bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Retrospective Review of the Primus First MTP Joint Double-Stemmed Silicone Implant
Authors: Lawrence Bruce R. , Thuen Eric 
Published: January 2013

Implant arthroplasty has been a surgical alternative for correction of hallux rigidus for many decades. A study is presented reviewing the authors’ experience using the (Tornier/Futura) Primus double-stemmed silicone implant. A total of 144 patients representing 201 implants were identified and invited to participate in the study. The postoperative period ranged from 32 to 108 months, with an average of 66.4 months. Chart review was performed on all cases. This review revealed that there were 2 implants that had been removed, each for reasons other than implant breakdown. Several indications in addition to hallux rigidus were found, including hallux valgus with arthritis, geriatric bunion, rheumatoid arthritis, and iatrogenic and traumatic arthritis. The outcomes are presented for all patients, with additional breakdown by their indication for surgery. In all, 54 patients involving 70 implants responded and were clinically evaluated. This study included a Visual Analogue Scale, Foot and Ankle (VAS FA) patient outcome and satisfaction questionnaire, clinical examination, and X-ray evaluation. Patients with hallux rigidus had an average postoperative American Orthopaedic Foot and Ankle Society (AOFAS) score of 88.2, and those with hallux valgus with arthritis had an average score of 88.6. The average AOFAS score for all patients was 87.4. The average VAS patient satisfaction for all patients was 8.5 (with 10 being highest satisfaction). Implant arthroplasty continues to be a viable alternative for surgical correction of hallux rigidus as well as other degenerative conditions of the first MTP joint. This procedure is particularly effective in older, less-active patients with lower functional demand. Levels of Evidence: Therapeutic, Level IV, Retrospective case series
Modified Minimal Incision Subcapital Osteotomy for Hallux Valgus Correction
Authors: Scala Andrea , Vendettuoli Domenico 
Published: January 2013

The potential advantages of minimal incision surgery for hallux valgus (HV) correction are the following: reduced surgical exposure, diminished soft-tissue stripping, and less blood supply impairment. These advantages imply fewer complications. We retrospectively reviewed patients who were consecutively treated with a modified minimally invasive osteotomy from January 2006 until December 2009 for HV deformity. We radiographically assessed the HV angle, 1-2 intermetatarsal (IM) angle, and tibial sesamoid position. Clinical outcomes were determined using the American Orthopaedic Foot and Ankle Society Hallux Metatarsophalangeal Interphalangeal (AOFAS HMI) Clinical Rating Scale. A paired Student’s t test was used to determine significance, with P < .01. There were 126 patients (146 feet) with an average age of 52.6 years and an average postoperative follow-up of 29.1 months. Preoperatively, the average HV angle was 32.3°, and postoperatively, it was 4.5° (P < .01). The preoperative average IM angle was 14.4°, whereas postoperatively, it was 4.8° (P < .01). The average tibial sesamoid position was 6.3 preoperatively and 2.5 postoperatively (P < .01). The average AOFAS HMI score was 54.6 preoperatively and 85.3 postoperatively (P < .01). There were 15 postoperative complications (10.3%) that included hallux varus, painful hardware, and delayed union. The results are comparable with those of traditional open techniques, with the additional advantages of a minimally invasive procedure. Level of Evidence: Therapeutic, Level IV: Retrospective case series
Exhaled breath profiling in diagnosing wheezy preschool children
Authors: van de Kant Kim D.G. , van Berkel Joep J.B.N. , Jöbsis Quirijn , Lima Passos Valéria , Klaassen Ester M.M. , van der Sande Linda , van Schayck Onno C.P. , de Jongste Johan C. , van Schooten Frederik Jan , Derks Eduard , Dompeling Edward , Dallinga Jan W. 
Published: January 2013

Although wheeze is common in preschool children, the underlying pathophysiology has not yet been disentangled. Volatile organic compounds (VOCs) in exhaled breath may serve as noninvasive markers of early wheeze. We aimed to assess the feasibility of VOC collection in preschool children, and to study whether a VOC profile can differentiate between children with and without recurrent wheeze.We included children (mean (range) age 3.3 (1.9–4.5) yrs) with (n=202) and without (n=50) recurrent wheeze. Exhaled VOCs were analysed by gas chromatography–time-of-flight mass spectrometry. VOC profiles were generated by ANOVA simultaneous component analysis (ASCA) and sparse logistic regression (SLR).Exhaled breath collection was possible in 98% of the children. In total, 913 different VOCs were detected. The signal-to-noise ratio improved after correction for age, sex and season using ASCA pre-processing. An SLR model with 28 VOCs correctly classified 83% of the children (84% sensitivity, 80% specificity). After six-fold cross-validation, 73% were correctly classified (79% sensitivity, 50% specificity).Assessment of VOCs in exhaled breath is feasible in young children. VOC profiles are able to distinguish children with and without recurrent wheeze with a reasonable accuracy. This proof of principle paves the way for additional research on VOCs in preschool wheezing.
New approaches for unravelling reassortment pathways
Authors: Svinti Victoria , Cotton James A , McInerney James O 
Published: January 2013

AbstractBackgroundEvery year the human population encounters epidemic outbreaks of influenza, and history reveals recurring pandemics that have had devastating consequences. The current work focuses on the development of a robust algorithm for detecting influenza strains that have a composite genomic architecture. These influenza subtypes can be generated through a reassortment process, whereby a virus can inherit gene segments from two different types of influenza particles during replication. Reassortant strains are often not immediately recognised by the adaptive immune system of the hosts and hence may be the source of pandemic outbreaks. Owing to their importance in public health and their infectious ability, it is essential to identify reassortant influenza strains in order to understand the evolution of this virus and describe reassortment pathways that may be biased towards particular viral segments. Phylogenetic methods have been used traditionally to identify reassortant viruses. In many studies up to now, the assumption has been that if two phylogenetic trees differ, it is because reassortment has caused them to be different. While phylogenetic incongruence may be caused by real differences in evolutionary history, it can also be the result of phylogenetic error. Therefore, we wish to develop a method for distinguishing between topological inconsistency that is due to confounding effects and topological inconsistency that is due to reassortment.ResultsThe current work describes the implementation of two approaches for robustly identifying reassortment events. The algorithms rest on the idea of significance of difference between phylogenetic trees or phylogenetic tree sets, and subtree pruning and regrafting operations, which mimic the effect of reassortment on tree topologies. The first method is based on a maximum likelihood (ML) framework (MLreassort) and the second implements a Bayesian approach (Breassort) for reassortment detection. We focus on reassortment events that are found by both methods. We test both methods on a simulated dataset and on a small collection of real viral data isolated in Hong Kong in 1999.ConclusionsThe nature of segmented viral genomes present many challenges with respect to disease. The algorithms developed here can effectively identify reassortment events in small viral datasets and can be applied not only to influenza but also to other segmented viruses. Owing to computational demands of comparing tree topologies, further development in this area is necessary to allow their application to larger datasets.
Injury-elicited stressors alter endogenous retrovirus expression in lymphocytes depending on cell type and source lymphoid organ
Authors: Lee Kang-Hoon , Lim Debora , Green Tajia , Greenhalgh David , Cho Kiho 
Published: January 2013

Abstract

Background
Murine leukemia virus-type endogenous retroviruses (MuLV-ERVs) constitute ~10% of the mouse genome and are associated with various pathophysiologic processes. In this study, we examined whether MuLV-ERVs’ response to burn-elicited stressors is specific for certain lymphocyte populations and/or locations of lymphoid organ.

Results
B- and T-cells, which were sorted from nine lymphoid organs of C57BL/6J mice after burn, were subjected to MuLV-ERV expression analyses. Overall, the post-burn MuLV-ERV expression pattern was dependent on lymphocyte type, time after injury, location of lymphoid organ, and MuLV-ERV type. For instance, the MuLV-ERV expression in T-cells from the thymus and three cervical lymph nodes decreased at 3 hours post-burn while the expression of some MuLV-ERVs was augmented in B-cells derived from the mesenteric lymph node. The MuLV-ERV U3 sequences population of the burn-24 hours group was less diverse in comparison to the no burn and burn-3 hours groups. In addition, it was apparent that at the 24 hours time point, the U3 populations of B-cells from both no burn and burn groups were less heterogeneous than the T-cells’ U3 populations. Using the U3 sequences, some of which were isolated only from specific experimental groups (B- vs. T-cells; no burn vs. burn), as probes, 51 putative MuLV-ERVs, including 16 full-length proviruses, were mapped followed by characterization of their biologic properties.

Conclusion
MuLV-ERVs’ response to burn-elicited stressors may be differentially controlled depending on lymphocyte type, location of lymphoid organ, MuLV-ERV type, and stress duration.
Allelotypes of lung adenocarcinomas featuring ALK fusion demonstrate fewer onco- and suppressor gene changes
Authors: Ninomiya Hironori , Kato Motohiro , Sanada Masashi , Takeuchi Kengo , Inamura Kentaro , Motoi Noriko , Nagano Hiroko , Nomura Kimie , Sakao Yukinori , Okumura Sakae , Mano Hiroyuki , Ogawa Seishi , Ishikawa Yuichi 
Published: January 2013

AbstractBackgroundA subset of lung adenocarcinomas harboring anEML4-ALKfusion gene resulting in dominant oncogenic activity has emerged as a target for specific therapy.EML4-ALKfusion confers a characteristic histology and is detected more frequently in never or light smokers and younger patients.MethodsTo gain insights into etiology and carcinogenic mechanisms we conducted analyses to compare allelotypes of 35ALKfusion-positive and 95 -negative tumours using single nucleotide polymorphism (SNP) arrays and especially designed software which enabled precise global genomic profiling.ResultsOverall aberration numbers (gains + losses) of chromosomal alterations were 8.42 and 9.56 in tumours with and withoutALKfusion, respectively, the difference not being statistically significant, although patterns of gain and loss were distinct. Interestingly, among selected genomic regions, oncogene-related examples such as 1p34.3(MYCL1), 7q11.2(EGFR), 7p21.1, 8q24.21(MYC), 16p13.3, 17q12(ERBB2) and 17q25.1 showed significantly less gain. Also, changes in tumour suppressor gene-related regions, such as 9p21.3 (CDKN2A) 9p23-24.1 (PTPRD), 13q14.2 (RB1), were significantly fewer in tumours withALKfusion.ConclusionGlobal genomic comparison with SNP arrays showed tumours withALKfusion to have fewer alterations in oncogenes and suppressor genes despite a similar overall aberration frequency, suggesting very strong oncogenic potency ofALKactivation by gene fusion.
Structural and functional characteristics of cGMP-dependent methionine oxidation in Arabidopsis thaliana proteins
Authors: Marondedze Claudius , Turek Ilona , Parrott Brian , Thomas Ludivine , Jankovic Boris , Lilley Kathryn S , Gehring Chris 
Published: January 2013

Abstract

Background
Increasing structural and biochemical evidence suggests that post-translational methionine oxidation of proteins is not just a result of cellular damage but may provide the cell with information on the cellular oxidative status. In addition, oxidation of methionine residues in key regulatory proteins, such as calmodulin, does influence cellular homeostasis. Previous findings also indicate that oxidation of methionine residues in signaling molecules may have a role in stress responses since these specific structural modifications can in turn change biological activities of proteins.

Findings
Here we use tandem mass spectrometry-based proteomics to show that treatment of Arabidopsis thaliana cells with a non-oxidative signaling molecule, the cell-permeant second messenger analogue, 8-bromo-3,5-cyclic guanosine monophosphate (8-Br-cGMP), results in a time-dependent increase in the content of oxidised methionine residues. Interestingly, the group of proteins affected by cGMP-dependent methionine oxidation is functionally enriched for stress response proteins. Furthermore, we also noted distinct signatures in the frequency of amino acids flanking oxidised and un-oxidised methionine residues on both the C- and N-terminus.

Conclusions
Given both a structural and functional bias in methionine oxidation events in response to a signaling molecule, we propose that these are indicative of a specific role of such post-translational modifications in the direct or indirect regulation of cellular responses. The mechanisms that determine the specificity of the modifications remain to be elucidated.
Softwares and methods for estimating genetic ancestry in human populations
Authors: Liu Yushi , Nyunoya Toru , Leng Shuguang , Belinsky Steven A , Tesfaigzi Yohannes , Bruse Shannon 
Published: January 2013

AbstractThe estimation of genetic ancestry in human populations has important applications in medical genetic studies. Genetic ancestry is used to control for population stratification in genetic association studies, and is used to understand the genetic basis for ethnic differences in disease susceptibility. In this review, we present an overview of genetic ancestry estimation in human disease studies, followed by a review of popular softwares and methods used for this estimation.
Coordinating transmit power and carrier phase for wireless networks with multi-packet reception capability
Authors: Choi Wooyeol , Kim Taewoon , Park Daeyoung , Lee Heung-No , Lim Hyuk 
Published: January 2013

Abstract
Driven by advances in signal processing and multiuser detection (MUD) technologies, it has become possible for a wireless node to simultaneously receive multiple signals from other transmitters. In order to take full advantage of MUD in multi-packet reception (MPR) capable wireless networks, it is highly desirable to make the compound signals from multiple transmitters more separable on its constellation at the receiver by coordinating both the transmit power level and carrier phase offsets of the transmitters. In this article, we propose a feedback-based transmit power and carrier phase adjustment scheme that estimates the symbol energy and the carrier phase offset for each transmitter’s received signal, computes the optimal received power level and carrier phase shift to maximize the minimum Euclidean distance between the constellation points, and finally feeds the optimal transmit power level and phase shift information back to the transmitters. We then evaluate the performance of the proposed transmit power and carrier phase adjustment scheme and subsequently show that the proposed scheme significantly reduces the error probability in a multiuser communication system having MPR capability.
Comparative modeling and docking studies of p16ink4/Cyclin D1/Rb pathway genes in lung cancer revealed functionally interactive residue of RB1 and its functional partner E2F1
Authors: e Zahra Syeda Naqsh , Khattak Naureen Aslam , Mir Asif 
Published: January 2013

AbstractBackgroundLung cancer is the major cause of mortality worldwide. Major signalling pathways that could play significant role in lung cancer therapy include (1) Growth promoting pathways (Epidermal Growth Factor Receptor/Ras/ PhosphatidylInositol 3-Kinase) (2) Growth inhibitory pathways (p53/Rb/P14ARF, STK11) (3) Apoptotic pathways (Bcl-2/Bax/Fas/FasL).Insilicostrategy was implemented to solve the mystery behind selected lung cancer pathway by applying comparative modeling and molecular docking studies.ResultsYASARA [v 12.4.1] was utilized to predict structural models ofP16-INK4andRB1genes using template 4ELJ-A and 1MX6-B respectively. WHAT CHECK evaluation tool demonstrated overall quality of predicted P16-INK4 and RB1 with Z-score of −0.132 and −0.007 respectively which showed a strong indication of reliable structure prediction. Protein-protein interactions were explored by utilizing STRING server, illustrated thatCDK4andE2F1showed strong interaction withP16-INK4andRB1based on confidence score of 0.999 and 0.999 respectively. In order to facilitate a comprehensive understanding of the complex interactions between candidate genes with their functional interactors, GRAMM-X server was used. Protein-protein docking investigation ofP16-INK4revealed four ionic bonds illustrating Arg47, Arg80,Cys72 and Met1 residues as actively participating in interactions withCDK4while docking results ofRB1showed four hydrogen bonds involving Glu864, Ser567, Asp36 and Arg861 residues which interact strongly with its respective functional interactorE2F1.ConclusionThis research may provide a basis for understanding biological insights ofP16-INK4andRB1proteins which will be helpful in future to design a suitable drug to inhibit the disease pathogenesis as we have determined the interacting amino acids which can be targeted in order to design a ligandin-vitroto propose a drug for clinical trials. Protein -protein docking of candidate genes and their important interacting residues likely to be provide a gateway for developing computer aided drug designing.
A specific family of interspersed repeats (SINEs) facilitates meiotic synapsis in mammals
Authors: Johnson Matthew E , Rowsey Ross A , Shirley Sofia , VandeVoort Catherine , Bailey Jeffrey , Hassold Terry 
Published: January 2013

Abstract

Background
Errors during meiosis that affect synapsis and recombination between homologous chromosomes contribute to aneuploidy and infertility in humans. Despite the clinical relevance of these defects, we know very little about the mechanisms by which homologous chromosomes interact with one another during mammalian meiotic prophase. Further, we remain ignorant of the way in which chromosomal DNA complexes with the meiosis-specific structure that tethers homologs, the synaptonemal complex (SC), and whether specific DNA elements are necessary for this interaction.

Results
In the present study we utilized chromatin immunoprecipitation (ChIP) and DNA sequencing to demonstrate that the axial elements of the mammalian SC are markedly enriched for a specific family of interspersed repeats, short interspersed elements (SINEs). Further, we refine the role of the repeats to specific sub-families of SINEs, B1 in mouse and AluY in old world monkey (Macaca mulatta).

Conclusions
Because B1 and AluY elements are the most actively retrotransposing SINEs in mice and rhesus monkeys, respectively, our observations imply that they may serve a dual function in axial element binding; i.e., as the anchoring point for the SC but possibly also as a suppressor/regulator of retrotransposition.
NucBase, an easy to use read mapper for small RNAs
Authors: Dufourt Jeremy , Pouchin Pierre , Peyret Pierre , Brasset Emilie , Vaury Chantal 
Published: January 2013

Abstract

Background
High-throughput deep-sequencing technology has generated an unprecedented number of expressed sequence reads that offer the opportunity to get insight into biological systems. Several databases report the sequence of small regulatory RNAs which play a prominent role in the control of transposable elements (TE). However, the huge amount of data reported in these databases remains mostly unexplored because the available tools are hard for biologists to use.

Results
Here we report NucBase, a new program designed to make an exhaustive search for sequence matches and to align short sequence reads from large nucleic acid databases to genomes or input sequences. NucBase includes a graphical interface which allows biologists to align sequences with ease and immediately visualize matched sequences, their number and their genomic position. NucBase identifies nucleic motives with strict identity to input sequences, and it capably finds candidates with one or several mismatches. It offers the opportunity to identify “core sequences” comprised of a chosen number of consecutive matching nucleotides. This software can be run locally on any Windows, Linux or Mac OS computer with 32-bit architecture compatibility.

Conclusions
Since this software is easy to use and can detect reads that were undetected by other software, we believe that it will be useful for biologists involved in the field of TE silencing by small non-coding RNAs. We hope NucBase will be useful for a larger community of researchers, since it makes exploration of small nucleic sequences in any organism much easier.
Gene encoding prolactin in cinnamon clownfish Amphiprion melanopus and its expression upon acclimation to low salinities
Authors: Noh Gyeong Eon , Rho Sum , Chang Yong Jin , Min Byung Hwa , Kim Jong-Myoung 
Published: January 2013

Abstract

Background
Prolactin (PRL) is a key hormone for osmoregulation in fish. Levels of PRL in the pituitary gland and plasma ion composition of clownfish seem to change to regulate their hydromineral balance during adaptation to waters of different salinities. In order to understand osmoregulatory mechanism and its association with growth performance and PRL in fish, the gene encoding PRL and its expression level in cinnamon clownfish Amphiprion melanopus upon acclimation to low salinity was analyzed.

Results
The PRL gene of A. melanopus encoded a protein of 212 amino acid residues comprised of a putative signal peptide of 24 amino acids and a mature protein of 188 amino acids. Analysis of growth performance under different salinities of 34, 25, 15, and 10 ppt indicated that cinnamon clownfish could survive under salinities as low as 10 ppt. A higher rate of growth was observed at the lower salinities as compared to that of 34 ppt. Upon shifting the salinity of the surrounding water from 34 ppt to 15 ppt, the level of the PRL transcripts gradually increased to reach the peak level until 24 h of acclimation at 15 ppt, but decreased back as adaptation continued to 144 h. In contrast, levels of plasma Na+, Cl-, and osmolality decreased at the initial stage (4–8 h) of acclimation at 15 pt but increased back as adaptation continued till 144 h.

Conclusion
Cinnamon clownfish could survive under salinities as low as 10 ppt. Upon shifting the salinity of the surrounding water from 34 ppt to 15 ppt, the level of the PRL transcripts gradually increased during the initial stage of acclimation but decreased back to the normal level as adaptation continued. An opposite pattern of changes - decrease at the beginning followed by an increase - in the levels of plasma Na+, Cl-, and osmolality was found upon acclimation to low salinity. The results suggest an involvement of PRL in the processes of osmoregulation and homeostasis in A. melanopus.