bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a recently active Prunus‐specific non‐autonomous Mutator element with considerable genome shaping force
Authors: Halász Júlia , Kodad Ossama , Hegedűs Attila 
Published: May 2014

SummaryMiniature inverted‐repeat transposable elements (MITEs) are known to contribute to the evolution of plants, but only limited information is available for MITEs in the Prunus genome. We identified a MITE that has been named Falling Stones, FaSt. All structural features (349‐bp size, 82‐bp terminal inverted repeats and 9‐bp target site duplications) are consistent with this MITE being a putative member of the Mutator transposase superfamily. FaSt showed a preferential accumulation in the short AT‐rich segments of the euchromatin region of the peach genome. DNA sequencing and pollination experiments have been performed to confirm that the nested insertion of FaSt into the S‐haplotype‐specific F‐box gene of apricot resulted in the breakdown of self‐incompatibility (SI). A bioinformatics‐based survey of the known Rosaceae and other genomes and a newly designed polymerase chain reaction (PCR) assay verified the Prunoideae‐specific occurrence of FaSt elements. Phylogenetic analysis suggested a recent activity of FaSt in the Prunus genome. The occurrence of a nested insertion in the apricot genome further supports the recent activity of FaSt in response to abiotic stress conditions. This study reports on a presumably active non‐autonomous Mutator element in Prunus that exhibits a major indirect genome shaping force through inducing loss‐of‐function mutation in the SI locus.
Wound healing in acutely injured fascia
Authors: Lau Frank H. , Pomahac Bohdan 
Published: May 2014

AbstractFascial healing following acute injury, such as that occurring during surgical procedures, is defined functionally. For example, failure of fascial healing following celiotomy is only identified when incisional hernias are diagnosed. Such hernias incur billions of dollars per year in medical costs. Despite the importance of fascial healing, there is a paucity of data regarding the quality such healing. In clinical settings, the quantification of fascial wound healing is limited to a binary state: either there is no clinically apparent functional deficit and full fascia healing is assumed, or an incisional hernia or other functional failure is visible and the fascia did not heal. There are no clinical methods to isolate and functionally test fascia in patients. Recent studies have revealed unexpected findings regarding the recovery of tensile strength, specific surgical methods that optimize fascial healing, and the potential impact of biological pharmaceuticals in eliminating fascial healing failure. However, much remains unknown about the biology of fascial healing.
Rotational alignment of the tibial component in total knee arthroplasty: the anterior tibial cortex is a reliable landmark
Authors: Baldini Andrea , Indelli Pier , De Luca Lapo , Mariani Pierpaolo , Marcucci Massimiliano 
Published: May 2014

Purpose: to compare the anterior tibial surface curvature, the Akagi’s line and the medial third of the tibial tubercle in order to assess which is the most reliable landmark for correct tibial component rotational positioning in total knee arthroplasty.
Methods: three independent investigators reviewed 124 knee MRI scans. The most suitable tibial baseplate tracing for the Nexgen Total Knee System (Zimmer, Warsaw, USA) was superimposed on the scan matching the anterior tibial cortex with the anterior aspect of the baseplate. The rotation of the tibial baseplate tracing was calculated with respect to the transepicondylar axis (TEA), the medial third of the tibial tubercle line, Akagi’s line and the femoral posterior condylar axis (PCA). Customized software was created and used for analysis of the MRI datasets.The reliability of each measurement was then calculated by using the intraclass correlation coefficient for interobserver agreement.
Results: observer agreement on the position of the Akagi’s line was within 3° in 64% of the cases and within 5°in 85% of the cases. Agreement on the position of the medial third of the tibial tubercle was within 3°in 29% of the cases and within 5°in 70% of the cases. Agreement on the localization of the anterior tibial surface curvature was within 3°in 89% of the cases and within 5°in 99% of the cases. Component alignment along the anterior cortex guaranteed full matching ± 3° with the epicondylar axis in 75% of the knees.
Conclusions: the anterior tibial surface curvature was found to be a more reliable and more easily identifiable landmark for correct tibial component alignment than either Akagi’s line or the medial third of the tibialtubercle.
Level of evidence: level III, retrospective cohort study.
Polyurethane scaffold for the treatment of partial meniscal tears. Clinical results with a minimum two-year follow-up
Authors: Bulgheroni Paolo , Bulgheroni Erica , Regazzola Gianmarco , Mazzola Claudio 
Published: May 2014

Purpose: to evaluate the safety and effectiveness of the polyurethane meniscal scaffold through clinical examination, MRI and arthroscopic second look, over a minimum two-year follow-up.
Methods: between 2009 and 2011, 19 patients underwent meniscal scaffold implantation in our department (medial meniscus in 16 cases lateral meniscus in two cases, and bilateral in one case). All the patients were clinically evaluated preoperatively, and at 6, 12, and 24 months after surgery using Lysholm score, Tegner score, and VAS. Ten patients were studied with MRI, and nine patients were evaluated arthroscopically.
Results: no adverse reactions to the implant were observed. The clinical scores showed a significant improvement at 6 months and increased progressively over time. On MRI studies, the implants showed a clear hyperintense signal, sometimes irregular, and the chondral surface was preserved in all cases. At arthroscopic second look in the first months after surgery, the scaffold size was unchanged and the scaffold appeared light yellowish in color and well integrated into the surrounding tissues. At arthroscopic second look at 12 and 24 months the scaffold was found to have an irregular morphology and to be slightly reduced in size.
Conclusions: polyurethane meniscal scaffold is a good alternative to a collagen scaffold, but a longer follow-up is needed to evaluate the scaffold degradation and chondral coverage.
Level of Evidence: level IV, therapeutic case series.
The treatment of chondral lesions of the knee with the microfracture technique and platelet-rich plasma
Authors: Manunta Andrea , Manconi Anna 
Published: May 2014

Purpose: to assess the efficacy of associating the microfracture technique with platelet-rich plasma (PRP) injections in the treatment of chondral lesions to promote acceleration and optimization of the healing process compared with the traditional microfracture approach.
Methods: from September 2011 to August 2012, 20 patients (9 males and 11 females, aged 30-55 years) were treated. All presented with chondral lesions of the medial femoral condyle of the knee and a pain duration ranging from 8 to 12 months.The patients were randomized into two groups (A and B). Group A was treated with the microfracture technique and a total of three intra-articular injections of PRP. Group B was treated with microfractures alone. Clinical follow-up was performed at 3, 6 and 12 months after treatment. Clinical function was assessed on the basis of the International Knee Documentation Committee (IKDC) score. Pain was evaluated using a visual analogue scale (VAS)
Results: the patients in group A had a mean baseline IKDC score of 31.2, which rose to 84.2 at 12 months. The IKDC scores in group B were at 30.1 at baseline and 81 at 12 months.
Conclusions: the results of our study suggest that functional recovery and resolution of pain are obtained more quickly in PRP-treated patients. We also observed a better functional outcome in the patients treated with the combination of PRP and microfractures, even at 12 months, although the difference was not statistically significant.
Level of evidence: level II, randomized clinical study.
Draft Genome Sequence of the First Isolate of Extensively Drug-Resistant Mycobacterium tuberculosis in New Zealand
Authors: O'Toole Ronan F. , Johari Bushra M. , Mac Aogáin Micheál , Rogers Thomas R. , Bower James E. , Basu Indira , Freeman Joshua T. 
Published: May 2014

ABSTRACT
Extensively drug-resistant (XDR) tuberculosis has now been described in >90 countries worldwide. The first case of XDR tuberculosis (XDR-TB) in New Zealand was recorded in 2010. We report the draft whole-genome sequence of the New Zealand isolate, NZXDR1, and describe a number of single-nucleotide polymorphisms that relate to drug resistance.
Draft Genome Sequence of Elizabethkingia meningoseptica Isolated from a Traumatic Wound
Authors: Quick Joshua , Constantinidou Chrystala , Pallen Mark J. , Oppenheim Beryl , Loman Nicholas J. 
Published: May 2014

ABSTRACT

We report the draft genome assembly of
Elizabethkingia meningoseptica
strain 502. The sample was isolated from the wound of a repatriated military serviceperson who suffered major trauma from an improvised explosive device (IED), resulting in wounds with extensive environmental contamination.
E. meningoseptica
was isolated from wounds in both legs. The draft genome assembly has 21 contigs with a total size of 3,960,744 bases. The genome contains genes encoding 26 putative β-lactamases.
Whole-Genome Sequence of a Classical Swine Fever Virus Isolated from the Uttarakhand State of India
Authors: Kumar Ravi , Rajak Kaushal Kishor , Chandra Tribhuwan , Thapliyal Ashish , Muthuchelvan Dhanavelu , Sudhakar Shashi Bhushan , Sharma Kuldeep , Saxena Arpit , Raut Sachin D. , Singh Vinod Kumar , Ahmad Zubair , Kumar Ajay , Chaudhary Dheeraj , Singh Raj Kumar , Pandey Awadh Bihari 
Published: May 2014

ABSTRACT
We report the first complete genome sequence of a classical swine fever (CSF) virus of subgenotype 2.2. The virus (CSFV/IND/UK/LAL-290) was isolated from the Uttarakhand state of India from a backyard pig suspected of having CSF. This genome sequence will give useful insight for future molecular epidemiological studies and the development of an effective vaccine in India.
Genome Sequence of Pseudomonas brassicacearum DF41
Authors: Loewen Peter C. , Switala Jack , Fernando W. G. Dilantha , de Kievit Teri 
Published: May 2014

ABSTRACT

Pseudomonas brassicacearum
DF41, a Gram-negative soil bacterium, is able to suppress the fungal pathogen
Sclerotinia sclerotiorum
through a process known as biological control. Here, we present a 6.8-Mb assembly of its genome, which is the second fully assembled genome of a
P. brassicacearum
strain.
Genome Sequence of Salmonella enterica subsp.
enterica
Strain Durban
Authors: Russell Daniel A. , Bowman Charles A. , Hatfull Graham F. 
Published: May 2014

ABSTRACT

We report the genome sequence of
Salmonella enterica
subsp.
enterica
strain Durban, isolated from a patient with salmonellosis and typhoid fever. The strain is closely related to
S. enterica
subsp.
enterica
strain P125109 but differs in loss of the ϕSE20 prophage and acquisition of a prophage similar to ELPhiS.
Draft Genome Sequence of Escherichia coli E1728 Isolated from Marine Sediment in Hong Kong
Authors: Lai Jennifer Y. H. , Zhang Hao , Chiang Miranda H. Y. , Yu Min , Zhang Rui , Lau Stanley C. K. 
Published: May 2014

ABSTRACT

Recent findings of
Escherichia coli
persisting autochthonously in environmental matrices outside animal bodies have revealed largely unknown facets of the lifestyle and ecophysiology of the species that have yet to be explored. Here, we report the draft genome sequence of
E. coli
E1728 isolated from marine sediment.
Poor Multi-Rater Reliability in Tcm Pattern Diagnoses and Variation in the Use of Symptoms to Obtain a Diagnosis
Authors: Birkeflet Oddveig , Laake Petter , Vøllestad Nina K 
Published: May 2014

Background Pattern differentiation and diagnosis are fundamental principles of Traditional Chinese Medicine (TCM). Studies have shown low inter-rater reliability in TCM pattern diagnoses. This variability may originate from both the identification and the interpretation of symptoms and signs. Objective To examine the inter-rater reliability in TCM pattern diagnoses made in the style of Maciocia for 25 case histories by eight acupuncturists and to explore the impact of demographic factors on the diagnostic conclusion. Further, the association between the diagnosis and the presence of symptoms was examined for a single TCM diagnosis. Methods Eight acupuncturists independently diagnosed 25 women (15 fertile, 10 infertile) based on written case histories. Descriptive statistics, logistic regression and inter-rater reliability (κ) were used. Results Poor inter-rater reliability on TCM patterns (κ<0.20) and large variation in the number of TCM pattern diagnoses were found. Sex, duration of practice and education had a highly significant effect (p<0.001) on the use of TCM patterns and working hours had a significant effect (p=0.029). There was considerable intra- and inter-rater variation in the use of symptoms to make a diagnosis. Symptoms occurring frequently as well as infrequently were inconsistently used to diagnose Liver Qi Stagnation. The study was limited by a small sample size. Conclusions The results showed extensive variation and poor inter-rater reliability in TCM diagnoses. Demographic variables influenced the frequency of diagnoses and symptoms were used inconsistently to set a diagnosis. The variability shown could impede individually tailored treatment.
A cross-sectional survey of essential surgical capacity in Somalia
Authors: Elkheir Natalie , Sharma Akshay , Cherian Meena , Saleh Omar Abdelrahman , Everard Marthe , Popal Ghulam Rabani , Ibrahim Abdi Awad 
Published: May 2014

ObjectiveTo assess life-saving and disability-preventing surgical services (including emergency, trauma, obstetrics, anaesthesia) of health facilities in Somalia and to assist in the planning of strategies for strengthening surgical care systems.DesignCross-sectional survey.SettingHealth facilities in all 3 administrative zones of Somalia; northwest Somalia (NWS), known as Somaliland; northeast Somalia (NES), known as Puntland; and south/central Somalia (SCS).Participants14 health facilities.MeasuresThe WHO Tool for Situational Analysis to Assess Emergency and Essential Surgical Care was employed to capture a health facility's capacity to deliver surgical and anaesthesia services by investigating four categories of data: infrastructure, human resources, interventions available and equipment.ResultsThe 14 facilities surveyed in Somalia represent 10 of the 18 districts throughout the country. The facilities serve an average patient population of 331 250 people, and 12 of the 14 identify as hospitals. While major surgical procedures were provided at many facilities (caesarean section, laparotomy, appendicectomy, etc), only 22% had fully available oxygen access, 50% fully available electricity and less than 30% had any management guidelines for emergency and surgical care. Furthermore, only 36% were able to provide general anaesthesia inhalation due to lack of skills, supplies and equipment. Basic supplies for airway management and the prevention of infection transmission were severely lacking in most facilities.ConclusionsAccording to the results of the WHO Tool for Situational Analysis to Assess Emergency and Essential Surgical Care survey, there exist significant gaps in the capacity of emergency and essential surgical services in Somalia including inadequacies in essential equipment, service provision and infrastructure. The information provided by the WHO tool can serve as a basis for evidence-based decisions on country-level policy regarding the allocation of resources and provision of emergency and essential surgical services.
Comparing responsible and non-responsible drivers to assess determinants of road traffic collisions: time to standardise and revisit
Authors: Salmi L Rachid , Orriols Ludivine , Lagarde Emmanuel 
Published: May 2014

ObjectivesIn 1994, Robertson and Drummer formalised the responsibility analysis as an alternative to case-control studies in the study of road traffic crashes. Our objective was to assess whether published responsibility studies respected standards defining adequate case-control studies.SettingUsing Web of Science, Scopus and Google Scholar, we identified responsibility studies indexed until October 2013, which cited Robertson and Drummer's paper. After reviewing titles, abstracts and reference lists, we selected original studies comparing responsible and non-responsible drivers, published in peer-reviewed journals or proceedings.Data and analysisWe applied a grid to judge the conformity of the responsibility assessment to the original definition, and whether methods addressing representativeness of selection, accuracy of measures of exposures, confounding variables, and power met standards defining adequate case-control studies.ResultsOf 205 titles, we identified 20 papers. Methods of responsibility assessment were the original in three papers. Variations across studies concerned the number of mitigating factors included, or the use of questionnaires rather than police data (n=3). The ratio responsible/non-responsible drivers varied from 0.90 to 5.31, due to major variations in sampling methods, threshold selection, and data completeness. Selection or measurement issues were discussed in 13 papers, but seldom addressed in the design. A comparison of confounding factors in responsible and non-responsible drivers was presented in five papers.ConclusionsBasic requirements of case-control studies are often not or not clearly met in responsibility studies. There is a need to revisit the method and to adapt existing publication standards to the way responsibility studies are reported.
Epigenetic inactivation ofDAPK1,p14ARF,mir-34aand-34b/cin acute promyelocytic leukaemia
Authors: Ng Ho Yin , Wan Thomas S , So Chi Chiu , Chim Chor Sang 
Published: May 2014

AimTP53mutation frequently occurs in solid cancers but not haematological cancers including acute promyelocytic leukaemia (APL) characterised by t(15;17). BothDAPK1andp14ARFpositively regulate p53 whereasmiR-34aand-34b/care direct transcriptional targets of p53. We studied if DNA methylation might contribute to inactivation of gene/microRNA (miRNA) in the TP53 tumour suppressor network.MethodsPromoter methylation ofDAPK1,p14ARF,miR-34aand -34b/cwere studied in 10 normal bone marrow samples, NB4 cell line and 60 APL primary samples at diagnosis by methylation-specific PCR (MSP).ResultsDAPK1, p14ARF,miR-34aand-34b/cwere completely unmethylated in normal bone marrow samples.DAPK1,miR-34aand-34b/cwere completely methylated in NB4. Treatment of NB4 by 5′-Aza-2′-deoxyctidine resulted in promoter demethylation together with re-expression ofDAPK1and both miRNAs. In primary APL samples, methylation ofmiR-34b/cwas detected in 43% in contrast to absence of methylation ofDAPK1,p14ARFormiR-34a. Overexpression ofmiR-34bin NB4 resulted in inhibition of proliferation.ConclusionsMethylation ofDAPK1,miR-34aand-34b/cis tumour-specific, and associated with gene/miRNAs silencing.miR-34b/cis a tumour suppressor miRNA in APL. Methylation ofmiR-34b/cmay contribute to APL leukaemogenesis.
Mortality on match days of the German national soccer team: a time series analysis from 1995 to 2009
Authors: Medenwald D , Kuss O 
Published: May 2014

BackgroundThere is inconsistent evidence on population mortality, especially cardiovascular disease mortality, on match days of national soccer teams during particular international tournaments. This study examines the number of deaths in Germany on match days of the national soccer team during a long-term period including several tournaments.MethodsWe analysed all registered daily deaths in Germany from 1995 to 2009 (11 225 966 cases) using time series analysis methods. Following the Box/Jenkins approach, we applied a seasonal autoregressive integrated moving average model. To assess the effect of match days, we performed an intervention analysis by including a transfer function model representing match days of the national team in the statistical analyses. We conducted separate analyses for all matches and for matches during international tournaments (European and World Championships) only. Time series and results were stratified in terms of sex, age (<50 years, 50–70 years, >70 years) and cause of death (cardiovascular deaths, injuries, others). We performed a further independent analysis focusing only on the effect of match results (victory, loss, draw) and kind of tournament (international championships, qualifications, friendly matches).ResultsMost of the results did not indicate a distinct effect of matches of the national team on general mortality. Moreover, all null value deviations were small when compared with the average number of daily deaths (n=2270).ConclusionsThere is no relevant increase or decrease in mortality on match days of the German national soccer team.
Stressful social relations and mortality: a prospective cohort study
Authors: Lund Rikke , Christensen Ulla , Nilsson Charlotte Juul , Kriegbaum Margit , Hulvej Rod Naja 
Published: May 2014

BackgroundFew studies have examined the relationship between stressful social relations in private life and all-cause mortality.ObjectiveTo evaluate the association between stressful social relations (with partner, children, other family, friends and neighbours, respectively) and all-cause mortality in a large population-based study of middle-aged men and women. Further, to investigate the possible modification of this association by labour force participation and gender.MethodsWe used baseline data (2000) from The Danish Longitudinal Study on Work, Unemployment and Health, including 9875 men and women aged 36–52 years, linked to the Danish Cause of Death Registry for information on all-cause mortality until 31 December 2011. Associations between stressful social relations with partner, children, other family, friends and neighbours, respectively, and all-cause mortality were examined using Cox proportional hazards models adjusted for age, gender, cohabitation status, occupational social class, hospitalisation with chronic disorder 1980–baseline, depressive symptoms and perceived emotional support. Modification by gender and labour force participation was investigated by an additive hazards model.ResultsFrequent worries/demands from partner or children were associated with 50–100% increased mortality risk. Frequent conflicts with any type of social relation were associated with 2–3 times increased mortality risk. Interaction between labour force participation and worries/demands (462 additional cases per 100 000 person-years, p=0.05) and conflicts with partner (830 additional cases per 100 000 person-years, p<0.01) was suggested. Being male and experiencing frequent worries/demands from partner produced 135 extra cases per 100 000 person-years, p=0.05 due to interaction.ConclusionsStressful social relations are associated with increased mortality risk among middle-aged men and women for a variety of different social roles. Those outside the labour force and men seem especially vulnerable to exposure.