bluuebunny/crossref_metadata_2025_split huggingface dataset:
MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C
α
only models, Alternative alignments, and Non-sequential alignments
Authors: Minami Shintaro , Sawada Kengo , Chikenji George 
Published: January 2013

Abstract

Background
Protein pairs that have the same secondary structure packing arrangement but have different topologies have attracted much attention in terms of both evolution and physical chemistry of protein structures. Further investigation of such protein relationships would give us a hint as to how proteins can change their fold in the course of evolution, as well as a insight into physico-chemical properties of secondary structure packing. For this purpose, highly accurate sequence order independent structure comparison methods are needed.

Results
We have developed a novel protein structure alignment algorithm, MICAN (a structure alignment algorithm that can handle M ultiple-chain complexes, I nverse direction of secondary structures, C

α
only models, A lternative alignments, and N on-sequential alignments). The algorithm was designed so as to identify the best structural alignment between protein pairs by disregarding the connectivity between secondary structure elements (SSE). One of the key feature of the algorithm is utilizing the multiple vector representation for each SSE, which enables us to correctly treat bent or twisted nature of long SSE. We compared MICAN with other 9 publicly available structure alignment programs, using both reference-dependent and reference-independent evaluation methods on a variety of benchmark test sets which include both sequential and non-sequential alignments. We show that MICAN outperforms the other existing methods for reproducing reference alignments of non-sequential test sets. Further, although MICAN does not specialize in sequential structure alignment, it showed the top level performance on the sequential test sets. We also show that MICAN program is the fastest non-sequential structure alignment program among all the programs we examined here.

Conclusions
MICAN is the fastest and the most accurate program among non-sequential alignment programs we examined here. These results suggest that MICAN is a highly effective tool for automatically detecting non-trivial structural relationships of proteins, such as circular permutations and segment-swapping, many of which have been identified manually by human experts so far. The source code of MICAN is freely download-able at http://www.tbp.cse.nagoya-u.ac.jp/MICAN.
Use of somatic mutations to quantify random contributions to mouse development
Authors: Zhou Wenyu , Tan Yunbing , Anderson Donovan J , Crist Eva M , Ruohola-Baker Hannele , Salipante Stephen J , Horwitz Marshall S 
Published: January 2013

Abstract

Background
The C. elegans cell fate map, in which the lineage of its approximately 1000 cells is visibly charted beginning from the zygote, represents a developmental biology milestone. Nematode development is invariant from one specimen to the next, whereas in mammals, aspects of development are probabilistic, and development exhibits variation between even genetically identical individuals. Consequently, a single defined cell fate map applicable to all individuals cannot exist.

Results
To determine the extent to which patterns of cell lineage are conserved between different mice, we have employed the recently developed method of “phylogenetic fate mapping” to compare cell fate maps in siblings. In this approach, somatic mutations arising in individual cells are used to retrospectively deduce lineage relationships through phylogenetic and—as newly investigated here—related analytical approaches based on genetic distance. We have cataloged genomic mutations at an average of 110 mutation-prone polyguanine (polyG) tracts for about 100 cells clonally isolated from various corresponding tissues of each of two littermates of a hypermutable mouse strain.

Conclusions
We find that during mouse development, muscle and fat arise from a mixed progenitor cell pool in the germ layer, but, contrastingly, vascular endothelium in brain derives from a smaller source of progenitor cells. Additionally, formation of tissue primordia is marked by establishment of left and right lateral compartments, with restricted cell migration between divisions. We quantitatively demonstrate that development represents a combination of stochastic and deterministic events, offering insight into how chance influences normal development and may give rise to birth defects.
Prediction of components of the sporopollenin synthesis pathway in peach by genomic and expression analyses
Authors: Ríos Gabino , Tadeo Francisco R , Leida Carmen , Badenes María L 
Published: January 2013

Abstract

Background
The outer cell wall of the pollen grain (exine) is an extremely resistant structure containing sporopollenin, a mixed polymer made up of fatty acids and phenolic compounds. The synthesis of sporopollenin in the tapetal cells and its proper deposition on the pollen surface are essential for the development of viable pollen. The beginning of microsporogenesis and pollen maturation in perennial plants from temperate climates, such as peach, is conditioned by the duration of flower bud dormancy. In order to identify putative genes involved in these processes, we analyzed the results of previous genomic experiments studying the dormancy-dependent gene expression in different peach cultivars.

Results
The expression of 50 genes induced in flower buds after the endodormancy period (flower-bud late genes) was compared in ten cultivars of peach with different dormancy behaviour. We found two co-expression clusters enriched in putative orthologs of sporopollenin synthesis and deposition factors in Arabidopsis. Flower-bud late genes were transiently expressed in anthers coincidently with microsporogenesis and pollen maturation processes. We postulated the participation of some flower-bud late genes in the sporopollenin synthesis pathway and the transcriptional regulation of late anther development in peach.

Conclusions
Peach and the model plant Arabidopsis thaliana show multiple elements in common within the essential sporopollenin synthesis pathway and gene expression regulatory mechanisms affecting anther development. The transcriptomic analysis of dormancy-released flower buds proved to be an efficient procedure for the identification of anther and pollen development genes in perennial plants showing seasonal dormancy.
Cost-effectiveness of supported self-management for CFS/ME patients in primary care
Authors: Richardson Gerry , Epstein David , Chew-Graham Carolyn , Dowrick Christopher , Bentall Richard P , Morriss Richard K , Peters Sarah , Riste Lisa , Lovell Karina , Dunn Graham , Wearden Alison J ,   the FINE Trial Writing group on behalf of the FINE Trial group
Published: January 2013

AbstractBackgroundNurse led self-help treatments for people with chronic fatigue syndrome/myalgic encephalitis (CFS/ME) have been shown to be effective in reducing fatigue but their cost-effectiveness is unknown.MethodsCost-effectiveness analysis conducted alongside a single blind randomised controlled trial comparing pragmatic rehabilitation (PR) and supportive listening (SL) delivered by primary care nurses, and treatment as usual (TAU) delivered by the general practitioner (GP) in North West England. A within trial analysis was conducted comparing the costs and quality adjusted life years (QALYs) measured within the time frame of the trial. 296 patients aged 18 and over with CFS/ME diagnosed using the Oxford criteria were included in the cost-effectiveness analysis.ResultsTreatment as usual is less expensive and leads to better patient outcomes compared with Supportive Listening. Treatment as usual is also less expensive than Pragmatic Rehabilitation. PR was effective at reducing fatigue in the short term, but the impact of the intervention on QALYs was uncertain. However, based on the results of this trial, PR is unlikely to be cost-effective in this patient population.ConclusionsThis analysis does not support the introduction of SL. Any benefits generated by PR are unlikely to be of sufficient magnitude to warrant recommending PR for this patient group on cost-effectiveness grounds alone. However, dissatisfaction with current treatment options means simply continuing with ‘treatment as usual’ in primary care is unlikely to be acceptable to patients and practitioners.Trial registrationThe trial registration number is IRCTN74156610
Co-culture of primary human tumor hepatocytes from patients with hepatocellular carcinoma with autologous peripheral blood mononuclear cells: study of their in vitro immunological interactions
Authors: Doumba Polyxeni P , Nikolopoulou Marilena , Gomatos Ilias P , Konstadoulakis Manousos M , Koskinas John 
Published: January 2013

AbstractBackgroundMany studies have suggested that the immune response may play a crucial role in the progression of hepatocellular carcinoma (HCC). Therefore, our aim was to establish a (i) functional culture of primary human tumor hepatocytes and non-tumor from patients with hepatocellular carcinoma (HCC) and (ii) a co-culture system of HCC and non-HCC hepatocytes with autologous peripheral blood mononuclear cells (PBMCs) in order to study in vitro cell-to-cell interactions.MethodsTumor (HCC) and non-tumor (non-HCC) hepatocytes were isolated from the liver resection specimens of 11 patients operated for HCC, while PBMCs were retrieved immediately prior to surgery. Four biopsies were obtained from patients with no liver disease who had surgery for non malignant tumor (normal hepatocytes). Hepatocytes were either cultured alone (monoculture) or co-cultured with PBMCs. Flow cytometry measurements for MHC class II expression, apoptosis, necrosis and viability (7AAD) were performed 24 h, 48 h and 72 h in co-culture and monocultures.ResultsHCC and non-HCC hepatocytes exhibited increased MHC-II expression at 48h and 72h in co-culture with PBMCs as compared to monoculture, with MHC II-expressing HCC hepatocytes showing increased viability at 72 h. PBMCs showed increased MHC-II expression (activation) in co-culture with HCC as compared to non-HCC hepatocytes at all time points. Moreover, CD8+ T cells had significantly increased apoptosis and necrosis at 48h in co-culture with HCC hepatocytes as compared to monocultures.Interestingly, MHC-II expression on both HCC and non-HCC hepatocytes in co-culture was positively correlated with the respective activated CD8+ T cells.ConclusionsWe have established an in vitro co-culture model to study interactions between autologous PBMCs and primary HCC and non-HCC hepatocytes. This direct interaction leads to increased antigen presenting ability of HCC hepatocytes, activation of PBMCs with a concomitant apoptosis of activated CD8+ T cells. Although, a partially effective immune response against HCC exists, still tumor hepatocytes manage to escape.
Frequency and antimicrobial resistance patterns of bacteria implicated in community urinary tract infections: a ten-year surveillance study (2000–2009)
Authors: Linhares Inês , Raposo Teresa , Rodrigues António , Almeida Adelaide 
Published: January 2013

Abstract

Background
Urinary tract infection (UTI) is one of the most common infectious diseases at the community level. In order to assess the adequacy of the empirical therapy, the prevalence and the resistance pattern of the main bacteria responsible for UTI in the community (in Aveiro, Portugal) was evaluated throughout a ten-year period.

Methods
In this retrospective study, all urine samples from patients of the District of Aveiro, in ambulatory regime, collected at the Clinical Analysis Laboratory Avelab during the period 2000–2009 were analysed. Samples with more than 105 CFU/mL bacteria were considered positive and, for these samples, the bacteria were identified and the profile of antibiotic susceptibility was characterized.

Results
From the 155597 samples analysed, 18797 (12.1%) were positive for bacterial infection. UTI was more frequent in women (78.5%) and its incidence varied with age, affecting more the elderly patients (38.6%). Although E. coli was, as usual, the most common pathogen implicated in UTI, it were observed differences related to the other bacteria more implicated in UTI relatively to previous studies. The bacteria implicated in the UTI varied with the sex of the patient, being P. aeruginosa a more important cause of infection in men than in women. The incidence of the main bacteria changed over the study period (P. aeruginosa, Klebsiella spp and Providencia spp increased and Enterobacter spp decreased). Although E. coli was responsible for more than an half of UTI, its resistance to antibiotics was low when compared with other pathogens implicated in UTI, showing also the lowest percentage of multidrug resistant (MDR) isolates (17%). Bacteria isolated from females were less resistant than those isolated from males and this difference increased with the patient age.

Conclusions
The differences in sex and age must be taken into account at the moment of empirical prescription of antimicrobials. From the recommended antimicrobials by the European Association of Urology guidelines, the first line drugs (pivmecillinam and nitrofurantoin) and the alternative antibiotic amoxicillin-clavulanic acid (AMX-CLA) are appropriate to treat community-acquired UTI, but the fluoroquinolones should not be suitable to treat male infections and the trimethoprim-sulfamethoxazole (SXT) shall not be used in the treatment of UTI at this level.
In situ molecular identification of the Influenza A (H1N1) 2009 Neuraminidase in patients with severe and fatal infections during a pandemic in Mexico City
Authors: Ocadiz-Delgado Rodolfo , Albino-Sanchez Martha Estela , Garcia-Villa Enrique , Aguilar-Gonzalez Maria Guadalupe , Cabello Carlos , Rosete Dora , Mejia Fidencio , Manjarrez-Zavala Maria Eugenia , Ondarza-Aguilera Carmen , Rivera-Rosales Rosa Ma , Gariglio Patricio 
Published: January 2013

Abstract

Background
In April 2009, public health surveillance detected an increased number of influenza-like illnesses in Mexico City’s hospitals. The etiological agent was subsequently determined to be a spread of a worldwide novel influenza A (H1N1) triple reassortant. The purpose of the present study was to demonstrate that molecular detection of pandemic influenza A (H1N1) 2009 strains is possible in archival material such as paraffin-embedded lung samples.

Methods
In order to detect A (H1N1) virus sequences in archived biological samples, eight paraffin-embedded lung samples from patients who died of pneumonia and respiratory failure were tested for influenza A (H1N1) Neuraminidase (NA) RNA using in situ RT-PCR.

Results
We detected NA transcripts in 100% of the previously diagnosed A (H1N1)-positive samples as a cytoplasmic signal. No expression was detected by in situ RT-PCR in two Influenza-like Illness A (H1N1)-negative patients using standard protocols nor in a non-related cervical cell line. In situ relative transcription levels correlated with those obtained when in vitro RT-PCR assays were performed. Partial sequences of the NA gene from A (H1N1)-positive patients were obtained by the in situ RT-PCR-sequencing method. Sequence analysis showed 98% similarity with influenza viruses reported previously in other places.

Conclusions
We have successfully amplified specific influenza A (H1N1) NA sequences using stored clinical material; results suggest that this strategy could be useful when clinical RNA samples are quantity limited, or when poor quality is obtained. Here, we provide a very sensitive method that specifically detects the neuraminidase viral RNA in lung samples from patients who died from pneumonia caused by Influenza A (H1N1) outbreak in Mexico City.
Association between family members of dialysis patients and chronic kidney disease: a multicenter study in China
Authors: Kong Xianglei , Liu Li , Zuo Li , Yuan Ping , Li Zhongxin , Li Wenge , Cai Meishun , Chen Xiangmei , Jiang Aili , Long Gang , Xu Jinsheng , Lin Hongli , Wang Shixiang , Huang Wen , Wang Yiping , Guo Yidan , Cao Po , Wu Hua , Jia Qiang , Zhang Luxia , Wang Mei , Wang Haiyan 
Published: January 2013

Abstract

Background
Family members of patients with end stage renal disease were reported to have an increased prevalence of chronic kidney disease (CKD). However, studies differentiated genetic and non-genetic family members are limited. We sought to investigate the prevalence of CKD among fist-degree relatives and spouses of dialysis patients in China.

Methods
Seventeen dialysis facilities from 4 cities of China including 1062 first-degree relatives and 450 spouses of dialysis patients were enrolled. Sex- and age- matched controls were randomly selected from a representative sample of general population in Beijing. CKD was defined as decreased estimated glomerular (eGFR < 60 mL/min/1.73 m2) or albuminuria.

Results
The prevalence of eGFR less than 60 mL/min/1.73 m2, albuminuria and the overall prevalence of CKD in dialysis spouses were compared with their counterpart controls, which was 3.8% vs. 7.8% (P < 0.01), 16.8% vs. 14.6% (P = 0.29) and 18.4% vs. 19.8% (P = 0.61), respectively. The prevalence of eGFR less than 60 mL/min/1.73 m2, albuminuria and the overall prevalence of CKD in dialysis relatives were also compared with their counterpart controls, which was 1.5% vs. 2.4% (P = 0.12), 14.4% vs. 8.4% (P < 0.01) and 14.6% vs. 10.5% (P < 0.01), respectively. Multivariable Logistic regression analysis indicated that being spouses of dialysis patients is negatively associated with presence of low eGFR, and being relatives of dialysis patients is positively associated with presence of albuminuria.

Conclusions
The association between being family members of dialysis patients and presence of CKD is different between first-degree relatives and spouses. The underlying mechanisms deserve further investigation.
MicroRNA-34a is a tumor suppressor in choriocarcinoma via regulation of Delta-like1
Authors: Pang Ronald TK , Leung Carmen ON , Lee Cheuk-Lun , Lam Kevin KW , Ye Tian-Min , Chiu Philip CN , Yeung William SB 
Published: January 2013

Abstract

Background
Choriocarcinoma is a gestational trophoblastic tumor which causes high mortality if left untreated. MicroRNAs (miRNAs) are small non protein-coding RNAs which inhibit target gene expression. The role of miRNAs in choriocarcinoma, however, is not well understood. In this study, we examined the effect of miR-34a in choriocarcinoma.

Methods
MiR-34a was either inhibited or ectopically expressed transiently in two choriocarcinoma cell lines (BeWo and JEG-3) respectively. Its actions on cell invasion, proliferation and colony formation at low cell density were examined. The miR-34a putative target Notch ligand Delta-like 1 (DLL1) was identified by adoption of different approaches including: in-silico analysis, functional luciferase assay and western blotting. Real-time quantitative polymerase chain reaction was used to quantify changes in the expression of matrix proteinase in the treated cells. To nullify the effect of miR-34a ectopic expression, we activated Notch signaling through force-expression of the Notch intracellular domain in the miR-34a force-expressed cells. In addition, we studied the importance of DLL1 in BeWo cell invasion through ligand stimulation and antibody inhibition. Furthermore, the induction in tumor formation of miR-34a-inhibited BeWo cells in SCID mice was investigated.

Results
Transient miR-34a force-expression significantly suppressed cell proliferation and invasion in BeWo and JEG-3 cells. In silicon miRNA target prediction, luciferase functional assays and Western blotting analysis demonstrated that miR-34a regulated DLL1 expression in both cell lines. Although force-expression of miR-34a suppressed the expression of DLL1 and NOTCH1, the extent of suppression was higher in DLL1 than NOTCH1 in both cell lines. MiR-34a-mediated DLL1 suppression led to reduced matrix metallopeptidase 9 and urokinase-type plasminogen activator expression. The effect of miR-34a on cell invasion was partially nullified by Notch signaling activation. DLL1 ligand stimulated while anti-DLL1 antibody treatment suppressed cell invasion. Mice inoculated with BeWo cells transfected with miR-34a inhibitor had significantly larger xenografts and stronger DLL1 expression than those with cells transfected with the control inhibitor.

Conclusions
MiR-34a reduced cell proliferation and invasiveness, at least, partially through its inhibitory effect on DLL1.
Reference intervals of serum hyaluronic acid corresponding to the radiographic severity of knee osteoarthritis in women
Authors: Kaneko Haruka , Ishijima Muneaki , Doi Tokuhide , Futami Ippei , Liu Lizu , Sadatsuki Ryo , Yusup Anwarjan , Hada Shinnosuke , Kubota Mitsuaki , Kawasaki Takayuki , Saita Yoshitomo , Takazawa Yuji , Ikeda Hiroshi , Kurosawa Hisashi , Kaneko Kazuo 
Published: January 2013

Abstract

Backgroud
While serum levels of hyarulonic acid (sHA) is known to be useful for a burden of disease biomarker in knee OA, it is far from practical. The reference intervals must be established for biomarkers to be useful for clinical interpretation. The aim of this study was to establish the reference intervals of sHA corresponding to the radiographic severity of knee OA for elucidating whether sHA can be useful as a burden of disease marker for individual patient with knee OA.

Methods
372 women with Kellgren & Lawrence grade (K/L) 1 through 4 painful knee OA were enrolled in this study. The patients included 54 with K/L 1, 96 with K/L 2, 97 with K/L 3, and 118 with K/L 4. Serum samples were obtained from all subjects on the day that radiographs taken. A HA binding protein based latex agglutination assay that employed an ELISA format was used to measure sHA. Age and BMI adjusted one way ANOVA was used to set the reference intervals of sHA.

Results
The reference intervals for sHA corresponding to the patients with K/L 4 (49.6 – 66.5 ng/ml) was established without any overlap against to those with K/L 1, 2 and 3, while those with K/L 1, 2 and 3 showed considerable overlap.

Conclusions
These results indicate that sHA can be available as a burden of disease marker for the individuals with severe knee OA (K/L 4), while it is not for those with primary to moderate knee OA (K/L 1–3).
Predictors of Dental caries among children 7–14 years old in Northwest Ethiopia: a community based cross-sectional study
Authors: Ayele Fenta A , Taye Belaynew W , Ayele Tadesse A , Gelaye Kassahun A 
Published: January 2013

Abstract

Background
Dental caries in children remains a significant public health problem. It is a disease with multifactorial causes. The aim of the study was to assess the prevalence and associated factors of dental caries among children between 7 to 14 years old.

Methods
A community based cross-sectional study was conducted in Gondar town from June 2011 to September 2011. A total of 842 children were involved in the study. Multi-stage sampling technique was used to select the children. Pretested and structured questionnaires were used to collect data from mothers. Clinical examination of children was done using dental caries criteria set by world health organization. Data were entered, cleaned and edited using EPI Info version 3.5.1 and exported to SPSS version 16.0 for analysis. Binary multiple logistic regression analyses was applied to test the association.

Results
Four hundred sixty three (55%) children were females. The prevalence of dental caries was 306(36.3%).The educational status of children’s father (AOR=0.3, 95%CI, 0.17, 0.80), monthly household income (AOR=0.59, 95%CI, 0.01, 0.45), regular teeth brushing (AOR=0.08, 95% CI, 0.03, 0.20) and using mouth rinsing (AOR=0.40, 95% CI, 0.2, 0.80) were found statistically significantly associated with dental caries.

Conclusions
Dental caries were high among children in Gondar town. Low socioeconomic status and poor oral hygiene practices were the influencing factors for dental caries. Oral hygiene, dietary habits and access to dental care services are supreme important for the prevention of the problem.