bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of low molecular weight nuclear complexes containing integrase during the early stages of HIV-1 infection
Authors: Gérard Annabelle , Soler Nicolas , Ségéral Emmanuel , Belshan Michael , Emiliani Stéphane 
Published: February 2013

Abstract

Background
HIV-1 replication requires integration of its reverse transcribed viral cDNA into a host cell chromosome. The DNA cutting and joining reactions associated to this key step are catalyzed by the viral protein integrase (IN). In infected cells, IN binds the viral cDNA, together with viral and cellular proteins, to form large nucleoprotein complexes. However, the dynamics of IN complexes formation is still poorly understood.

Results
Here, we characterized IN complexes during the early stages of T-lymphocyte infection. We found that following viral entry into the host cell, IN was rapidly targeted to proteasome-mediated degradation. Interactions between IN and cellular cofactors LEDGF/p75 and TNPO3 were detected as early as 6 h post-infection. Size exclusion chromatography of infected cell extracts revealed distinct IN complexes in vivo. While at 2 h post-infection the majority of IN eluted within a high molecular weight complex competent for integration (IN complex I), IN was also detected in a low molecular weight complex devoid of full-length viral cDNA (IN complex II, ~440 KDa). At 6 h post-infection the relative proportion of IN complex II increased. Inhibition of reverse transcription or integration did not alter the elution profile of IN complex II in infected cells. However, in cells depleted for LEDGF/p75 IN complex II shifted to a lower molecular weight complex (IN complex III, ~150 KDa) containing multimers of IN. Notably, cell fractionation experiments indicated that both IN complex II and III were exclusively nuclear. Finally, IN complex II was not detected in cells infected with a virus harboring a mutated IN defective for LEDGF/p75 interaction and tetramerization.

Conclusions
Our findings indicate that, shortly after viral entry, a significant portion of DNA–free IN that is distinct from active pre-integration complexes accumulates in the nucleus.
Sero-epidemiological survey of human cytomegalovirus-infected children in Weifang (Eastern China) between 2009 and 2012
Authors: Sun Xiuning , Liu Zhijun , Wang Bin , Shi Lihong , Liang Ruiwen , Li Ling , Qian Dongmeng , Song Xuxia 
Published: February 2013

Abstract

Background
To understand the prevalence and characteristics of human cytomegalovirus (HCMV) infection in children in the Weifang area, and to provide information for its prevention and treatment.

Methods
A comprehensive survey was performed from 2009 to 2012 in 7582 children from birth to 6 years of age hospitalized in the Maternity and Child Health Hospital of Weifang. ELISA HCMV serology results and survey data were analyzed by age group and socio-economic level. The infection rates were based on IgG and IgM serology.

Results and conclusions
The overall infection rate from IgG and IgM in the Weifang area from 2009 to 2012 was 42.5% (3496/7582), among which 34.2% were HCMV-IgG positive, suggesting past infection. Overall, the probability of active HCMV infection showed no gender difference in any age group (P >0.05). Recent infections centered on the first 6 months of life, presumably due to breastfeeding. Among the 654 children hospitalized for active HCMV infection, 379 (57.9%) were from rural areas and 275 (42.1%) from urban areas, showing that active infection in the countryside was higher than that in the city (χ2 = 32.65, p <0.01).
The prevalence and risk factors of cytomegalovirus infection in inflammatory bowel disease in Wuhan, Central China
Authors: Yi Fengming , Zhao Jie , Luckheeram Rishi Vishal , Lei Yuan , Wang Changgao , Huang Sha , Song Lu , Wang Wei , Xia Bing 
Published: February 2013

Abstract

Background
The etiology of inflammatory bowel disease (IBD) is not clear and cytomegalovirus (CMV) infection is often associated with IBD patients. The etiologic link between IBD and CMV infection needs to be studied. The objective of the present study is to investigate the prevalence and risk factors of CMV in a cohort of IBD patients from Central China.

Methods
Two hundred and twenty six IBD patients (189 ulcerative colitis (UC) and 37 patients with Crohn’s disease (CD)), and 290 age and sex matched healthy controls were recruited. CMV DNA was detected by nested PCR, while serum anti-CMV IgG and anti-CMV IgM was determined by ELISAs. Colonoscopy/enteroscopy with biopsy of diseased tissues and subsequent H&E stain were then conducted in IBD patients with positive anti-CMV IgM. Finally, we analyzed the prevalence and clinical risk factors of CMV infection in IBD patients.

Results
The prevalence of CMV DNA and anti-CMV IgG positive rate in IBD patients were 84.07% and 76.11%, respectively, higher than those in healthy controls (59.66% and 50.69%, respectively, P < 0.05), However, anti-CMV IgM positive rate was no different with healthy controls (1.77% vs 0.34%, P = 0.235). In univariate analysis of risk factors, the recent use of corticosteroid was associated with increase of CMV DNA and IgM positive rate in UC (P = 0.035 and P = 0.015, respectively), aminosalicylic acid drug therapy was correlated with positivity of CMV DNA and IgG in UC and CMV DNA in CD (P = 0.041, P < 0.001 and P = 0.014, respectively), the treatment of immunosuppresent was correlated with CMV IgM (P < 0.001). Furthermore, patients with severe UC were significantly associated with CMV DNA and IgM (P = 0.048 and P = 0.031, respectively). Malnutrition (albumin < 35 G/L) was also found to be related with CMV recent infection (P = 0.031). In multivariate analysis of risk factors in UC, pancolitis was significantly associated with CMV DNA positivity (P = 0.001). Severe UC and pancolitis seemed to be related with IgG positivity. For CD, there was just single factor associated with CMV positive in each group, multivariate analysis was unnecessary.

Conclusions
CMV positive rate in IBD patients was significantly higher, than in healthy controls. The use of aminosalicylic acid, corticosteroid, immunosuppressants, pancolitis and severe IBD patients seemed to be more susceptible to CMV infection in univariate analysis of risk factors. However, no risk factor was found to be significantly correlated with CMV infection in multivariate analysis of risk factors.
In-office bacteria test for a microbial monitoring during the conventional and self-ligating orthodontic treatment
Authors: Mummolo Stefano , Marchetti Enrico , Giuca Maria Rita , Gallusi Gianni , Tecco Simona , Gatto Roberto , Marzo Giuseppe 
Published: February 2013

Abstract
This study investigated the microbial level of Streptococcus mutans and Lactobacillus spp. during an orthodontic treatment, and compare the data with untreated control subjects.
Sixty young adult subjects were selected (average 20.5, DS 1.62), among which 40 underwent an orthodontic treatment (20 were treated with self-ligating brackets and 20 with conventional brackets) and 20 were controls. Plaque Index, salivary flow and buffering capacity of saliva were assessed before the beginning of the orthodontic treatment. Then the microbial counts were obtained by using an in-office bacteria test.
The plaque index (PI) increased over time in each group as well as salivary flow, mostly in subjects treated with self-ligating brackets, suggesting a difference between conventional and self-ligating brackets. S.mutans showed a different trend of colonization in the two treated groups, as for subjects treated with conventional brackets it showed the greater value at the early stage of treatment (T1), followed by a decrease at T2. Lactobacillus spp. showed significant increase over time in the two treated groups, respect to the control group. Linear regression analysis showed no significant predictor for the microbial count at T2.
The assortment of the various species of bacteria change over time during the orthodontic treatment, and seems to show different trends, depending on the type of orthodontic device. Consequently a periodical microbial monitoring using in-office bacteria tests, seems indicated.
Resection of a methicillin-resistant Staphylococcus aureus liver abscess in a patient with Crohn’s disease under infliximab treatment: a case report
Authors: Togashi Junichi , Sugawara Yasuhiko , Akamatsu Nobuhisa , Aoki Taku , Ijichi Masayoshi , Tanabe Mami , Kusaka Koji , Shibazaki Masayuki , Tadami Tokuma , Sakou Minako , Takazoe Masakazu , Bandai Yasutsugu , Kokudo Norihiro 
Published: February 2013

Abstract

Introduction
A liver abscess in Crohn’s disease is a rare but important entity that is associated with a poor prognosis and high mortality when treatment is delayed. We report a case of successful liver segmentectomy for a methicillin-resistant Staphylococcus aureus liver abscess in a patient with Crohn’s disease under infliximab treatment.

Case presentation
A 31-year-old Japanese man, who had been treated with infliximab infusions for Crohn’s disease, was referred to our hospital presenting with an abrupt onset of high fever and an elevated white blood cell count and serum C-reactive protein level. Computed tomography revealed a liver abscess occupying segment 8. The limited effect of percutaneous transhepatic abscess drainage and antibiotics led us to perform radical resection of the abscess. The patient recovered quickly after surgery and the postoperative course was uneventful.

Conclusion
The present case suggests that surgical removal of an abscess should be considered for patients under immunosuppression or refractory to conventional treatment.
A review of the foot function index and the foot function index – revised
Authors: Budiman‐Mak Elly , Conrad Kendon J , Mazza Jessica , Stuck Rodney M 
Published: February 2013

AbstractBackgroundThe Foot Function Index (FFI) is a self‐report, foot‐specific instrument measuring pain and disability and has been widely used to measure foot health for over twenty years. A revised FFI (FFI‐R) was developed in response to criticism of the FFI. The purpose of this review was to assess the uses of FFI and FFI‐R as were reported in medical and surgical literature and address the suggestions found in the literature to improve the metrics of FFI‐R.MethodsA systematic literature search of PubMed/Medline and Embase databases from October 1991 through December 2010 comprised the main sources of literature. To enrich the bibliography, the search was extended to BioMedLib and Scopus search engines and manual search methods. Search terms included FFI, FFI scores, FFI‐R. Requirements included abstracts/full length articles, English‐language publications, and articles containing the term “foot complaints/problems.” Articles selected were scrutinized; EBM abstracted data from literature and collected into tables designed for this review. EBM analyzed tables, KJC, JM, RMS reviewed and confirmed table contents. KJC and JM reanalyzed the original database of FFI‐R to improve metrics.ResultsSeventy‐eight articles qualified for this review, abstracts were compiled into 12 tables. FFI and FFI‐R were used in studies of foot and ankle disorders in 4700 people worldwide. FFI Full scale or the Subscales and FFI‐R were used as outcome measures in various studies; new instruments were developed based on FFI subscales. FFI Full scale was adapted/translated into other cultures. FFI and FFI‐R psychometric properties are reported in this review. Reanalysis of FFI‐R subscales’ confirmed unidimensionality, and the FFI‐R questionnaires’ response categories were edited into four responses for ease of use.ConclusionThis review was limited to articles published in English in the past twenty years. FFI is used extensively worldwide; this instrument pioneered a quantifiable measure of foot health, and thus has shifted the paradigm of outcome measure to subjective, patient‐centered, valid, reliable and responsive hard data endpoints. Edited FFI‐R into four response categories will enhance its user friendliness for measuring foot health.
Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)
Authors: Benachenhou Farid , Sperber Göran O , Bongcam-Rudloff Erik , Andersson Göran , Boeke Jef D , Blomberg Jonas 
Published: February 2013

Abstract

Background
Long terminal repeats (LTRs, consisting of U3-R-U5 portions) are important elements of retroviruses and related retrotransposons. They are difficult to analyse due to their variability.
The aim was to obtain a more comprehensive view of structure, diversity and phylogeny of LTRs than hitherto possible.

Results
Hidden Markov models (HMM) were created for 11 clades of LTRs belonging to Retroviridae (class III retroviruses), animal Metaviridae (Gypsy/Ty3) elements and plant Pseudoviridae (Copia/Ty1) elements, complementing our work with Orthoretrovirus HMMs. The great variation in LTR length of plant Metaviridae and the few divergent animal Pseudoviridae prevented building HMMs from both of these groups.
Animal Metaviridae LTRs had the same conserved motifs as retroviral LTRs, confirming that the two groups are closely related. The conserved motifs were the short inverted repeats (SIRs), integrase recognition signals (5´TGTTRNR…YNYAACA 3´); the polyadenylation signal or AATAAA motif; a GT-rich stretch downstream of the polyadenylation signal; and a less conserved AT-rich stretch corresponding to the core promoter element, the TATA box. Plant Pseudoviridae LTRs differed slightly in having a conserved TATA-box, TATATA, but no conserved polyadenylation signal, plus a much shorter R region.
The sensitivity of the HMMs for detection in genomic sequences was around 50% for most models, at a relatively high specificity, suitable for genome screening.
The HMMs yielded consensus sequences, which were aligned by creating an HMM model (a ‘Superviterbi’ alignment). This yielded a phylogenetic tree that was compared with a Pol-based tree. Both LTR and Pol trees supported monophyly of retroviruses. In both, Pseudoviridae was ancestral to all other LTR retrotransposons. However, the LTR trees showed the chromovirus portion of Metaviridae clustering together with Pseudoviridae, dividing Metaviridae into two portions with distinct phylogeny.

Conclusion
The HMMs clearly demonstrated a unitary conserved structure of LTRs, supporting that they arose once during evolution. We attempted to follow the evolution of LTRs by tracing their functional foundations, that is, acquisition of RNAse H, a combined promoter/ polyadenylation site, integrase, hairpin priming and the primer binding site (PBS). Available information did not support a simple evolutionary chain of events.
Bacterial diversity of the rock-water interface in an East Antarctic freshwater ecosystem, Lake Tawani(P)†
Authors: Huang Jonathan P , Swain Ashit K , Thacker Robert W , Ravindra Rasik , Andersen Dale T , Bej Asim K 
Published: February 2013

Abstract
Schirmacher Oasis is one of the few ice-free plateaus in East Antarctica that maintains a unique distribution of over 120 microbial-rich, dynamic freshwater lakes, most of which are unexplored. In this study, we describe the bacterial diversity of the rock-water interface in Lake Tawani(P) using culture-independent Bacterial Tag Encoded FLX Amplicon Pyrosequencing (bTEFAP), clone library construction, and culture-based analysis targeting the eubacterial 16S rRNA gene. Lake Tawani(P)was formed in a fossil valley by the accumulation of snow and glacial melt through surface channels into a low-catchment depression. Overall this lake exhibited thirteen bacterial phyla and one-hundred and twelve genera. The Qiime bioinformatics analysis on the bTEFAP alone exhibited higher coverage of the bacterial composition in Lake Tawani(P) than the clone library construction or culture-based methodology. Particularly due to the higher sensitivity of the bTEFAP approach, we detected and differentiated members of the phyla: Chloroflexi, Gemmatimonadetes, Planctomycetes, Nitrospira, and Candidate Division TM7 that other methods were unable to reveal. Nevertheless we found that the use of multiple approaches identified a more complete bacterial community than by using any single approach. Investigating the bacterial diversity of the Schirmacher Oasis lakes, especially those connected through surface channels and encompassed by valleys, will help unravel the dynamic nature of these unique seasonal, freshwater lakes, which potentially harbors highly adapted bacterial taxa with defined ecological functions.
Leflunomide inhibits the apoptosis of human embryonic lung fibroblasts infected by human cytomegalovirus
Authors: Qi Ren , Hua-Song Zeng , Xiao-Feng Zeng 
Published: February 2013

Abstract

Background
The immunomodulatory drug leflunomide (LEF) is frequently used for treating human cytomegalovirus (HCMV), but its antiviral mechanism is still unclear. In this study,we therefore investigated the effects of the active LEF metabolite A771726 on the HCMV lifecycle in human embryonic lung fibroblasts. We clarified the mechanism of LEF antiviral infection, and provide a new way to treat immune dysfunction patients with HCMV infection.

Methods
The experiment was divided into four groups: the control group, the HCMV group, the ganciclovir + HCMV group as well as the LEF + HCMV group. MTT was usedfor assessment of the cell inhibitory rate. Apoptosis was measured by staining with fluorescein isothiocyanate Annexin V and propidium iodide. Statistical significance was determined by paired t- test using SPSS software.

Results
The results of the study showed that cell proliferation was significantly inhibited by HCMV at 24 hours and 48 hours. With increasing HCMV concentration, the value-added inhibition of the cells was significantly decreased compared with the control group, and was statistically significant (P <0.01). Ganciclovir can increase proliferation of cellsinfected with HCMV; compared with the control group it was statistically significant (P <0.05). Meanwhile, with LEF treatment cell proliferation was significantly improved at 24 hours and 48 hours, with statistical significance (P <0.05). The apoptosis rate of human embryonic lung fibroblasts infected with HCMV increased significantly at 24 hours, 48 hours and 72 hours, and as time goes on the apoptosis rate increases statistically significantly (P <0.01) compared with the control group The apoptosis rate of theHCMV infection group decreased by adding LEF,and was statistically significant (P <0.05).

Conclusions
In this studywe show that LEF is an exciting new drug for cytomegalovirus infection. LEF significantly inhibited HCMV infection-induced apoptosis and proliferation, playing an important role in the treatment of patients infected by HCMV. In this study we explored the potential usefulness of LEF for cytomegalovirus infection and found it to be a cost-effective new treatment for cytomegalovirus infection that deserves further study.
Rilonacept in the treatment of acute gouty arthritis: a randomized, controlled clinical trial using indomethacin as the active comparator
Authors: Terkeltaub Robert A , Schumacher H Ralph , Carter John D , Baraf Herbert SB , Evans Robert R , Wang Jian , King-Davis Shirletta , Weinstein Steven P 
Published: February 2013

Abstract
Introduction
In phase-3 clinical trials, the interleukin (IL-1) blocker, rilonacept (IL-1 Trap), demonstrated efficacy for gout flare prevention during initiation of urate-lowering therapy. This trial evaluated rilonacept added to a standard-of-care, indomethacin, for treatment of acute gout flares.

Methods
Adults, aged 18-70 years, with gout presenting within 48 hours of flare onset and having at least moderate pain as well as swelling and tenderness in the index joint were randomized to subcutaneous (SC) rilonacept 320 mg at baseline plus oral indomethacin 50 mg TID for 3 days followed by 25 mg TID for up to 9 days (n = 74); SC placebo at baseline plus oral indomethacin as above (n = 76); or SC rilonacept 320 mg at baseline plus oral placebo (n = 75). The primary efficacy endpoint was change in pain in the index joint (patient-reported using a Likert scale (0 = none; 4 = extreme)) from baseline to the average of values at 24, 48 and 72 hours (composite time point) for rilonacept plus indomethacin versus indomethacin alone. Comparison of rilonacept monotherapy with indomethacin monotherapy was dependent on demonstration of significance for the primary endpoint. Safety evaluation included clinical laboratory and adverse event (AE) assessments.

Results
Patient characteristics were comparable among the groups; the population was predominantly male (94.1%), white (75.7%), with mean ± SD age of 50.3 ± 10.6 years. All treatment groups reported within-group pain reductions from baseline (P < 0.0001). Although primary endpoint pain reduction was greater with rilonacept plus indomethacin (-1.55 ± 0.92) relative to indomethacin alone (-1.40 ± 0.96), the difference was not statistically significant (P = 0.33), so formal comparison between monotherapy groups was not performed. Pain reduction over the 72-hour period with rilonacept alone (-0.69 ± 0.97) was less than that in the other groups, but pain reduction was similar among groups at 72 hours. Treatment with rilonacept was well-tolerated with no reported serious AEs related to rilonacept. Across all groups, the most frequent AEs were headache and dizziness.

Conclusions
Although generally well-tolerated, rilonacept in combination with indomethacin and rilonacept alone did not provide additional pain relief over 72 hours relative to indomethacin alone in patients with acute gout flare.

Trial registration
ClinicalTrials.gov registration number NCT00855920.
Serum adipocyte fatty acid-binding protein levels in patients with critical illness are associated with insulin resistance and predict mortality
Authors: Huang Chi-Lun , Wu Yen-Wen , Hsieh Ai-Ru , Hung Yu-Hsuan , Chen Wen-Jone , Yang Wei-Shiung 
Published: February 2013

Abstract
Introduction
Hyperglycemia and insulin resistance are commonplace in critical illness, especially in patients with sepsis. Recently, several hormones secreted by adipose tissue have been determined to be involved in overall insulin sensitivity in metabolic syndrome-related conditions, including adipocyte fatty-acid binding protein (A-FABP). However, little is known about their roles in critical illness. On the other hand, there is evidence that several adipose tissue gene expressions change in critically ill patients.

Methods
A total of 120 patients (72 with sepsis, 48 without sepsis) were studied prospectively on admission to a medical ICU and compared with 45 healthy volunteers as controls. Various laboratory parameters and metabolic and inflammatory profiles were assessed within 48 hours after admission. Clinical data were collected from medical records.

Results
Compared with healthy controls, serum A-FABP concentrations were higher in all critically ill patients, and there was a trend of higher A-FABP in patients with sepsis. In multivariate correlation analysis in all critically ill patients, the serum A-FABP concentrations were independently related to serum creatinine, fasting plasma glucose, total cholesterol, TNF-alpha, albumin, and the Acute Physiology and Chronic Health Evaluation II scores. In survival analysis, higher A-FABP levels (> 40 ng/ml) were associated with an unfavorable overall survival outcome, especially in sepsis patients.

Conclusions
Critically ill patients have higher serum A-FABP concentrations. Moreover, A-FABP may potentially serve as a prognostic biomarker in critically ill patients with sepsis.