bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns
Authors: Meyer Fernando , Kurtz Stefan , Beckstette Michael 
Published: July 2013

Abstract

Background
It is well known that the search for homologous RNAs is more effective if both sequence and structure information is incorporated into the search. However, current tools for searching with RNA sequence-structure patterns cannot fully handle mutations occurring on both these levels or are simply not fast enough for searching large sequence databases because of the high computational costs of the underlying sequence-structure alignment problem.

Results
We present new fast index-based and online algorithms for approximate matching of RNA sequence-structure patterns supporting a full set of edit operations on single bases and base pairs. Our methods efficiently compute semi-global alignments of structural RNA patterns and substrings of the target sequence whose costs satisfy a user-defined sequence-structure edit distance threshold. For this purpose, we introduce a new computing scheme to optimally reuse the entries of the required dynamic programming matrices for all substrings and combine it with a technique for avoiding the alignment computation of non-matching substrings. Our new index-based methods exploit suffix arrays preprocessed from the target database and achieve running times that are sublinear in the size of the searched sequences. To support the description of RNA molecules that fold into complex secondary structures with multiple ordered sequence-structure patterns, we use fast algorithms for the local or global chaining of approximate sequence-structure pattern matches. The chaining step removes spurious matches from the set of intermediate results, in particular of patterns with little specificity. In benchmark experiments on the Rfam database, our improved online algorithm is faster than the best previous method by up to factor 45. Our best new index-based algorithm achieves a speedup of factor 560.

Conclusions
The presented methods achieve considerable speedups compared to the best previous method. This, together with the expected sublinear running time of the presented index-based algorithms, allows for the first time approximate matching of RNA sequence-structure patterns in large sequence databases. Beyond the algorithmic contributions, we provide with RaligNAtor a robust and well documented open-source software package implementing the algorithms presented in this manuscript. The RaligNAtor software is available at http://www.zbh.uni-hamburg.de/ralignator.
Dynamic compartment specific changes in glutathione and ascorbate levels in Arabidopsis plants exposed to different light intensities
Authors: Heyneke Elmien , Luschin-Ebengreuth Nora , Krajcer Iztok , Wolkinger Volker , Müller Maria , Zechmann Bernd 
Published: July 2013

Abstract

Background
Excess light conditions induce the generation of reactive oxygen species (ROS) directly in the chloroplasts but also cause an accumulation and production of ROS in peroxisomes, cytosol and vacuoles. Antioxidants such as ascorbate and glutathione occur in all cell compartments where they detoxify ROS. In this study compartment specific changes in antioxidant levels and related enzymes were monitored among Arabidopsis wildtype plants and ascorbate and glutathione deficient mutants (vtc2-1 and pad2-1, respectively) exposed to different light intensities (50, 150 which was considered as control condition, 300, 700 and 1,500 μmol m-2 s-1) for 4 h and 14 d.

Results
The results revealed that wildtype plants reacted to short term exposure to excess light conditions with the accumulation of ascorbate and glutathione in chloroplasts, peroxisomes and the cytosol and an increased activity of catalase in the leaves. Long term exposure led to an accumulation of ascorbate and glutathione mainly in chloroplasts. In wildtype plants an accumulation of ascorbate and hydrogen peroxide (H2O2) could be observed in vacuoles when exposed to high light conditions. The pad2-1 mutant reacted to long term excess light exposure with an accumulation of ascorbate in peroxisomes whereas the vtc2-1 mutant reacted with an accumulation of glutathione in the chloroplasts (relative to the wildtype) and nuclei during long term high light conditions indicating an important role of these antioxidants in these cell compartments for the protection of the mutants against high light stress.

Conclusion
The results obtained in this study demonstrate that the accumulation of ascorbate and glutathione in chloroplasts, peroxisomes and the cytosol is an important reaction of plants to short term high light stress. The accumulation of ascorbate and H2O2 along the tonoplast and in vacuoles during these conditions indicates an important route for H2O2 detoxification under these conditions.
Unexpected random urinary protein:creatinine ratio results–limitations of the pyrocatechol violet-dye method
Authors: De Silva Dane A , Halstead Anne C , Côté Anne-Marie , Sabr Yasser , von Dadelszen Peter , Magee Laura A 
Published: July 2013

Abstract

Background
For clinicians, it is important to rely on accurate laboratory results for patient care and optimal use of health care resources. We sought to explore our observations that urine protein:creatinine ratios (PrCr) ≥30 mg/mmol are seen not infrequently associated with normal pregnancy outcome.

Methods
Urine samples were collected prospectively from 160 pregnant women attending high-risk maternity clinics at a tertiary care facility. Urinary protein was measured using a pyrocatechol violet assay and urinary creatinine by an enzymatic method on Vitros analysers. Maternal/perinatal outcomes were abstracted from hospital records.

Results
91/233 (39.1%) samples had a PrCr ≥30 mg/mmol, especially when urinary creatinine concentration was <3 mM (94.1%) vs. ≥3 mM (16.4%) (p < 0.001). When using the last sample before delivery, 47/160 (29.4%) had a PrCr ≥30 mg/mmol in diluted urine vs. only 17/160 (15.4%) in more concentrated urine (p < 0.001); PrCr positive results were also more frequent among the 32 (20.0%) women with known normal pregnancy outcome (90.9% vs. 0) (p < 0.001). Using the same analyser, 0.12 g/L urinary protein was ‘detected’ in deionised water. Re-analysis of data from two cohorts revealed substantially less inflation of PrCr in dilute urine using a pyrogallol red assay.

Conclusions
Random urinary PrCr was overestimated in dilute urine when tested using a common pyrocatechol violet dye-based method. This effect was reduced in cohorts when pyrogallol red assays were used. False positive results can impact on diagnosis and patient care. This highlights the need for both clinical and laboratory quality improvement projects and standardization of laboratory protein measurement.
CXCR7 is induced by hypoxia and mediates glioma cell migration towards SDF-1α
Authors: Esencay Mine , Sarfraz Yasmeen , Zagzag David 
Published: July 2013

Abstract

Background
Glioblastomas, the most common and malignant brain tumors of the central nervous system, exhibit high invasive capacity, which hinders effective therapy. Therefore, intense efforts aimed at improved therapeutics are ongoing to delineate the molecular mechanisms governing glioma cell migration and invasion.

Methods
In order to perform the studies, we employed optimal cell culture methods and hypoxic conditions, lentivirus-mediated knockdown of protein expression, Western Blot analysis, migration assays and immunoprecipitation. We determined statistical significance by unpaired t-test.

Results
In this report, we show that U87MG, LN229 and LN308 glioma cells express CXCR7 and that exposure to hypoxia upregulates CXCR7 protein expression in these cell lines. CXCR7-expressing U87MG, LN229 and LN308 glioma cells migrated towards stromal-derived factor (SDF)-1α/CXCL12 in hypoxic conditions in the Boyden chamber assays. While shRNA-mediated knockdown of CXCR7 expression did not affect the migration of any of the three cell lines in normoxic conditions, we observed a reduction in the migration of LN229 and LN308, but not U87MG, glioma cells towards SDF-1α in hypoxic conditions. In addition, knockdown of CXCR7 expression in LN229 and LN308 glioma cells decreased levels of SDF-1α-induced phosphorylation of ERK1/2 and Akt. Inhibiting CXCR4 in LN229 and LN308 glioma cells that were knocked down for CXCR7 did not further reduce migration towards SDF-1α in hypoxic conditions and did not affect the levels of phosphorylated ERK1/2 and Akt. Analysis of immunoprecipitated CXCR4 from LN229 and LN308 glioma cells revealed co-precipitated CXCR7.

Conclusions
Taken together, our findings indicate that both CXCR4 and CXCR7 mediate glioma cell migration towards SDF-1α in hypoxic conditions and support the development of therapeutic agents targeting these receptors.
The overall health and risk factor profile of Australian Aboriginal and Torres Strait Islander participants from the 45 and up study
Authors: Gubhaju Lina , McNamara Bridgette J , Banks Emily , Joshy Grace , Raphael Beverley , Williamson Anna , Eades Sandra J 
Published: July 2013

Abstract

Background
Despite large disparities in health outcomes between Aboriginal and non-Aboriginal Australians, detailed evidence on the health and lifestyle characteristics of older Aboriginal Australians is lacking. The aim of this study is to quantify socio-demographic and health risk factors and mental and physical health status among Aboriginal participants from the 45 and Up Study and to compare these with non-Aboriginal participants from the study.

Methods
The 45 and Up Study is a large-scale study of individuals aged 45 years and older from the general population of New South Wales, Australia responding to a baseline questionnaire distributed from 2006–2008. Odds ratios (OR) and 95% confidence intervals (CI) of self-reported responses from the baseline questionnaire for Aboriginal versus non-Aboriginal participants relating to socio-demographic factors, health risk factors, current and past medical and surgical history, physical disability, functional health limitations and levels of current psychological distress were calculated using unconditional logistic regression, with adjustments for age and sex.

Results
Overall, 1939 of 266,661 45 and Up Study participants examined in this study identified as Aboriginal and/or Torres Strait Islander (0.7%). Compared to non-Aboriginal participants, Aboriginal participants were significantly more likely to be: younger (mean age 58 versus 63 years); without formal educational qualifications (age- and sex- adjusted OR = 6.2, 95% CI 5.3-7.3); of unemployed (3.7, 2.9-4.6) or disabled (4.6, 3.9-5.3) work status; and with a household income < $20,000/year versus ≥ $70,000/year (5.8, 5.0-6.9). Following additional adjustment for income and education, Aboriginal participants were significantly more likely than non-Aboriginal participants to: be current smokers (2.4, 2.0-2.8), be obese (2.1, 1.8-2.5), have ever been diagnosed with certain medical conditions (especially: diabetes [2.1, 1.8-2.4]; depression [1.6, 1.4-1.8] and stroke [1.8, 1.4-2.3]), have care-giving responsibilities (1.8, 1.5-2.2); have a major physical disability (2.6, 2.2-3.1); have severe physical functional limitation (2.9, 2.4-3.4) and have very high levels of psychological distress (2.4, 2.0-3.0).

Conclusions
Aboriginal participants from the 45 and Up Study experience greater levels of disadvantage and have greater health needs (including physical disability and psychological distress) compared to non-Aboriginal participants. The study highlights the need to address the social determinants of health in Australia and to provide appropriate mental health services and disability support for older Aboriginal people.
Insulin resistance is significantly associated with the metabolic syndrome, but not with sonographically proven peripheral arterial disease
Authors: Vonbank Alexander , Saely Christoph H , Rein Philipp , Drexel Heinz 
Published: July 2013

Abstract

Objective
Insulin resistance (IR) is the key feature of the metabolic syndrome (MetS); its association with peripheral arterial disease (PAD) is unclear. We hypothesized that IR is associated with both the MetS and sonographically proven PAD.

Methods
IR was determined by the Homeostasis Model Assessment (HOMA) index in 214 patients with sonographically proven PAD as well as in 197 controls, who did not have a history of PAD and in whom coronary artery disease was ruled out angiographically; the MetS was defined according to NCEP-ATPIII criteria.

Results
HOMA IR scores were significantly higher in MetS patients than in subjects without the MetS (5.9 ± 6.2 vs. 2.9 ± 3.9; p <0.001). However, HOMA IR did not differ significantly between patients with PAD and controls (4.2 ± 5.4 vs. 3.3 ± 4.3; p = 0.124). When both, the presence of MetS and of PAD were considered, HOMA IR was significantly higher in patients with the MetS both among those with PAD (6.1 ± 5.7 vs. 3.6 ± 5.2; p<0.001) and among controls (5.8 ± 6.8 vs. 2.3 ± 1.8; p <0.001), whereas it did not differ significantly between patients with PAD and controls among patients with the MetS (5.8 ± 6.8 vs. 6.1 ± 5.7; p = 0.587) nor among those without the MetS (2.3 ± 1.8 vs. 3.6 ± 5.2; p = 0.165). Similar results were obtained with the International Diabetes Federation definition of the MetS.

Conclusion
IR is significantly associated with the MetS but not with sonographically proven PAD.
Video-assisted thoracoscopic surgery versus robotic-assisted thoracoscopic surgery in the surgical treatment of Masaoka stage I thymoma
Authors: Ye Bo , Tantai Ji-Cheng , Li Wang , Ge Xiao-Xiao , Feng Jian , Cheng Ming , Zhao Heng 
Published: July 2013

Abstract

Background
The purpose of this study was to compare perioperative outcomes in patients who underwent video-assisted thoracoscopic surgery or robot-assisted thoracoscopic surgery and assess the feasibility of robotic-assisted thymectomy for the treatment of Masaoka stage I.

Methods
We evaluated the short-term outcomes of 46 patients who underwent surgery for Masaoka stage I thymoma without myasthenia gravis between January 2009 and June 2012. Of these patients, 25 received unilateral video-assisted thoracoscopic surgery (VATS group) and the rest 21 recieved unilateral robotic-assisted thoracoscopic surgery (RATS group). We evaluated the duration of surgery, amount of intraoperative blood loss, duration of chest drainage, duration of postoperative hospital stay, hospitalization costs, postoperative complications and oncological outcomes.

Results
The duration of surgery was not significantly different between the two groups. Intraoperative blood loss volumes did not differ significantly between the VATS and RATS groups (86.8 mL and 58.6 mL, respectively; P=0.168). The postoperative hospital stay was significantly shorter in the RATS group (3.7 days vs. 6.7 days; P <0.01), and the postoperative pleural drainage volume of the RATS group was significantly less than VATS group (1.1 days vs. 3.6 days; P <0.01). No patients in the RATS group needed conversion to open surgery. However, in the VATS series, one patient had conversion to an open procedure. No surgical complications were observed except that one case had pulmonary atelectasis in the RATS group and one case developed pneumonia after surgery. Use of robot is much more expensive than video. No early recurrence was observed in both groups.

Conclusions
Robotic thymectomy is feasible and safe for Masaoka stage I thymoma. RATS is equally minimally invasive as VATS and results in a shorter drainage period and reduced hospital stay compared with the VATS approach.
Diagnosis and treatment of cystic renal cell carcinoma
Authors: Zhang Jiexiu , Liu Bianjiang , Song Ninghong , Hua Lixin , Wang Zengjun , Gu Min , Yin Changjun 
Published: July 2013

Abstract

Background
To summarize the diagnosis and treatment of cystic renal cell carcinoma (CRCC).

Methods
A retrospective study was conducted on 13 patients with CRCC at our center from August 2004 to April 2012. The pathologic features, clinical manifestation, imaging characteristics, treatment, and prognosis of CRCC were summarized according to available literature.

Results
Of the 13 patients, 11 were diagnosed with CRCC by preoperative B ultrasonography and computed tomography (CT) scan. The remaining two cases were initially misdiagnosed with simple renal cysts. Open radical nephrectomy was performed on two of the 13 cases, laparoscopic radical nephrectomy on seven cases, and open partial nephrectomy on four cases. All diagnoses of CRCC were confirmed by pathological examination. After the operation, all patients had an uneventful recovery. During the follow-up (range, 6–60 months), the serum creatinine concentrations and GFR of the partially removed kidneys remained stable within the normal range. No tumor recurrence or metastasis occurred.

Conclusions
By combining imaging examinations (B ultrasonography and CT scan) with intraoperative pathological examination, most cases of CRCC can be diagnosed and treated promptly and accurately. Nephrectomy is the first-line therapy. Nephron-sparing surgery should be preferred for CRCC. After a successful operation, the prognosis of CRCC is good.
M-CSF increases proliferation and phagocytosis while modulating receptor and transcription factor expression in adult human microglia
Authors: Smith Amy M , Gibbons Hannah M , Oldfield Robyn L , Bergin Peter M , Mee Edward W , Curtis Maurice A , Faull Richard L M , Dragunow Mike 
Published: July 2013

AbstractBackgroundMicroglia are the primary immune cells of the brain whose phenotype largely depends on their surrounding micro-environment. Microglia respond to a multitude of soluble molecules produced by a variety of brain cells. Macrophage colony-stimulating factor (M-CSF) is a cytokine found in the brain whose receptor is expressed by microglia. Previous studies suggest a critical role for M-CSF in brain development and normal functioning as well as in several disease processes involving neuroinflammation.MethodsUsing biopsy tissue from patients with intractable temporal epilepsy and autopsy tissue, we cultured primary adult human microglia to investigate their response to M-CSF. Mixed glial cultures were treated with 25 ng/ml M-CSF for 96 hours. Proliferation and phagocytosis assays, and high through-put immunocytochemistry, microscopy and image analysis were performed to investigate microglial phenotype and function.ResultsWe found that the phenotype of primary adult human microglia was markedly changed following exposure to M-CSF. A greater number of microglia were present in the M-CSF- treated cultures as the percentage of proliferating (BrdU and Ki67-positive) microglia was greatly increased. A number of changes in protein expression occurred following M-CSF treatment, including increased transcription factors PU.1 and C/EBPβ, increased DAP12 adaptor protein, increased M-CSF receptor (CSF-1R) and IGF-1 receptor, and reduced HLA-DP, DQ, DR antigen presentation protein. Furthermore, a distinct morphological change was observed with elongation of microglial processes. These changes in phenotype were accompanied by a functional increase in phagocytosis of Aβ1-42peptide.ConclusionsWe show here that the cytokine M-CSF dramatically influences the phenotype of adult human microglia. These results pave the way for future investigation of M-CSF-related targets for human therapeutic benefit.
Pediatric femoral shaft fractures: treatment strategies according to age - 13 years of experience in one medical center
Authors: Sela Yaron , Hershkovich Oded , Sher-Lurie Nir , Schindler Amos , Givon Uri 
Published: July 2013

Abstract

Objective
The objective of this study was to analyze our experience in treating femoral shaft fractures with different strategies, focusing on the first year after injury when the choice of method would have the greatest impact.

Methods
We reviewed the medical records of all children treated for femoral shaft fractures in our institution between 1997 and 2010. They were divided according to therapeutic approach: spica cast, skin traction, titanium elastic nail (TEN), external fixator, intramedullary medullary nail (IMN), and plating.

Results
The 212 patients included 150 boys and 62 girls (M/F ratio 2.4:1, mean age 5 years, range 0–16). The postoperative radiographic results demonstrated solid union in all patients, with no malunions. Of the 151 children in the spica cast group, 10 required re-manipulation and casting due to loss of reduction with unaccepted angulation, 10 had contact dermatitis, and 2 had fever and pressure sores. All 21 elastic nail group children underwent re-operation to remove the hardware: 3 had soft tissue irritation at the insertion points, and 3 had leg length discrepancy (LLD). Of the 14 external fixation patients, 4 had LLD, 1 had a pin tract infection, and 1 had a fracture through a pinhole after a fall. There were no complications in the 12 IMN patients, the 3 plating patients, or the 11 skin traction patients. LLD rates in the spica group were 10.5% higher compared to those in the control group (other treatment modalities) (P = .03).

Conclusions
TEN treatment was superior to spica casting for children who had reached an average age of 4 years.
Implementing a new EPR lineshape parameter for organic radicals in carbonaceous matter
Authors: Bourbin Mathilde , Du Yann Le , Binet Laurent , Gourier Didier 
Published: July 2013

Abstract

Background
Electron Paramagnetic Resonance (EPR) is a non-destructive, non-invasive technique useful for the characterization of organic moieties in primitive carbonaceous matter related to the origin of life. The classical EPR parameters are the peak-to-peak amplitude, the linewidth and the g factor; however, such parameters turn out not to suffice to fully determine a single EPR line.

Results
In this paper, we give the definition and practical implementation of a new EPR parameter based on the signal shape that we call the R
10 factor. This parameter was originally defined in the case of a single symmetric EPR line and used as a new datation method for organic matter in the field of exobiology.

Conclusion
Combined to classical EPR parameters, the proposed shape parameter provides a full description of an EPR spectrum and opens the way to novel applications like datation. Such a parameter is a powerful tool for future EPR studies, not only of carbonaceous matter, but also of any substance which spectrum exhibits a single symmetric line.

Reproducibility
The paper is a literate program—written using Noweb within the Org-mode as provided by the Emacs editor— and it also describes the full data analysis pipeline that computes the R
10 on a real EPR spectrum.