bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intelligent query by humming system based on score level fusion of multiple classifiers
Authors: Nam Gi Pyo , Luong Thi Thu Trang , Nam Hyun Ha , Park Kang Ryoung , Park Sung-Joo 
Published: August 2011

Abstract
Recently, the necessity for content-based music retrieval that can return results even if a user does not know information such as the title or singer has increased. Query-by-humming (QBH) systems have been introduced to address this need, as they allow the user to simply hum snatches of the tune to find the right song. Even though there have been many studies on QBH, few have combined multiple classifiers based on various fusion methods. Here we propose a new QBH system based on the score level fusion of multiple classifiers. This research is novel in the following three respects: three local classifiers [quantized binary (QB) code-based linear scaling (LS), pitch-based dynamic time warping (DTW), and LS] are employed; local maximum and minimum point-based LS and pitch distribution feature-based LS are used as global classifiers; and the combination of local and global classifiers based on the score level fusion by the PRODUCT rule is used to achieve enhanced matching accuracy. Experimental results with the 2006 MIREX QBSH and 2009 MIR-QBSH corpus databases show that the performance of the proposed method is better than that of single classifier and other fusion methods.
Krüppel-like factor 6 regulates transforming growth factor-β gene expression during human respiratory syncytial virus infection
Authors: Mgbemena Victoria , Segovia Jesus , Chang TeHung , Bose Santanu 
Published: August 2011

Abstract

Background
Human respiratory syncytial virus (RSV) infection is associated with airway remodeling and subsequent asthma development. Transforming growth factor-beta (TGF) plays a crucial role in asthma development. The mechanism regulating TGF gene expression during RSV infection is not known. Kruppel-like factor family of transcription factors are critical regulators of cellular/tissue homeostasis. Previous studies have shown that Kruppel-like factor 6 (KLF6) could function as a trans-activator of TGF gene; however, whether KLF members play a role during infection is unknown. In the current study we have evaluated the role of KLF6 during TGF expression in RSV infected cells.

Findings
Silencing KLF6 expression by shRNA led to drastic inhibition in TGF production during RSV infection, as assessed by ELISA analysis of medium supernatants. RT-PCR analysis revealed loss of TGF expression in KLF6 silenced cells. Chromatin-immunoprecipitation assay conducted with RSV infected cells showed binding of KLF6 protein to the TGF promoter during RSV infection. We further observed reduced RSV infectivity in KLF6 silenced cells and in cells incubated with TGF neutralizing antibody. In contrast, enhanced RSV infection was noted in cells incubated with purified TGF.

Conclusion
We have identified KLF6 as a key transcription factor required for trans-activation of TGF gene during RSV infection. Moreover, TGF production is required for efficient RSV infection and thus, KLF6 is also required for efficient RSV infection by virtue of KLF6 dependent TGF production during infection.
Reducing the worst case running times of a family of RNA and CFG problems, using Valiant’s approach
Authors: Zakov Shay , Tsur Dekel , Ziv-Ukelson Michal 
Published: August 2011

AbstractBackgroundRNA secondary structure prediction is a mainstream bioinformatic domain, and is key to computational analysis of functional RNA. In more than 30 years, much research has been devoted to defining different variants of RNA structure prediction problems, and to developing techniques for improving prediction quality. Nevertheless, most of the algorithms in this field follow a similar dynamic programming approach as that presented by Nussinov and Jacobson in the late 70's, which typically yields cubic worst case running time algorithms. Recently, some algorithmic approaches were applied to improve the complexity of these algorithms, motivated by new discoveries in the RNA domain and by the need to efficiently analyze the increasing amount of accumulated genome-wide data.ResultsWe study Valiant's classical algorithm for Context Free Grammar recognition in sub-cubic time, and extract features that are common to problems on which Valiant's approach can be applied. Based on this, we describe several problem templates, and formulate generic algorithms that use Valiant's technique and can be applied to all problems which abide by these templates, including many problems within the world of RNA Secondary Structures and Context Free Grammars.ConclusionsThe algorithms presented in this paper improve the theoretical asymptotic worst case running time bounds for a large family of important problems. It is also possible that the suggested techniques could be applied to yield a practical speedup for these problems. For some of the problems (such as computing the RNA partition function and base-pair binding probabilities), the presented techniques are the only ones which are currently known for reducing the asymptotic running time bounds of the standard algorithms.
Isolated complete avulsion of the gallbladder (near traumatic cholecystectomy): a case report and review of the literature
Authors: Pavlidis Theodoros E , Lalountas Miltiadis A , Psarras Kyriakos , Symeonidis Nikolaos G , Tsitlakidis Anastasios , Pavlidis Efstathios T , Ballas Konstantinos , Flaris Nikolaos , Marakis Georgios N , Sakantamis Athanassios K 
Published: August 2011

Abstract

Introduction
Injury of the gallbladder after blunt abdominal trauma is an unusual finding; the reported incidence is less than 2%. Three groups of injuries are described: simple contusion, laceration, and avulsion, the last of which can be partial, complete, or total traumatic cholecystectomy.

Case presentation
A case of isolated complete avulsion of the gallbladder (near traumatic cholecystectomy) from its hepatic bed in a 46-year-old Caucasian man without any other sign of injury is presented. The avulsion was due to blunt abdominal trauma after a car accident. The rarity of this injury and the stable condition of our patient at the initial presentation warrant a description. The diagnosis was made incidentally after a computed tomography scan, and our patient was treated successfully with ligation of the cystic duct and artery, removal of the gallbladder, coagulation of the bleeding points, and placement of a drain.

Conclusions
Early diagnosis of such injuries is quite difficult because abdominal signs are poor, non-specific, or even absent. Therefore, a computed tomography scan should be performed when the mechanism of injury is indicated.
A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1
Authors: Blasius Melanie , Forment Josep V , Thakkar Neha , Wagner Sebastian A , Choudhary Chunaram , Jackson Stephen P 
Published: August 2011

Abstract
Background
The cell-cycle checkpoint kinase Chk1 is essential in mammalian cells due to its roles in controlling processes such as DNA replication, mitosis and DNA-damage responses. Despite its paramount importance, how Chk1 controls these functions remains unclear, mainly because very few Chk1 substrates have hitherto been identified.

Results
Here, we combine a chemical genetics approach with high-resolution mass spectrometry to identify novel Chk1 substrates and their phosphorylation sites. The list of targets produced reveals the potential impact of Chk1 function not only on processes where Chk1 was already known to be involved, but also on other key cellular events such as transcription, RNA splicing and cell fate determination. In addition, we validate and explore the phosphorylation of transcriptional co-repressor KAP1 Ser473 as a novel DNA-damage-induced Chk1 site.

Conclusions
By providing a substantial set of potential Chk1 substrates, we present opportunities for studying unanticipated functions for Chk1 in controlling a wide range of cellular processes. We also refine the Chk1 consensus sequence, facilitating the future prediction of Chk1 target sites. In addition, our identification of KAP1 Ser473 phosphorylation as a robust readout for Chk1 activity could be used to explore the in vivo effects of Chk1 inhibitors that are being developed for clinical evaluation.
PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data
Authors: Corcoran David L , Georgiev Stoyan , Mukherjee Neelanjan , Gottwein Eva , Skalsky Rebecca L , Keene Jack D , Ohler Uwe 
Published: August 2011

AbstractCrosslinking and immunoprecipitation (CLIP) protocols have made it possible to identify transcriptome-wide RNA-protein interaction sites. In particular, PAR-CLIP utilizes a photoactivatable nucleoside for more efficient crosslinking. We present an approach, centered on the novel PARalyzer tool, for mapping high-confidence sites from PAR-CLIP deep-sequencing data. We show that PARalyzer delineates sites with a high signal-to-noise ratio. Motif finding identifies the sequence preferences of RNA-binding proteins, as well as seed-matches for highly expressed microRNAs when profiling Argonaute proteins. Our study describes tailored analytical methods and provides guidelines for future efforts to utilize high-throughput sequencing in RNA biology. PARalyzer is available at http://www.genome.duke.edu/labs/ohler/research/PARalyzer/.
Efficacy of Dosimetric Versus Empiric Prescribed Activity of 131I for Therapy of Differentiated Thyroid Cancer
Authors: Klubo-Gwiezdzinska Joanna , Van Nostrand Douglas , Atkins Frank , Burman Kenneth , Jonklaas Jacqueline , Mete Mihriye , Wartofsky Leonard 
Published: August 2011

Abstract

Background:
The optimal management of high-risk patients with differentiated thyroid cancer (DTC) consists of thyroidectomy followed by radioiodine (131I) therapy. The prescribed activity of 131I can be determined using two approaches: 1) empiric prescribed activity of 131I (E-Rx); and 2) dosimetry-based prescribed activity of 131I (D-Rx).

Aim:
The aim of the study was to compare the relative treatment efficacy and side effects of D-Rx vs. E-Rx.

Methods:
A retrospective analysis was performed of patients with distant metastases and/or locoregionally advanced radioiodine-avid DTC who were treated with either D-Rx or E-Rx. Response to treatment was based on RECIST (Response Evaluation Criteria in Solid Tumors) 1.1 criteria.

Results:
The study group consisted of 87 patients followed for 51 ± 35 months, of whom 43 were treated with D-Rx and 44 with E-Rx. Multivariate analysis, controlling for age, gender, and status of metastases revealed that the D-Rx group tended to be 70% less likely to progress (odds ratio, 0.29; 95% confidence interval, 0.087–1.02; P = 0.052) and more likely to obtain complete response (CR) compared to the E-Rx group (odds ratio, 8.2; 95% confidence interval, 1.2–53.5; P = 0.029). There was an association in the D-Rx group between the observed CR and percentage of maximum tolerable activity given as a first treatment of 131I (P = 0.030). The advantage of D-Rx was specifically apparent in the locoregionally advanced group because CR was significantly higher in D-Rx vs. E-Rx in this group of patients (35.7 vs. 3.3%; P = 0.009). The rates of partial response, stable disease, and progression-free survival, as well as the frequency of side effects, were not significantly different between the two groups.

Conclusion:
Higher efficacy of D-Rx with a similar safety profile compared to E-Rx supports the rationale for employing individually prescribed activity in high-risk patients with DTC.
Does Growth Hormone Replacement Therapy Reduce Mortality in Adults with Growth Hormone Deficiency? Data from the Dutch National Registry of Growth Hormone Treatment in Adults
Authors: van Bunderen Christa C. , van Nieuwpoort I. Caroline , Arwert Lucia I. , Heymans Martijn W. , Franken Anton A. M. , Koppeschaar Hans P. F. , van der Lely Aart J. , Drent Madeleine L. 
Published: August 2011

Abstract

Context:
Adults with GH deficiency (GHD) have a decreased life expectancy. The effect of GH treatment on mortality remains to be established.

Objective:
This nationwide cohort study investigates the effect of GH treatment on all-cause and cause-specific mortality and analyzes patient characteristics influencing mortality in GHD adults.

Design, Setting, and Patients:
Patients in the Dutch National Registry of Growth Hormone Treatment in Adults were retrospectively monitored (1985–2009) and subdivided into treatment (n = 2229), primary (untreated, n = 109), and secondary control (partly treated, n = 356) groups.

Main Outcome Measures:
Standardized mortality ratios (SMR) were calculated for all-cause, malignancy, and cardiovascular disease (CVD) mortality. Expected mortality was obtained from cause, sex, calendar year, and age-specific death rates from national death and population counts.

Results:
In the treatment group, 95 patients died compared to 74.6 expected [SMR 1.27 (95% confidence interval, 1.04–1.56)]. Mortality was higher in women than in men. After exclusion of high-risk patients, the SMR for CVD mortality remained increased in women. Mortality due to malignancies was not elevated. In the control groups mortality was not different from the background population. Univariate analyses demonstrated sex, GHD onset, age, and underlying diagnosis as influencing factors.

Conclusions:
GHD men receiving GH treatment have a mortality rate not different from the background population. In women, after exclusion of high-risk patients, mortality was not different from the background population except for CVD. Mortality due to malignancies was not elevated in adults receiving GH treatment. Next to gender, the heterogeneous etiology is of influence on mortality in GHD adults with GH treatment.
Consumption of Fructose and High Fructose Corn Syrup Increase Postprandial Triglycerides, LDL-Cholesterol, and Apolipoprotein-B in Young Men and Women
Authors: Stanhope Kimber L. , Bremer Andrew A. , Medici Valentina , Nakajima Katsuyuki , Ito Yasuki , Nakano Takamitsu , Chen Guoxia , Fong Tak Hou , Lee Vivien , Menorca Roseanne I. , Keim Nancy L. , Havel Peter J. 
Published: August 2011

Abstract

Context:
The American Heart Association Nutrition Committee recommends women and men consume no more than 100 and 150 kcal of added sugar per day, respectively, whereas the Dietary Guidelines for Americans, 2010, suggests a maximal added sugar intake of 25% or less of total energy.

Objective:
To address this discrepancy, we compared the effects of consuming glucose, fructose, or high-fructose corn syrup (HFCS) at 25% of energy requirements (E) on risk factors for cardiovascular disease.

Participants, Design and Setting, and Intervention:
Forty-eight adults (aged 18–40 yr; body mass index 18–35 kg/m2) resided at the Clinical Research Center for 3.5 d of baseline testing while consuming energy-balanced diets containing 55% E complex carbohydrate. For 12 outpatient days, they consumed usual ad libitum diets along with three servings per day of glucose, fructose, or HFCS-sweetened beverages (n = 16/group), which provided 25% E requirements. Subjects then consumed energy-balanced diets containing 25% E sugar-sweetened beverages/30% E complex carbohydrate during 3.5 d of inpatient intervention testing.

Main Outcome Measures:
Twenty-four-hour triglyceride area under the curve, fasting plasma low-density lipoprotein (LDL), and apolipoprotein B (apoB) concentrations were measured.

Results:
Twenty-four-hour triglyceride area under the curve was increased compared with baseline during consumption of fructose (+4.7 ± 1.2 mmol/liter × 24 h, P = 0.0032) and HFCS (+1.8 ± 1.4 mmol/liter × 24 h, P = 0.035) but not glucose (−1.9 ± 0.9 mmol/liter × 24 h, P = 0.14). Fasting LDL and apoB concentrations were increased during consumption of fructose (LDL: +0.29 ± 0.082 mmol/liter, P = 0.0023; apoB: +0.093 ± 0.022 g/liter, P = 0.0005) and HFCS (LDL: +0.42 ± 0.11 mmol/liter, P &lt; 0.0001; apoB: +0.12 ± 0.031 g/liter, P &lt; 0.0001) but not glucose (LDL: +0.012 ± 0.071 mmol/liter, P = 0.86; apoB: +0.0097 ± 0.019 g/liter, P = 0.90).

Conclusions:
Consumption of HFCS-sweetened beverages for 2 wk at 25% E increased risk factors for cardiovascular disease comparably with fructose and more than glucose in young adults.
Prevention of Fractures after Solid Organ Transplantation: A Meta-Analysis
Authors: Stein Emily M. , Ortiz Dionisio , Jin Zhezhen , McMahon Donald J. , Shane Elizabeth 
Published: August 2011

AbstractContext:Bone loss and fracture are serious sequelae of organ transplantation, particularly in the first posttransplant year. Most interventional studies have been inadequately powered to detect effects on fracture.Objective:The objective of the study was to determine whether treatment with bisphosphonates (BP) or active vitamin D analogs (vitD) during the first year after transplantation reduces fracture risk and estimate the effect of these interventions on bone loss.Data Sources:Sources included PUBMED, MEDLINE, Cochrane Library, and abstracts from scientific meetings (presented 2003–2010).Study Selection:Randomized controlled clinical trials of BP or vitD in solid organ transplant recipients were included if treatment was initiated at the time of transplantation and fracture data were collected.Data Extraction:Two investigators independently extracted data and rated study quality. Fixed effect and random-effects models were used to obtain pooled estimates.Data Synthesis:Eleven studies of 780 transplant recipients (134 fractures) were included. Treatment with BP or vitD reduced the number of subjects with fracture [odds ratio (OR) 0.50 (0.29, 0.83)] and number of vertebral fractures, [OR 0.24 (0.07, 0.78)]. An increase in bone mineral density at the lumbar spine [2.98% (1.31, 4.64)] and femoral neck [3.05% (2.16, 3.93)] was found with treatment. When BP trials (nine studies, 625 subjects) were examined separately, there was a reduction in number of subjects with fractures [OR 0.53 (0.30, 0.91)] but no significant reduction in vertebral fractures [OR 0.34 (0.09, 1.24)].Conclusions:Treatment with BP or vitD during the first year after solid organ transplant was associated with a reduction in the number of subjects with fractures and fewer vertebral fractures.
Assessment of the right ventricular function in patients with chronic obstructive pulmonary disease using MRI
Authors: Gao Yan , Du Xiangying , Qin Wen , Li Kuncheng 
Published: August 2011

Background Chronic obstructive pulmonary disease (COPD) is often associated with changes of the structure and the function of the right ventricle (RV). Therefore, the assessment of right ventricular function and myocardial mass (MM) is clinically important for the evaluation of the severity of COPD, which may provide an objective basis for therapeutic strategy. Purpose To assess the right ventricular function and RV MM in patients with mild to severe COPD using magnetic resonance imaging (MRI). Material and Methods We prospectively studied 49 COPD patients determined by the pulmonary function test (PFT). Using the Global Initiative for COPD classification, the COPD patients were divided into three groups according to the severity of the disease: group I = mild ( n = 18); group II = moderate ( n = 16); and group III = severe ( n = 15). The patient groups were compared to a control group consisting of 30 age-matched, healthy, non-smoking subjects. The RV function and RV MM were obtained by 1.5T cardiac MRI in all of the four groups. The results were compared among the four groups using the ANOVA. Pearson's correlation was used to evaluate the relationship between the right ventricular ejection fraction (RVEF) and MM with the PFT results in COPD patients. Results The RVEF was significantly lower in group III than in the other groups ( P < 0.01). The RV MM differed significantly among all groups ( P < 0.01) and gradually increased with the severity of COPD ( P < 0.01). The correlation was significant between the MRI results and forced expiratory volume in 1 s (r = 0.860 for RVEF, r = –0.838 for RV MM) in COPD patients. Conclusion The RVEF and RV MM measured by MRI correlate significantly with the severity of disease as determined by PFT in patients with COPD.
Fungal biodegradation of genetically modified and lignin-altered quaking aspen (Populus tremuloides Michx.)
Authors: Giles Richard , Peszlen Ilona , Peralta Perry , Chang Hou-Min , Farrell Roberta , Grand Larry , Horvath Balazs 
Published: August 2011

AbstractBetter access to wood carbohydrates as a result of reduced, or altered, lignin is a goal of biopulping, as well as biofuel research. In the present article, woods from three transgenic trees and one wild-type quaking aspen (Populus tremuloidesMichx.) were analyzed in terms of mass loss of cellulose and lignin after incubation with lignocellulolytic fungi. The transgenic trees had reduced lignin content through transfer of an antisense -4CL gene, elevated syringyl/guaiacyl (S/G) ratio through insertion of a sense CAld5H gene and low lignin content and elevated S/G ratio through simultaneous insertion of -4CL and CAld5H genes, respectively. The lignocellulolytic fungi employed were a lignin-selective white rot fungusCeriporiopsis subvermispora, a simultaneous white rot fungusTrametes versicolorand a brown rot fungusPostia placenta. Reduced lignin degradation was observed in woods with increased S/G ratios indicating that this analytical feature influences decay resistance, regardless of the fungal decay mechanism.
Die phraseologische Konstruktionsfamilie [X Präp Hand Verb]
Authors: Staffeldt Sven 
Published: August 2011

Abstract
The subject of this paper is the presentation of the analysis of details of various German phraseologisms containing the constituent Hand [hand]. It will be shown that a considerable improvement in clarity can be achieved by analyzing these phraseolgisms as belonging to a specific construction family. The analysis follows in its classification previous studies from the project “Linguistik des Körpers” [Linguistics of the Human Body]. The essential objectives of this project are:

(I)
identification of the semantic potential of the body and

(II)
analysis and description of the meaning of phraseologisms containing body part terms (so called somatisms).

As considered from a methodological point of view (II) would be the conditio sine qua non with regard to (I). The thesis is the following: Although phraseologisms – following Goldberg – are not absolutely predictable, the body part terms still allow the identification of a specific contribution to the phraseological meaning. To a certain extent the phraseological meaning turns out to be compositional as if moved along a metonymic guide.
Analysis of the meaning will be the main focus of this investigation. Meanings occur in daily use. The only way to get further knowledge about the meaning(s) of linguistic entities is by analyzing their (actual) use.
Der Wortartenstatus des Elements je in der komparativen Korrelativkonstruktion
Authors: Meinunger André 
Published: August 2011

Abstract
Most grammars and text books list the element je in its correlative use as a subordinate conjunction. The present study shows that this classification is not correct. Je is rather a word or word-like element which introduces a larger constituent which occupies the clause initial position much like a question word, or more precisely an interrogative constituent. One of the pieces of evidence is the multiple occurrence of je(-constituents) inside the same clause, a finding which has never been recognized before. Furthermore it is shown – contrary to Bech (1964) – that je clauses are compatible with negation. The contribution ends with a speculative part in which je is proposed to be either a particle or else even a bound morpheme, lacking word status at altogether.