bluuebunny/crossref_metadata_2025_split huggingface dataset:
Full sequence analysis and characterization of the South Korean Norovirus GII-4 variant CUK-3
Authors: Park Jeong-Woong , Lee Sung-Geun , Lee Young-Min , Jheong Weon-Hwa , Ryu Sangryeol , Paik Soon-Young 
Published: April 2011

Abstract

Background
Many of researchers have focused on the emerging pathogen, Norovirus, since its first identification as the causing agent of nonbacterial acute gastroenteritis in humans. One of the virulence factors of norovirus, the great genetic diversity attributed to point mutations and recombinations, has brought forth the result of significant changes in the circulating norovirus genotype patterns.

Findings
In recognition of the necessity for tracking and monitoring of genetic diversity, a norovirus variant among the most prevalent genotype GII-4, Norovirus Hu/GII-4/CUK-3/2008/KR (CUK-3), was isolated from stool samples and analyzed on the level of whole genome sequence. Whole genome sequence analysis revealed three ORF composites of the whole genome, ORF1 (5100 bp), ORF2 (1623 bp), and ORF3 (807 bp). Each genetic relationship of CUK-3 variant analysis located the ORF1 (5,100 bp) in Cluster I, ORF2 (1623 bp) in Cluster I (2006b), ORF3 (807 bp) in Cluster I, and the whole genome sequence (about 5.1 kb) in Cluster I in the phylogenetic tree. And the phylogenetic analyses showed the same location of CUK-3 strain with the GII-4/2006b cluster in the phylogenetic tree.

Conclusions
In This study, a first concerning the full-length sequence of a NoV variant in South Korea is meaningful in that it can be used not only as a full-length NoV variant sequence standard for future comparison studies, but also as useful material for the public health field by enabling the diagnosis, vaccine development, and prediction of new emerging variants.
Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors
Authors: Miller Christopher A , Settle Stephen H , Sulman Erik P , Aldape Kenneth D , Milosavljevic Aleksandar 
Published: April 2011

Abstract

Background
Assays of multiple tumor samples frequently reveal recurrent genomic aberrations, including point mutations and copy-number alterations, that affect individual genes. Analyses that extend beyond single genes are often restricted to examining pathways, interactions and functional modules that are already known.

Methods
We present a method that identifies functional modules without any information other than patterns of recurrent and mutually exclusive aberrations (RME patterns) that arise due to positive selection for key cancer phenotypes. Our algorithm efficiently constructs and searches networks of potential interactions and identifies significant modules (RME modules) by using the algorithmic significance test.

Results
We apply the method to the TCGA collection of 145 glioblastoma samples, resulting in extension of known pathways and discovery of new functional modules. The method predicts a role for EP300 that was previously unknown in glioblastoma. We demonstrate the clinical relevance of these results by validating that expression of EP300 is prognostic, predicting survival independent of age at diagnosis and tumor grade.

Conclusions
We have developed a sensitive, simple, and fast method for automatically detecting functional modules in tumors based solely on patterns of recurrent genomic aberration. Due to its ability to analyze very large amounts of diverse data, we expect it to be increasingly useful when applied to the many tumor panels scheduled to be assayed in the near future.
Thrombomodulin phenotype of a distinct monocyte subtype is an independent prognostic marker for disseminated intravascular coagulation
Authors: Hwang Sang Mee , Kim Ji-Eun , Han Kyou-Sup , Kim Hyun Kyung 
Published: April 2011

Abstract
Introduction
Thrombomodulin, which is expressed solely on monocytes, along with tissue factor (TF), takes part in coagulation and inflammation. Circulating blood monocytes can be divided into 3 major subtypes on the basis of their receptor phenotype: classical (CD14brightCD16negative, CMs), inflammatory (CD14brightCD16positive; IMs), and dendritic cell-like (CD14dimCD16positive DMs). Monocyte subtype is strongly regulated, and the balance may influence the clinical outcomes of disseminated intravascular coagulation (DIC). Therefore, we investigated the phenotypic difference in thrombomodulin and TF expression between different monocyte subtypes in coagulopathy severity and prognosis in patients suspected of having DIC.

Methods
In total, 98 patients suspected of having DIC were enrolled. The subtypes of circulating monocytes were identified using CD14 and CD16 and the thrombomodulin and TF expression in each subtype, expressed as mean fluorescence intensity, was measured by flow cytometry. Plasma level of tissue factor was measured by ELISA. In cultures of microbead-selected, CD14-positive peripheral monocytes, lipopolysaccharide (LPS)- or interleukin-10-induced expression profiles were analyzed, using flow cytometry.

Results
The proportion of monocyte subtypes did not significantly differ between the overt and non-overt DIC groups. The IM thrombomodulin expression level was prominent in the overt DIC group and was well correlated with other coagulation markers. Of note, IM thrombomodulin expression was found to be an independent prognostic marker in multivariate Cox regression analysis. In addition, in vitro culture of peripheral monocytes showed that LPS stimulation upregulated thrombomodulin expression and TF expression in distinct populations of monocytes.

Conclusions
These findings suggest that the IM thrombomodulin phenotype is a potential independent prognostic marker for DIC, and that thrombomodulin-induced upregulation of monocytes is a vestige of the physiological defense mechanism against hypercoagulopathy.
Characterization of DXZ4 conservation in primates implies important functional roles for CTCF binding, array expression and tandem repeat organization on the X chromosome
Authors: McLaughlin Christine R , Chadwick Brian P 
Published: April 2011

Abstract
Background
Comparative sequence analysis is a powerful means with which to identify functionally relevant non-coding DNA elements through conserved nucleotide sequence. The macrosatellite DXZ4 is a polymorphic, uninterrupted, tandem array of 3-kb repeat units located exclusively on the human X chromosome. While not obviously protein coding, its chromatin organization suggests differing roles for the array on the active and inactive X chromosomes.

Results
In order to identify important elements within DXZ4, we explored preservation of DNA sequence and chromatin conformation of the macrosatellite in primates. We found that DXZ4 DNA sequence conservation beyond New World monkeys is limited to the promoter and CTCF binding site, although DXZ4 remains a GC-rich tandem array. Investigation of chromatin organization in macaques revealed that DXZ4 in males and on the active X chromosome is packaged into heterochromatin, whereas on the inactive X, DXZ4 was euchromatic and bound by CTCF.

Conclusions
Collectively, these data suggest an important conserved role for DXZ4 on the X chromosome involving expression, CTCF binding and tandem organization.
Hepatic Glucokinase Expression Is Associated with Lipogenesis and Fatty Liver in Humans
Authors: Peter Andreas , Stefan Norbert , Cegan Alexander , Walenta Mareike , Wagner Silvia , Königsrainer Alfred , Königsrainer Ingmar , Machicao Fausto , Schick Fritz , Häring Hans-Ulrich , Schleicher Erwin 
Published: April 2011

Abstract

Background/Aims:
Glucokinase (GCK) phosphorylates glucose to form glucose 6-phosphate and thereby regulates hepatic glucose disposal and activates hepatic lipogenesis. Hepatic GCK activity is regulated on the level of GCK mRNA expression and by the inhibitory glucokinase regulatory protein. In this study, we aimed to investigate the relation between GCK mRNA expression and markers of lipogenesis as well as liver fat content in human liver biopsies. Additionally, we investigated whether genetic variation in the liver specific GCK promoter determines liver fat content in humans.

Methods:
Hepatic mRNA expression and liver triglyceride content was analyzed in 50 human liver biopsies. In a second cohort of 330 individuals, liver fat was precisely measured by 1H magnetic resonance spectroscopy.

Results:
Hepatic GCK mRNA expression is associated with triglyceride content in human liver biopsies (r = 0.50, P = 0.0002). Furthermore, hepatic GCK mRNA expression is associated with lipogenic gene expression (fatty acid synthase, r = 0.49, P = 0.0003; acetyl-coenzyme A carboxylase-α, r = 0.44, P = 0.0015, and acetyl-coenzyme A carboxylase-β, r = 0.48, P = 0.0004) and the de novo lipogenesis index (r = 0.36, P = 0.01). In support of these findings, the single-nucleotide polymorphism rs2041547 in the liver-specific GCK promoter is associated with liver fat content in prediabetic individuals (P = 0.047).

Conclusions:
In this study, we demonstrate for the first time that GCK mRNA expression is associated with markers of de novo lipogenesis and liver triglyceride content in humans. This suggests that increased GCK activity may induce fatty liver and its metabolic and hepatic consequences in humans. Thus, the widely used approach to nonspecifically activate β-cell and hepatic GCK to treat diabetes mellitus is therefore questionable and may cause serious side effects.
ASP, The Art and Science of Practice: Taking the Measure of Lean: Efficiency and Effectiveness
Authors: Schonberger Richard J. 
Published: April 2011

Part I: As a long-time (29 years and counting) researcher and writer about lean, I gave no thought to addressing lean efficiency and effectiveness until data began to show trouble in lean land. I saw that big, “best-managed” companies had mixed, long-term lean results, most of which were not good. The main measure of merit in my “leanness” research is the common one, inventory—a measure that is visible and countable in lean action zones and is readily available up the hierarchy as a standard, audited metric for publicly traded companies. Despite that, I have found the inventory metric to be subject to misunderstanding and misuse. In this two-part paper, I address the merits, uses, and abuses of this metric in terms of lean efficiency and lean effectiveness. With exceptions, inventory works well as a dominant, gratifying lean result and as a low-level indicator of lean efficiency. However, examples from five companies show inventory to be equivocal as an upper-management-level marker of lean effectiveness. Part II: In part I of this two-part paper, I stated that lean's dominant purpose should be seen as cycle-time (wait-time) reduction, which—counted in units of inventory, its close relative—is visually prominent and easily measured at low (efficiency) levels and high (effectiveness) levels in the hierarchy. Part II continues with observations on lean's strategic value; additional cautions about uses of inventory trends at the executive level; examination of lean metrics in retailing, wholesaling, and services; and lean's relationship to quality and other elements of continuous-process improvement. More data from my “leanness studies” offer support for my observations.
The Hydrostatic Stress Board of Plastics Pipe Institute: The First 50 Years
Authors: Mruk Stanley A. 
Published: April 2011

Abstract
The activities and the policies issued by the Hydrostatic Stress Board (HSB) of the Plastics Pipe Institute have significantly enhanced the reliability of pressure rated thermoplastics pipe and the quality of ASTM, American Water Works Association, and other standards that cover such pipes. HSB policies define procedures for the forecasting of the long-term hydrostatic strength of thermoplastics piping materials and for the reducing of this strength into a hydrostatic design stress (HDS). HSB policies have been developed and are periodically updated under the light of our most current understanding of the factors that affect significant strength under actual service conditions. In support of the development of the most appropriate policies the HSB has also conducted various investigative activities. This paper reports on the major contributions that have been made by the HSB. Furthermore, it does so with reference to an overview of the factors that are now recognized as affecting the significant strength under actual service conditions and those that need to be considered when reducing a particular measure of strength into the most appropriate value of a HDS for an intended application.
Post-operative hypothalamic lesions and obesity in childhood craniopharyngioma: results of the multinational prospective trial KRANIOPHARYNGEOM 2000 after 3-year follow-up
Authors: Müller Hermann L , Gebhardt Ursel , Teske Carmen , Faldum Andreas , Zwiener Isabella , Warmuth-Metz Monika , Pietsch Torsten , Pohl Fabian , Sörensen Niels , Calaminus Gabriele 
Published: April 2011

BackgroundHypothalamic obesity has major impact on prognosis and quality of life (QoL) in childhood craniopharyngioma.Patients and methodsFor this study, 120 patients were prospectively recruited during 2001 and 2007 and evaluated after 3 years of follow-up (KRANIOPHARYNGEOM 2000). Body mass index (BMI) and QoL at diagnosis and 36 months after diagnosis were analysed based on the reference assessment of tumour localisation and post-surgical hypothalamic lesions. Treatment was analysed based on the neurosurgical strategy of 50 participating neurosurgical centres, the centre size based on the patient load.ResultsBMI SDS at diagnosis was similar in patients with or without hypothalamic involvement. Surgical lesions of anterior and posterior hypothalamic areas were associated with higher increase in BMI SDS during 36 months post-diagnosis compared with patients without or only anterior lesion (+1.8 BMISD, P=0.033, +2.1 BMISD; P=0.011), negative impact on QoL in patients with posterior hypothalamic lesions. Surgical strategies varied among the 50 neurosurgical centres (three large-sized, 24 middle-sized and 23 small-sized centres). Patients treated in small-sized centres presented with a higher rate of hypothalamic involvement compared with those treated in the middle- and large-sized centres. Treatment in large-sized centres was less radical, and the rates of complete resection and hypothalamic surgical lesions were lower in large-sized centres than those of the middle- and small-sized centres. However, a multivariable analysis showed that pre-operative hypothalamic involvement was the only independent risk factor for severe obesity (P=0.002).ConclusionsRadical neurosurgical strategies leading to posterior hypothalamic lesions are not recommended due to the potential to exacerbate hypothalamic obesity and impaired QoL. Treatment should be confined to experienced multidisciplinary teams.
Association of bone microarchitecture with parathyroid hormone concentration and calcium intake in men: the STRAMBO study
Authors: Chaitou A , Boutroy S , Vilayphiou N , Varennes A , Richard M , Blaizot S , Munoz F , Delmas P D , Goudable J , Chapurlat R , Szulc P 
Published: April 2011

ObjectiveIn the elderly, vitamin D deficit, low calcium intake, and impaired bone microarchitecture are associated with higher risk of hip fracture. We assessed the association of bone microarchitecture with calcium intake and serum concentrations of 25-hydroxycholecalciferol (25OHD) and parathyroid hormone (PTH) in men.DesignCross-sectional analysis was performed in 1064 men aged 20–87 years not taking vitamin D or calcium supplements.MethodsDaily calcium intake was assessed using a food frequency questionnaire. Bone microarchitecture was assessed at distal radius and tibia by high-resolution peripheral quantitative computed tomography. We measured serum and urinary levels of biochemical bone turnover markers (BTMs). Statistical models were adjusted for age, weight, height, and glomerular filtration rate.ResultsIn 500 men aged <65 years, lower 25OHD levels and low calcium intake were associated with lower trabecular volumetric bone mineral density (Dtrab) at the distal tibia, due to lower trabecular number (Tb.N). Low calcium intake was associated with lower cortical thickness (Ct.Th). Higher PTH level was associated with higher BTM levels. In 563 men aged ≥65 years, the highest PTH quartile was associated with lower Ct.Th (tibia), lower Dtrab (both sites), and lower Tb.N (radius) compared with the lowest quartile. Low calcium intake was associated with lower Tb.N and more heterogenous trabecular distribution. BTM positively correlated with the PTH concentration.ConclusionIn older men, elevated PTH concentration is associated with high bone turnover, poor trabecular microarchitecture (radius and tibia), and, at the distal tibia, lower Ct.Th. Low calcium intake is associated with lower Tb.N and more heterogenous trabecular distribution.
A Novel Approach to the Use of Subgingival Controlled‐Release Chlorhexidine Delivery in Chronic Periodontitis: A Randomized Clinical Trial
Authors: Gonzales Jose R. , Harnack Lutz , Schmitt‐Corsitto Gabriella , Boedeker Rolf H. , Chakraborty Trinad , Domann Eugen , Meyle Joerg 
Published: April 2011

Background: We aimed to analyze clinical, microbiologic, and serologic effects of chlorhexidine (CHX) chips used as a subgingival controlled‐release delivery device before and immediately after scaling and root planing (SRP).Methods: Twenty‐four patients presenting with ≥12 teeth with probing depth (PD) ≥5 mm and bleeding on probing were assigned in test or control groups. After prophylaxis, CHX chips (test) or placebo chips (control) were placed in pockets with PD ≥5 mm. Ten days later, SRP was performed in all teeth with PD ≥4 mm in a single appointment. Immediately after SRP, new chips were inserted in all pockets with PD ≥5 mm. Parameters were assessed at baseline; beginning of SRP; and 1, 3, and 6 months after treatment. Subgingival samples were obtained at baseline; beginning of SRP; and at 1 month after treatment. Periodontal pathogens Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Tannerella forsythia, and Treponema denticola were analyzed. Serum levels of high sensitive C‐reactive and lipopolysaccharide‐binding proteins were measured. The changes of the parameters between and within the groups were tested by Mann‐Whitney U test (P <0.05).Results: All clinical and serologic parameters improved in both groups over time. There was a significant difference in clinical attachment level (CAL) gain from baseline to 6 months between groups (1.17 mm in the test group versus 0.79 mm in the placebo group) (P <0.05). The treatment with CHX chips showed a greater reduction of the microorganisms of the “red complex” after 1 month (P = 0.02).Conclusion: The use of CHX chips before and immediately after SRP improved CAL and reduced the subgingival microorganisms of the red complex in the treatment of chronic periodontitis.
A rare case of intestinal obstruction due to ascariasis in Niš, south Serbia
Authors: Stojanovic Miroslava , Slavkovic Andjelka , Stojanovic Miroslav , Marjanovic Zoran , Bojanovic Milan 
Published: April 2011

Abstract
Ascariasis is a helminthic infection of global distribution, and intestinal obstruction is its most common gastrointestinal complication. This is a case of a 7-year-old boy admitted to Pediatric Surgery because of intestinal obstruction caused by ascariasis. On admission, the patient presented with colicky abdominal pain, bile-stained vomiting and meteorism. On physical examination, the patient was thin, pale, and dehydrated. An abdominal examination showed distention and diffuse tenderness. After admission, the patient had fecal vomiting and expulsion of worms through the mouth. Laboratory-test results showed leucocytosis, eosinophilia, hypoalbuminaemia, and hypochloremia. Abdominal radiographs and ultrasound studies were indicative of small-bowel obstruction due to roundworms, which led to the performance of an exploratory laparotomy. On bowel exploration, an intraluminal mass, 10 by 6 cm in diameter, consisting of roundworms in the middle third of the ileum was found. A longitudinal enterotomy was performed, and the worms were meticulously extracted manually. Postoperatively, broad-spectrum antibiotics and antihelminthic drugs were administered. Our case of intestinal obstruction caused by ascariasis is the first to be reported in Serbia, according to the Serbian literature.
Intelligibility of Foreign-Accented Speech for Older Adults with and without Hearing Loss
Authors: Ferguson Sarah Hargus , Jongman Allard , Sereno Joan A. , Keum Kyung Ae 
Published: April 2011

Background:Numerous studies have demonstrated that the negative effect of noise and other distortions on speech understanding is greater for older adults than for younger adults. Anecdotal evidence suggests that older adults may also be disproportionately negatively affected
by foreign accent. While two previous studies found no interaction between foreign accent and listener age, these studies reported no audiometric data and assessed speech understanding in quiet only.Purpose:To examine the effects of foreign accent, listening condition, and listener
age and hearing status on word identification.Research Design:A cross-sectional descriptive study.Study Sample:Experiments 1 and 2 tested young adults with normal hearing (n = 20 and n = 5, respectively), older adults with essentially normal
hearing (n = 20 and n = 10, respectively), and older adults with sloping sensorineural hearing loss (n = 20 and n = 10, respectively).Data Collection and Analysis:The intelligibility of English words produced by a native
speaker of English and by a native speaker of Spanish was assessed. In Experiment 1, word intelligibility was measured in quiet, in noise (+3 dB signal-to-babble ratio, or SBR), and in a telephone filter condition. In Experiment 2, intelligibility was measured in three additional noise
conditions (+6, +9, and +12 dB SBR).Results:English words produced by the native speaker of English were significantly more intelligible than those produced by the native speaker of Spanish. While the negative effect of noise was significantly greater for older listeners than
for younger listeners, the effect of foreign accent was independent of listener age, listener hearing status, and listening condition.Conclusion:The results suggest that, unlike with other forms of distortion, older adults are not disproportionately affected by foreign accent. This
suggests, in turn, that talker-related distortions of the speech signal have a qualitatively different impact on speech perception than distortions that are applied to the signal after it has been produced. The nature of these different types of distortion may be a fruitful area for future
investigations of speech understanding in older adults.