bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virtual CGH: an integrative approach to predict genetic abnormalities from gene expression microarray data applied in lymphoma
Authors: Geng Huimin , Iqbal Javeed , Chan Wing C , Ali Hesham H 
Published: April 2011

Abstract

Background
Comparative Genomic Hybridization (CGH) is a molecular approach for detecting DNA Copy Number Alterations (CNAs) in tumor, which are among the key causes of tumorigenesis. However in the post-genomic era, most studies in cancer biology have been focusing on Gene Expression Profiling (GEP) but not CGH, and as a result, an enormous amount of GEP data had been accumulated in public databases for a wide variety of tumor types. We exploited this resource of GEP data to define possible recurrent CNAs in tumor. In addition, the CNAs identified by GEP would be more functionally relevant CNAs in the disease pathogenesis since the functional effects of CNAs can be reflected by altered gene expression.

Methods
We proposed a novel computational approach, coined virtual CGH (vCGH), which employs hidden Markov models (HMMs) to predict DNA CNAs from their corresponding GEP data. vCGH was first trained on the paired GEP and CGH data generated from a sufficient number of tumor samples, and then applied to the GEP data of a new tumor sample to predict its CNAs.

Results
Using cross-validation on 190 Diffuse Large B-Cell Lymphomas (DLBCL), vCGH achieved 80% sensitivity, 90% specificity and 90% accuracy for CNA prediction. The majority of the recurrent regions defined by vCGH are concordant with the experimental CGH, including gains of 1q, 2p16-p14, 3q27-q29, 6p25-p21, 7, 11q, 12 and 18q21, and losses of 6q, 8p23-p21, 9p24-p21 and 17p13 in DLBCL. In addition, vCGH predicted some recurrent functional abnormalities which were not observed in CGH, including gains of 1p, 2q and 6q and losses of 1q, 6p and 8q. Among those novel loci, 1q, 6q and 8q were significantly associated with the clinical outcomes in the DLBCL patients (p < 0.05).

Conclusions
We developed a novel computational approach, vCGH, to predict genome-wide genetic abnormalities from GEP data in lymphomas. vCGH can be generally applied to other types of tumors and may significantly enhance the detection of functionally important genetic abnormalities in cancer research.
Role of the ATPase/helicase maleless (MLE) in the assembly, targeting, spreading and function of the male-specific lethal (MSL) complex of Drosophila
Authors: Morra Rosa , Yokoyama Ruth , Ling Huiping , Lucchesi John C 
Published: April 2011

Abstract

Background
The male-specific lethal (MSL) complex of Drosophila remodels the chromatin of the X chromosome in males to enhance the level of transcription of most X-linked genes, and thereby achieve dosage compensation. The core complex consists of five proteins and one of two non-coding RNAs. One of the proteins, MOF (males absent on the first), is a histone acetyltransferase that specifically acetylates histone H4 at lysine 16. Another protein, maleless (MLE), is an ATP-dependent helicase with the ability to unwind DNA/RNA or RNA/RNA substrates in vitro. Recently, we showed that the ATPase activity of MLE is sufficient for the hypertranscription of genes adjacent to a high-affinity site by MSL complexes located at that site. The helicase activity is required for the spreading of the complex to the hundreds of positions along the X chromosome, where it is normally found. In this study, to further understand the role of MLE in the function of the MSL complex, we analyzed its relationship to the other complex components by creating a series of deletions or mutations in its putative functional domains, and testing their effect on the distribution and function of the complex in vivo.

Results
The presence of the RB2 RNA-binding domain is necessary for the association of the MSL3 protein with the other complex subunits. In its absence, the activity of the MOF subunit was compromised, and the complex failed to acetylate histone H4 at lysine 16. Deletion of the RB1 RNA-binding domain resulted in complexes that maintained substantial acetylation activity but failed to spread beyond the high-affinity sites. Flies bearing this mutation exhibited low levels of roX RNAs, indicating that these RNAs failed to associate with the proteins of the complex and were degraded, or that MLE contributes to their synthesis. Deletion of the glycine-rich C-terminal region, which contains a nuclear localization sequence, caused a substantial level of retention of the other MSL proteins in the cytoplasm. These data suggest that the MSL proteins assemble into complexes or subcomplexes before entering the nucleus.

Conclusions
This study provides insights into the role that MLE plays in the function of the MSL complex through its association with roX RNAs and the other MSL subunits, and suggests a hypothesis to explain the role of MLE in the synthesis of these RNAs.
The shallow turn of a worm
Authors: Kim Daeyeon , Park Sungsu , Mahadevan L. , Shin Jennifer H. 
Published: April 2011

SUMMARY
When crawling on a solid surface, the nematode Caenorhabditis elegans (C. elegans) moves forward by propagating sinusoidal dorso-ventral retrograde contraction waves. A uniform propagating wave leads to motion that undulates about a straight line. When C. elegans turns as it forages or navigates its environment, it uses several different strategies of reorientation. These modes include the well-known omega turn, in which the worm makes a sharp angle turn forming an Ω-shape, and the reversal, in which the worm draws itself backwards. In these two modes of reorientation, C. elegans strongly disrupts its propagating sinusoidal wave, either in form or in direction, leading to abrupt directional change. However, a third mode of reorientation, the shallow turn, involves a gentler disruption of the locomotory gait. Analyzing the statistics of locomotion suggests that the shallow turn is by far the most frequent reorienting maneuver in navigation in the absence of food. We show that the worm executes a shallow turn by modulating the amplitude and wavelength of its curvature during forward movement, and provide a minimal description of the process using a three-parameter mathematical model. The results of our study augment the understanding of how these parameters are controlled at the neuromotor circuit level.
Physiological responses of the scleractinian coral Pocillopora damicornis to bacterial stress from Vibrio coralliilyticus
Authors: Vidal-Dupiol Jeremie , Ladrière Ophélie , Meistertzheim Anne-Leila , Fouré Laurent , Adjeroud Mehdi , Mitta Guillaume 
Published: April 2011

SUMMARY
As the effects of climate change have become increasingly visible over the past three decades, coral reefs have suffered from a number of natural and anthropogenic disturbances that have caused a critical decline in coral populations. Among these disturbances are coral diseases, which have appeared with increasing frequency and severity, often in correlation with increases in water temperature. Although the crucial role played by Vibrio species in coral disease has been widely documented, the scientific community does not yet fully understand the infection process of Vibrio or its impact on coral physiology and immunology. Here, we investigated the physiological and transcriptomic responses of a major reef-building coral, Pocillopora damicornis, when exposed to a specific pathogen (Vibrio coralliilyticus) under virulent (increasing water temperature) and non-virulent (constant low temperature) conditions. The infection process was examined by electron microscopy and quantitative reverse-transcription PCR, and coral health was monitored by visual observations and measurements of zooxanthellar density. The results obtained suggest that coral tissue invasion occurs upon increasing water temperature only. Transcriptomic variations were investigated using a suppression–subtractive–hybridization approach, and the expression levels of six candidate immune-related genes were examined during bacterial exposure. These genes correspond to three lectin-like molecules putatively involved in the recognition of pathogens, two metal-binding proteins putatively involved in antibacterial response and one cystein protease inhibitor. The transcription patterns of these selected genes provide new insights into the responses of coral colonies to virulent versus non-virulent bacteria.
Condensation Reaction of Phenols with 1,5-Pentanedial for Synthesis of Noria-like Ladder-cyclic Oligomer by Dynamic Covalent Chemistry Mechanism
Authors: Seki Hiroyuki , Kuwabara Shingo , Kudo Hiroto , Nishikubo Tadatomi 
Published: April 2011

Abstract
Condensation reaction of 2-methylresorcinol and pyrogallol with 1,5-pentanedial [CH2(CH2CHO)2] in the presence of concentrated HCl in ethanol at 80 °C for 48 h proceeded according to a dynamic covalent chemistry (DCC) mechanism to afford the noria-like ladder-cyclic oligomers noriaMR and noriaPY, respectively.
Photoinduced Surface-relief-grating Formation Using a Mixed Film of 4-[Bis(4-methylphenyl)amino]azobenzene and 4,4′,4′′-Tris[3-methylphenyl(phenyl)amino]triphenylamine
Authors: Nakano Hideyuki 
Published: April 2011

Abstract
The ability of photoinduced surface-relief-grating (SRG) formation of 4-[bis(4-methylphenyl)amino]azobenzene (BMAB) was found to be drastically enhanced by mixing with 4,4′,4′′-tris[3-methylphenyl(phenyl)amino]triphenylamine (m-MTDATA) due to the increase in glass-transition temperature (Tg). The resulting SRG inscribed on the mixed amorphous film remained even after annealing at 55 °C, which was considerably higher than the Tg of BMAB. These results suggest that the m-MTDATA molecules in the mixed film were transported together with BMAB molecules upon irradiation with the writing beams.
Molecular Dynamics Simulation for Irreversibility of Green Fluorescent Protein before and after Photoactivation
Authors: Koseki Jun , Kita Yukiumi , Tachikawa Masanori 
Published: April 2011

Abstract
To elucidate the irreversible photoreaction of green fluorescent protein (GFP), we have theoretically analyzed hydrogen-bonding networks and distributions of water molecules around a chromophore (CRO) of GFP before and after photoactivation. Our molecular dynamics simulation clearly shows that such irreversibility arises from the migration of water molecules to the hollowed out region due to the reorientation of amino acid residues together with the disappearance of hydrogen-bonding networks around the CRO.
Is CA-125 an additional help to radiologic findings for differentiation borderline ovarian tumor from stage I carcinoma?
Authors: Lee Eun Joo , Kim See Hyung , Kim Young Hwan , Lee Hee Jung 
Published: April 2011

Background Borderline ovarian tumors (BOTs) are difficult to differentiate from stage I carcinoma using radiological findings. Little is known about the correlation between CA-125 levels and radiological findings for predicting BOTs or carcinoma. Purpose To assess the role of CA-125, in addition to that of radiological findings, in differentiating BOTs from stage I carcinoma. Material and Methods The study received institutional review board approval, with waiver of informed consent. We evaluated 100 patients (two groups: BOT, 58 patients; stage I carcinoma, 42 patients) using radiological findings, including location and size of each tumor, number and size of septations, papillary projections and vegetations, peritoneal implants, ascites, and preoperative CA-125 levels. The differences in CA-125 levels according to bilateral location, solid components, and thickness of septations between the two groups were evaluated using the McNemar test. Correlations of CA-125 level to size and number of septations were evaluated by the independent sample t test. Results No statistical correlation was found between CA-125 level and location, size, and number of septations between the two groups. Solid components within the tumors were similar in the two groups, but the CA-125 level was significantly higher in stage I carcinoma than in BOTs. The number of septations per tumor was similar in the two groups; thick septations were more frequent in stage I carcinoma than in BOTs, and a significantly higher titer of CA-125 was found in stage I carcinoma. Discriminant analysis of solid components and thickness of septations resulted in accurate diagnosis of 70.6% of the tumors (80.6% of BOTs and 69.7% of stage I carcinomas). Conclusion CA-125 levels for solid components and thickness of septations are lower in BOTs. These may be helpful in predicting the risk of carcinoma, even if BOTs cannot be conclusively differentiated from stage I carcinoma.
Ultrasonographic detection and characterization of asymptomatic ductal carcinomain situwith histopathologic correlation
Authors: Gwak Yeon Ju , Kim Hye Jung , Kwak Jin Young , Lee Sang Kwon , Shin Kyung Min , Lee Hui Joong , Kim Gab Chul , Jang Yun-Jin , Han Man Hoon , Park Ji Young , Jung Jin Hyang 
Published: April 2011

BackgroundMost ductal carcinoma in situ (DCIS) of the breast is asymptomatic and usually manifests as calcifications in screening mammography. On the other hand, little is known about ultrasonographic (US) features of asymptomatic DCIS, for US is rarely used for the diagnosis and evaluation of DCIS because of low sensitivity in detecting microcalcifications.PurposeTo evaluate US detection and characterization of DCIS in asymptomatic women and correlate these imaging findings with the histopathologic features.Material and MethodsThis retrospective study evaluated mammographic and US images of 60 DCIS cases from 59 asymptomatic women. US was performed in knowledge of mammographic findings. The following histopathologic parameters were analyzed: Van Nuys classification, architectural pattern, and presence of microinvasion. Image detectability and US features were correlated with these histopathologic parameters.ResultsOf the 54 cases (90.0%) detected on mammography, 48 cases (88.9%) had microcalcifications only, 5 (9.3%) had microcalcifications with associated density, and 1 (1.9%) had soft tissue density alone. Of the 38 cases (63.3%) identified by US, 29 cases (76.3%) had a mass with or without microcalcifications, six (15.8%) had microcalcifications only, and three (7.9%) had other findings. US identified lesions were associated with higher Van Nuys groups, microinvasion and comedocarcinoma ( P = 0.044, P = 0.024, and P = 0.032, respectively). The most common US finding was a not-circumscribed, oval mass with parallel orientation and normal acoustic transmission. Microcalcifications were seen on US in 31 (81.6%) of the 38 US visible cases; this finding showed a trend of association with Van Nuys group 2 and 3 but was not statistically significant ( P = 0.063).ConclusionWhen DCIS was identified on US, it was associated with more aggressive histopathologic type. However, mammographic correlation is essential to differentiate benign from malignant lesion in cases seen by US; US findings of asymptomatic DCIS had a low suspicion of malignancy.
The optimal contrast media policy in CT of the liver. Part I: Technical notes
Authors: Rengo Marco , Bellini Davide , De Cecco Carlo N , Osimani Marcello , Vecchietti Fabrizio , Caruso Damiano , Maceroni Marco M , Lucchesi Paola , Iafrate Franco , Paolantonio Pasquale , Ferrari Riccardo , Laghi Andrea 
Published: April 2011

Latest developments of multidetector computed tomography (MDCT), which is today considered a real volumetric technique, have revolutionized abdominal imaging. Technological improvements such as higher spatial resolution, larger volume coverage and higher temporal resolution, have reduced scan times allowing CT studies of the abdomen within a single breath-hold. Furthermore, the increased number of slices, the submillimetric collimation, and the use of multiple dynamic post-contrast phases per single examination, may all contribute to increase the radiation exposure of single patients. The aim of this review is to discuss different parameters affecting contrast media enhancement, as vascular enhancement, parenchymal enhancement and timing, in order to minimize the amount of contrast medium injected and the radiation exposure.
Fluorine-18-fluorodeoxyglucose PET/CT for the evaluation of suspected recurrent uterine leiomyosarcomas
Authors: Kao Yung Hsiang , Saad U , Tan Andrew EH , Magsombol Butch M , Padhy Ajit Kumar 
Published: April 2011

Background Uterine leiomyosarcomas are rare and aggressive malignancies of the uterine corpus with high recurrence rates and poor prognoses. The current recommendation for detection of recurrent uterine leiomyosarcoma involves periodic physical examination and conventional imaging such as CT or MRI. The role of fluorine-18-fluorodeoxyglucose positron emission tomography with integrated computed tomography (FDG-PET/CT) in the detection of recurrent uterine leiomyosarcomas is not yet established. Purpose To evaluate the use of FDG-PET/CT as a single integrated modality for the evaluation of suspected recurrent uterine leiomyosarcomas. Material and Methods A retrospective study was performed on patients who underwent FDG-PET/CT scans for suspected recurrent uterine leiomyosarcoma. Only patients with follow-up data were included in the study. FDG-PET/CT was evaluated as a single integrated imaging modality. A positive lesion on FDG-PET/CT was defined as a focal abnormality detected on either the PET or CT components, or both. Results Sixteen consecutive patients over 5 years underwent FDG-PET/CT for suspected recurrent uterine leiomyosarcoma. Five patients were excluded due to incomplete follow-up data. The remaining 11 patients were aged 36–58 years (mean age 48). FDG-PET/CT had a sensitivity of 100% (95% CI 63–100) and specificity of 100% (95% CI 20–100) for the detection of recurrent uterine leiomyosarcomas. Sites of metastases include lungs, peritoneum, liver, pancreas and breast, of which lungs and peritoneum were the most common. Two (18%) patients had discordant findings: FDG-PET negative metastatic nodules in the breast and lung detected on the CT component. The maximum standardized uptake value (SUVmax) of metastatic lesions ranged from 2.0 to 16.0 (mean 7.6). Conclusion FDG-PET/CT as a single integrated modality may be a useful for the evaluation of suspected recurrent uterine leiomyosarcomas. FDG-PET negative discordant nodules detected on the CT component may represent metastases and should be followed up closely.
Injury in an Elderly Population Before and After Initiating a Skeletal Muscle Relaxant
Authors: Billups Sarah J , Delate Thomas , Hoover Barbara 
Published: April 2011

Background Quality guidelines recommend avoidance of skeletal muscle relaxants in patients 65 years and older, but this recommendation is based on expert opinion, not evidence. Objective: To describe an elderly population using skeletal muscle relaxants and compare the incidence of physical injury among these patients before and after initiation of the medication. Methods: This was a retrospective, pre-post cohort analysis, with each patient serving as his/her own control. In a population of elderly patients who purchased a prescription for a skeletal muscle relaxant, the primary outcome was to compare the proportion of patients experiencing an injury in a 60-day period prior to initiating the drug to the proportion experiencing an injury in the 60 days immediately following the purchase date. Results: Of the 11,875 patients included in the study. 108 (0.9%) experienced an injury during the baseline period and 144 (1.2%) experienced an injury in the 60-day follow-up period (unadjusted OR 1.35; 95% CI 1.05 to 1.75; adjusted OR 1.35; 95% CI 1.01 to 1.81). A total of 333 patients needed to be treated with a skeletal muscle relaxant to result in 1 additional injury. Independent predictors of an injury included a history of an injury in the previous 6 months (OR 3.01; 95% CI 1.54 to 5.88) and older age (OR 1.06; 95% CI 1.04 to 1.09). Conclusions: The absolute increase in risk of injury in this population using a skeletal muscle relaxant was small but statistically significant. Cautionary use of these medications in the elderly continues to be advisable, but their use in selected patients 65 years and older could be considered if the expected benefits outweigh the small increased risk of injury. More study is needed to quantify the benefits versus risks of these medications in this population.
Acute Pancreatitis Associated with Liraglutide
Authors: Lee Phillip H , Stockton M David , Franks Andrea S 
Published: April 2011

Objective: To report what is, to our knowledge, the first postmarketing case of acute pancreatitis associated with liraglutide Case Summary: A 60-year-old female with type 2 diabetes presented with a 16-hour history of mid-epigastric pain 3 weeks after treatment was changed from exenatide 10 μg twice daily, which she had taken for 4 years, to liraglutide 1.8 mg daily. Her serum lipase level was elevated (478 units/L) at admission, and other laboratory values were within normal limits. Liraglutide was discontinued at admission. Standard therapy for pancreatitis resulted in symptom resolution and a significant decrease in serum lipase (131 units/L) by hospital day 4; she was discharged on hospital day 5. Discussion: Based on the Naranjo scale, this case represents a probable adverse drug reaction. Eight cases of pancreatitis were observed in liraglutide-treated patients in premarketing clinical trials. Extensive literature describing exenatide-related pancreatitis and premarketing reports of liraglutide-related pancreatitis, along with the temporal relationship between the initiation of liraglutide and the onset of this patient's symptoms, suggest that the episode of pancreatitis was induced by liraglutide. Conclusions: Liraglutide should be used cautiously in patients with a history of pancreatitis, and clinicians should have a high index of suspicion for this rare, but potentially serious, adverse effect.
Discovering constructions by means of collostruction analysis: The English Denominative Construction
Authors: Hampe Beate 
Published: April 2011

Abstract
Complex-transitive argument structures have received a large amount of attention from syntacticians of both formalist and cognitive-functional orientations. To account for expressions with causative resultative meanings, construction grammar has postulated a family of argument-structure constructions whose core is constituted by the Caused-Motion Construction and the Resultative Construction, exhibiting a locative complement and a predicative complement in the form of an AjP, respectively. Argument structures with NP complements, however, have been largely neglected. The present study investigates these patterns in the International Corpus of English (ICE-GB) by means “collostruction analysis”. It shows that the formal distinction between AjP and NP complements corresponds to a constructional distinction hitherto unrevealed, viz. that between the Resultative Construction and another argument-structure construction, here called the “Denominative Construction”. Apart from improving existing descriptions of the network of complex-transitive argument-structure constructions, this study demonstrates that collostruction analysis can be employed in an exploratory way to discover constructions.