bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of cytogenetic abnormalities with gene expression profiles
Authors: Zhou Yiming , Zhang Qing , Stephens Owen , Heuck Christoph J. , Tian Erming , Sawyer Jeffrey R. , Cartron-Mizeracki Marie-Astrid , Qu Pingping , Keller Jason , Epstein Joshua , Barlogie Bart , Shaughnessy John D. 
Published: April 2012

Abstract
Cytogenetic abnormalities are important clinical parameters in various types of cancer, including multiple myeloma. We developed a model to predict cytogenetic abnormalities in patients with multiple myeloma using gene expression profiling and validated it by different cytogenetic techniques. The model has an accuracy rate up to 0.89. These results provide proof of concept for the hypothesis that gene expression profiling is a superior genomic method for clinical molecular diagnosis and/or prognosis.
The impact of platelet transfusion characteristics on posttransfusion platelet increments and clinical bleeding in patients with hypoproliferative thrombocytopenia
Authors: Triulzi Darrell J. , Assmann Susan F. , Strauss Ronald G. , Ness P. M. , Hess John R. , Kaufman Richard M. , Granger Suzanne , Slichter Sherrill J. 
Published: April 2012

Abstract
Platelet characteristics, such as platelet dose, platelet source (apheresis vs pooled), platelet donor-recipient ABO compatibility, and duration of platelet storage, can affect posttransfusion platelet increments, but it is unclear whether these factors impact platelet transfusion efficacy on clinical bleeding. We performed secondary analyses of platelet transfusions given in the prospective randomized Platelet Dose Study, which included 1272 platelet-transfused hematology-oncology patients who received 6031 prophylactic platelet transfusions. The primary outcome of these analyses was time from first transfusion to first World Health Organization ≥ grade 2 bleeding. Platelet transfusion increments were assessed at 0.25 to 4 hours and 16 to 32 hours after platelet transfusion. There were 778 patients evaluable for analysis of time to bleeding. Adjusted models showed that randomized dose strategy, platelet source, ABO compatibility, and duration of storage did not predict this outcome. Platelet increments were generally higher for transfusions of apheresis platelets, ABO-identical platelets, and platelets stored 3 days versus 4 to 5 days. Thus, although platelet source, ABO compatibility, and duration of storage exert a modest impact on both absolute and corrected posttransfusion platelet increments, they have no measurable impact on prevention of clinical bleeding. This trial was registered at www.clinicaltrials.gov as #NCT00128713.
Broadening the factor V Leiden paradox: pulmonary embolism and deep-vein thrombosis as 2 sides of the spectrum
Authors: van Langevelde Kirsten , Flinterman Linda E. , van Hylckama Vlieg Astrid , Rosendaal Frits R. , Cannegieter Suzanne C. 
Published: April 2012

AbstractRisk factors for deep-vein thrombosis have been shown not to be always the same as for pulmonary embolism. A well-known example is the factor V Leiden (FVL) paradox: the FVL mutation poses a clearly higher risk for deep-vein thrombosis (DVT) than for pulmonary embolism. We aimed to expand this paradox and therefore present risk estimates for several established risk factors for DVT and pulmonary embolism separately. When such separate risk estimates could not be retrieved from the literature, we calculated these risks in our own data, a large population-based case-control study on venous thrombosis (the MEGA study). Our results showed that the FVL paradox can be broadened (ie, the risk factors oral contraceptive use, pregnancy, puerperium, minor leg injuries, and obesity have an effect comparable with FVL). Furthermore, we found that pulmonary conditions, such as chronic obstructive pulmonary disease, pneumonia, and sickle cell disease, were risk factors with an opposite effect: a higher risk of pulmonary embolism, but little or no effect on DVT. These findings suggest that pulmonary embolism and DVT may not always have the same etiology, and encourage unraveling this phenomenon in further studies.
Improvement of defective cystic fibrosis airway epithelial wound repair after CFTR rescue
Authors: Trinh Nguyen Thu Ngan , Bardou Olivier , Privé Anik , Maillé Emilie , Adam Damien , Lingée Sarah , Ferraro Pasquale , Desrosiers Martin-Yvon , Coraux Christelle , Brochiero Emmanuelle 
Published: April 2012

Airway damage and remodelling are important components of lung pathology progression in cystic fibrosis (CF). Although repair mechanisms are engaged to restore the epithelial integrity, these processes are obviously insufficient to maintain lung function in CF airways. Our aims were therefore to study how the basic cystic fibrosis transmembrane conductance regulator (CFTR) defect could impact epithelial wound healing and to determine if CFTR correction could improve it.Wound-healing experiments, as well as cell migration and proliferation assays, were performed to study the early phases of epithelial repair in human CF and non-CF airway cells. CFTR function was evaluated using CFTR small interferring (si)RNA and inhibitor GlyH101 in non-CF cells, and conversely after CFTR rescue with the CFTR corrector VRT-325 in CF cells.Wound-healing experiments first showed that airway cells from CF patients repaired slower than non-CF cells. CFTR inhibition or silencing in non-CF primary airway cells significantly inhibited wound closure. GlyH101 also decreased cell migration and proliferation. Interestingly, wild-type CFTR transduction in CF airway cell lines or CFTR correction with VRT-325 in CFBE-ΔF508 and primary CF bronchial monolayers significantly improved wound healing.Altogether our results demonstrated that functional CFTR plays a critical role in wound repair, and CFTR correction may represent a novel strategy to promote the airway repair processes in CF.
EnzyBase: a novel database for enzybiotic studies
Authors: Wu Hongyu , Lu Hairong , Huang Jinjiang , Li Guodong , Huang Qingshan 
Published: April 2012

Abstract

Background
Enzybiotics are becoming increasingly recognized as potential alternative therapies for drug-resistant bacteria. Although only a few enzybiotics are currently well characterized, much information is still missing or is unavailable for researchers. The construction of an enzybiotics database would therefore increase efficiency and convenience in investigating these bioactive proteins and thus help reduce or delay the recent increase in antibiotic resistance.

Description
In the present manuscript, we describe the development of a novel and original database called EnzyBase, which contains 1144 enzybiotics from 216 natural sources. To ensure data quality, we limited the source of information to authoritative public databases and published scientific literature. The interface of EnzyBase is easy to use and allows users to rapidly retrieve data according to their desired search criteria and blast the database for homologous sequences. We also describe examples of database-aided enzybiotics discovery and design.

Conclusion
EnzyBase serves as a unique tool for enzybiotic studies. It has several potential applications, e.g. in silico enzybiotic combination as cocktails, and novel enzybiotic design, in response to continuously emerging drug-resistant pathogens. This database is a valuable platform for researchers who are interested in enzybiotic studies. EnzyBase is available online at http://biotechlab.fudan.edu.cn/database/EnzyBase/home.php.
Dexmedetomidine is neuroprotective in an in vitro model for traumatic brain injury
Authors: Schoeler Marc , Loetscher Philip D , Rossaint Rolf , Fahlenkamp Astrid V , Eberhardt Georg , Rex Steffen , Weis Joachim , Coburn Mark 
Published: April 2012

Abstract

Background
The α2-adrenoreceptor agonist dexmedetomidine is known to provide neuroprotection under ischemic conditions. In this study we investigated whether dexmedetomidine has a protective effect in an in vitro model for traumatic brain injury.

Methods
Organotypic hippocampal slice cultures were subjected to a focal mechanical trauma and then exposed to varying concentrations of dexmedetomidine. After 72 h cell injury was assessed using propidium iodide. In addition, the effects of delayed dexmedetomidine application, of hypothermia and canonical signalling pathway inhibitors were examined.

Results
Dexmedetomidine showed a protective effect on traumatically injured hippocampal cells with a maximum effect at a dosage of 1 μM. This effect was partially reversed by the simultaneous administration of the ERK inhibitor PD98059.

Conclusion
In this TBI model dexmedetomidine had a significant neuroprotective effect. Our results indicate that activation of ERK might be involved in mediating this effect.
Genistein cooperates with the histone deacetylase inhibitor vorinostat to induce cell death in prostate cancer cells
Authors: Phillip Cornel J , Giardina Christopher K , Bilir Birdal , Cutler David J , Lai Yu-Heng , Kucuk Omer , Moreno Carlos S 
Published: April 2012

AbstractBackgroundAmong American men, prostate cancer is the most common, non-cutaneous malignancy that accounted for an estimated 241,000 new cases and 34,000 deaths in 2011. Previous studies have suggested that Wnt pathway inhibitory genes are silenced by CpG hypermethylation, and other studies have suggested that genistein can demethylate hypermethylated DNA. Genistein is a soy isoflavone with diverse effects on cellular proliferation, survival, and gene expression that suggest it could be a potential therapeutic agent for prostate cancer. We undertook the present study to investigate the effects of genistein on the epigenome of prostate cancer cells and to discover novel combination approaches of other compounds with genistein that might be of translational utility. Here, we have investigated the effects of genistein on several prostate cancer cell lines, including the ARCaP-E/ARCaP-M model of the epithelial to mesenchymal transition (EMT), to analyze effects on their epigenetic state. In addition, we investigated the effects of combined treatment of genistein with the histone deacetylase inhibitor vorinostat on survival in prostate cancer cells.MethodsUsing whole genome expression profiling and whole genome methylation profiling, we have determined the genome-wide differences in genetic and epigenetic responses to genistein in prostate cancer cells before and after undergoing the EMT. Also, cells were treated with genistein, vorinostat, and combination treatment, where cell death and cell proliferation was determined.ResultsContrary to earlier reports, genistein did not have an effect on CpG methylation at 20 μM, but it did affect histone H3K9 acetylation and induced increased expression of histone acetyltransferase 1 (HAT1). In addition, genistein also had differential effects on survival and cooperated with the histone deacteylase inhibitor vorinostat to induce cell death and inhibit proliferation.ConclusionOur results suggest that there are a number of pathways that are affected with genistein and vorinostat treatment such as Wnt, TNF, G2/M DNA damage checkpoint, and androgen signaling pathways. In addition, genistein cooperates with vorinostat to induce cell death in prostate cancer cell lines with a greater effect on early stage prostate cancer.
Bean and rice meals reduce postprandial glycemic response in adults with type 2 diabetes: a cross-over study
Authors: Thompson Sharon V , Winham Donna M , Hutchins Andrea M 
Published: April 2012

Abstract

Background
Around the world, beans and rice are commonly consumed together as a meal. With type 2 diabetes increasing, the effect of this traditional diet pattern on glycemic response has not been studied fully.

Methods
We evaluated the glycemic response of bean and rice traditional meals compared to rice alone in adults with type 2 diabetes. Seventeen men and women with type 2 diabetes controlled by metformin (n = 14) or diet/exercise (n = 3) aged 35–70 years participated in the randomized 4 × 4 crossover trial. The white long grain rice control, pinto beans/rice, black beans/rice, red kidney beans/rice test meals, matched for 50 grams of available carbohydrate, were consumed at breakfast after a 12 hour fast. Capillary blood glucose concentrations at baseline and at 30 minute intervals up to 180 minutes postprandial were collected. MANOVA for repeated measures established glucose differences between treatments. Paired t tests identified differences between bean types and the rice control following a significant MANOVA.

Results
Postprandial net glucose values were significantly lower for the three bean/rice treatments in contrast to the rice control at 90, 120 and 150 minutes. Incremental area under the curve values were significantly lower for the pinto and black bean/rice meals compared to rice alone, but not for kidney beans.

Conclusions
Pinto, dark red kidney and black beans with rice attenuate the glycemic response compared to rice alone. Promotion of traditional foods may provide non-pharmaceutical management of type 2 diabetes and improve dietary adherence with cultural groups.

Trial registration
Clinical Trials number NCT01241253
Removal of 10-nm contaminant particles from Si wafers using CO2 bullet particles
Authors: Kim Inho , Hwang Kwangseok , Lee JinWon 
Published: April 2012

Abstract
Removal of nanometer-sized contaminant particles (CPs) from substrates is essential in successful fabrication of nanoscale devices. The particle beam technique that uses nanometer-sized bullet particles (BPs) moving at supersonic velocity was improved by operating it at room temperature to achieve higher velocity and size uniformity of BPs and was successfully used to remove CPs as small as 10 nm. CO2 BPs were generated by gas-phase nucleation and growth in a supersonic nozzle; appropriate size and velocity of the BPs were obtained by optimizing the nozzle contours and CO2/He mixture fraction. Cleaning efficiency greater than 95% was attained. BP velocity was the most important parameter affecting removal of CPs in the 10-nm size range. Compared to cryogenic Ar or N2 particles, CO2 BPs were more uniform in size and had higher velocity and, therefore, cleaned CPs more effectively.
Joint parameter estimation and Cramer-Rao bound analysis in ground-based forward scatter radar
Authors: Zeng Tao , Hu Cheng , Cherniakov Mikhail , Zhuo Chao , Mao Cong 
Published: April 2012

Abstract
Forward scatter radar (FSR) has potential applications such as target detection, classification, and recognition. The success of these issues depends on the accuracy of parameter estimation. Many parameter estimation methods for air-based FSR have been given, but cannot directly be applied in the ground-based ones for the different system functions. The received signal in ground-based FSR depends on the target's electrical size and trajectory, which are unknown a priori. It is impossible to construct an optimal reception with accurate reference function in practical situations. An adaptive method of parameter estimation is therefore proposed in this article, which includes the construction of reference function and the two-dimensional parameter estimation. Furthermore, the Crammer-Rao bounds of estimation accuracy are obtained via the analytical derivation, which can be in turn utilized to determine the estimation step in the algorithm. Finally, the effectiveness of the algorithm is shown using both simulated and experimental data.
Age-related guanine nucleotide exchange factor, mouse Zizimin2, induces filopodia in bone marrow-derived dendritic cells
Authors: Sakabe Isamu , Asai Azusa , Iijima Junko , Maruyama Mitsuo 
Published: April 2012

Abstract

Background
We recently isolated and identified Zizimin2 as a functional factor that is highly expressed in murine splenic germinal center B cells after immunization with T-cell-dependent antigen. Zizimin2 was revealed to be a new family member of Dock (dedicator of cytokinesis), Dock11, which is the guanine nucleotide exchange factor for Cdc42, a low-molecular-weight GTPase. However, the molecular function of Zizimin2 in acquired immunity has not been elucidated.

Results
In this study, we show that the protein expression of Zizimin2, which is also restricted to lymphoid tissues and lymphocytes, is reduced in aged mice. Over-expression of full-length Zizimin2 induced filopodial formation in 293T cells, whereas expression of CZH2 domain inhibited it. Stimulation of Fcγ receptor and Toll-like receptor 4 triggered Zizimin2 up-regulation and Cdc42 activation in bone marrow-derived dendritic cells.

Conclusions
These data suggest that Zizimin2 is an immune-related and age-regulated guanine nucleotide exchange factor, which facilitates filopodial formation through activation of Cdc42, which results in activation of cell migration.
Emergency total thyroidectomy due to non traumatic disease. Experience of a surgical unit and literature review
Authors: Testini Mario , Logoluso Francesco , Lissidini Germana , Gurrado Angela , Campobasso Giuseppe , Cortese Rocco , De Luca Giuseppe Massimiliano , Franco Ilaria Fabiola , De Luca Alessandro , Piccinni Giuseppe 
Published: April 2012

AbstractBackgroundAcute respiratory failure due to thyroid compression or invasion of the tracheal lumen is a surgical emergency requiring urgent management. The aim of this paper is to describe a series of six patients treated successfully in the emergency setting with total thyroidectomy due to ingravescent dyspnoea and asphyxia, as well as review related data reported in literature.MethodsDuring 2005-2010, of 919 patients treated by total thyroidectomy at our Academic Hospital, 6 (0.7%; 4 females and 2 men, mean age: 68.7 years, range 42-81 years) were treated in emergency. All the emergency operations were performed for life-threatening respiratory distress. The clinical picture at admission, clinical features, type of surgery, outcomes and complications are described. Mean duration of surgery was 146 minutes (range: 53-260).ResultsIn 3/6 (50%) a manubriotomy was necessary due to the extension of the mass into the upper mediastinum. In all cases total thyroidectomy was performed. In one case (16.7%) a parathyroid gland transplantation and in another one (16.7%) a tracheotomy was necessary due to a condition of tracheomalacia. Mean post-operative hospital stay was 6.5 days (range: 2-10 days). Histology revealed malignancy in 4/6 cases (66.7%), showing 3 primitive, and 1 secondary tumors. Morbidity consisted of 1 transient recurrent laryngeal palsy, 3 transient postoperative hypoparathyroidism, and 4 pleural effusions, treated by medical therapy in 3 and by drains in one. There was no mortality.ConclusionOn the basis of our experience and of literature review, we strongly advocate elective surgery for patients with thyroid disease at the first signs of tracheal compression. When an acute airway distress appears, an emergency life-threatening total thyroidectomy is recommended in a high-volume centre.
RAC1 GTPase plays an important role in γ-irradiation induced G2/M checkpoint activation
Authors: Yan Ying , Greer Patrick M , Cao Phu T , Kolb Ryan H , Cowan Kenneth H 
Published: April 2012

Abstract
Introduction
In response to gamma-irradiation (IR)-induced double-strand DNA breaks, cells undergo cell-cycle arrest, allowing time for DNA repair before reentering the cell cycle. G2/M checkpoint activation involves activation of ataxia telangiectasia mutated (ATM)/ATM- and rad3-related (ATR) kinases and inhibition of Cdc25 phosphatases, resulting in inhibition of Cdc2 kinase and subsequent G2/M cell-cycle arrest. Previous studies from our laboratory showed that the G2/M checkpoint activation after IR exposure of MCF-7 breast cancer cells is dependent on the activation of extracellular signal-regulated protein kinase 1 and 2 (ERK1/2) signaling. In the present studies, we investigated the role of Ras-related C3 botulinum toxin substrate 1 (Rac1) guanosine triphosphatase (GTPase) in IR-induced G2/M checkpoint response and ERK1/2 activation, as well as in cell survival after IR.

Methods
With Rac1-specific inhibitor, dominant negative mutant Rac1 (N17Rac1) and specific small interfering RNA, the effect of Rac1 on IR-induced G2/M checkpoint response and ERK1/2 activation was examined in human breast cancer cells. In addition, the effect of Rac1 on cell survival after irradiation was assessed by using Rac1-specific inhibitor.

Results
IR exposure of MCF-7 breast cancer cells was associated with a marked activation of Rac1 GTPase. Furthermore, inhibition of Rac1 by using specific inhibitor, dominant-negative Rac1 mutant, or specific siRNA resulted in attenuation of IR-induced G2/M arrest and concomitant diminution of IR-induced activation of ATM, ATR, Chk1, and Chk2 kinases, as well as phosphorylation of Cdc2-Tyr15. Moreover, Rac1 inhibition or decreased Rac1 expression also abrogated IR-induced phosphorylation of mitogen-activated protein kinase kinase 1 and 2 (MEK1/2) and ERK1/2. Ultimately, inhibition of Rac1 markedly increased cellular sensitivity to IR exposure, which involves induction of apoptosis.

Conclusion
Studies in this report suggest that Rac1 GTPase plays an essential role in the activation of IR-induced ERK1/2 signaling and subsequent G2/M checkpoint response. Furthermore, results also support a role for Rac1 in promoting cell survival after irradiation treatment.
Correlation between high blood IL-6 level, hyperglycemia, and glucose control in septic patients
Authors: Nakamura Masataka , Oda Shigeto , Sadahiro Tomohito , Watanabe Eizo , Abe Ryuzo , Nakada Taka-aki , Morita Yasumasa , Hirasawa Hiroyuki 
Published: April 2012

Abstract
Introduction
The aim of the present study was to investigate the relationship between the blood IL-6 level, the blood glucose level, and glucose control in septic patients.

Methods
This retrospective observational study in a general ICU of a university hospital included a total of 153 patients with sepsis, severe sepsis, or septic shock who were admitted to the ICU between 2005 and 2010, stayed in the ICU for 7 days or longer, and did not receive steroid therapy prior to or after ICU admission. The severity of stress hyperglycemia, status of glucose control, and correlation between those two factors in these patients were investigated using the blood IL-6 level as an index of hypercytokinemia.

Results
A significant positive correlation between blood IL-6 level and blood glucose level on ICU admission was observed in the overall study population (n = 153; r = 0.24, P = 0.01), and was stronger in the nondiabetic subgroup (n = 112; r = 0.42, P < 0.01). The rate of successful glucose control (blood glucose level < 150 mg/dl maintained for 6 days or longer) decreased with increase in blood IL-6 level on ICU admission (P < 0.01). The blood IL-6 level after ICU admission remained significantly higher and the 60-day survival rate was significantly lower in the failed glucose control group than in the successful glucose control group (P < 0.01 and P < 0.01, respectively).

Conclusions
High blood IL-6 level was correlated with hyperglycemia and with difficulties in glucose control in septic patients. These results suggest the possibility that hypercytokinemia might be involved in the development of hyperglycemia in sepsis, and thereby might affect the success of glucose control.
Aestivation: signaling and hypometabolism
Authors: Storey Kenneth B. , Storey Janet M. 
Published: April 2012

Summary
Aestivation is a survival strategy used by many vertebrates and invertebrates to endure arid environmental conditions. Key features of aestivation include strong metabolic rate suppression, strategies to retain body water, conservation of energy and body fuel reserves, altered nitrogen metabolism, and mechanisms to preserve and stabilize organs, cells and macromolecules over many weeks or months of dormancy. Cell signaling is crucial to achieving both a hypometabolic state and reorganizing multiple metabolic pathways to optimize long-term viability during aestivation. This commentary examines the current knowledge about cell signaling pathways that participate in regulating aestivation, including signaling cascades mediated by the AMP-activated kinase, Akt, ERK, and FoxO1.