bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene expression profiles in liver of mouse after chronic exposure to drinking water
Authors: Wu Bing , Zhang Yan , Zhao Dayong , Zhang Xuxiang , Kong Zhiming , Cheng Shupei 
Published: May 2009

AbstractcDNA micorarray approach was applied to hepatic transcriptional profile analysis in male mouse (Mus musculus, ICR) to assess the potential health effects of drinking water in Nanjing, China. Mice were treated with continuous exposure to drinking water for 90 days. Hepatic gene expression was analyzed with Affymetrix Mouse Genome 430A 2.0 arrays, and pathway analysis was carried out by Molecule Annotation System 2.0 and KEGG pathway database. A total of 836 genes were found to be significantly altered (1.5‐fold, P ≤ 0.05), including 294 up‐regulated genes and 542 down‐regulated genes. According to biological pathway analysis, drinking water exposure resulted in aberration of gene expression and biological pathways linked to xenobiotic metabolism, signal transduction, cell cycle and oxidative stress response. Further, deregulation of several genes associated with carcinogenesis or tumor progression including Ccnd1, Egfr, Map2k3, Mcm2, Orc2l and Smad2 was observed. Although transcription changes in identified genes are unlikely to be used as a sole indicator of adverse health effects, the results of this study could enhance our understanding of early toxic effects of drinking water exposure and support future studies on drinking water safety. Copyright © 2009 John Wiley & Sons, Ltd.
CHARMM: The biomolecular simulation program
Authors: Brooks B. R. , Brooks C. L. , Mackerell A. D. , Nilsson L. , Petrella R. J. , Roux B. , Won Y. , Archontis G. , Bartels C. , Boresch S. , Caflisch A. , Caves L. , Cui Q. , Dinner A. R. , Feig M. , Fischer S. , Gao J. , Hodoscek M. , Im W. , Kuczera K. , Lazaridis T. , Ma J. , Ovchinnikov V. , Paci E. , Pastor R. W. , Post C. B. , Pu J. Z. , Schaefer M. , Tidor B. , Venable R. M. , Woodcock H. L. , Wu X. , Yang W. , York D. M. , Karplus M. 
Published: May 2009

AbstractCHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model‐building capabilities. The CHARMM program is applicable to problems involving a much broader class of many‐particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical‐molecular mechanical force fields, to all‐atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983. © 2009 Wiley Periodicals, Inc.J Comput Chem, 2009.
Salivary simulation with ascorbic acid enhances sonographic diagnosis of obstructive sialadenitis
Authors: Bozzato Alessandro , Hertel Victoria , Bumm Klaus , Iro Heinrich , Zenk Johannes 
Published: May 2009

AbstractPurpose.High‐frequency ultrasound (US) is routinely used to evaluate various diseases of the salivary glands. Normally, the duct network of the submandibular and parotid glands is not visible during US assessment. In obstructive sialadenitis of the parotid and submandibular glands, localization of the obstacle is often difficult.Methods.In a case‐control study, the sonographic visibility of the duct before and after stimulation with oral ascorbic acid (vitamin C) was compared with sialendoscopy as the gold standard. Twenty male and 23 female patients suffering from salivary gland diseases were included in this study and compared with 25 healthy volunteers. US examination of the parotid and submandibular glands was performed before and after oral ascorbic acid stimulation. Changes in visibility of the main excretory duct were recorded and US diagnoses were compared with results of sialendoscopy.Results.In 7 of 25 controls, the main duct became partially visible after stimulation. In the group of 43 patients, the main duct was depicted before stimulation in 27 patients (63%). After ascorbic acid stimulation, the main duct became visible in 41 patients (95%). Grading the stimulated duct dilation by measuring diameters at different points revealed no correlation with the underlying type of pathology.Conclusions.Application of ascorbic acid prior to diagnostic US examination facilitates the sonographic evaluation of obstructive salivary gland diseases. © 2009 Wiley Periodicals, Inc. J Clin Ultrasound 2009
Is thermal oxidation at different temperatures suitable to isolate soil organic carbon fractions with different turnover?
Authors: Helfrich Mirjam , Flessa Heiner , Dreves Alexander , Ludwig Bernard 
Published: May 2009

AbstractFindings of previous studies suggest that there are relations between thermal stability of soil organic matter (SOM), organo‐mineral associations, and stability of SOM against microbial decay. We aimed to test whether thermal oxidation at various temperatures (200°C, 225°C, 275°C, 300°C, 400°C, or 500°C) is capable of isolating SOM fractions with increasing stability against microbial degradation. The investigation was carried out on soils (Phaeozem and Luvisol) under different land‐use regimes (field, grassland, forest). The stability of the obtained soil organic carbon (SOC) fractions was determined using the natural‐13C approach for continuously maize‐cropped soils and radiocarbon dating. In the Luvisol, thermal oxidation with increasing temperatures did not yield residual SOC fractions of increasing microbial stability. Even the SOC fraction resistant to thermal oxidation at 300°C contained considerable amounts of young, maize‐derived C. In the Phaeozem, the mean 14C age increased considerably (from 3473 y BP in the mineral‐associated SOC fraction to 9116 y BP in the residual SOC fraction after thermal oxidation at 300°C). An increasing proportion of fossil C (calculated based on 14C data) in residual SOC fractions after thermal oxidation with increasing temperatures indicated that this was mainly due to the relative accumulation of thermally stable fossil C. We conclude that thermal oxidation with increasing temperature was not generally suitable to isolate mineral‐associated SOC fractions of increasing microbial stability.
Sulfur in soils
Authors: Wilhelm Scherer Heinrich 
Published: May 2009

AbstractSulfur (S) deficiency of crops, which has been reported with increasing frequency over the past two decades on a worldwide scale, is a factor that reduces yield and affects the quality of harvested products. Especially in Western European countries, incidence of S deficiency has increasingly been reported in Brassicaceae. For this reason, more attention should be paid to the optimization of S‐fertilizer application, in order to cover plant S requirements whilst minimizing environmental impacts. In soils, S exists in inorganic and organic forms. While sulfate (SO$ _4^{2-} $), which is a direct S source for plants, contributes up to 5% of total soil S, generally more than 95% of soil S are organically bound. Organic S is divided into sulfate ester and carbon‐bonded S. Although not directly plant‐available, organically bound S may potentially contribute to the S supply of plants, especially in deficiency situations. Sulfur turnover involves both biochemical and biological mineralization. Biochemical mineralization, which is the release of SO$ _4^{2-} $ from the ester sulfate pool through enzymatic hydrolysis, is controlled by S supply, while the biological mineralization is driven by the microbial need for organic C to provide energy.
A comparison of PTSD symptom patterns in three types of civilian trauma
Authors: Kelley Lance P. , Weathers Frank W. , McDevitt‐Murphy Meghan E. , Eakin David E. , Flood Amanda M. 
Published: May 2009

AbstractPosttraumatic stress disorder (PTSD) is assumed to be an equivalent syndrome regardless of the type of traumatic event that precipitated it. However, the Diagnostic and Statistical Manual of Mental Disorders (4th ed.; DSM‐IV; American Psychiatric Association, 1994) and previous research suggest that the clinical presentation of PTSD varies by trauma type. This study compared PTSD symptom profiles in three types of civilian trauma: sexual assault (n = 86), motor vehicle accident (n = 162), and sudden loss of a loved one (n = 185). Groups differed in overall PTSD severity and displayed distinct PTSD symptom patterns. Results suggest that different trauma types lead to unique variants of the PTSD syndrome, which may result from different etiological factors and may require different treatment approaches.
Imagery rehearsal therapy for posttraumatic nightmares in U.S. veterans
Authors: Lu Mary , Wagner Amy , Van Male Lynn , Whitehead Ashlee , Boehnlein James 
Published: May 2009

AbstractImagery rehearsal therapy (IRT) may help reduce residual nightmares and posttraumatic stress disorder (PTSD) symptoms in veterans after trauma‐focused PTSD treatment. Fifteen male U.S. veterans with PTSD and trauma‐related nightmares, who had not previously completed trauma‐focused PTSD treatment, attended 6 IRT group sessions. No benefits were observed immediately posttreatment. At 3‐ and 6‐month follow‐up, however, trauma‐related nightmare frequency (nights/week) decreased (p < .01). The number of trauma‐related nightmares/week (p < .01), number of total nightmares/week (p < .05), and PTSD symptoms (p < .05) also decreased at 3 months. The overall F test for time was significant (p < .05) for nightmare severity and fear of sleep. No effects were found on measures of the impact of nightmares, sleep quality, or depression. Clinical and research implications are discussed.
Parasympathetic reactivity to recalled traumatic and pleasant events in trauma‐exposed individuals
Authors: Arditi‐Babchuk Hadar , Feldman Ruth , Gilboa‐Schechtman Eva 
Published: May 2009

AbstractParasympathetic and heart rate (HR) reactivity to memories of traumatic and pleasant events were investigated in trauma‐exposed individuals (n = 40). Vagal tone and HR were recorded before, during, and following recall of traumatic and pleasant events. Posttraumatic stress (PTS) was related to blunted parasympathetic reactivity among trauma‐exposed individuals. Specifically, PTS severity was related to lower parasympathetic activation and lower recovery following trauma recall, and to lower parasympathetic activation (but not recovery) in response to a pleasant event recall. No association was observed between PTS severity and initial parasympathetic tone. However, PTS severity was associated with initial HR. Assessment of parasympathetic reactivity may enhance our understanding of the normative and pathological reactions to trauma and stress.
National laryngopharyngectomy and reconstructive surgery survey
Authors: Richmon Jeremy D. , Samji Hussein A. , Deschler Daniel G. 
Published: May 2009

AbstractObjectives/Hypothesis:To understand the various methods available to reconstruct total laryngopharyngectomy defects and to understand which, and to what degree, various factors influence the surgeon in choosing a particular reconstructive method.Methods:Otolaryngologists and plastic surgeons who perform head and neck reconstruction were surveyed regarding preference of laryngopharyngectomy reconstruction. Numerical and rank‐order data was analyzed using T statistics and Fisher exact test.Results:Two hundred surveys were mailed and 72 physicians (36% response rate) provided data, with otolaryngologists comprising 54% of the respondents. Otolaryngologists were more likely to consider voice (P = .003) and swallowing (P = .02) outcomes compared to plastic surgeons. In contrast, plastic surgeons more often included cosmesis (P = .05) among those factors influencing their reconstructive choice. However, rank‐order analysis demonstrated no statistical difference between plastic surgeons and otolaryngologists with respect to each factor.Conclusions:Our study sought to examine what motivates surgeons from several specialties to choose one reconstructive method over another for laryngopharyngeal defects. Otolaryngologists were more likely to consider voice and swallowing function in contrast to plastic surgeons, who more frequently included cosmesis as a factor. However, when physicians were asked to rank the importance of each of the eight factors from most to least important in influencing their reconstructive option, there was no statistical difference between plastic surgeons and otolaryngologists with respect to each factor. Further research is necessary to provide an evidence base for which reconstructive method offers the optimal functional restoration. Laryngoscope, 2009
Proteomic identification of serum biomarkers for head and neck cancer surveillance
Authors: Gourin Christine G. , Zhi Wenbo , Adam Bao‐Ling 
Published: May 2009

AbstractObjectives/Hypothesis:Serum protein profiling by SELDI‐TOF‐MS distinguishes pretreatment and post‐treatment samples from patients with head and neck squamous cell cancer (HNSCC) by disease status (disease‐free or recurrence) with a high degree of sensitivity and specificity. We sought to identify biomarkers for recurrence with potential utility for surveillance and incorporated 2‐D DIGE and MALDI‐TOF‐MS techniques to overcome the limitations of SELDI‐TOF‐MS in determining biomarker identity.Methods:Serum samples were collected prospectively from 143 HNSCC patients and analyzed based on disease status following treatment.Results:Recurrent HNSCC occurred in 46 patients. MALDI‐TOF‐MS following immunodepletion of major plasma proteins followed by 2‐D DIGE identified 181 proteins with differential expression between pretreatment and post‐treatment samples collected 6 months or more following treatment. Classification by disease status revealed significant differential expression of 16 proteins, with recurrent HNSCC associated with underexpression of kininogen and serine protease inhibitors C‐1 inhibitor, kininogen, angiotensinogen, serine/cysteine proteinase inhibitor clade G member 1, and overexpression of thiol‐specific antioxidant proteins (TSA), apolipoprotein A1 and proapolipoprotein, and epidermal cytokeratin 2.Conclusions:Serum protein profiling using 2D DIGE/MALDI‐TOF‐MS identifies proteins with significant differential expression in HNSCC based on disease status. Recurrent HNSCC was associated with underexpression of several protease inhibitors and kininogen, which has antiangiogenic properties, and overexpression of TSA, which is a free radical scavenger, as well as several forms of apolipoprotein A1 that may serve as a carrier molecule but may also indirectly promote tumor survival through kinase activation. This profile is consistent with a more aggressive disease variant and warrants further investigation. Laryngoscope, 2009
Morphometric bronchoscopy in adults with central airway obstruction: Case illustrations and review of the literature
Authors: Murgu Septimiu , Colt Henri G. 
Published: May 2009

AbstractThe severity of airway narrowing impacts ventilatory function, quality of life, and choice of therapy for patients with central airway obstruction. The quantification of airway caliber remains a subjective estimate that depends on patient positioning, technique, and operator experience. In this article, we describe how morphometric bronchoscopy, a software processing method whereby bronchoscopic digital images are analyzed in order to measure airway lumen diameter, can be used to objectively quantify the degree of airway narrowing in adult patients with central airway obstruction. Laryngoscope, 2009
Middle turbinate hinge flap for frontal recess obliteration following prior cranialization
Authors: Soler Zachary M. , Khalid Ayesha N. , Smith Timothy L. 
Published: May 2009

AbstractFrontal sinus cranialization is an established procedure utilized in instances wherein the posterior table has been irreversibly compromised. A known complication of this procedure is pneumocephalus, which may develop if the frontal recess has not been fully separated from the cranialized sinus. We report 3 cases wherein massive pneumocephalus developed after cranialization of the frontal sinus. In each case, a novel endoscopic repair was undertaken utilizing a middle turbinate hinge flap to obliterate the frontal recess. In each instance, obliteration of the frontal recess resulted in durable resolution of pneumocephalus. Laryngoscope, 2009
Prognostic significance of vascular endothelial growth factor‐C expression and lymphatic vessel density in supraglottic squamous cell carcinoma
Authors: Baek Seung‐Kuk , Jung Kwang‐Yoon , Lee Sang‐Hag , Woo Jeong‐Soo , Kwon Soon‐Young , Chung Eun‐Jae , Kim Tae‐Hoon , Chae Yang‐Seok 
Published: May 2009

AbstractObjectives/Hypothesis:Regional lymph node metastases are very common findings of supraglottic cancer. The mechanism of lymphatic metastasis is as yet unknown because there have been no specific markers that could definitely distinguish lymphatic vessels from blood vessels. The aim of this study is to identify the prognostic significance of vascular endothelial growth factor‐C (VEGF‐C) expression and lymphatic vessel density (LVD) in supraglottic cancer.Study Design:The prognostic value of the VEGF‐C and LVD was retrospectively evaluated in an unselected series of patients treated with curative intent for supraglottic cancer.Methods:We investigated lymphatic vessels in 43 subjects who had previously been diagnosed with supraglottic cancer. Immunohistochemical staining was performed with VEGF‐C, D2‐40, and CD31 monoclonal antibodies on the paraffin‐embedded tissues obtained from these patients. The association among the semiquantitative score of VEGF‐C stained cancer cells, the density of immunohistochemically stained microvessels, and the prognostic factors of supraglottic cancers were investigated to evaluate the prognostic significance.Results:VEGF‐C and LVD showed a statistically significant difference according to the presence of lymph node metastasis and regional recurrence (P < .05). VEGF‐C was only associated with disease‐free survival and regional recurrence in multivariate analysis (P < .05).Conclusions:VEGF‐C and LVD might be useful as predictors of the risk of lymph node metastasis and regional recurrence. Laryngoscope, 2009
Cartilage grafts in dorsal nasal augmentation of traumatic saddle nose deformity: A long‐term follow‐up
Authors: Mao Johnny , Carron Michael , Tomovic Senja , Narasimhan Kailash , Allen Shannon , Mathog Robert H. 
Published: May 2009

AbstractObjectives/Hypothesis:To document the long‐term advantages and disadvantages of cartilage grafts used to correct traumatic saddle nose deformity. Additionally, to demonstrate functional improvement and cosmetic satisfaction with the use of this graft.Study Design:Retrospective chart review and prospective follow‐up telephone survey of 20 patients after dorsal augmentation of saddle nose deformity secondary to trauma.Methods:This is a single‐surgeon, single‐institution investigation within an academic tertiary care medical center. All patients presented for correction of saddle nose deformity after trauma, and cartilage grafts were used for augmentation of the dorsum. Minimum postoperative follow‐up period of 1 year was required. A modified and expanded Nasal Obstructive Symptoms Evaluation survey, which included questions pertaining to the appearance of their nose, was used to assess both functional and cosmetic changes after surgery.Results:Only 1 of the 20 patients was dissatisfied with the overall outcome. Three (15%) were extremely satisfied, 12 (60%) were very satisfied, three (15%) were somewhat satisfied, and one (5%) was indifferent. In terms of function, four (20%) experienced excellent relief in nasal obstruction, five (25%) moderate relief, four (20%) mild relief, and seven (35%) noted no difference. Regarding cosmesis, two (10%) noted excellent improvement, three (15%) moderate improvement, nine (45%) mild improvement, and five (25%) noted no significant change. One (5%) patient reported worsening due to tip edema. Mean follow‐up time was 6.8 years.Conclusions:Autogenous cartilage grafts are useful in the correction of mild to moderate traumatic saddle nose deformity. The graft is readily available, preserves long‐term structural stability, and achieves functional and cosmetic satisfaction in most patients. Laryngoscope, 2009
Solid‐state NMR spectroscopic studies on the interaction of sorbic acid with phospholipid membranes at different pH levels
Authors: Chu Shidong , Hawes John W. , Lorigan Gary A. 
Published: May 2009

Abstract2H,31P, and1H‐magic‐angle‐spinning (MAS) solid‐state NMR spectroscopic methods were used to elucidate the interaction between sorbic acid, a widely used weak acid food preservative, and 1,2‐dimyristoyl‐sn‐glycero‐3‐phosphocholine (DMPC) bilayers under both acidic and neutral pH conditions. The linewidth broadening observed in the31P NMR powder pattern spectra and the changes in the31P longitudinal relaxation time (T1) indicate interaction with the phospholipid headgroup upon titration of sorbic acid or decanoic acid into DMPC bilayers over the pH range from 3.0 to 7.4. The peak intensities of sorbic acid decrease upon addition of paramagnetic Mn2+ions in DMPC bilayers as recorded in the1H MAS NMR spectra, suggesting that sorbic acid molecules are in close proximity with the membrane/aqueous surface. No significant2H quadrupolar splitting (ΔνQ) changes are observed in the2H NMR spectra of DMPC‐d54upon titration of sorbic acid, and the change of pH has a slight effect on ΔνQ, indicating that sorbic acid has weak influence on the orientation order of the DMPC acyl chains in the fluid phase over the pH range from 3.0 to 7.4. This finding is in contrast to the results of the decanoic acid/DMPC‐d54systems, where ΔνQincreases as the concentration of decanoic acid increases. Thus, in the membrane association process, sorbic acids are most likely interacting with the headgroups and shallowly embedded near the top of the phospholipid headgroups, rather than inserting deep into the acyl chains. Thus, antimicrobial mode of action for sorbic acid may be different from that of long‐chain fatty acids. Copyright © 2009 John Wiley & Sons, Ltd.
Mixed finite element methods for incompressible flow: Stationary Stokes equations
Authors: Cai Zhiqiang , Tong Charles , Vassilevski Panayot S. , Wang Chunbo 
Published: May 2009

AbstractIn this article, we develop and analyze a mixed finite element method for the Stokes equations. Our mixed method is based on the pseudostress‐velocity formulation. The pseudostress is approximated by the Raviart‐Thomas (RT) element of index k ≥ 0 and the velocity by piecewise discontinuous polynomials of degree k. It is shown that this pair of finite elements is stable and yields quasi‐optimal accuracy. The indefinite system of linear equations resulting from the discretization is decoupled by the penalty method. The penalized pseudostress system is solved by the H(div) type of multigrid method and the velocity is then calculated explicitly. Alternative preconditioning approaches that do not involve penalizing the system are also discussed. Finally, numerical experiments are presented. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2010