bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multifactor dimensionality reduction reveals a three-locus epistatic interaction associated with susceptibility to pulmonary tuberculosis
Authors: Collins Ryan L , Hu Ting , Wejse Christian , Sirugo Giorgio , Williams Scott M , Moore Jason H 
Published: February 2013

Abstract

Background
Identifying high-order genetics associations with non-additive (i.e. epistatic) effects in population-based studies of common human diseases is a computational challenge. Multifactor dimensionality reduction (MDR) is a machine learning method that was designed specifically for this problem. The goal of the present study was to apply MDR to mining high-order epistatic interactions in a population-based genetic study of tuberculosis (TB).

Results
The study used a previously published data set consisting of 19 candidate single-nucleotide polymorphisms (SNPs) in 321 pulmonary TB cases and 347 healthy controls from Guniea-Bissau in Africa. The ReliefF algorithm was applied first to generate a smaller set of the five most informative SNPs. MDR with 10-fold cross-validation was then applied to look at all possible combinations of two, three, four and five SNPs. The MDR model with the best testing accuracy (TA) consisted of SNPs rs2305619, rs187084, and rs11465421 (TA = 0.588) in PTX3, TLR9 and DC-Sign, respectively. A general 1000-fold permutation test of the null hypothesis of no association confirmed the statistical significance of the model (p = 0.008). An additional 1000-fold permutation test designed specifically to test the linear null hypothesis that the association effects are only additive confirmed the presence of non-additive (i.e. nonlinear) or epistatic effects (p = 0.013). An independent information-gain measure corroborated these results with a third-order epistatic interaction that was stronger than any lower-order associations.

Conclusions
We have identified statistically significant evidence for a three-way epistatic interaction that is associated with susceptibility to TB. This interaction is stronger than any previously described one-way or two-way associations. This study highlights the importance of using machine learning methods that are designed to embrace, rather than ignore, the complexity of common diseases such as TB. We recommend future studies of the genetics of TB take into account the possibility that high-order epistatic interactions might play an important role in disease susceptibility.
Erosive potential of energy drinks on the dentine surface
Authors: Pinto Shelon CS , Bandeca Matheus C , Silva Carolina N , Cavassim Rodrigo , Borges Alvaro H , Sampaio José E C 
Published: February 2013

AbstractBackgroundConsidering the current high consumption of energy drinks, the aim of the present study is to evaluate the influence of energy drinks in removing the smear layer and exposing dentinal tubules on root surface.MethodsDentine root surfaces were exposed using a diamond bur. Forty movements of scaling were performed in the area prepared in order to create a smear layer. One hundred and thirty specimens were obtained from 35 teeth. Specimens were randomly distributed into 12 groups (n = 10) and divided into subgroups according to the application: topical (n = 5) and friction (n = 5). Twelve energy drinks were evaluated: RedBull™, Burn™, TNT™, Flash Power™, Flying Horse™, Sports Drink™, Ionic™, Hot Power™, Army Power™, Gladiator™ and Bug™. Distilled water was used as a control group. The specimens were analysed by scanning electron microscopy.ResultsTopical application: a significant influence of energy drinks on smear layer removal was found for FlyingHorse™ and Bug™ when compared with the control group. Friction application: significant smear layer removal was found for Burn™, FlyingHorse™, Gladiator™, SportsDrinks™, when compared with the control group. Comparing the different application forms, a statistically significant difference was found for Army Power™.ConclusionConsidering the significant smear layer removal, energy drinks can be an important etiological factor for cervical dentine hypersensitivity.
Breast cancer in women using digoxin: tumor characteristics and relapse risk
Authors: Biggar Robert J , Andersen Elisabeth W , Kroman Niels , Wohlfahrt Jan , Melbye Mads 
Published: February 2013

Abstract
Introduction
Digoxin use is associated with increased incidence of breast and uterus cancers. We postulated that digoxin use might affect tumor characteristics and increase relapse risk in women with breast cancer.

Methods
Incident breast cancer cases in Danish women (n = 49,312; 1995 to 2008) were identified. Analyses were conducted in women 20 to 74 years old. Relapse hazard ratios (HR) were compared in women using and not using digoxin, adjusting for age, calendar period, protocol, tumor size, nodal involvement, histology grade, estrogen-receptor (ER) status, and anti-estrogen therapy in Cox regression models.

Results
At diagnosis, tumors in digoxin users were more likely ER+ (85.4% vs. 78.6%: P = 0.002) and have grade 1 ductal histology (37.2% vs. 25.7%; P = 0.004), compared to non-users. 45 relapses occurred in women already using digoxin at breast cancer diagnosis (1,487 person-years); 24 relapses occurred in women later starting digoxin (384 person-years). Overall relapse risk HR in digoxin users was 1.13 (95% confidence interval: 0.88, 1.46) compared to non-users. Relapse risk in digoxin users was significantly increased in the first year (2.19; 1.26, 3.78) but not thereafter (0.99; 0.74, 1.32) (P = 0.02 for difference in HRs). First-year relapse hazard was high in digoxin-using women with ER+ tumors (2.51; 1.39, 4.55) but not ER- tumors (0.72; 0.10, 5.27). Recurrence hazard was not significantly changed among digoxin-using women also using tamoxifen.

Conclusions
Breast cancers arising in digoxin-using women had better prognostic features. After adjustment for markers, overall breast cancer relapse risk in digoxin users was not increased significantly, although recurrence hazards for ER+ tumors were higher in the first year following diagnosis.
Energy metabolism and energy-sensing pathways in mammalian embryonic and adult stem cell fate
Authors: Rafalski Victoria A. , Mancini Elena , Brunet Anne 
Published: February 2013

Summary
Metabolism is influenced by age, food intake, and conditions such as diabetes and obesity. How do physiological or pathological metabolic changes influence stem cells, which are crucial for tissue homeostasis? This Commentary reviews recent evidence that stem cells have different metabolic demands than differentiated cells, and that the molecular mechanisms that control stem cell self-renewal and differentiation are functionally connected to the metabolic state of the cell and the surrounding stem cell niche. Furthermore, we present how energy-sensing signaling molecules and metabolism regulators are implicated in the regulation of stem cell self-renewal and differentiation. Finally, we discuss the emerging literature on the metabolism of induced pluripotent stem cells and how manipulating metabolic pathways might aid cellular reprogramming. Determining how energy metabolism regulates stem cell fate should shed light on the decline in tissue regeneration that occurs during aging and facilitate the development of therapies for degenerative or metabolic diseases.
Empfehlungen zur Hygiene bei der Sklerotherapie
Authors: Breu F.X. , Gerlach H. , Stücker M. , Meyer E. , Dettenkofer M. , Hahn M. 
Published: February 2013

ZusammenfassungEinleitung: In den letzten Jahren sind die Anforderungen in Deutschland an die Hygiene in Arztpraxen stetig gewachsen. Hintergrund ist unter anderem der Grundsatz der prozessbezogenen Gleichstellung der Hygieneanforderungen zwischen ambulantem und stationärem Bereich.Diskussion: Schwierig gestaltet sich die Situation einerseits hinsichtlich bundesweit einheitlicher Anforderungen und andererseits dem relativen Mangel an praxisbezogenen und prozessorientierten Empfehlungen für die therapeutisch tätigen Ärzte. Diesem Problem tragen einerseits die Veröffentlichungen des Robert Koch-Instituts Rechnung. Andererseits sollen mit diesen hier vorgestellten Empfehlungen konkrete, prozessorientierte, klar strukturierte Handlungsempfehlungen für den praktisch tätigen Sklerotherapeuten gegeben werden.
Free radical-mediated cytosine C-5 methylation triggers epigenetic changes during carcinogenesis
Authors: Kasai Hiroshi , Kawai Kazuaki , Li Yun-Shan 
Published: February 2013

Abstract
The methylation of the C-5 position of deoxycytidine (dC) in the promoter regions of tumor suppressor genes is often observed in cancer cells. We found that various environmental agents, as well as endogenous compounds such as methionine sulfoxide (MetO), generate methyl radicals and modify dC to form 5-methyl-dC in DNA in vitro. We confirmed that both DNA methylation and cancer incidence in the liver were increased by the administration of MetO to oxidatively stressed mice. In this review, we summarize previous reports on methyl radical generation in vitro and in vivo and DNA modifications by methyl radicals, including our discoveries, as well as our recent experimental evidence suggesting that free radical-mediated dC methylation triggers epigenetic changes.
Synthesis, crystal structure, and bioactivity of N-dichloroacetyl diazabicyclo compounds
Authors: Ye Fei , Li Guan-Yu , Ding Li , Fu Ying , Xing Zhi-Yong 
Published: February 2013

Abstract
A short and efficient route to synthesis of a series of N-dichloroacetyl diazabicyclo derivatives has been developed. The compounds were obtained by cycloaddition of levulinic acid or ester with diamine, followed by acylation with dichloroacetyl chloride. All products were characterized by IR, 1H NMR, 13C NMR, MS, and elemental analysis. The single crystal of compound 4c was determined by X-ray crystallographic analysis. All compounds were tested for their herbicide safeners activity of protecting maize from injury with acetochlor.
Assessment of In Situ Scour Profile in Sand Using a Jet Probe
Authors: Gabr Mo , Caruso Cary , Key Austin , Kayser Mohammad 
Published: February 2013

Abstract
Work in this paper presents a device and a process for in situ assessment of erosion potential with depth. The proposed device is termed “in situ erosion evaluation probe” (ISEEP), and the process is developed based upon advancing a rod fitted with a truncated cone jet nozzle into the soil. As water exits the nozzle with controllable velocity and flow rate (induced by an external pump) the probe advances into the subsurface profile and the rate of advancement is measured. The jet flow velocity and the advancement rate of the probe are correlated with a stream power value, and used to estimate soil erodibility parameters. Results from laboratory testing show the feasibility of the concept. An approach for the estimation of a critical stream power and a detachment rate coefficient is presented. Numerical modeling and deployment of the device at a North Carolina barrier island site after hurricane Irene are used to demonstrate the applicability of the proposed concept. Correlations between scour magnitudes, estimated by ISEEP parameters, and those estimated through modeling and field observation are presented and illustrate the viability of ISEEP’s soil erosion parameters as defined by a critical stream power and a detachment rate coefficient.
Free–Free Resonance Testing of In Situ Deep Mixed Soils
Authors: Guimond-Barrett Antoine , Nauleau Elodie , Le Kouby Alain , Pantet Anne , Reiffsteck Philippe , Martineau François 
Published: February 2013

Abstract
This paper focuses on the use of free–free resonance testing (FFR testing) applied to the characterization of stabilized silt and sand specimens treated in situ by deep soil mixing. The aim of FFR testing is to measure the natural frequencies of free vibration of the tested specimen. Compression and shear wave velocities, seismic moduli and Poisson’s ratio can be determined from these frequencies. Block samples were taken from soil–cement columns installed at a test site near Paris, France. Specimens of 100 by 50 mm (height to diameter ratio of 2) were cored from these blocks and submitted to FFR testing in the laboratory. The measured resonant frequencies were very repeatable for all specimens tested, validating the use of free–free resonance as a rapid testing method for the characterization of fairly heterogeneous stabilized soil specimens. It was found that both P-wave and S-wave velocities increase nonlinearly with unconfined compressive strength. A linear correlation between strength and dynamic stiffness was observed. Free–free resonance test results can be correlated with index parameters such as density and porosity and used for preliminary assessments of static stiffness as all these parameters varied linearly with measured wave velocities.
Electro-Osmotic Chemical Treatment of Clay on Shear Modulus
Authors: Teng Fu-Chen , Chien Shao-Chi , Ou Chang-Yu 
Published: February 2013

Abstract
Electro-osmosis chemical treatment (ECT) is one of the soil improvement methods used to improve the engineering properties of soft soils. The injected chemical solutions are usually a calcium chloride solution in combination with sodium silicate solution. Previous laboratory studies have shown that the injection of a calcium chloride solution followed by the injection of a sodium silicate solution during electro-osmosis is effective in strengthening soft silty clay. Very stiff cemented soil near the anode is formed after treatment due to the cementation of two chemical solutions and soil particles under applied electric field. However, most works focused on the improvement of the strength of the soil with treatment. The variation of the shear modulus on soils after electro-osmosis chemical treatment is rarely discussed. Thus, a field test of electro-osmosis chemical treatment on Taipei silty clay was carried out in this study. Six electrodes were installed with electrode spacing of 1.5 and 2.0 m. The shear wave velocity of the treated clay was measured by multi-orientation bender elements. The bender element test results show that the maximum improvement ratio of the shear modulus is about 200 % at positions near the anode and the cathode. The pH value and concentration of Ca2+ was determined by the inductively coupled plasma atomic emission spectrometer (ICP-AES) test at all positions that shear moduli was measured. Strong cementation which enhanced the shear modulus of the soft clay were also observed at the anode and cathode. Results presented in this study demonstrate that the electro-osmosis chemical treatment is effective in improving soil strength and soil stiffness.
Numerical Methodology to Minimize Resolution and Sensitivity Effects in P-Wave Measurements
Authors: Amaral M. F. , Viana da Fonseca A. , Rios S. 
Published: February 2013

Abstract
This paper presents a new numerical methodology aiming at facilitating the identification of seismic wave’s propagation time, using a time domain approach. The solution uses first- and second-order differential computing, namely divided differences methods. Results of extensive laboratory seismic wave tests over aggregate–cement mixtures with different voids ratios (densities) and cement contents (1 %, 2 %, 3 %, 4 %, and 5 %) are discussed. The results indicated relevant differences in values of longitudinal modulus (or P-wave modulus) derived with and without this methodology. This was considered especially important in stiff specimens with high-seismic wave velocities and low-energy input signals.
New Approach to Resonant Column Testing
Authors: Werden Salim K. , Drnevich Vincent P. , Hall John R. , Hankour Chafik , Conlee Carolyn T. , Allen Marr W. 
Published: February 2013

Abstract
This paper describes a new type of torsional resonant column device that has a quasi-fixed base and free top. In this device, a relatively rigid torque transducer is placed between the bottom platen and the fixed chamber base. A large capacity torque motor excites the top platen. The primary measurements during the test are the rotation of the top platen, the torque at the specimen base and excitation frequency. An equilibrium equation for the bottom platen relates the torque transducer output to the torque applied by the specimen to the bottom platen. Using equivalent linear viscoelastic theory, a stiffness matrix is generated that relates the torque and rotation at each end of the specimen to specimen properties. A hybrid magnification factor is defined as the ratio of motion at the top of the specimen to that at the base. These two measurements provide the data needed to determine the shear modulus and damping ratio in the specimen for each frequency. The benefit of this approach is that the modulus and damping ratio of the soil are determined independent of the torque applied by the torque motor to the top platen. This removes the problems of torque motor characteristics, bearing friction, back EMF, and eddy current damping that occur with torque motors, which in turn allow more precise and repeatable determination of shear modulus and damping ratio over a wide range of shear strain and frequency. The paper outlines the theory, describes the apparatus and calibration procedures, and provides sample test data.
Effect of Resin Cure Recipe and Ambient Processing Temperature on the Material Properties of Marine Grade Polymer Matrix Composite Materials
Authors: Berube Keith A. , Lopez-Anido Roberto A. 
Published: February 2013

AbstractThe effects of the resin curing recipe and ambient processing temperature on the mechanical properties of composite laminates were investigated. Woven roving E-glass/vinyl-ester composite plates were fabricated with a pliable-bag vacuum assisted resin transfer molding process over a range of ambient temperatures and resin gel times commonly encountered when fabricating polymer composite parts for the marine industry. Standardized tests for Mode-I interlaminar fracture toughness, compression, constituent volume fraction, and Barcol hardness were conducted. Interlaminar fracture toughness exhibited the most variability among the measured properties. Although there were few direct correlations between the measured properties and the parameters in the study, there were several statistically significant differences that could not be discarded as random, as they were consistent among the replicate panels fabricated for each combination of parameters in the study.
Neonatal Visual Evoked Potentials in Infants Born to Mothers Prescribed Methadone
Authors: McGlone Laura , Hamilton Ruth , McCulloch Daphne L. , Boulton Richard , Bradnam Michael S. , Weaver Lawrence T. , Mactier Helen 
Published: February 2013

OBJECTIVE:
Drug misuse in pregnancy is associated with impaired infant visual development. Pilot data showed abnormal flash visual evoked potentials (VEPs) in neonates exposed to methadone in utero, but results were confounded by intrauterine growth restriction, gestation, and ongoing drug misuse. This large cohort study aimed to clarify the effects on neonatal flash VEPs of maternal drug misuse in pregnancy, including prescription of substitute methadone and subsequent development of neonatal abstinence syndrome.

METHODS:
This was a prospective cohort study. Flash VEPs were recorded within 3 days of birth from 100 healthy infants of drug-misusing mothers prescribed substitute methadone during pregnancy and 50 comparison infants matched for birth weight, gestation, and socioeconomic deprivation. VEP morphology was classified as mature, typical, or immature, and amplitudes and implicit times of the major waveform components measured. Drug exposure was determined by maternal history, maternal and infant urine, and meconium toxicology.

RESULTS:
VEPs from maternal drug-exposed infants were more likely to be of immature waveform (P &lt; .001) and were smaller in overall amplitude (median 27 µV vs 39 µV, P &lt; .001) compared with non–drug-exposed infants. Most infants were exposed to illicit drugs in addition to prescribed methadone; differences in VEP parameters were independently associated with maternal prescribed methadone and persisted after correcting for birth weight, cigarette smoking, and excess in utero alcohol exposure.

CONCLUSIONS:
In utero exposure to prescribed substitute methadone is associated with altered flash VEPs in the newborn period and these infants may warrant early clinical visual assessment.
A Quality Improvement Program to Reduce Unnecessary Referrals for Adolescent Scoliosis
Authors: Vernacchio Louis , Trudell Emily K. , Hresko M. Timothy , Karlin Lawrence I. , Risko Wanessa 
Published: February 2013

OBJECTIVE:
Adolescent idiopathic scoliosis (AIS) is a relatively common reason for referral to orthopedic surgery, but most referred patients do not require bracing or surgery. We developed a quality improvement (QI) program within the Pediatric Physicians’ Organization at Children’s, an independent practice association affiliated with Boston Children’s Hospital, to reduce unnecessary specialty referrals for AIS.

METHODS:
The QI program consisted of physician education, decision support tools available at the point of care, and longitudinal feedback of data on physician referrals for AIS. Referral patterns in the 2-year postintervention period were tracked and compared with those of the 2-year preintervention period. Clinical characteristics of referred patients were compared through claims analysis and chart review.

RESULTS:
Initial visits to orthopedic surgery for AIS declined from 5.1 to 4.1 per 1000 adolescents per year, a reduction of 20.4% (P = .01). Process control chart analysis showed a rapid change in referral patterns after the initiation of the program which was sustained over the 2-year postintervention period and demonstrated that 66 initial and 131 total AIS specialty visits were avoided as a result of the program.

CONCLUSIONS:
A QI program consisting of physician education, decision support available at the point of care, and longitudinal data feedback led to a sustained reduction in unnecessary referrals for AIS. This program can serve as a model for other programs that seek to shift the locus of care from specialists to primary care providers.
Hydrogel Composites Containing Carbon Nanobrushes as Tissue Scaffolds
Authors: Marks William H. , Yang Sze C. , Dombi George W. , Bhatia Sujata K. 
Published: February 2013

ABSTRACTThe objective of this work is to examine the feasibility of electrically conductive hydrogel composites as scaffolds in tissue engineering and tissue regeneration, and to understand the properties of the composites as a growth matrix for clinically relevant cell lines. The composite is comprised of carbon nanobrushes embedded in a biocompatible poloxamer gel. This work assesses the ability of such composite gels to support the growth of fibroblasts and myocytes and eventually serve as a matrix to stimulate wound closure. In such a model, fibroblasts and myocytes are seeded on the hydrogel and bathed in culture medium. The experimental model assesses the ability of fibroblasts and myocytes to grow into and adhere to the gel. The work demonstrates that carbon nanobrushes can be dispersed within poloxamer gels, and that fibroblasts and myocytes can proliferate within homogenously dispersed carbon nanobrush-containing poloxamer gels. This work also examines the effects of carbon nanobrush content on the rheological properties of the poloxamer gel matrix and shows an improvement in several areas in the presence of carbon nanobrushes. Future work will examine the effects of design parameters such as carbon nanobrush content and matrix structure on wound healing, as well as the growth of tendons and other cell lines within the hydrogel composites. This work has relevance for tissue and cellular engineering and tissue regeneration in clinical medicine.