bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioconversion of lignocellulose: inhibitors and detoxification
Authors: Jönsson Leif J , Alriksson Björn , Nilvebrant Nils-Olof 
Published: January 2013

Abstract
Bioconversion of lignocellulose by microbial fermentation is typically preceded by an acidic thermochemical pretreatment step designed to facilitate enzymatic hydrolysis of cellulose. Substances formed during the pretreatment of the lignocellulosic feedstock inhibit enzymatic hydrolysis as well as microbial fermentation steps. This review focuses on inhibitors from lignocellulosic feedstocks and how conditioning of slurries and hydrolysates can be used to alleviate inhibition problems. Novel developments in the area include chemical in-situ detoxification by using reducing agents, and methods that improve the performance of both enzymatic and microbial biocatalysts.
Preliminary study of ventilation with 4 ml/kg tidal volume in acute respiratory distress syndrome: feasibility and effects on cyclic recruitment - derecruitment and hyperinflation
Authors: Retamal Jaime , Libuy Javiera , Jiménez Magdalena , Delgado Matías , Besa Cecilia , Bugedo Guillermo , Bruhn Alejandro 
Published: January 2013

Abstract
Introduction
Cyclic recruitment-derecruitment and overdistension contribute to ventilator-induced lung injury. Tidal volume (Vt) may influence both, cyclic recruitment-derecruitment and overdistension. The goal of this study was to determine if decreasing Vt from 6 to 4 ml/kg reduces cyclic recruitment-derecruitment and hyperinflation, and if it is possible to avoid severe hypercapnia.

Methods
Patients with pulmonary acute respiratory distress syndrome (ARDS) were included in a crossover study with two Vt levels: 6 and 4 ml/kg. The protocol had two parts: one bedside and other at the CT room. To avoid severe hypercapnia in the 4 ml/kg arm, we replaced the heat and moisture exchange filter by a heated humidifier, and respiratory rate was increased to keep minute ventilation constant. Data on lung mechanics and gas exchange were taken at baseline and after 30 minutes at each Vt (bedside). Thereafter, a dynamic CT (4 images/sec for 8 sec) was taken at each Vt at a fixed transverse region between the middle and lower third of the lungs. Afterward, CT images were analyzed and cyclic recruitment-derecruitment was determined as non-aerated tissue variation between inspiration and expiration, and hyperinflation as maximal hyperinflated tissue at end-inspiration, expressed as % of lung tissue weight.

Results
We analyzed 10 patients. Decreasing Vt from 6 to 4 ml/kg consistently decreased cyclic recruitment-derecruitment from 3.6 (2.5 to 5.7) % to 2.9 (0.9 to 4.7) % (P <0.01) and end-inspiratory hyperinflation from 0.7 (0.3 to 2.2) to 0.6 (0.2 to 1.7) % (P = 0.01). No patient developed severe respiratory acidosis or severe hypercapnia when decreasing Vt to 4 ml/kg (pH 7.29 (7.21 to 7.46); PaCO2 48 (26 to 51) mmHg).

Conclusions
Decreasing Vt from 6 to 4 ml/kg reduces cyclic recruitment-derecruitment and hyperinflation. Severe respiratory acidosis may be effectively prevented by decreasing instrumental dead space and by increasing respiratory rate.
Data Submission and Quality in Microarray-Based MicroRNA Profiling
Authors: Witwer Kenneth W 
Published: January 2013

BACKGROUND
Public sharing of scientific data has assumed greater importance in the omics era. Transparency is necessary for confirmation and validation, and multiple examiners aid in extracting maximal value from large data sets. Accordingly, database submission and provision of the Minimum Information About a Microarray Experiment (MIAME)3 are required by most journals as a prerequisite for review or acceptance.

METHODS
In this study, the level of data submission and MIAME compliance was reviewed for 127 articles that included microarray-based microRNA (miRNA) profiling and were published from July 2011 through April 2012 in the journals that published the largest number of such articles—PLOS ONE, the Journal of Biological Chemistry, Blood, and Oncogene—along with articles from 9 other journals, including Clinical Chemistry, that published smaller numbers of array-based articles.

RESULTS
Overall, data submission was reported at publication for &lt;40% of all articles, and almost 75% of articles were MIAME noncompliant. On average, articles that included full data submission scored significantly higher on a quality metric than articles with limited or no data submission, and studies with adequate description of methods disproportionately included larger numbers of experimental repeats. Finally, for several articles that were not MIAME compliant, data reanalysis revealed less than complete support for the published conclusions, in 1 case leading to retraction.

CONCLUSIONS
These findings buttress the hypothesis that reluctance to share data is associated with low study quality and suggest that most miRNA array investigations are underpowered and/or potentially compromised by a lack of appropriate reporting and data submission.
Liquid Structure and Cluster Formation in Ionic Liquid/Water Mixtures – An Extensive ab initio Molecular Dynamics Study on 1-Ethyl-3-Methylimidazolium Acetate/Water Mixtures – Part
Authors: Brehm Martin , Weber Henry , Pensado Alfonso S. , Stark Annegret , Kirchner Barbara 
Published: January 2013

Abstract
We present an extensive ab initio molecular dynamics study on mixtures of the room temperature ionic liquid 1-ethyl-3-methylimidazolium acetate with water. To show the dependence of the properties on the concentration, we simulated four different systems: Pure IL, pure water, and two binary mixtures with different mixing ratios. We found that the imidazolium rings are stacking on top of each other in the pure ionic liquid, which is a result of the strong dispersion interactions between the cations. With increasing water content, this ordering is disturbed. While in the pure IL the anions are located almost exclusively within the cation's ring plane, they occupy both the in-plane and the on-top position in the mixture. For very high water content, the anions are mainly found on top of the imidazolium ring. The ethyl chains of the cations attract each other via dispersion force and form clusters, indicating the existence of microheterogeneity in our simulations. We also analyzed the topology of the hydrogen bond network and found that the cation is forming hydrogen bonds to multiple anions at the same time, and is therefore a bridging agent. Likewise, the anion is bridging between different cations. At moderate water content, two acetate ions are frequently coordinated to the same water molecule, leading to the formation of acetate/water clusters.
Interaction between Zwitterionic Surfactants and Amphiphilic Drug: A Tensiometric Study
Authors: Ansari Wajid Husain , Noori Sahar , Naqvi Andleeb , ud - Din Kabir - 
Published: January 2013

AbstractThe physicochemical properties, viz, critical micelle concentration (cmc), surface excess concentration (Γmax), minimum area per head group (Amin) of zwitterionic surfactants (designated asn(−)-2-m(+);n= 8, 10, 12 andm= 12, 14, 16) and their mixtures with amphiphilic antidepressant drug amitriptyline hydrochloride (AMT) were determined by using surface tension measurements. The cmc and ideal cmc (cmcid) values along with interaction parameters,βmandβσ(calculated using Rubingh's and Rosen's models), suggest attractive interactions among the components. The Krafft temperature measurements also indicate strong attractive interactions.Γmax(orAmin) increases (or decreases) with the addition of gemini surfactant; the values being closer to that of the drug. These values and micellar mole fraction (X1m-calculated from Rubingh's model andX1Moto-calculated from Motomura's model) indicate larger contribution of gemini surfactants in mixed micelles and smaller contribution at air/solution interface (as mole fraction values at interface,X1σ, are slightly smaller thanX1m). The standard Gibbs energy of micellization (ΔGmicº) and adsorption (ΔGadº) as well as excess energy of mixing (ΔGexm) are all negative. All these results suggest higher stability of the mixed systems. UV absorbance results also suggest that the mixed micelles are stable for several days.
Fracture Optimization in a Giant Gas Field, Wamsutter, Wyoming, USA
Authors: Brake Al 
Published: January 2013

Abstract
Optimization of fracture stimulation treatments in BP's giant Wamsutter Field is an important aspect of efficient and viable development of this tight gas asset. This paper integrates historical fracturing data, well performance, surveillance data, and data from fracturing field trials to provide a clearer view of created fracture geometry and resulting well performance. This integrated understanding of Wamsutter fracturing is being used to design additional field trials with a calibrated, more predictive fracture model.
The results of this analysis could directly apply to similar tight gas fields. The evaluation technique of integrating field results with surveillance data and field trials would be beneficial for any unconventional gas asset in defining the most effective fracturing techniques.
Major conclusions of this study:
Fluid Volumes pumped during fracture stimulation have a strong correlation to the well performance in Wamsutter Field. Shale boundaries within the Almond are not always effective in preventing frac height growth. Microseismic indicates that stages frequently grow into each other. A predictive fracture model with a calibrated geomechanical profile is essential for designing and understanding stimulation results. A field trial program to test fracture design concepts and calibrate fracture models is an important aspect of fracture optimization.
Fracture geometry is difficult to model and design accurately. This case study, based on a large data set, provides some "ground truth" to measure the accuracy of design versus actual results.
Creating Value Through Permanent Down Hole Gauges in Oman Block A Tight Gas Appraisal
Authors: Al Busafi Badar , Clark Robert A , Adil Imtiaz 
Published: January 2013

Abstract
BP's down hole instrumentation of the Khazzan tight gas appraisal wells provides a rare opportunity to quantify reservoir pressure and temperature dynamics. Several appraisal wells were initially tested for 3-4 weeks and subsequently shut-in for about a year. The continuous downhole gauge recordings of the resulting pressure build ups were then analyzed to quantify understanding of stimulation effectiveness, reservoir quality away from the wellbore, total producible connected gas, geomechanics and wellbore hydraulics. History matching of this gauge data provided confidence in predicting production profiles for full field development. This paper examines the pressure transient analysis (PTA) of one representative well in the field. The high quality build-up indicated that good quality rock extends to beyond the radius of investigation of the pressure transient and PTA did not reveal any barriers in an area of ~20 sq. km around the wellbore. The absence of boundaries and the possible extension of better quality reservoir have given BP the confidence to place an additional (and successful) appraisal well in the southwest of the block, thus extending the area that potentially will be a focus for early full field development. Installing permanent down hole gauges carried a high initial cost, but the value gained in quantifying subsurface uncertainty has proven the success of this technology application. It has also proved invaluable in executing hydraulic fracture stimulation. This high quality information boosts confidence in reservoir performance and long term deliverability leading to better informed business decisions regarding potential full field development.
Numerical simulation of surface acoustic wave actuated cell sorting
Authors: Franke Thomas , Hoppe Ronald , Linsenmann Christopher , Zeleke Kidist 
Published: January 2013

Abstract
We consider the mathematical modeling and numerical simulation of high throughput sorting of two different types of biological cells (type I and type II) by a biomedical micro-electro-mechanical system (BioMEMS) whose operating behavior relies on surface acoustic wave (SAW) manipulated fluid flow in a microchannel. The BioMEMS consists of a separation channel with three inflow channels for injection of the carrier fluid and the cells, two outflow channels for separation, and an interdigital transducer (IDT) close to the lateral wall of the separation channel for generation of the SAWs. The cells can be distinguished by fluorescence. The inflow velocities are tuned so that without SAW actuation a cell of type I leaves the device through a designated outflow channel. However, if a cell of type II is detected, the IDT is switched on and the SAWs modify the fluid flow so that the cell leaves the separation channel through the other outflow boundary. The motion of a cell in the carrier fluid is modeled by the Finite Element Immersed Boundary method (FE-IB). Numerical results are presented that illustrate the feasibility of the surface acoustic wave actuated cell sorting approach.
Growth and Yield Performance of Bari Mung-5 Under Different Time of Sowing
Authors: Jahan Nargis , Adam M M Golam 
Published: January 2013

A field experiment was carried out at University of Dhaka from March to July, 2011 to study the effect of time of sowing on the growth and yield of BARI mung-5. The treatments consisted of three dates of sowing viz. March 15, April 15 and May 15. The crop responded significantly to sowing time and 15 April sowing seeds produced plants having maximum plant height (68.4 cm), leaves/plant (29.33), total dry matter/plant (17.99), branches/plant (8.17), pods/plant (11.33), pod length (8.78 cm), seeds/pod (11.17), 1000 seed weight (46.52 g), seed yield/plant (5.33 g), yield/ha (1.77 t) and harvest index (29.58 %) at harvest. The seed yield decreased by 36.8 and 49.9% when seed sown early (15 March) or late (15 May) due to production of lower yield components. DOI: http://dx.doi.org/10.3329/jbas.v36i2.12966 Journal of Bangladesh Academy of Sciences, Vol. 36, No. 2, 227-231, 2012
Exceptional Acid–Base Organogelators for a Wide Variety of Organic Liquids and Their Many Applications
Authors: Chen Yi‐Chang , Wang Huan , Li Dong‐Mi , Zheng Yan‐Song 
Published: January 2013

AbstractIt was found that 2‐amino‐1,2‐diphenylethanol forms organogels with a wide variety of acidic compounds in a large number of organic liquids, in which short contacts such as CH–π hydrogen bonds play a key role in gel formation. This new kind of acid–base, two‐component organogelator has potential application as a fluorescence switch and in the preparation of organic nanotubes, silver nanofibers, and ultrathin silver nanoparticles of less than 3 nm, which could be used as catalysts for the reduction of nitroaniline.
Development of an albuminous reactive oxygen species assay for photosafety evaluation under experimental biomimetic conditions
Authors: Onoue Satomi , Kato Masashi , Yamada Shizuo 
Published: January 2013

ABSTRACTThe generation of reactive oxygen species (ROS) from an ultraviolet (UV)‐exposed chemical can be an experimental indicator of phototoxic potential. The aim of the present study was to develop a new ROS assay using serum albumin to provide photosafety assessment under experimental biomimetic conditions. To assess assay robustness, a validation study on an albuminous ROS (aROS) assay was conducted with a focus on intra‐ and inter‐day precisions and Z’‐factor reflecting both the assay signal‐to‐noise ratio and variation associated with signal measurements. In the aROS assay on quinine HCl (200 μM), a typical phototoxic drug, both intra‐ and inter‐day precisions (coefficient of variation; CV) were found to be below 4%, and the Z’‐factors for singlet oxygen and superoxide suggested a large separation band between samples and blank signals. To evaluate the prediction capacity, the aROS and ROS assays were applied to 21 phototoxins and 10 non‐phototoxic chemicals. Upon aROS assay on these model chemicals, the individual specificity was 100%, and the positive and negative predictivities were found to be 100% and 81.8%, respectively. The aROS assay can be employed for poorly soluble chemicals for which the ROS assay is unavailable. Comparing the ROS assay data, there seemed to be a photochemical transition of some chemicals in albuminous solution. A molecular interaction between albumin and chemical was also assessed by UV and fluorescent spectroscopic analyses, and the results suggested the limited relationship between the albumin–chemical interaction and the photochemical change. The aROS assay may allow photosafety assessment of new drug entities with a wide range of applicability partly under experimental biomimetic conditions. Copyright © 2013 John Wiley & Sons, Ltd.
Photoisomerizable and Thermoresponsive N‐isopropylacrylamide–Surfmer Copolymer Hydrogels Prepared upon Electrostatic Self‐Assembly of an Azobenzene Bolaamphiphile
Authors: Friedrich Tatjana , Mielke Tamara , Domogalla Monika , Hentschel Maria , Kraus Katharina , Tieke Bernd 
Published: January 2013

AbstractPhotoreactive and thermoresponsive N‐isopropylacrylamide (NIPAM)–surfmer copolymer hydrogels containing 4,4′‐di(6‐sulfato‐hexyloxy)azobenzene (DSHA) dianions are described. The functional hydrogels are obtained in a two steps. First a micellar aqueous solution of (11‐(acryloyloxy)undecyl)trimethylammonium bromide (AUTMAB) and NIPAM is exposed to 60Co‐gamma irradiation, and a thermoresponsive copolymer gel is obtained. Second, DSHA is included by shrinking the gel at 50 °C and subsequent reswelling in an aqueous solution of DSHA disodium salt at 20 °C. Reswelling is accompanied by electrostatic adsorption of DSHA dianions at the positively charged AUTMAB headgroups replacing the bromide ions. Gels containing trans‐DSHA are transparent yellow at room temperature (λmax = 370 nm), while gels containing cis‐rich DSHA are orange (λmax = 460 and 330 nm). Energy dispersive X‐ray measurements indicate that 41% of the bromide ions are exchanged if trans‐DSHA is used for adsorption, and only 7.5% if cis‐DSHA is used. The incorporation of DSHA lowers the lower critical solution temperature (LCST) from 34 to 32 °C. Below the LCST, DSHA can be switched from the trans‐ to the cis‐rich state and vice versa upon irradiation with UV (λ = 366 nm) or visible light (λ ≥ 450 nm). Above the LCST no photoreaction takes place.
Surgical management of external auditory canal lesions
Authors: Spielmann P M , McKean S , White R D , Hussain S S M 
Published: January 2013

AbstractBackground:Lesions arising in the external auditory canal that require surgical excision are uncommon. They are associated with a range of pathologies, including bony abnormalities, infections, benign and malignant neoplasms, and epithelial disorders.Methods:This paper describes a 10-year personal case series of external auditory canal lesions with chart, imaging and histopathology review.Results:In total, 48 lesions required surgical management, consisting of: 13 bony lesions; 14 infective lesions; 14 neoplasms with 11 histological types (including ceruminous adenoma and the extremely rare cavernous haemangioma); 3 epithelial abnormalities; and 4 other benign lesions. The surgical management is described.Conclusion:This study emphasises the diagnostic differences between exostoses and osteomas, and between external auditory canal cholesteatoma and keratosis obturans. It also discusses the management of aural polyps, and highlights the need to excise external auditory canal masses for histology in order to guide subsequent treatment.
English exposure in the home and classroom: Predictions to Spanish-speaking preschoolers’ English vocabulary skills
Authors: PALERMO FRANCISCO , MIKULSKI ARIANA M. , FABES RICHARD A. , HANISH LAURA D. , MARTIN CAROL LYNN , STARGEL LAUREN E. 
Published: January 2013

ABSTRACTThis study examined the combined and unique contributions of home, teacher, and peer English exposure levels on Spanish-speaking preschoolers’ (N= 107) English receptive and expressive vocabulary skills. The combined levels of English exposure during the fall of preschool were positively associated with children's English receptive and expressive vocabulary skills in the spring. Furthermore, English exposure levels at home were uniquely and positively associated with children's English receptive and expressive vocabularies, whereas peer English exposure levels were uniquely and positively associated with children's English expressive vocabulary. Teachers’ English exposure levels were not uniquely associated with children's English vocabulary. The findings highlight the importance of the home environment and peer experiences in the classroom for maximizing Spanish-speaking children's early English vocabulary skills.
Antimicrobial and antiproliferative activities of stingless bee Melipona scutellaris geopropolis
Authors: da Cunha Marcos Guilherme , Franchin Marcelo , Galvão LíviaCâmaradeCarvalho , de Ruiz AnaLúciaTascaGóis , de Carvalho João Ernesto , Ikegaki Masarahu , de Alencar Severino Matias , Koo Hyun , Rosalen Pedro Luiz 
Published: January 2013

Abstract

Background
Geopropolis is a type of propolis containing resin, wax, and soil, collected by threatened stingless bee species native to tropical countries and used in folk medicine. However, studies concerning the biological activity and chemical composition of geopropolis are scarce. In this study, we evaluated the antimicrobial and antiproliferative activity of the ethanolic extract of geopropolis (EEGP) collected by Melipona scutellaris and its bioactive fraction against important clinical microorganisms as well as their in vitro cytotoxicity and chemical profile.

Methods
The antimicrobial activity of EEGP and fractions was examined by determining their minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) against six bacteria strains as well as their ability to inhibit Streptococcus mutans biofilm adherence. Total growth inhibition (TGI) was chosen to assay the antiproliferative activity of EEGP and its bioactive fraction against normal and cancer cell lines. The chemical composition of M. scutellaris geopropolis was identified by reversed-phase high-performance liquid chromatography and gas chromatography–mass spectrometry.

Results
EEGP significantly inhibited the growth of Staphylococcus aureus strains and S. mutans at low concentrations, and its hexane fraction (HF) presented the highest antibacterial activity. Also, both EEGP and HF inhibited S. mutans biofilm adherence (p < 0.05) and showed selectivity against human cancer cell lines, although only HF demonstrated selectivity at low concentrations. The chemical analyses performed suggest the absence of flavonoids and the presence of benzophenones as geopropolis major compounds.

Conclusions
The empirical use of this unique type of geopropolis by folk medicine practitioners was confirmed in the present study, since it showed antimicrobial and antiproliferative potential against the cancer cell lines studied. It is possible that the major compounds found in this type of geopropolis are responsible for its properties.
Existence of positive ground states for some nonlinear Schrödinger systems
Authors: Zhang Hui , Xu Junxiang , Zhang Fubao 
Published: January 2013

Abstract
We prove the existence of positive ground states for the nonlinear Schrödinger system

{

−
Δ
u
+
(
1
+
a
(
x
)
)
u
=

F
u

(
u
,
v
)
+
λ
v
,

−
Δ
v
+
(
1
+
b
(
x
)
)
v
=

F
v

(
u
,
v
)
+
λ
u
,

where a, b are periodic or asymptotically periodic and F satisfies some superlinear conditions in

(
u
,
v
)

. The proof is based on the method of Nehari manifold and the concentration-compactness principle.

MSC:35J05, 35J50, 35J61.