bluuebunny/crossref_metadata_2025 huggingface dataset:
Understanding metalinguistic development in beginning writers
Authors: Chen Honglin , Jones Pauline
Published: December 2013

Internationally, English curricula increasingly emphasize the explicit teaching of knowledge about language. This paper reports on a small pilot study of an ongoing project investigating the relationship between explicit teaching about language and its uptake by students. Drawing on the underpinnings of Vygotskian sociocultural theory and Hallidayan systemic functional linguistics, this paper presents an interdisciplinary approach to the analysis of development in students’ metalinguistic understanding. The approach recognizes the centrality of the expert's mediation via classroom interaction involving data drawn from observations of lessons, interviews and writing conversations with students. The findings demonstrate some of the complexity involved in learning a grammatical concept: that is, in recognizing, acquiring and applying metalinguistic knowledge to the task of becoming increasingly literate. The paper argues that the purpose of teaching metalinguistic knowledge should be to support learners to become confident and successful users of language. Our findings also make some important suggestions for pedagogic practice with respect to teaching knowledge about language to young learners.
A Long-Term Clinical and Cephalometric Study of Cleft Lip and Palate Patients following Intraoral Maxillary Quadrangular Le Fort I Osteotomy
Authors: Karabekmez Furkan E. , Keller Eugene E. , Stork James T. , Regennitter Frederick J. , Bite Uldis
Published: December 2013

Objective

To evaluate the horizontal and vertical stability of the quadrangular Le Fort I in patients with congenital cleft lip and palate.

Design

Prospective longitudinal study.

Patients

A total of 15 congenital cleft lip and palate patients treated with the maxillary quadrangular Le Fort I were enrolled.

Intervention

Lateral cephalometric radiographic examinations were obtained preoperatively, early postoperatively, and late postoperatively for four dental and skeletal landmarks. A questionnaire regarding patients' satisfaction with treatment and functional/cosmetic outcomes (airway, speech, mastication) was administered.

Main Outcome Measures

Surgical horizontal and vertical movement, late postsurgical horizontal and vertical movement, and surgical and postsurgical movement in relation to age and cleft type were evaluated using Spearman correlation coefficients, Wilcoxon signed rank tests, and Mann-Whitney tests.

Results

Surgical horizontal movements of all measured points showed significant changes. Significant differences of postsurgical horizontal movement were observed in younger patients versus adult patients. Significant differences of postsurgical horizontal movement were observed in unilateral cleft patients versus bilateral cleft patients. A high percentage of patients showed significant functional improvement in nasal airflow, speech, mastication, temporomandibular joint function, and mouth versus nose breathing.

Conclusions

The quadrangular Le Fort I is a functionally stable and a surgically predictable procedure for cleft lip and palate patients who present with midface deficiency. Patients under the age of 18 at the time of the osteotomy had a higher relapse rate than patients over 18 years of age. Younger patients who need surgery should be advised regarding the increased risk of skeletal relapse. Patients' satisfaction was high in all aesthetic- and function-related items on the questionnaire.
Seed photosynthesis enhances Posidonia oceanica seedling growth
Authors: Celdrán David , Marín Arnaldo
Published: December 2013

Posidonia oceanica seeds demonstrate photosynthetic activity during germination as well as throughout seedling development, a fact which suggests that seed photosynthesis can influence seedling growth. This study examines the contribution of seed photosynthesis to changes in leaf and root biomass, the concentration of seed carbohydrate reserves (free sugars and starch) and elemental C, N and P content in seedlings exposed to different light/dark treatments. Green seeds attached to seedlings remained photosynthetically active for three months and photosynthetic activity in the seeds enhanced seedling growth in leaves and roots. It was estimated that ca. 29.26% of leaf biomass and ca. 42.31% of root biomass production was due to seed photosynthetic activity. Photosynthesis occurred at a higher rate in seeds than in leaves during early seedling growth, and extreme light limitation reduced the mobilization of carbon reserves stored in the seeds. These adaptations control leaf self‐shading and plant competition in well‐established P. oceanica beds while also promoting increased seedling survival rates in open, uncolonised areas where clonal growth is limited.
Spatiotemporal variation in range‐wide Golden‐cheeked Warbler breeding habitat
Authors: Duarte Adam , Jensen Jennifer L. R. , Hatfield Jeff S. , Weckerly Floyd W.
Published: December 2013

Habitat availability ultimately limits the distribution and abundance of wildlife species. Consequently, it is paramount to identify where wildlife habitat is and understand how it changes over time in order to implement large‐scale wildlife conservation plans. Yet, no work has quantified the degree of change in range‐wide breeding habitat for the Golden‐cheeked Warbler (Setophaga chrysoparia), despite the species being listed as endangered by the U.S. Federal Government. Thus, using available GIS data and Landsat imagery we quantified range‐wide warbler breeding habitat change from 1999–2001 to 2010–2011. We detected a 29% reduction in total warbler breeding habitat and found that warbler breeding habitat was removed and became more fragmented at uneven rates across the warbler's breeding range during this time period. This information will assist researchers and managers in prioritizing breeding habitat conservation efforts for the species and provides a foundation for more realistic carrying capacity scenarios when modeling Golden‐cheeked Warbler populations over time. Additionally, this study highlights the need for future work centered on quantifying Golden‐cheeked Warbler movement rates and distances in order to assess the degree of connectivity between increasingly fragmented habitat patches.
Egg crypsis in a ground‐nesting shorebird influences nest survival
Authors: Skrade P. D. B. , Dinsmore S. J.
Published: December 2013

Coloration of exposed eggs of ground‐nesting birds is thought to reduce predation, with camouflaged eggs that more closely match the area around the nest having greater survival. We tested this hypothesis using digital photographs of 374 Mountain Plover (Charadrius montanus) nests and the substrate surrounding each nest to produce covariates in nest survival models. Covariates included values representing the difference between the color of the eggs and that of the substrate, the average egg and substrate colors, and variation in both egg and substrate color. Nest survival decreased as the difference between the color of the eggs and substrate increased (accounted for by two different methods of quantifying color: βΔE = −0.021, SE = 0.024, 95% CI = −0.069, 0.026 and βΔRGB = −0.004, SE = 0.005, 95% CI = −0.013, 0.005) and increased with increasing variability in substrate color (βΔSDsub = 2.624, SE = 2.846, 95% CI = −2.954, 8.202), although after model‐averaging these effects were not well‐supported. Model‐averaged estimates of daily nest survival ranged from 0.90 to 0.98 (unconditional SEs from 0.004 to 0.129). Our results support the egg crypsis hypothesis because eggs that closely match their surroundings have greater survival.
Casing During Drilling With Rotary-Steerable Technology in the Stag Field—Offshore Australia
Authors: Graves Kyle S. , Herrera Delimar C.
Published: December 2013

Originally discovered in 1993, the Stag oil field, located on the Northwest shelf of Western Australia, has produced more than 58 million bbl since production began in 1998 (Goodacre et al. 2000). The field is shallow (680 m subsea), encompassing highly unconsolidated and highly permeable sandstone. Reservoir depletion, unconsolidated rock, water breakthrough, and sand production have created conditions under which infill-drilling campaigns have become increasingly problematic in the Stag field in recent years. There have been numerous papers documenting the history of the Stag field (McDiarmid et al. 2001; Muecke et al. 2002; Wibawa et al. 2008).

On three recent infill wells, the intermediate 12¼-in. intervals were drilled and cased with casing-while-drilling (CWD) technology with a rotary-steerable system (RSS). This was used to navigate wellbore congestion, to drill designer well paths to avoid "incoherencies" [a seismic attribute that is mappable and correlates with drilling problems (Chima et al. 2012)], to land the horizontal section, and then to drill horizontal tangent sections out to the initial reservoir penetration (liner point). The CWD applications progressed from a "new technology" trial to a stretch reach and performance goal, to finally successfully being used as a key enabling technology to drill a well that might otherwise be undrillable because of instability issues.

The directional CWD 12¼-in.-hole intervals were drilled from just below the 13-⅜in. surface casing to the 9⅝-in.-casing point, building from 25° inclination to horizontal and holding thereafter. This program (the first applications of this type in Australia) resulted in two consecutive world-record runs. The result is that CWD is a viable enabling technology that will be used to drill future Stag infill wells and should be considered as a viable alternative on other drilling projects.

This paper will discuss the identification of the technology application, planning, implementation, results, and lessons learned. This paper will end with a notional conversation regarding CWD becoming a mainstream method.
Modeling the viscosity of silicate melts containing manganese oxide
Authors: Kim Wan-Yi , Pelton Arthur , Bale Christopher , Bélisle Eve , Decterov Sergei
Published: December 2013

Our recently developed model for the viscosity of silicate melts is applied
to describe and predict the viscosities of oxide melts containing manganese
oxide. The model requires three pairs of adjustable parameters that describe
the viscosities in three systems: pure MnO, MnO-SiO2 and MnO-Al2O3-SiO2. The
viscosity of other ternary and multicomponent silicate melts containing MnO
is then predicted by the model without any additional adjustable model
parameters. Experimental viscosity data are reviewed for melts formed by MnO
with SiO2, Al2O3, CaO, MgO, PbO, Na2O and K2O. The deviation of the available
experimental data from the viscosities predicted by the model is shown to be
within experimental error limits.
Liquidus temperatures of Na3AlF6-AlF3-CaF2-KF-LiF-Al2O3 melts
Authors: Peng J.P. , Di Y.Z. , Wang Y.W. , Bai Y.B. , Feng N.X.
Published: December 2013

Temperatures for the primary crystallization of
Na3AlF6-AlF3-CaF2-KF-LiF-Al2O3 system adopted in aluminum electrolysis
process were determined by thermal analysis. An empirical equation was
derived to describe the liquidus temperatures for the primary
crystallization of this multicomponent electrolyte system: t/?=1011 +
0.7w(AlF3) - 0.232w(AlF3)2 - 7.65w(Al2O3) + 0.523w(Al2O3)2 - 8.96w(LiF) +
0.043w(LiF)2 - 3.32w(KF) - 0.12w(KF)2 - 3.28w(CaF2) +0.037w(CaF2)2 +
0.091w(AlF3)w(LiF) + 0.074w(AlF3)w(KF) + 0.084w(AlF3)w(CaF2) -
0.27w(Al2O3)w(LiF), where w(AlF3) denotes the mass fraction of excess
aluminum fluoride with respect to cryolite. While w(Al2O3) ranges from 2% to
4%, w(LiF), w(KF) and w(CaF2) from 0 to 7%, and the molar ratio of NaF/AlF3
from 2.2 to 3.
Study of solid state interactions in the systems ZnFe2O4 - CaO, ZnFe2O4 - MgO and zinc cake with CaO and MgO
Authors: Peltekov A.B. , Boyanov B.S.
Published: December 2013

The solid state interactions of CaO and MgO with synthetic and industrial
ZnFe2O4 (in zinc cake) have been studied using chemical, XRD analysis and
M?ssbauer spectroscopy. The exchange reactions in the systems ZnFe2O4 - CaO
and ZnFe2O4 - MgO have been investigated in the range of 850-1200?C and
duration up to 180 min. It has been established that Ca2+ and Mg2+ ions
exchange Zn2+ in ferrite partially and the solubility of zinc in a 7%
sulfuric acid solution increases. The possibilities for utilization of the
obtained results in zinc hydrometallurgy have been discussed.
Bagasse wastewater treatment using biopolymer: A novel approach
Authors: Thirugnanasambandham K. , Sivakumar V. , Maran Prakash
Published: December 2013

In this present study, the removal of turbidity, biological oxygen demand
(BOD) and chemical oxygen demand (COD) were investigated under different
operating conditions such as agitation time (X1: 15-25 min), initial pH
(X2:4-8), chitosan dose (X3:1.2-2 g L-1) and settling time (X4:40-80 min) to
treat bagasse based paper and pulp industry wastewater via response surface
methodology (RSM). The experimental data obtained were fitted to a
second-order polynomial equation using multiple regression analysis and ANOVA
(analysis of variance) was used to examine the significance of the developed
mathematical models. The 3-D response surface plots were derived from the
mathematical models in order to study the interactive effects process
variables on the treatment efficiency. Derringer?s desired function
methodology were applied to determine the optimal conditions and it was found
to be: agitation time of 20 min, initial pH of 6, chitosan dose of 1.8 gL-1
and settling time of 60 min. Under these conditions, the removal of
turbidity, BOD and COD were found to be 84 %, 90 % and 93 % respectively.
Incidence of acute lung injury in dogs receiving transfusions
Authors: Thomovsky Elizabeth J. , Bach Jonathan
Published: December 2013

Objective—To document the existence and incidence of acute lung injury (ie, veterinary acute lung injury [VetALI] per the 2007 consensus definition) in a population of client-owned dogs receiving transfusions for various clinical reasons.

Design—Prospective observational study.

Animals—54 client-owned dogs.

Procedures—Arterial blood gas analysis was performed for dogs receiving a transfusion (blood and plasma products) at 0 to 12 hours before and 24 to 48 hours after transfusion; dogs also underwent thoracic radiography 0 to 24 hours before and 24 to 48 hours after transfusion. The ratio of Pao2 to fraction of inspired oxygen (Fio2) was calculated. Dogs with posttransfusion radiographic signs of pulmonary infiltrates, a Pao2:Fio2 ratio < 300, or clinical signs of respiratory compromise were suspected of having VetALI and underwent echocardiography to exclude left-sided heart failure. The incidence of VetALI was calculated, and χ2 tests were used to compare the incidence in study dogs with the historical reported incidence of acute respiratory distress syndrome (ARDS) in ill dogs (not receiving transfusions) and transfusion-related acute lung injury (TRALI) in humans.

Results—The incidence of VetALI (2/54 [3.7%]; 95% confidence interval, 0% to 8.73%) in study dogs was significantly less than the reported incidence of TRALI in humans (25%) and not significantly different from the reported incidence of ARDS in ill dogs (10%).

Conclusions and Clinical Relevance—VetALI occurred in dogs that received transfusions at a frequency similar to that previously reported for ARDS in ill dogs that did not receive transfusions.
Histopathologic findings in uterine biopsy samples from subfertile bitches: 399 cases (1990–2005)
Authors: Gifford Angela T. , Scarlett Janet M. , Schlafer Donald H.
Published: December 2013

Objective—To determine the prevalence of various lesion types detected by histologic evaluation of uterine biopsy samples collected from subfertile bitches.

Design—Retrospective case series.

Animals—399 sexually intact bitches.

Procedures—Results of histologic evaluation of canine uterine biopsy samples submitted by a single veterinary practice and clinical histories of dogs from which samples were obtained were reviewed. Clinical data including age, reason for biopsy, and histopathologic findings were recorded. The prevalence of specific lesions was determined, categorized by severity and age, and statistically analyzed.

Results—Endometritis (170/399 [42.6%] cases) and cystic endometrial changes, including cystic endometrial hyperplasia (133/399 [33.3%]) were the most prevalent lesions in the study population. Eighty-nine of 170 (52.4%) cases of endometritis were characterized as chronic with predominantly lymphocytic or lymphoplasmacytic inflammatory infiltrates, 51 (30.0%) included mixed inflammatory reactions, and 30 (17.6%) were characterized as having acute inflammation with neutrophils, eosinophils, or both. Fibrosis was common (101/399 [25.3%] cases). Eosinophilic endometritis was significantly associated with a history of fetal loss during the same breeding cycle. No significant difference was found in prevalence of lesions among age groups.

Conclusions and Clinical Relevance—The high prevalence of endometritis in this population of dogs suggested that acute and chronic endometritis may be related to subfertility in bitches. The association of eosinophilic endometrial infiltrates with a history of fetal loss may be an important diagnostic finding in dogs with endometritis.
Second intention healing after wide local excision of soft tissue sarcomas in the distal aspects of the limbs in dogs: 31 cases (2005–2012)
Authors: Prpich Cassandra Y. , Santamaria Alessandra C. , Simcock James O. , Wong Hoong Kien , Nimmo Judith S. , Kuntz Charles A.
Published: December 2013

Objective—To determine outcomes for dogs with soft tissue sarcomas in the distal aspects of the limbs that underwent second intention healing after wide excision (2-cm lateral surgical margins and a margin 1 fascial plane deep) of the tumors.

Design—Retrospective case series.

Animals—31 dogs with soft tissue sarcomas in the distal aspects of the limbs that underwent second intention healing following wide local excision of their tumors.

Procedures—Tumors were excised with 2-cm lateral margins and a margin 1 fascial plane deep to tumors. Wounds healed by means of second intention. Time to healing, complications during healing, and information regarding tumor recurrence were recorded.

Results—All tumors were excised with histologically tumor-free margins. Twenty-nine (93.5%) wounds healed completely by second intention (median time, 53 days). Two (6.5%) dogs required free skin graft procedures to facilitate healing. Complications during open wound management developed for 7 (22.6%) dogs. Long-term complications were detected for 8 (25.8%) dogs, including intermittent epidermal disruption (5/31 [16.1%]) and wound contracture (3/31 [9.7%]). All complications were managed conservatively. Local tumor recurrence was detected for 1 (3.2%) dog. Median follow-up time was 980 days (range, 380 to 2,356 days). No patients died because of tumor-related causes.

Conclusions and Clinical Relevance—Results of this study indicated second intention healing of large wounds in the distal aspects of the limbs was complete and typically without complications for dogs that underwent wide excision of soft tissue sarcomas. Wide local excision of soft tissue sarcomas in the distal aspects of the limbs with 2-cm lateral margins and margins 1 fascial plane deep to the tumors provided excellent long-term local tumor control.
Intramedullary spinal cord mass presumptively associated with leishmaniasis in a dog
Authors: José-López Roberto , de la Fuente Cristian , Pumarola Martí , Añor Sonia
Published: December 2013

Case Description—A 9-year-old male Miniature Poodle was evaluated because of progressive severe right hemiparesis, right forelimb lameness, and signs of cervical pain.

Clinical Findings—A low body condition score (2/9) and popliteal lymphadenopathy were detected. Results of a CBC, serum biochemical analyses, urinalysis, cytologic examination of bone marrow and popliteal lymph node aspirates, and serum ELISA were consistent with systemic leishmaniasis. Magnetic resonance imaging of the cervical spinal cord revealed an intramedullary mass extending from the caudal aspect of the C5 vertebral body to the C5–6 intervertebral disk space with a contrast medium–enhanced pattern that had 3 zones (central contrast medium–enhanced core, intermediate isointense zone, and peripheral contrast medium–enhanced ring). Surgical biopsy of the mass was performed by means of a right C5–6 dorsal hemilaminectomy. Results of PCR assays for detection of Leishmania DNA in CSF and tissue biopsy samples were positive.

Treatment and Outcome—Treatment for systemic leishmaniasis was initiated. Two months later, body condition, neurologic signs, and gait of the dog had substantially improved; the dog had mild right forelimb paresis at that time. Results of follow-up MRI indicated resolution of the cervical spinal cord lesion. Four months after diagnosis, the dog's neurologic condition was stable.

Clinical Relevance—To the authors’ knowledge, this report is the first in which clinical findings, clinicopathologic data, and MRI characteristics of an intramedullary inflammatory spinal cord lesion presumptively attributable to leishmaniasis in a dog have been reported, and the first report of CNS leishmaniasis in a dog with MRI resolution and a successful clinical response to treatment.
Impact of colic surgery on return to function in racing Thoroughbreds: 59 cases (1996–2009)
Authors: Hart Samantha K. , Southwood Louise L. , Aceto Helen W.
Published: December 2013

Objective—To determine the effect of colic surgery on return to function in Thoroughbred racehorses, identify clinical variables associated with successful return to racing, and compare racing performance between horses undergoing colic surgery and an untreated cohort.

Design—Retrospective cohort study.

Animals—59 Thoroughbred racehorses 2 to 5 years of age that underwent colic surgery and survived to hospital discharge and 90 untreated Thoroughbred racehorses equivalent in class.

Procedures—Medical records of patients evaluated for colic between January 1996 and July 2009 were reviewed, and horses with a Jockey Club Information Systems record were included. Physical examination and laboratory findings on hospital admission, lesion location and type, duration of surgery, duration of hospitalization, and any postoperative complications were recorded. The untreated cohort comprised 2 untreated horses randomly selected from runners in each treated horse's last race immediately prior to the date of colic surgery. Records were obtained from the Jockey Club Information Systems in April 2011. Only horses that raced at least once before and after surgery were included in the performance analysis. Number of starts, earnings per start, and total earnings were determined from race records for all horses. Quarterly earnings and number of starts for 12 quarters following the date of surgery were compared between treated and untreated horses via a Wilcoxon rank sum test. Longevity of racing was assessed by means of survival analysis. Poisson regression was used to compare rates of return to racing and active quarters aggregated across the first 12 quarters after surgery and for the available follow-up period for treated and untreated horses.

Results—45 of 59 (76%) horses that raced prior to surgery returned to racing. Return to racing was significantly associated with admission heart rate and blood lactate concentration. From quarters 3 to 12, treated and untreated horses had slight differences in the number of starts but no difference in earnings per quarter. Treated and untreated horses had no difference in total number of quarters raced, number of starts, or earnings after surgery. Treated horses had higher earnings per start, compared with untreated horses.

Conclusions and Clinical Relevance—In the present study, racing Thoroughbreds that underwent colic surgery and successfully returned to racing had no differences in performance variables, compared with their untreated cohorts.
Effect of constant exposure to cattle persistently infected with bovine viral diarrhea virus on morbidity and mortality rates and performance of feedlot cattle
Authors: Grooms Daniel L. , Brock Kenny V. , Bolin Steven R. , Grotelueschen Dale M. , Cortese Victor S.
Published: December 2013

Objective—To determine the effects of constant exposure to cattle persistently infected (PI) with bovine viral diarrhea virus (BVDV) on health and performance of feedlot cattle.

Design—3 controlled trials.

Animals—Crossbred feedlot cattle (trial 1, n = 184; trial 2, 138; trial 3, 138).

Procedures—Weaned calves were or were not vaccinated against BVDV at feedlot arrival (trial 1) or 2 (trial 2) or 3 (trial 3) weeks before feedlot arrival. During trial 1, half of the calves were commingled with PI cattle throughout the feeding period. During trial 2, 63 calves were exposed to PI cattle before weaning and all calves were exposed to PI cattle throughout the feeding period. During trial 3, all study calves were exposed to PI cattle throughout the feeding period. Morbidity and mortality rates and average daily gain (ADG) data were analyzed.

Results—During trial 1, calves maintained with PI cattle had a higher morbidity rate regardless of BVDV vaccination than did calves not exposed to PI cattle; however, for calves maintained with PI cattle, the morbidity rate for those vaccinated against BVDV was less than that for those not vaccinated against BVDV. During trial 2, calves exposed to PI cattle before weaning or vaccinated against BVDV had lower morbidity and mortality rates and increased ADG, compared with those for calves not exposed to PI cattle before weaning or vaccinated against BVDV. During trial 3, health and performance did not vary between calves that were and were not vaccinated against BVDV.

Conclusions and Clinical Relevance—Exposure of cattle to BVDV naturally or through vaccination before or at feedlot arrival mitigated the negative effects of constant exposure to PI cattle.
Swelling Properties of Hydrogels Containing Phenylboronic Acids
Authors: Kim Arum , Mujumdar Siddharthya , Siegel Ronald
Published: December 2013

Phenylboronic acids are a class of compounds that bind glucose and other sugars. When polymerized into hydrogels, they provide a convenient nonenzymatic means for sensing glucose concentration, provided competing sugars are present at negligible concentrations. In this paper we provide a comprehensive study of swelling of hydrogels containing methacrylamidophenylboronic acid (MPBA), as a function of pH and concentration of either glucose or fructose. In one set of hydrogels, MPBA is substituted at 20 mol·% in a polyacrylamide hydrogel [p(MPBA-co-AAm)], while in a second set of hydrogels, 20 mol·% MPBA is supplemented with 20 mol·% of N-3-(dimethylaminopropyl methacrylamide) [p(MPBA-co-DMP-co-AAm)]. Swelling curves are markedly different for fructose and glucose, and for the two sets of hydrogels. While fructose alters swelling by binding and contributing to the ionization of MPBA, glucose does the same, but it also can form crosslinking bridges between separate chains, leading to hydrogel shrinkage. While the [p(MPBA-co-AAm)] hydrogels behaved as polyacids, swelling monotonically with increasing pH, the [p(MPBA-co-DMP-co-AAm)] hydrogels exhibited polyampholyte behavior, with swelling minima at intermediate pH values.
Markov State Models for Rare Events in Molecular Dynamics
Authors: Sarich Marco , Banisch Ralf , Hartmann Carsten , Schütte Christof
Published: December 2013

Rare, but important, transition events between long-lived states are a key feature of many molecular systems. In many cases, the computation of rare event statistics by direct molecular dynamics (MD) simulations is infeasible, even on the most powerful computers, because of the immensely long simulation timescales needed. Recently, a technique for spatial discretization of the molecular state space designed to help overcome such problems, so-called Markov State Models (MSMs), has attracted a lot of attention. We review the theoretical background and algorithmic realization of MSMs and illustrate their use by some numerical examples. Furthermore, we introduce a novel approach to using MSMs for the efficient solution of optimal control problems that appear in applications where one desires to optimize molecular properties by means of external controls.
First Principles Methods: A Perspective from Quantum Monte Carlo
Authors: Morales Miguel , Clay Raymond , Pierleoni Carlo , Ceperley David
Published: December 2013

Quantum Monte Carlo methods are among the most accurate algorithms for predicting properties of general quantum systems. We briefly introduce ground state, path integral at finite temperature and coupled electron-ion Monte Carlo methods, their merits and limitations. We then discuss recent calculations using these methods for dense liquid hydrogen as it undergoes a molecular/atomic (metal/insulator) transition. We then discuss a procedure that can be used to assess electronic density functionals, which in turn can be used on a larger scale for first principles calculations and apply this technique to dense hydrogen and liquid water.
Modeling Potential Energy Surfaces: From First-Principle Approaches to Empirical Force Fields
Authors: Ballone Pietro
Published: December 2013

Explicit or implicit expressions of potential energy surfaces (PES) represent the basis of our ability to simulate condensed matter systems, possibly understanding and sometimes predicting their properties by purely computational methods. The paper provides an outline of the major approaches currently used to approximate and represent PESs and contains a brief discussion of what still needs to be achieved. The paper also analyses the relative role of empirical and ab initio methods, which represents a crucial issue affecting the future of modeling in chemical physics and materials science.
Characterization of Rare Events in Molecular Dynamics
Authors: Hartmann Carsten , Banisch Ralf , Sarich Marco , Badowski Tomasz , Schütte Christof
Published: December 2013

A good deal of molecular dynamics simulations aims at predicting and quantifying rare events, such as the folding of a protein or a phase transition. Simulating rare events is often prohibitive, especially if the equations of motion are high-dimensional, as is the case in molecular dynamics. Various algorithms have been proposed for efficiently computing mean first passage times, transition rates or reaction pathways. This article surveys and discusses recent developments in the field of rare event simulation and outlines a new approach that combines ideas from optimal control and statistical mechanics. The optimal control approach described in detail resembles the use of Jarzynski’s equality for free energy calculations, but with an optimized protocol that speeds up the sampling, while (theoretically) giving variance-free estimators of the rare events statistics. We illustrate the new approach with two numerical examples and discuss its relation to existing methods.
Financial Markets, Banking and the Design of Monetary Policy: A Stable Baseline Scenario
Authors: Hartmann Florian , Flaschel Peter
Published: December 2013

A baseline integration of commercial banks into the disequilibrium framework with behavioral traders of Charpe et al. (2011, 2012) is presented. At the core of the analysis is the impact the banking sector exerts on the interaction of real and financial markets. Potentially destabilizing feedback channels in the presence of imperfect macroeconomic portfolio adjustment and heterogeneous expectations are investigated. Given the possible financial market instability, various policy instruments have to be applied in order to guarantee viable dynamics in the highly interconnected macroeconomy. Among those are open market operations reacting to the state-of-confidence in the economy and Tobin-type capital gain taxes. The need for policy intervention is even more striking, as the banking sector is modeled in a rather stability enhancing way, fulfilling its fundamental tasks of term transformation of savings and credit granting without engaging in investment activities itself.
Subsurface Transport Behavior of Micro-Nano Bubbles and Potential Applications for Groundwater Remediation
Authors: Li Hengzhen , Hu Liming , Song Dejun , Al-Tabbaa Abir
Published: December 2013

Micro-nano bubbles (MNBs) are tiny bubbles with diameters on the order of micrometers and nanometers, showing great potential in environmental remediation. However, the application is only in the beginning stages and remains to be intensively studied. In order to explore the possible use of MNBs in groundwater contaminant removal, this study focuses on the transport of MNBs in porous media and dissolution processes. The bubble diameter distribution was obtained under different conditions by a laser particle analyzer. The permeability of MNB water through sand was compared with that of air-free water. Moreover, the mass transfer features of dissolved oxygen in water with MNBs were studied. The results show that the bubble diameter distribution is influenced by the surfactant concentration in the water. The existence of MNBs in pore water has no impact on the hydraulic conductivity of sand. Furthermore, the dissolved oxygen (DO) in water is greatly increased by the MNBs, which will predictably improve the aerobic bioremediation of groundwater. The results are meaningful and instructive in the further study of MNB research and applications in groundwater bioremediation.
Analysis of Phthalate Migration to Food Simulants in Plastic Containers during Microwave Operations
Authors: Moreira Miriany , André Leiliane , Cardeal Zenilda
Published: December 2013

Phthalates used as plasticizers in the manufacture of household containers can potentially be transferred to foods that are stored or heated in these plastic containers. Phthalates are endocrine disruptor compounds (EDC) and are found in very low concentrations in foods, thus, highly sensitive analytical techniques are required for their quantification. This study describes the application of a new method developed for analyzing the migration of dibutylphthalate (DBP) and benzylbutylphthalate (BBP) from plastic food containers into liquid food simulants. This new method employs the technique of solid phase microextraction cooled with liquid nitrogen. The analysis was conducted by gas chromatography/mass spectrometry (GC/MS) using a polyacrylate fiber. Ultrapure water was used as a simulant for liquids foods, and both new and used plastic containers were placed in a domestic microwave oven for different periods of time at different power levels. The limits of detection for DBP and BBP were 0.08 µg/L and 0.31 µg/L, respectively. BBP was not found in the samples that were analyzed. DBP was found in concentrations ranging from <LOQ to 7.5 µg/L. In general, an increase in migration was observed in containers that were used for a prolonged time, which correlated with increasing heating time.
Gender-Specific Associations between Perceived Neighbourhood Walkability and Meeting Walking Recommendations When Walking for Transport and Recreation for Czech Inhabitants over 50 Years of Age
Authors: Pelclová Jana , Frömel Karel , Cuberek Roman
Published: December 2013

Few studies have investigated the different effects that the built environment may have on the physical activity behaviours of men and women. Therefore, the aim of this study was to estimate the gender differences in meeting walking recommendations in relation to perceived neighbourhood walkability attributes within the active transportation and leisure-time domains for Czech inhabitants over 50 years of age. The sample included 1,417 men and 1,422 women who were randomly selected. The Abbreviated Neighbourhood Environment Walkability Scale (ANEWS) was used to obtain information about the perceived environment. The self-administered long version of the IPAQ was used to assess physical activity levels. When walking for transport, men living in neighbourhoods with high street connectivity (OR = 1.47, CI = 1.04–2.9) and higher traffic and crime safety (OR = 1.28, CI = 1.02–1.6) and women living in neighbourhoods with high proximity (OR = 1.36, CI = 1.04–1.77) and high neighbourhood aesthetics (OR = 1.36, CI = 1.04–1.76) were more likely to meet recommended levels of walking. No environmental attributes were found to significantly influence the accomplishment of walking recommendations by men or women when walking for leisure. The study results indicate the gender-specific associations between transportation-related walking and the environment factors. The consideration of those factors in the design of gender-specific walking interventions for Czech inhabitants may help the interventions to be more effective in promotion of physical activity.
Traumatic Brain Injury Pathophysiology and Treatments: Early, Intermediate, and Late Phases Post-Injury
Authors: Algattas Hanna , Huang Jason
Published: December 2013

Traumatic Brain Injury (TBI) affects a large proportion and extensive array of individuals in the population. While precise pathological mechanisms are lacking, the growing base of knowledge concerning TBI has put increased emphasis on its understanding and treatment. Most treatments of TBI are aimed at ameliorating secondary insults arising from the injury; these insults can be characterized with respect to time post-injury, including early, intermediate, and late pathological changes. Early pathological responses are due to energy depletion and cell death secondary to excitotoxicity, the intermediate phase is characterized by neuroinflammation and the late stage by increased susceptibility to seizures and epilepsy. Current treatments of TBI have been tailored to these distinct pathological stages with some overlap. Many prophylactic, pharmacologic, and surgical treatments are used post-TBI to halt the progression of these pathologic reactions. In the present review, we discuss the mechanisms of the pathological hallmarks of TBI and both current and novel treatments which target the respective pathways.
Pyrene-Fullerene C60 Dyads as Light-Harvesting Antennas
Authors: Zaragoza-Galán Gerardo , Ortíz-Palacios Jesús , Valderrama Bianca , Camacho-Dávila Alejandro , Chávez-Flores David , Ramos-Sánchez Víctor , Rivera Ernesto
Published: December 2013

A series of pyrene-fullerene C60 dyads bearing pyrene units (PyFC12, PyFPy, Py2FC12 and PyFN) were synthesized and characterized. Their optical properties were studied by absorption and fluorescence spectroscopies. Dyads were designed in this way because the pyrene moeities act as light-harvesting molecules and are able to produce “monomer” (PyFC12) or excimer emission (PyFPy, Py2FC12 and PyFN). The fluorescence spectra of the dyads exhibited a significant decrease in the amount of pyrene monomer and excimer emission, without the appearance of a new emission band due to fullerene C60. The pyrene fluorescence quenching was found to be almost quantitative, ranging between 96%–99% depending on the construct, which is an indication that energy transfer occurred from one of the excited pyrene species to the fullerene C60.
A SAR and QSAR Study of New Artemisinin Compounds with Antimalarial Activity
Authors: Santos Cleydson , Vieira Josinete , Lobato Cleison , Hage-Melim Lorane , Souto Raimundo , Lima Clarissa , Costa Elizabeth , Brasil Davi , Macêdo Williams , Carvalho José
Published: December 2013

The Hartree-Fock method and the 6-31G** basis set were employed to calculate the molecular properties of artemisinin and 20 derivatives with antimalarial activity. Maps of molecular electrostatic potential (MEPs) and molecular docking were used to investigate the interaction between ligands and the receptor (heme). Principal component analysis and hierarchical cluster analysis were employed to select the most important descriptors related to activity. The correlation between biological activity and molecular properties was obtained using the partial least squares and principal component regression methods. The regression PLS and PCR models built in this study were also used to predict the antimalarial activity of 30 new artemisinin compounds with unknown activity. The models obtained showed not only statistical significance but also predictive ability. The significant molecular descriptors related to the compounds with antimalarial activity were the hydration energy (HE), the charge on the O11 oxygen atom (QO11), the torsion angle O1-O2-Fe-N2 (D2) and the maximum rate of R/Sanderson Electronegativity (RTe+). These variables led to a physical and structural explanation of the molecular properties that should be selected for when designing new ligands to be used as antimalarial agents.
Metabolism of Cholesterol and Bile Acids by the Gut Microbiota
Authors: Gérard Philippe
Published: December 2013

The human gastro-intestinal tract hosts a complex and diverse microbial community, whose collective genetic coding capacity vastly exceeds that of the human genome. As a consequence, the gut microbiota produces metabolites from a large range of molecules that host’s enzymes are not able to convert. Among these molecules, two main classes of steroids, cholesterol and bile acids, denote two different examples of bacterial metabolism in the gut. Therefore, cholesterol is mainly converted into coprostanol, a non absorbable sterol which is excreted in the feces. Moreover, this conversion occurs in a part of the human population only. Conversely, the primary bile acids (cholic and chenodeoxycholic acids) are converted to over twenty different secondary bile acid metabolites by the gut microbiota. The main bile salt conversions, which appear in the gut of the whole human population, include deconjugation, oxidation and epimerization of hydroxyl groups at C3, C7 and C12, 7-dehydroxylation, esterification and desulfatation. If the metabolisms of cholesterol and bile acids by the gut microbiota are known for decades, their consequences on human health and disease are poorly understood and only start to be considered.
Immunosuppressive Therapy in Immune-Mediated Liver Disease in the Non-Transplanted Patient
Authors: Abhyankar Anita , Tapper Elliot , Bonder Alan
Published: December 2013

Autoimmune liver disease management goals are primarily slowing disease progression and symptomatic treatment. There are few options for curative medical management other than transplant for a spectrum of autoimmune liver disease that encompasses autoimmune hepatitis, primary biliary cirrhosis, primary sclerosing cholangitis as well as their overlap syndromes. These diseases are managed primarily with immunosuppressive therapy. Herein, we review the current literature, detailing the promise and pitfalls of the recommended immunosuppressive therapy for these challenging diseases.
Are AMPA Receptor Positive Allosteric Modulators Potential Pharmacotherapeutics for Addiction?
Authors: Watterson Lucas , Olive M.
Published: December 2013

Positive allosteric modulators (PAMs) of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors are a diverse class of compounds that increase fast excitatory transmission in the brain. AMPA PAMs have been shown to facilitate long-term potentiation, strengthen communication between various cortical and subcortical regions, and some of these compounds increase the production and release of brain-derived neurotrophic factor (BDNF) in an activity-dependent manner. Through these mechanisms, AMPA PAMs have shown promise as broad spectrum pharmacotherapeutics in preclinical and clinical studies for various neurodegenerative and psychiatric disorders. In recent years, a small collection of preclinical animal studies has also shown that AMPA PAMs may have potential as pharmacotherapeutic adjuncts to extinction-based or cue-exposure therapies for the treatment of drug addiction. The present paper will review this preclinical literature, discuss novel data collected in our laboratory, and recommend future research directions for the possible development of AMPA PAMs as anti-addiction medications.
Modified Johnston Failure Criterion from Rock Mechanics to Predict the Ultimate Strength of Fiber Reinforced Polymer (FRP) Confined Columns
Authors: Girgin Zehra
Published: December 2013

The failure criteria from rock mechanics, Hoek-Brown and Johnston failure criteria, may be extended and modified to assess the ultimate compressive strength of axially loaded circular fiber reinforced polymer (FRP)-confined concrete columns. In addition to the previously modified Hoek-Brown criterion, in this study, the Johnston failure criterion is extended to scope of FRP-confined concrete, verified with the experimental data and compared with the significant relationships from the current literature. Wide-range compressive strengths from 7 to 108 MPa and high confinement ratios up to 2.0 are used to verify the ultimate strengths in short columns. The results are in good agreement with experimental data for all confinement levels and concrete strengths.
Improved Accuracy of Chlorophyll-a Concentration Estimates from MODIS Imagery Using a Two-Band Ratio Algorithm and Geostatistics: As Applied to the Monitoring of Eutrophication Processes over Tien Yen Bay (Northern Vietnam)
Authors: Ha Nguyen , Koike Katsuaki , Nhuan Mai
Published: December 2013

Sea eutrophication is a natural process of water enrichment caused by increased nutrient loading that severely affects coastal ecosystems by decreasing water quality. The degree of eutrophication can be assessed by chlorophyll-a concentration. This study aims to develop a remote sensing method suitable for estimating chlorophyll-a concentrations in tropical coastal waters with abundant phytoplankton using Moderate Resolution Imaging Spectroradiometer (MODIS)/Terra imagery and to improve the spatial resolution of MODIS/Terra-based estimation from 1 km to 100 m by geostatistics. A model based on the ratio of green and blue band reflectance (rGBr) is proposed considering the bio-optical property of chlorophyll-a. Tien Yen Bay in northern Vietnam, a typical phytoplankton-rich coastal area, was selected as a case study site. The superiority of rGBr over two existing representative models, based on the blue-green band ratio and the red-near infrared band ratio, was demonstrated by a high correlation of the estimated chlorophyll-a concentrations at 40 sites with values measured in situ. Ordinary kriging was then shown to be highly capable of predicting the concentration for regions of the image covered by clouds and, thus, without sea surface data. Resultant space-time maps of concentrations over a year clarified that Tien Yen Bay is characterized by natural eutrophic waters, because the average of chlorophyll-a concentrations exceeded 10 mg/m3 in the summer. The temporal changes of chlorophyll-a concentrations were consistent with average monthly air temperatures and precipitation. Consequently, a combination of rGBr and ordinary kriging can effectively monitor water quality in tropical shallow waters.