bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling the Agility MLC in the Monaco treatment planning system
Authors: Snyder Michael , Halford Robert , Knill Cory , Adams Jeffrey N. , Bossenberger Todd , Nalichowski Adrian , Hammoud Ahmad , Burmeister Jay 
Published: February 2017

We investigate the relationship between the various parameters in the Monaco MLC model and dose calculation accuracy for an Elekta Agility MLC. The vendor‐provided MLC modeling procedure — completed first with external vendor participation and then exclusively in‐house — was used in combination with our own procedures to investigate several sets of MLC modeling parameters to determine their effect on dose distributions and point‐dose measurements. Simple plans provided in the vendor procedure were used to elucidate specific mechanical characteristics of the MLC, while ten complex treatment plans — five IMRT and five VMAT — created using TG‐119‐based structure sets were used to test clinical dosimetric effects of particular parameter choices. EDR2 film was used for the vendor fields to give high spatial resolution, while a combination of MapCHECK and ion chambers were used for the in‐house TG‐119‐based procedures. The vendor‐determined parameter set provided a reasonable starting point for the MLC model and largely delivered acceptable gamma pass rates for clinical plans — including a passing external evaluation using the IROC H&N phantom. However, the vendor model did not provide point‐dose accuracy consistent with that seen in other treatment systems at our center. Through further internal testing it was found that there existed many sets of MLC parameters, often at opposite ends of their allowable ranges, that provided similar dosimetric characteristics and good agreement with planar and point‐dose measurements. In particular, the leaf offset and tip leakage parameters compensated for one another if adjusted in opposite directions, which provided a level curve of acceptable parameter sets across all plans. Interestingly, gamma pass rates of the plans were less dependent upon parameter choices than point‐dose measurements, suggesting that MLC modeling using only gamma evaluation may be generally an insufficient approach. It was also found that exploring all parameters of the very robust MLC model to find the best match to the vendor‐provided QA fields can reduce the pass rates of the TG‐119‐based clinical distributions as compared to simpler models. A wide variety of parameter sets produced MLC models capable of meeting RPC passing criteria for their H&N IMRT phantom. The most accurate models were achievable using a combination of vendor‐provided and in‐house procedures. The potential existed for an over‐modeling of the Agility MLC in an effort to obtain the fine structure of certain quality assurance fields, which led to a reduction in agreement between calculation and measurement of more typical clinical dose distributions.PACS number(s): 87.56.nk, 87.53.Kn, 87.55.km, 87.55.Qr
Quantification of the margin required for treating intraprostatic lesions
Authors: Studenski Matthew T. , Valenciaga Yanisley , Abramowitz Matthew C. , Stoyanova Radka , Bossart Elizabeth , Dogan Nesrin , Pollack Alan 
Published: February 2017

Advances in magnetic resonance imaging (MRI) sequences allow physicians to define the dominant intraprostatic lesion (IPL) in prostate radiation therapy treatments allowing for dose escalation and potentially increased tumor control. This work quantifies the margin required around the MRI‐defined IPL accounting for both prostate motion and deformation. Ten patients treated with a simultaneous integrated intraprostatic boost (SIIB) were retrospectively selected and replanned with incremental 1 mm margins from 0‐5 mm around the IPL to determine if there were any significant differences in dosimetric parameters. Sensitivity analysis was then performed accounting for random and systematic uncertainties in both prostate motion and deformation to ensure adequate dose was delivered to the IPL. Prostate deformation was assessed using daily CBCT imaging and implanted fiducial markers. The average IPL volume without margin was 2.3% of the PTV volume and increased to 11.8% with a 5 mm margin. Despite these changes in volume, the only statistically significant dosimetric difference was found for the PTV maximum dose, which increased with increasing margin. The sensitivity analysis demonstrated that a 3.0 mm margin ensures IPL coverage accounting for both motion and deformation. We found that a margin of 3.0 mm around the MRI defined IPL is sufficient to account for random and systematic errors in IPL position for the majority of cases.PACS number(s): 87.55.de
Evaluation of a combined respiratory‐gating system comprising the TrueBeam linear accelerator and a new real‐time tumor‐tracking radiotherapy system: a preliminary study
Authors: Shiinoki Takehiro , Kawamura Shinji , Uehara Takuya , Yuasa Yuki , Fujimoto Koya , Koike Masahiro , Sera Tatsuhiro , Emoto Yuki , Hanazawa Hideki , Shibuya Keiko 
Published: February 2017

A combined system comprising the TrueBeam linear accelerator and a new real‐time, tumor‐tracking radiotherapy system, SyncTraX, was installed in our institution. The goals of this study were to assess the capability of SyncTraX in measuring the position of a fiducial marker using color fluoroscopic images, and to evaluate the dosimetric and geometric accuracy of respiratory‐gated radiotherapy using this combined system for the simple geometry. For the fundamental evaluation of respiratory‐gated radiotherapy using SyncTraX, the following were performed: 1) determination of dosimetric and positional characteristics of sinusoidal patterns using a motor‐driven base for several gating windows; 2) measurement of time delay using an oscilloscope; 3) positional verification of sinusoidal patterns and the pattern in the case of a lung cancer patient; 4) measurement of the half‐value layer (HVL in mm AL), effective kVp, and air kerma, using a solid‐state detector for each fluoroscopic condition, to determine the patient dose. The dose profile in a moving phantom with gated radiotherapy having a gating window was in good agreement with that under static conditions for each photon beam. The total time delay between TrueBeam and SyncTraX was for each photon beam. The mean of the positional tracking error was for sinusoidal patterns and for the pattern in the case of a lung cancer patient. The air‐kerma rates from one fluoroscopy direction were , , , , and for 70, 80, 90, 100, and 110 kV X‐ray beams at 80 mA, respectively. The combined system comprising TrueBeam and SyncTraX could track the motion of the fiducial marker and control radiation delivery with reasonable accuracy; therefore, this system provides significant dosimetric improvement. However, patient exposure dose from fluoroscopy was not clinically negligible.PACS number(s): 87.53.Bn, 87.55.km, 87.55.Qr
A novel phantom and procedure providing submillimeter accuracy in daily QA tests of accelerators used for stereotactic radiosurgery*
Authors: Brezovich Ivan A. , Popple Richard A. , Duan Jun , Shen Sui , Wu Xingen , Benhabib Sidi , Huang Mi , Cardan Rex A. 
Published: February 2017

Stereotactic radiosurgery (SRS) places great demands on spatial accuracy. Steel BBs used as markers in quality assurance (QA) phantoms are clearly visible in MV and planar kV images, but artifacts compromise cone‐beam CT (CBCT) isocenter localization. The purpose of this work was to develop a QA phantom for measuring with sub‐mm accuracy isocenter congruence of planar kV, MV, and CBCT imaging systems and to design a practical QA procedure that includes daily Winston‐Lutz (WL) tests and does not require computer aid. The salient feature of the phantom (Universal Alignment Ball (UAB)) is a novel marker for precisely localizing isocenters of CBCT, planar kV, and MV beams. It consists of a 25.4 mm diameter sphere of polymethylmetacrylate (PMMA) containing a concentric 6.35 mm diameter tungsten carbide ball. The large density difference between PMMA and the polystyrene foam in which the PMMA sphere is embedded yields a sharp image of the sphere for accurate CBCT registration. The tungsten carbide ball serves in finding isocenter in planar kV and MV images and in doing WL tests. With the aid of the UAB, CBCT isocenter was located within of its true positon, and MV isocenter was pinpointed in planar images to within . In clinical morning QA tests extending over an 18 months period the UAB consistently yielded measurements with sub‐mm accuracy. The average distance between isocenter defined by orthogonal kV images and CBCT measured . In WL tests the central ray of anterior beams defined by a MLC field agreed with CBCT isocenter within in the lateral direction and within in the longitudinal direction. Lateral MV beams approached CBCT isocenter within in the vertical direction and within longitudinally. It took therapists about 10 min to do the tests. The novel QA phantom allows pinpointing CBCT and MV isocenter positions to better than 0.2 mm, using visual image registration. Under CBCT guidance, MLC‐defined beams are deliverable with sub‐mm spatial accuracy. The QA procedure is practical for daily tests by therapists.PACS number(s): 87.53.Ly, 87.56.Fc
Resolution of Mismatched Overlap Holliday Junction Intermediates by the Tyrosine Recombinase IntDOT
Authors: Ringwald Kenneth , Yoneji Sumiko , Gardner Jeffrey 
Published: February 2017

ABSTRACT

CTnDOT is an integrated conjugative element found in
Bacteroides
species. CTnDOT contains and transfers antibiotic resistance genes. The element integrates into and excises from the host chromosome via a Holliday junction (HJ) intermediate as part of a site-specific recombination mechanism. The CTnDOT integrase, IntDOT, is a tyrosine recombinase with core-binding, catalytic, and amino-terminal (N) domains. Unlike well-studied tyrosine recombinases, such as lambda integrase (Int), IntDOT is able to resolve Holliday junctions containing heterology (mismatched bases) between the sites of strand exchange. All known natural isolates of CTnDOT contain mismatches in the overlap region between the sites of strand exchange. Previous work showed that IntDOT was unable to resolve synthetic Holliday junctions containing mismatched bases to products in the absence of the arm-type sites and a DNA-bending protein. We constructed synthetic HJs with the arm-type sites and tested them with the
Bacteroides
host factor (BHFa). We found that the addition of BHFa stimulated resolution of HJ intermediates with mismatched overlap regions to products. In addition, the L1 site is required for directionality of the reaction, particularly when the HJ contains mismatches. BHFa is required for product formation when the overlap region contains mismatches, and it stimulates resolution to products when the overlap region is identical. Without this DNA bending, the N domain of IntDOT is likely unable to bind the L1 arm-type site. These findings suggest that BHFa bends DNA into the necessary conformation for the higher-order complexes, including the L1 site, that are required for product formation.

IMPORTANCE
CTnDOT is a mobile element that carries antibiotic resistance genes and moves by site-selective recombination and subsequent conjugation. The recombination reaction is catalyzed by an integrase IntDOT that is a member of the tyrosine recombinase family. The reaction proceeds through ordered strand exchanges that generate a Holliday junction (HJ) intermediate. Unlike other tyrosine recombinases, IntDOT can resolve HJs containing mismatched bases in the overlap region
in vivo
, as is the case under natural conditions. However, HJ intermediates including only IntDOT core-type sites cannot be resolved to products if the HJ intermediate contains mismatched bases. We added arm-type sites in
cis
and in
trans
to the HJ intermediates and the protein BHFa to study the requirements for higher-order nucleoprotein complexes.
Comparing Cancellous Bone Volume of the Manubrium to Iliac Crest in Fresh Cadavers
Authors: Smith Aaron , Kortebein Sarah , Eid Anas , Boughter John , Cary Nathan , Brooks Jeffrey , Sebelik Merry 
Published: February 2017

ObjectiveThe iliac crest is the gold standard for cancellous bone grafting. This site is distant from head and neck reconstruction and may lead to significant postoperative morbidity. We propose an alternative harvest site within the head and neck with potentially less mobility deficits, the manubrium.Study DesignFresh‐frozen cadaveric study.SettingGross anatomy laboratory.Subjects and MethodsAccess to 18 cadavers was granted from the Medical Education and Research Institute in Memphis, Tennessee. The anterior iliac crests were exposed and H‐type osteotomies performed. The manubrium was accessed through a substernal notch incision and a cortical window created through the anterior manubrium. Cancellous bone was harvested from these sites. Cadaveric demographics and noncompressed and compressed volumes were recorded with statistical comparisons.ResultsThe population was predominantly male (12/18) with a mean age of 69.6 (95% confidence interval [CI], 64.0‐75.3) years. The mean body mass index was 22.9 (95% CI, 18.8‐27.1) kg/m2 with no sex propensity. Uncompressed volumes did not vary, ranging from 6.4 to 7.5 mL. Compressed volumes (mL) for the right iliac crest (4.3; 95% CI, 3.0‐5.6), left iliac crest (3.5; 95% CI, 2.7‐4.2), and manubrium (2.4; 95% CI, 1.8‐3.0) varied (1‐way analysis of variance: F(2, 51) = 4.63; P <. 02). Furthermore, there was correlation between compressed volumes taken from either area (r = 0.58; P <. 02).ConclusionsThe manubrium can be used for cancellous bone grafting. This site affords a proximity to the head and neck rather than the distant iliac crest but with slightly lower yields. Potential applications include reconstructing small mandibular defects, mandible nonunion, or alveolar bone grafting.
An Experimental Study on Strengthening of Reinforced Concrete Flexural Members using Steel Wire Mesh
Authors: Al Saadi Hamza Salim Mohammed , Mohandas Hoby P. , Namasivayam Aravind 
Published: February 2017

Abstract One of the major challenges and contemporary research in the field of structural engineering is strengthening of existing structural elements using readily available materials in the market. Several investigations were conducted on strengthening of various structural components using traditional and advanced materials. Many researchers tried to enhance the reinforced concrete (RC) beams strength using steel plate, Glass and Carbon Fibre Reinforced Polymers (GFRP & CFRP). For the reason that high weight to the strength ratio and compatibility in strength between FRP composites and steel bars, steel plates and GFRP and CFRP composites are not used for strengthening works practically. Hence, in this present work the suitability of using wire mesh for the purpose of strengthening the RC flexural members is studied by conducting experimental works. New technique of strengthening system using wire mesh with a view to improve sectional properties and subsequently flexural strength of RC beams is adopted in this work. The results for experimental and theoretical analysis were compared and found that good correlation exists between them. The experimental results indicate that RC beams strengthened with steel wire mesh are easy technique for strengthening of existing flexural members.
Is new spread of the European beaver in Pannonian basin an evidence of the species recovery?
Authors: Čanády Alexander , Krišovský Peter , Bajomi Bálint , Huber Attila , Czabán Dávid , Olekšák Milan 
Published: February 2017

Abstract
Abstract: During fieldwork from 6 June to 20 July 2016, the first records of the European beaver (Castor fiber)
in south-eastern Slovakia were made. Beavers are mainly nocturnal animals, and as such, they are rarely observed;
therefore, our observations were based on searching for beaver presence signs: damaged trees, dams,
signs of food consumption (chewed/felled trees) and footprints in the mud. The southern part of the Košická
kotlina basin, from the city of Košice down to the state border and the surrounding villages in Hungary, was
checked. We found two beaver locations via feeding signs in the vicinity of the Slovakia–Hungary state border,
at the villages of Milhosť (Miglécnémeti) and Buzica (Buzita), in Slovakia. According to our calculations, the present
total beaver population in Hungary is between 4,000 and 5,000 and 14,600–18,300 beavers with potential
support. For Slovakia, we estimated the potential population size to be 7,700–9,600. Our findings in northern
Pannonian lowland (Slovakia–Hungary border) are an important evidence of beaver expansion. Although we
don’t know the exact origin of investigated population, these new records indicate the possibility of merging the
populations of different origin, which could enable gene flow and increase the genetic diversity. This could lead
to improved recovery of species and its stabilisation in nature. However, it is necessary to carry out a detailed
investigation of the presence of beaver in these regions in future.
Investigation of ischemia modified albumin levels in iron deficiency anemia
Authors: Bilgili Sibel , Bozkaya Giray , Tütüncüler Funda Kırtay , Akşit Murat , Yavuz Mehmet 
Published: February 2017

Abstract

Objective
The aim of this study was to evaluate the levels of ischemia-modified albumin (IMA), before and after oral iron supplementation in iron deficiency anemia and to determine the correlations between IMA and hemoglobin values.

Study design
IMA, hemoglobin, hematocrit, mean corpuscular volume, ferritin, iron, total iron binding capacity and albumin levels were measured in 140 female patients with newly established as iron deficiency anemia before and after treatment and in 84 female healthy controls.

Results
IMA levels were higher in the anemia group [0.340±0.082 absorbance units (ABSU)] compared to control group (0.291±0.077 ABSU). After oral iron therapy we saw that IMA values (0.392±0.080 ABSU) were higher than the IMA levels of the anemia group and the control group (p<0.05). Only in the anemia group there were negative correlations between IMA and hemoglobin, hematocrit.

Conclusion
We conclude that the high levels of IMA in the anemia group might be attributed to hypoxia due to low hemoglobin levels. Iron is an oxidant element and oral iron supplementation may be associated with oxidative stress and may increase IMA levels by changing the albumin molecule. We thought that, IMA can be demonstrative of the severity of anemia since it was correlated with hemoglobin in the anemia group.
Preterm Infant Growth Velocity Calculations: A Systematic Review
Authors: Fenton Tanis R. , Chan Hilton T. , Madhu Aiswarya , Griffin Ian J. , Hoyos Angela , Ziegler Ekhard E. , Groh-Wargo Sharon , Carlson Susan J. , Senterre Thibault , Anderson Diane , Ehrenkranz Richard A. 
Published: February 2017

CONTEXT:Clinicians assess the growth of preterm infants and compare growth velocity using a variety of methods.OBJECTIVE:We determined the numerical methods used to describe weight, length, and head circumference growth velocity in preterm infants; these methods include grams/kilogram/day (g/kg/d), grams/day (g/d), centimeters/week (cm/week), and change in z scores.DATA SOURCES:A search was conducted in April 2015 of the Medline database by using PubMed for studies that measured growth as a main outcome in preterm neonates between birth and hospital discharge and/or 40 weeks’ postmenstrual age. English, French, German, and Spanish articles were included. The systematic review was conducted by using Preferred Reporting Items for Systematic Reviews and Meta-analyses methods.STUDY SELECTION:Of 1543 located studies, 373 (24%) calculated growth velocity.DATA EXTRACTION:We conducted detailed extraction of the 151 studies that reported g/kg/d weight gain velocity.RESULTS:A variety of methods were used. The most frequently used method to calculate weight gain velocity reported in the 1543 studies was g/kg/d (40%), followed by g/d (32%); 29% reported change in z score relative to an intrauterine or growth chart. In the g/kg/d studies, 39% began g/kg/d calculations at birth/admission, 20% at the start of the study, 10% at full feedings, and 7% after birth weight regained. The kilogram denominator was not reported for 62%. Of the studies that did report the denominators, the majority used an average of the start and end weights as the denominator (36%) followed by exponential methods (23%); less frequently used denominators included birth weight (10%) and an early weight that was not birth weight (16%). Nineteen percent (67 of 355 studies) made conclusions regarding extrauterine growth restriction or postnatal growth failure. Temporal trends in head circumference growth and length gain changed from predominantly cm/wk to predominantly z scores.LIMITATIONS AND CONCLUSIONSThe lack of standardization of methods used to calculate preterm infant growth velocity makes comparisons between studies difficult and presents an obstacle to using research results to guide clinical practice.
Alginate Lyase from Indonesian Bacillus megaterium S245 Shows Activities Toward Polymannuronate and Polyguluronate
Authors: Subaryono Subaryono , Ardilasari Yuwanita , Peranginangin Rosmawaty , Zakaria Fransisca Rungkat , Suhartono Maggy Thenawidjaja 
Published: February 2017

Screening of alginate lyase producing bacteria associated with seaweed Sargassum crassifolium was carried out, and isolate S245, identified as Bacillus megaterium S245 was found to produce high alginate lyase activity. This research was conducted to evaluate activity of the alginate lyase enzyme at various pHs, temperatures and substrates. Polymannuronate and polyguluronate were used to evaluate substrate specificities. Alginate lyase activity was assayed by analysis of reducing sugar released using the 3,5 dinitrosalicylic acid (DNS) method. The research showed that the activity of alginate lyase was optimum at pH of 7.0 and temperature of 45 0C. This enzyme was active for both polymannuronate and polyguluronate susbtrates. The Vmax and Km of this enzyme for polymannuronate and polyguluronate were 200 unit/ml/min and 79.8 mg/ml for polymannuronate substrate and 27.78 unit/ml/min and 13.17 mg/ml for polyguluronate substrate. This enzyme showed unique characteristic in working toward the two substrates.