bluuebunny/crossref_metadata_2025_split huggingface dataset:
Creation of an atlas of filter positions for fluence field modulated CT
Authors: Szczykutowicz Timothy P. , Hermus James 
Published: March 2015

Purpose:Fluence field modulated CT (FFMCT) and volume of interest (VOI) CT imaging applications require adjustment of the profile of the x‐ray fluence incident on a patient as a function of view angle. Since current FFMCT prototypes can theoretically take on an infinite number of configurations, measuring a calibration data set for all possible positions would not be feasible. The present work details a methodology for calculating an atlas of configurations that will span all likely body regions, patient sizes, patient positioning, and imaging modes. The hypothesis is that there exists a finite number of unique modulator configurations that effectively span the infinite number of possible fluence profiles with minimal loss in performance.Methods:CT images of a head, shoulder, thorax, abdominal, wrist, and leg anatomical slices were dilated and contracted to model small, medium, and large sized patients. Additionally, the images were positioned from iso‐center by three different amounts. The modulator configurations required to compensate for each image were computed assuming a FFMCT prototype, digital beam attenuator, (DBA), was set to equalize the detector exposure. Each atlas configuration should be different from the other atlas configurations. The degree of difference was quantified using the sum of the absolute differences in filter thickness between configurations. Using this metric, a set of unique wedge configurations for which no two configurations have a metric value smaller than some threshold can be constructed. Differences in the total number of incident photons between the unconstrained filters and the atlas were studied as a function of the number of atlas positions for each anatomical site and size/off‐centering combination.Results:By varying the threshold used in creating the atlas, it was found that roughly 322 atlas positions provided an incident number of photons within 20% of using 19 440 unique filters (the number of atlas entries ranged from 7213 to 1). Additionally, for VOI applications implemented with a single VOI region, the number of required filter configurations was expressed in a simple closed form solution.Conclusions:The methodology proposed in this work will enable DBA‐FFMCT and DBA‐VOI imaging in the clinic without the need for patient specific air‐scans to be performed. In addition, the methodology proposed here is directly applicable to other modulator designs such as piecewise linear, TomoTherapy multi leaf collimators, 2D fluid arrays, and inverse geometry CT.
Draft Genome Sequences of 33 Salmonella enterica Clinical and Wildlife Isolates from Chile
Authors: Toro Magaly , Retamal Patricio , Allard Marc , Brown Eric W. , Evans Peter , Gonzalez-Escalona Narjol 
Published: March 2015

ABSTRACT

Salmonella enterica
causes health problem worldwide. The relationships among strains that are from the same serotype but different hosts, countries, and continents remain elusive. Few genome sequences are available from
S. enterica
isolates from South America. Therefore, we sequenced the genomes of 33 strains from diverse sources isolated in Chile and determined that they were of different serotypes. These genomes will improve phylogenetic analysis of Salmonella strains from Chile and the rest of South America.
Complete Genome Sequence of Raoultella ornithinolytica Strain S12, a Lignin-Degrading Bacterium Isolated from Forest Soil
Authors: Bao Wenying , Zhou Yun , Jiang Jingwei , Xu Zhihui , Hou Liyuan , Leung Frederick Chi-Ching 
Published: March 2015

ABSTRACT

We report the complete genome sequence of
Raoultella ornithinolytica
strain S12, isolated from a soil sample collected from areas bordering rotten wood and wet soil on Mt. Zijin, Nanjing. The complete genome of this bacterium may contribute toward the discovery of efficient lignin-degrading pathways.
Draft Genome Sequence of Thauera sp. Strain SWB20, Isolated from a Singapore Wastewater Treatment Facility Using Gel Microdroplets
Authors: Dichosa Armand E. K. , Davenport Karen W. , Li Po-E , Ahmed Sanaa A. , Daligault Hajnalka , Gleasner Cheryl D. , Kunde Yuliya , McMurry Kim , Lo Chien-Chi , Reitenga Krista G. , Daughton Ashlynn R. , Shen Xiaohong , Frietze Seth , Wang Dongping , Johnson Shannon L. , Drautz-Moses Daniela I. , Schuster Stephan , Chain Patrick S. , Han Cliff 
Published: March 2015

ABSTRACT
We report here the genome sequence of Thauera sp. strain SWB20, isolated from a Singaporean wastewater treatment facility using gel microdroplets (GMDs) and single-cell genomics (SCG). This approach provided a single clonal microcolony that was sufficient to obtain a 4.9-Mbp genome assembly of an ecologically relevant Thauera species.
Complete Genome Sequence of Escherichia coli Strain BL21
Authors: Jeong Haeyoung , Kim Hyun Ju , Lee Sang Jun 
Published: March 2015

ABSTRACT

Escherichia coli
strain BL21 is one of the widely used bacterial hosts for high-level recombinant protein production and for other applications. Here, we present the complete genome sequence of a commercial version of the
Escherichia coli
BL21 strain.
Draft Genome Sequence of Lactobacillus kunkeei AR114 Isolated from Honey Bee Gut
Authors: Porcellato Davide , Frantzen Cyril , Rangberg Anbjørg , Umu Ozgun C. , Gabrielsen Christina , Nes Ingolf F. , Amdam Gro V. , Diep Dzung B. 
Published: March 2015

ABSTRACT

Lactobacillus kunkeei
is a common inhabitant in honey bee gut, being present in several parts of the world. Here, we describe the draft genome of L. kunkeei AR114, an isolate from late foraging season in Norway.
Complete Genome Sequence of the Persistent Listeria monocytogenes Strain R479a
Authors: Schmitz-Esser Stephan , Gram Lone , Wagner Martin 
Published: March 2015

ABSTRACT

The complete genome sequence of the persistent
Listeria monocytogenes
strain R479a isolated from smoked salmon in Denmark and belonging to lineage II, serovar 1/2a, and multilocus sequence type 8 (ST8) is presented here.
Resource management and a Best Available Concept for aggregate sustainability
Authors: Danielsen S. W. , Kuznetsova E. 
Published: March 2015

Abstract
Aggregates are major constituents in construction, the global demand for which approaches some 22 billion tonnes per year. Some major challenges follow: firstly, the dependency on geological conditions and the availability of resources; secondly, the traffic, emissions and energy use connected with transportation; thirdly, the technology of utilizing resources with a variety of properties to meet user requirements; and finally, the need for increased awareness, particularly over issues like land-use conflicts, environmental impact of the aggregate and quarrying industry, and the need to make these activities sustainable.
Aggregate standards have primarily been written by engineers, and engineers are first of all concerned with technical requirements. However, in the future, there will be a greater focus on environmental impact and sustainability.
Geological resources are non-renewable, which, for example, can be seen in the rapid depletion of natural sand/gravel deposits. This causes increasing awareness along with environmental impact, conflicts of interest concerning land use, sustainability in mass balance and – not least – increasing transport distances required to get the materials to the places of use.
The principle of a Best Available Concept (BAC) for aggregate production and use is introduced, working with four essential phases: inventory and planning; quarrying and production; use of aggregates; and reclamation of mined-out areas. In order to compare alternatives and calculate environmental and economic consequences of decisions, it is recommended that new LCC (Life Cycle Cost) and LCA (Life Cycle Assessment) tools are worked with, which have been recently developed in two EU (European Union) funded research projects.
Microenvironmental Remodeling as a Parameter and Prognostic Factor of Heterogeneous Leukemogenesis in Acute Myelogenous Leukemia
Authors: Kim Jin-A , Shim Jae-Seung , Lee Ga-Young , Yim Hyeon Woo , Kim Tae-Min , Kim Myungshin , Leem Sun-Hee , Lee Jong-Wook , Min Chang-Ki , Oh Il-Hoan 
Published: March 2015

Abstract
Acute myelogenous leukemia (AML) is a heterogeneous disorder characterized by clonal proliferation of stem cell-like blasts in bone marrow (BM); however, their unique cellular interaction within the BM microenvironment and its functional significance remain unclear. Here, we assessed the BM microenvironment of AML patients and demonstrate that the leukemia stem cells induce a change in the transcriptional programming of the normal mesenchymal stromal cells (MSC). The modified leukemic niche alters the expressions of cross-talk molecules (i.e., CXCL12 and JAG1) in MSCs to provide a distinct cross-talk between normal and leukemia cells, selectively suppressing normal primitive hematopoietic cells while supporting leukemogenesis and chemoresistance. Of note, AML patients exhibited distinct heterogeneity in the alteration of mesenchymal stroma in BM. The distinct pattern of stromal changes in leukemic BM at initial diagnosis was associated with a heterogeneous posttreatment clinical course with respect to the maintenance of complete remission for 5 to 8 years and early or late relapse. Thus, remodeling of mesenchymal niche by leukemia cells is an intrinsic self-reinforcing process of leukemogenesis that can be a parameter for the heterogeneity in the clinical course of leukemia and hence serve as a potential prognostic factor. Cancer Res; 75(11); 2222–31. ©2015 AACR.
De Novo Mutation in X-Linked Hearing Loss–Associated POU3F4 in a Sporadic Case of Congenital Hearing Loss
Authors: Moteki Hideaki , Shearer A. Eliot , Izumi Shuji , Kubota Yamato , Azaiez Hela , Booth Kevin T. , Sloan Christina M. , Kolbe Diana L. , Smith Richard J. H. , Usami Shin-ichi 
Published: March 2015

Objectives: In this report, we present a male patient with no family history of hearing loss, in whom we identified a novel de novo mutation in the POU3F4 gene. Methods: One hundred ninety-four (194) Japanese subjects from unrelated and nonconsanguineous families were enrolled in this study. We used targeted genomic enrichment and massively parallel sequencing of all known nonsyndromic hearing loss genes for identifying the genetic causes of hearing loss. Results: A novel de novo frameshift mutation of POU3F4 to c.727_728insA (p.N244KfsX26) was identified. The patient was a 7-year-old male with congenital progressive hearing loss and inner ear deformity. Although the patient had received a cochlear implant, auditory skills were still limited. The patient also exhibited developmental delays similar to those previously associated with POU3F4 mutation. Conclusion: This is the first report of a mutation in POU3F4 causing hearing loss in a Japanese patient without a family history of hearing loss. This study underscores the importance of comprehensive genetic testing of patients with hearing loss for providing accurate prognostic information and guiding the optimal management of patient rehabilitation.
Mutations in the MYO15A Gene Are a Significant Cause of Nonsyndromic Hearing Loss
Authors: Miyagawa Maiko , Nishio Shin-ya , Hattori Mitsuru , Moteki Hideaki , Kobayashi Yumiko , Sato Hiroaki , Watanabe Tomoo , Naito Yasushi , Oshikawa Chie , Usami Shin-ichi 
Published: March 2015

Objectives: Screening for MYO15A mutations was carried out using a large cohort to clarify the frequency and clinical characteristics of patients with MYO15A (DFNB3) mutations in a hearing loss population. Methods: Genetic analysis of 63 previously reported deafness genes based on massively parallel DNA sequencing (MPS) in 1120 Japanese hearing loss patients from 53 otorhinolaryngology departments was performed. Detailed clinical features of the patients with MYO15A mutations were then collected and analyzed. Results: Eleven patients from 10 families were found to have compound heterozygosity for MYO15A. Audiograms showed profound or high frequency hearing loss, with some patients showing progressive hearing loss. Age at onset was found to vary from 0 to 14 years, which seemed to be associated with the mutation. Four children underwent bilateral cochlear implantation for congenital hearing loss, with all showing good results. Conclusion: Mutations in the MYO15A gene are a notable cause of nonsyndromic hearing loss. MPS technology successfully detected mutations in relatively rare deafness genes such as MYO15A.
Virtue ethics – an old answer to a new dilemma? Part 2. The case for inclusive virtue ethics
Authors: Misselbrook David 
Published: March 2015

Summary While Principlism is a widely accepted consensus statement for ethics, the moral theory that underpins it faces serious challenges. This two-part paper proposes a version of virtue theory as a more grounded system of moral analysis. Part 2 examines the role of basic moral theory as the foundation to ethics and suggests how virtue theory can be used as a central framework for ethics while being inclusive of insights from deontology and consequentialism.
Vestibular Schwannoma Excision in Sporadic versus Neurofibromatosis Type 2 Populations
Authors: Mahboubi Hossein , Maducdoc Marlon M. , Yau Amy Y. , Ziai Kasra , Ghavami Yaser , Badran Karam W. , Al‐Thobaiti Majid , Brandon Bryan , Djalilian Hamid R. 
Published: March 2015

ObjectiveTo understand the differences in characteristics of neurofibromatosis type 2 (NF2) and sporadic patients with surgically excised vestibular schwannomas in the state of California.Study DesignCross‐sectional.Setting, Subjects, and MethodsThe records of all patients who underwent vestibular schwannoma excision between 1997 and 2011 were extracted from the California Hospital Inpatient Discharge Databases (CHIDD). NF2 cases were identified using ICD‐9‐CM diagnosis code 237.72, neurofibromatosis, type 2. All other cases were recoded as sporadic. Trends in total number and population‐adjusted rates (per 1 million California residents) of surgery, demographics, hospital case volume, state of residency, complications, length of stay, total charges, expected source of payment, and disposition were examined.ResultsVestibular schwannoma (VS) excision was performed on 7017 patients, of which 464 patients (6.6%) had NF2. The population‐adjusted surgery rate declined from 11.8 to 6.2 (P <. 001) for sporadic cases and from 0.3 to 0.2 (P =. 01) for NF2 cases over the study period. NF2 was associated with younger age (mean, 32.9 vs 51.3), higher rate of other complications (8.8% vs 4.4%) and facial nerve complications (32.3% vs 16.8%), higher total charges (median $70,106 vs $46,395), longer stay (median 5 vs 4), and high volume hospitals (80.4% vs 48.8%) (all P <. 001).ConclusionThe surgery rates for vestibular schwannoma excision for both sporadic and NF2 patients have declined, but the decline is more prominent for sporadic cases. NF2 patients tend to be younger and have a longer hospitalization and possibly higher corresponding hospital charges compared to patients with sporadic VS.
Dental pulp tissue engineering with bFGF-incorporated silk fibroin scaffolds
Authors: Yang Jing-wen , Zhang Yu-feng , Sun Zhe-yi , Song Guang-tai , Chen Zhi 
Published: March 2015

The clinical translation of regenerative endodontics demands further development of suitable scaffolds. Here, we assessed the possibility of using silk fibroin scaffold for pulp regeneration with dental pulp stem cells (DPSCs) and basic fibroblast growth factor (bFGF) in ectopic root canal transplantation model. Porous silk fibroin scaffolds were fabricated using freeze-drying technique (with or without bFGF incorporation), and characterized by scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy. DPSCs were isolated, characterized, seeded onto scaffolds, and inserted into the tooth root fragments. Cell viability and morphology were tested in the 3D model in vitro using CCK8 assay and SEM. Furthermore, the ectopic transplantation model was used to verify the generation of pulp-like tissue in DPSCs seeded silk fibroin scaffold with bFGF, as examined by histological analysis. DPSCs seeded in silk fibroin scaffold survived, exhibited cytoplasmic elongation in scaffolds at least 4 weeks in culture. bFGF promoted DPSCs viability in tooth fragments/scaffolds (TSS) between 7 and 28 days. Pulp-like tissue was generated in the bFGF-incorporated TSS with DPSCs. Histologically, the generated tissue was shown to be with well vascularity, have new matrix deposition and dentin-like tissue formation, and consist of both the transplanted and host-derived cells. Collectively, these data support the use of bFGF-incorporated silk fibroin scaffold as a highly promising scaffold candidate for future treatment concepts in regenerative endodontics to save teeth.
Corticospinal tract integrity is related to primary motor cortex thinning in relapsing–remitting multiple sclerosis
Authors: Bergsland Niels , Laganà Maria Marcella , Tavazzi Eleonora , Caffini Matteo , Tortorella Paola , Baglio Francesca , Baselli Giuseppe , Rovaris Marco 
Published: March 2015

Background: The relationship between white matter injury and cortical atrophy development in relapsing–remitting multiple sclerosis (RRMS) remains unclear. Objectives: To investigate the associations between corticospinal tract integrity and cortical morphology measures of the primary motor cortex in RRMS patients and healthy controls. Methods: 51 RRMS patients and 30 healthy controls underwent MRI examination for cortical reconstruction and assessment of corticospinal tract integrity. Partial correlation and multiple linear regression analyses were used to investigate the associations of focal and normal appearing white matter (NAWM) injury of the corticospinal tract with thickness and surface area measures of the primary motor cortex. Relationships between MRI measures and clinical disability as assessed by the Expanded Disability Status Scale and disease duration were also investigated. Results: In patients only, decreased cortical thickness was related to increased corticospinal tract NAWM mean, axial and radial diffusivities in addition to corticospinal tract lesion volume. The final multiple linear regression model for PMC thickness retained only NAWM axial diffusivity as a significant predictor (adjusted R2= 0.270, p= 0.001). Clinical measures were associated with NAWM corticospinal tract integrity measures. Conclusions: Primary motor cortex thinning in RRMS is related to alterations in connected white matter and is best explained by decreased NAWM integrity.
Potential Benefits from Heating the High-Dose rtPA Boluses Used in Catheter-Directed Thrombolysis for Acute/Subacute Lower Limb Ischemia
Authors: Tsetis Dimitrios K. , Katsamouris Asterios N. , Giannoukas Athanasios D. , Hatzidakis Adam A. , Kostas Theodoros , Chamalakis Konstantinos , Ioannou Christos , Gourtsoyiannis Nicholas C. 
Published: March 2015

Purpose: To explore the potential benefits from heating recombinant tissue plasminogen activator (rtPA) before catheter-directed thrombolysis in patients with lower-limb ischemia of <30 days' duration. Methods: Over a 2-year period, 34 patients (26 men; mean age 63.5 years, range 39–80) with 10 iliac and 24 infrainguinal arterial occlusions (5 embolic and 29 thrombotic) were treated with two 5-mg boluses of rtPA injected into the proximal clot, followed by 2 additional 5-mg boluses of rtPA. In the first 18 patients (group A), room temperature rtPA was administered, whereas in the last 16 patients (group B), the rtPA boluses were heated to 38°C for 30 minutes before injection. Residual thrombus was treated with a continuous infusion of 2.5 mg/h of rtPA for 4 hours then at a reduced dose (1 mg/h). Results: Successful thrombolysis was achieved in 28 (82%) arteries. Unmasked lesions were treated with balloon angioplasty/stenting in 17 cases and with surgery in 4. One fatal retroperitoneal hematoma occurred in group A. Heating the rtPA did not significantly alter the outcome of thrombolysis. However, a statistically significant reduction in the total rtPA dose was observed in group B (24.28 mg versus 27.9 mg in group A, p = 0.05), as well as quicker lysis (2 hours, 42 minutes versus 6 hours, 12 minutes in group A, p = 0.001). There was no statistical difference in the amputation-free survival at 30 days between the groups. Conclusions: In patients with acute or subacute lower limb ischemia treated with catheter-directed thrombolysis, heating the rtPA results in faster lysis with a considerable reduction in the total dose of the lytic agent.
Open versus Endovascular Repair of Para-Anastomotic Aneurysms in Patients Who Were Morphological Candidates for Endovascular Treatment
Authors: Gawenda Michael , Zaehringer Markus , Brunkwall Jan 
Published: March 2015

Purpose: To compare the outcomes of open versus endovascular repair of para-anastomotic aneurysms (PAA) in the aortic and iliac arteries in a cohort of patients who fulfilled morphological criteria for endovascular repair. Methods: A retrospective review of 31 consecutive patients with PAA treated between 1985 and 2002 identified 26 (84%) patients who would have been candidates for endovascular repair based on preoperative computed tomography and angiography. Of these 26 patients, 10 (9 men; median age 65 years, range 60–75) underwent endovascular repair; the remaining 16 patients (14 men; median age 61.5 years, range 49–78) had open repair. The baseline data and outcome measures were compared between the treatment groups. Results: The patient groups were well matched for age, sex, weight, risk factors, comorbidities, aneurysm length, and elapsed time from initial graft placement. Both groups had technically successful PAA repairs; however, median blood loss (300 versus 1000 mL; p = 0.05) and procedural time (100 versus 215 minutes; p<0.001) were significantly reduced in the endovascular group. Median transfusion volume was significantly greater (1000 versus 0 mL; p = 0.01) in the surgically treated patients. The median stay in ICU was similar (18 versus 24 hours in the surgical cohort). Length of stay was significantly shorter in the endovascular group: 7.5 versus 17.0 days (p = 0.001) after the repair and 11 versus 22 days (p = 0.01) for overall hospitalization. One (10%) patient in the endovascular group died from a myocardial infarction on the third postoperative day. In the open group, there were 3 (19%) procedure-related deaths. Conclusions: Patients with PAA who were endograft candidates but who were treated with open repair experienced more morbidity and had more complications than patients treated with stent-grafts. If long-term follow-up demonstrates durable results, stent-graft repair may become the therapy of choice in PAAs.