bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prospective Assessment of the Oncogenic Risk to Patients From Fluoroscopy During Trauma Surgery
Authors: Beebe Michael J. , Jenkins Peter , Rothberg David L. , Kubiak Erik N. , Higgins Thomas F. 
Published: January 2016

Objective:
Concern about radiation exposure during surgery has focused on surgeon exposure. However, the patient receives exposure that is more direct and, in surgery about the pelvis and hip, internal pelvic nonskeletal organs often cannot be shielded without obscuring the region of surgical interest. The purpose of this study was to prospectively evaluate patients' radiation exposure during fracture surgery of the acetabulum, pelvic ring, and femur to calculate future cancer incidence (CI).

Design:
Prospective descriptive cohort.

Setting:
Level-1 trauma center.

Patients/Participants:
One hundred eight patients with acetabulum, pelvic, or femur fractures requiring operative repair were prospectively enrolled.

Intervention:
Dosimeters were placed in locations determined for each surgery type by a medical physicist.

Main Outcome Measurements:
Demographics, operative records, and average x-ray emission energy were recorded. Effective dose, specific organ doses, and lifetime CI for a 30-year-old patient were calculated.

Results:
Diagnoses included 27 acetabular fractures, 30 intertrochanteric femur fractures, 26 femoral shafts, and 25 pelvic ring injuries. Patients with pelvic ring injuries received the highest effective dose at 0.91 ± 0.74 mSv. The average lifetime increase in CI, for any cancer type, after pelvic ring fixation is 0.0097% for females and 0.0062% for males. The greatest mean single-organ dose to the ovaries (3.82 ± 3.34 mGy) occurred during pelvic ring surgery, correlating to an increased ovarian cancer risk of 0.0013%. The greatest mean single-organ dose to the prostate (6.81 ± 5.91 mSv) also occurred during pelvic surgery, correlating to increased prostate cancer risk of 0.0024%.

Conclusions:
Fracture surgery to the pelvis and femur is exceptionally fluoroscopy-dependent; however, the radiation exposure incurred represents a relatively small increased risk of future cancer development in patients.

Level of Evidence:
Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.
Intramedullary Nailing of Tibial Shaft Fractures: Size Matters
Authors: Donegan Derek J. , Akinleye Sheriff , Taylor Ryan M. , Baldwin Keith , Mehta Samir 
Published: January 2016

Objectives:
To determine optimal ratio of intramedullary nail diameter to tibial canal diameter that leads to reliable and timely healing in tibial shaft fractures.

Design:
Retrospective case series.

Setting:
Level I trauma center.

Patients:
One hundred thirty-three fractures in 132 patients with tibial shaft fractures that underwent intramedullary nailing as definitive fixation were identified between June 2004 and July 2012 at our level I trauma center. Of these, 78 had serial radiographs out to 12 months that could be analyzed for radiographic healing with an average age of 37 years old (range 16–86 years). There were 52 males and 26 females.

Intervention:
All patients underwent intramedullary nailing of the tibia with documentation of both the diameter of the nail and radiographic canal width at the isthmus to determine the nail to canal ratio.

Main Outcome Measures:
Patients were followed with serial radiographs for at least 12 months to determine time to healing as a function of nail to canal ratio. The senior author assessed healing at 3, 6, 9, and 12 months using RUST criteria.

Results:
Patients with an intramedullary nail to canal diameter ratio of less than 0.8 or greater than 0.99 were 4.4 times more likely not to heal than patients with a ratio of between 0.8 and 0.99.

Conclusion:
The ideal intramedullary nail to tibial canal diameter ratio to optimize tibial shaft fracture healing is between 0.8 and 0.99.

Level of Evidence:
Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
Focused Critical Care Echocardiography: Development and Evaluation of an Image Acquisition Assessment Tool*
Authors: Gaudet Jonathan , Waechter Jason , McLaughlin Kevin , Ferland André , Godinez Tomás , Bands Colin , Boucher Paul , Lockyer Jocelyn 
Published: January 2016

Objectives:
Little attention has been placed on assessment tools to evaluate image acquisition quality for focused critical care echocardiography. We designed a novel assessment tool to objectively evaluate the image acquisition skills of critical care trainees learning focused critical care echocardiography and examined the tool for evidence of validity.

Design:
Prospective observational study.

Setting:
Medical-surgical ICUs at a tertiary care teaching hospital.

Subjects:
Trainees in our critical care medicine fellowship program.

Interventions:
Six trainees completed a focused critical care echocardiography training curriculum followed by performing 20 transthoracic echocardiograms on patients receiving invasive mechanical ventilation. At three assessment intervals (the 1st and 2nd examinations, 10th and 11th examinations, and 19th and 20th examinations), echocardiograms performed by trainees were compared with those of critical care physicians certified in echocardiography and scored according to the focused critical care echocardiography assessment tool. The primary outcome was an efficiency score (overall assessment tool score divided by examination time). Differences in mean efficiency scores between echocardiographers of differing skill levels and changes in trainees’ mean efficiency scores with increasing focused critical care echocardiography experience were compared by using t tests.

Measurements and Main Results:
On the initial assessment, mean efficiency scores (sd) for trainees and experienced physicians were 1.55 (0.95) versus 2.78 (1.38), respectively (p = 0.02), and for the second and third assessments, the corresponding efficiency ratings for trainees and experienced physicians were 2.48 (0.97) versus 4.55 (1.32) (p < 0.01) and 2.61 (1.37) versus 4.17 (2.12) (p = 0.04), respectively.

Conclusions:
Trainees’ efficiency in focused critical care echocardiography image acquisition improved quickly in the first 10 studies, yet, it could not match with the performance of experienced physicians after 20 focused critical care echocardiography studies. The focused critical care echocardiography assessment tool demonstrated evidence of validity and could discern changes in trainees’ image acquisition performance with increasing experience.
SUCCESSFUL REPAIR OF RECURRENT OPTIC DISK PIT MACULOPATHY WITH AUTOLOGOUS PLATELET RICH PLASMA: REPORT OF A SURGICAL TECHNIQUE
Authors: Todorich Bozho , Sharma Sumit , Vajzovic Lejla 
Published: January 2016

Purpose:
To describe vitreoretinal surgical technique of using autologous platelet-rich plasma to aid in surgical repair of optic pit maculopathy refractive to previous vitrectomy.

Methods:
A case of an 18-year-old woman presenting with serous macular detachment secondary to optic pit is reported. Patient had previously undergone vitrectomy and peripapillary laser, but had recurrence of subretinal fluid and worsening visual acuity. Autologous platelet-rich plasma was harvested from the patient's blood and purified using Arthrex ACP kit (Arthrex, Inc, Naples, FL). Repeat pars plana vitrectomy was performed with internal limiting membrane peeling extending to the optic nerve. Platelet-rich plasma was layered over the pit and long-acting gas tamponade performed with face-down positioning.

Results:
At 8 months of follow-up, subretinal fluid was resolved, the connection between optic pit and subretinal space collapsed and the ellipsoid zone near completely reconstituted on optical coherence tomography. The patient's vision improved significantly from 20/100 to 20/50, which is largely limited by posterior subcapsular cataract.

Conclusion:
Platelet-rich plasma can augment anatomical and visual outcomes in surgical repair of optic pit maculopathy.
SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments
Authors: Page Andrew J. , Taylor Ben , Delaney Aidan J. , Soares Jorge , Seemann Torsten , Keane Jacqueline A. , Harris Simon R. 
Published: January 2016

ABSTRACTRapidly decreasing genome sequencing costs have led to a proportionate increase in the number of samples used in prokaryotic population studies. Extracting single nucleotide polymorphisms (SNPs) from a large whole genome alignment is now a routine task, but existing tools have failed to scale efficiently with the increased size of studies. These tools are slow, memory inefficient and are installed through non-standard procedures. We presentSNP-siteswhich can rapidly extract SNPs from a multi-FASTA alignment using modest resources and can output results in multiple formats for downstream analysis. SNPs can be extracted from a 8.3 GB alignment file (1,842 taxa, 22,618 sites) in 267 seconds using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers. It is easy to install through the Debian and Homebrew package managers, and has been successfully tested on more than 20 operating systems.SNP-sitesis implemented in C and is available under the open source license GNU GPL version 3.
ELF3 polyQ variation inArabidopsis thalianareveals PIF4-independent role in thermoresponsive flowering
Authors: Press Maximilian O. , Lanctot Amy , Queitsch Christine 
Published: January 2016

ABSTRACTPlants have evolved elaborate mechanisms controlling developmental responses to environmental stimuli. A particularly important stimulus is temperature. Previous work has identified the interplay of PIF4 and ELF3 as a central circuit underlying thermal responses inArabidopsis thaliana. However, thermal responses vary widely among strains, possibly offering mechanistic insights into the wiring of this circuit. ELF3 contains a polyglutamine (polyQ) tract that is crucial for ELF3 function and varies in length across strains. Here, we use transgenic analysis to test the hypothesis that natural polyQ variation in ELF3 is associated with the observed natural variation in thermomorphogenesis. We found little evidence that the polyQ tract plays a specific role in thermal responses beyond modulating general ELF3 function. Instead, we made the serendipitous discovery that ELF3 plays a crucial, PIF4-independent role in thermoresponsive flowering under conditions more likely to reflect field conditions. We present evidence that ELF3 acts through the photoperiodic pathway, pointing to a previously unknown symmetry between low and high ambient temperature responses. Moreover, in analyzing two strain backgrounds with vastly different thermal responses, we demonstrate that responses may be shifted rather than fundamentally rewired across strains. Our findings tie together disparate observations into a coherent framework in which multiple pathways converge in accelerating flowering in response to temperature, with some such pathways modulated by photoperiod.
Dynamic Distribution and Interaction of the Arabidopsis SRSF1 Subfamily Splicing Factors
Authors: Stankovic Nancy , Schloesser Marie , Joris Marine , Sauvage Eric , Hanikenne Marc , Motte Patrick 
Published: January 2016

Abstract
Ser/Arg-rich (SR) proteins are essential nucleus-localized splicing factors. Our prior studies showed that Arabidopsis (Arabidopsis thaliana) RSZ22, a homolog of the human SRSF7 SR factor, exits the nucleus through two pathways, either dependent or independent on the XPO1 receptor. Here, we examined the expression profiles and shuttling dynamics of the Arabidopsis SRSF1 subfamily (SR30, SR34, SR34a, and SR34b) under control of their endogenous promoter in Arabidopsis and in transient expression assay. Due to its rapid nucleocytoplasmic shuttling and high expression level in transient assay, we analyzed the multiple determinants that regulate the localization and shuttling dynamics of SR34. By site-directed mutagenesis of SR34 RNA-binding sequences and Arg/Ser-rich (RS) domain, we further show that functional RRM1 or RRM2 are dispensable for the exclusive protein nuclear localization and speckle-like distribution. However, mutations of both RRMs induced aggregation of the protein whereas mutation in the RS domain decreased the stability of the protein and suppressed its nuclear accumulation. Furthermore, the RNA-binding motif mutants are defective for their export through the XPO1 (CRM1/Exportin-1) receptor pathway, but retain nucleocytoplasmic mobility. We performed a yeast two hybrid screen with SR34 as bait and discovered SR45 as a new interactor. SR45 is an unusual SR splicing factor bearing two RS domains. These interactions were confirmed in planta by FLIM-FRET and BiFC and the roles of SR34 domains in protein-protein interactions were further studied. Altogether, our report extends our understanding of shuttling dynamics of Arabidopsis SR splicing factors.
The Physiology of Adventitious Roots
Authors: Steffens Bianka , Rasmussen Amanda 
Published: January 2016

AbstractAdventitious roots are plant roots that form from any nonroot tissue and are produced both during normal development (crown roots on cereals and nodal roots on strawberry [Fragaria spp.]) and in response to stress conditions, such as flooding, nutrient deprivation, and wounding. They are important economically (for cuttings and food production), ecologically (environmental stress response), and for human existence (food production). To improve sustainable food production under environmentally extreme conditions, it is important to understand the adventitious root development of crops both in normal and stressed conditions. Therefore, understanding the regulation and physiology of adventitious root formation is critical for breeding programs. Recent work shows that different adventitious root types are regulated differently, and here, we propose clear definitions of these classes. We use three case studies to summarize the physiology of adventitious root development in response to flooding (case study 1), nutrient deficiency (case study 2), and wounding (case study 3).
Engineering Triterpene and Methylated Triterpene Production in Plants Provides Biochemical and Physiological Insights into Terpene Metabolism
Authors: Jiang Zuodong , Kempinski Chase , Bush Caroline J. , Nybo S. Eric , Chappell Joe 
Published: January 2016

Abstract
Linear, branch-chained triterpenes, including squalene (C30), botryococcene (C30), and their methylated derivatives (C31–C37), generated by the green alga Botryococcus braunii race B have received significant attention because of their utility as chemical and biofuel feedstocks. However, the slow growth habit of B. braunii makes it impractical as a production system. In this study, we evaluated the potential of generating high levels of botryococcene in tobacco (Nicotiana tabacum) plants by diverting carbon flux from the cytosolic mevalonate pathway or the plastidic methylerythritol phosphate pathway by the targeted overexpression of an avian farnesyl diphosphate synthase along with two versions of botryococcene synthases. Up to 544 µg g−1 fresh weight of botryococcene was achieved when this metabolism was directed to the chloroplasts, which is approximately 90 times greater than that accumulating in plants engineered for cytosolic production. To test if methylated triterpenes could be produced in tobacco, we also engineered triterpene methyltransferases (TMTs) from B. braunii into wild-type plants and transgenic lines selected for high-level triterpene accumulation. Up to 91% of the total triterpene contents could be converted to methylated forms (C31 and C32) by cotargeting the TMTs and triterpene biosynthesis to the chloroplasts, whereas only 4% to 14% of total triterpenes were methylated when this metabolism was directed to the cytoplasm. When the TMTs were overexpressed in the cytoplasm of wild-type plants, up to 72% of the total squalene was methylated, and total triterpene (C30+C31+C32) content was elevated 7-fold. Altogether, these results point to innate mechanisms controlling metabolite fluxes, including a homeostatic role for squalene.
THI1, a Thiamine Thiazole Synthase, Interacts with Ca2+-Dependent Protein Kinase CPK33 and Modulates the S-Type Anion Channels and Stomatal Closure in Arabidopsis
Authors: Li Chun-Long , Wang Mei , Wu Xiao-Meng , Chen Dong-Hua , Lv Hong-Jun , Shen Jian-Lin , Qiao Zhu , Zhang Wei 
Published: January 2016

Abstract
Thiamine is required for both plant growth and development. Here, the involvement of a thiamine thiazole synthase, THI1, has been demonstrated in both guard cell abscisic acid (ABA) signaling and the drought response in Arabidopsis (Arabidopsis thaliana). THI1 overexpressors proved to be more sensitive to ABA than the wild type with respect to both the activation of guard cell slow type anion channels and stomatal closure; this effectively reduced the rate of water loss from the plant and thereby enhanced its level of drought tolerance. A yeast two-hybrid strategy was used to screen a cDNA library from epidermal strips of leaves for THI1 regulatory factors, and identified CPK33, a Ca2+-dependent protein kinase, as interactor with THI1 in a plasma membrane-delimited manner. Loss-of-function cpk33 mutants were hypersensitive to ABA activation of slow type anion channels and ABA-induced stomatal closure, while the CPK33 overexpression lines showed opposite phenotypes. CPK33 kinase activity was essential for ABA-induced stomatal closure. Consistent with their contrasting regulatory role over stomatal closure, THI1 suppressed CPK33 kinase activity in vitro. Together, our data reveal a novel regulatory role of thiamine thiazole synthase to kinase activity in guard cell signaling.
A higher frequency of IL‐10‐producing B cells in Hepatitis B virus‐associated membranous nephropathy
Authors: Liu Yong , Wang Haifeng , Hu Xintong , Qu Zhihui , Zhang Huimao , Crew Rebecca , Ayana Desalegn Admassu , Li Man , Qiu Jinpeng , Jiang Yanfang 
Published: January 2016

SummaryThe purpose of this study is to elucidate the potential role of interleukin (IL)‐10+ regulatory B cells and other B cell subsets in the development of hepatitis B virus‐associated membranous nephropathy (HBV‐MN). A total of 14 patients with new onset HBV‐MN, 12 individuals with immune‐tolerant HBV infection (HBV‐IT), and 12 healthy controls (HC) were examined for the percentages of CD38+, CD86+, CD27+, CD95+ and IL‐10+ B cells by flow cytometry. Serum IL‐10 concentration was examined by enzyme‐linked immunosorbent assay (ELISA). The percentages of CD38+CD19+, CD86+CD19+, CD38+CD86+CD19+, and CD95+CD19+ B cells were significantly higher in HBV‐MN patients than the HBV‐IT and HC. The percentages of CD5+CD19+, IL‐10+CD19+ B cells and serum IL‐10 level in HBV‐MN patients were significantly higher than the HC, and lower than the HBV‐IT. Percentages of CD38+CD19+, and CD86+CD19+ B cells were reduced after treatment, while the percentages of CD5+CD1d+CD19+, CD5+CD1d+IL‐10+CD19+, and IL‐10+CD19+ B cells were increased. The 24 h urinary protein concentration was positively correlated with the percentage of CD38+CD19+, and negatively correlated with the percentage of IL‐10+CD19+ B cells and serum IL‐10 level. Similarly, the value of eGFR was negatively correlated with the percentage of CD38+CD19+, and positively correlated with the percentage of IL‐10+CD19+ B cells and serum IL‐10 level. Serum IL‐10 level and the percentage of IL‐10+CD19+ were negatively correlated with the percentages of CD38+CD19+, and CD86+CD19+ B cells. These results suggest that CD86+CD19+, CD38+CD86+CD19+, CD95+CD19+, and especially CD38+CD19+ and IL‐10+CD19+ cells may participate in the pathogenesis of HBV‐MN.
Effects of sample design and landscape features on a measure of environmental heterogeneity
Authors: Christianson Danielle S. , Kaufman Cari G. 
Published: January 2016

Summary

Environmental heterogeneity, an important influence on organisms and ecological processes, can be quantified by the variance of an environmental characteristic over all locations within a study extent. However on landscapes with autocorrelation and gradient patterns, estimating this variance from a sample of locations may lead to errors that cannot be corrected with statistical techniques.

We analytically derived the relative expected sampling error of sample designs on landscapes with particular gradient pattern and autocorrelation features. We applied this closed‐form approach to temperature observations from an existing study. The expected heterogeneity differed, both in magnitude and direction, amongst sample designs over the study site's likely range of autocorrelation and gradient features.

We conducted a simulation study to understand the effects of (i) landscape variability and (ii) design variability on an average sampling error. On 10 000 simulated landscapes with varying gradient and autocorrelation features, we compared estimates of variance from a variety of structured and random sample designs. While gradient patterns and autocorrelation cause large errors for some designs, others yield near‐zero average sampling error. Sample location spacing is a key factor in sample design performance. Random designs have larger range of possible sampling errors than structured designs due to the potential for sample arrangements that over‐ and under‐sample certain areas of the landscape.

When implementing a new sample design to quantify environmental heterogeneity via variance, we recommend using a simple structured design with appropriate sample spacing. For existing designs, we recommend calculating the relative expected sampling error via our analytical derivation.
Childhood trauma, family history, and their association with mood disorders in early adulthood
Authors: Jansen K. , Cardoso T. A. , Fries G. R. , Branco J. C. , Silva R. A. , Kauer‐Sant'Anna M. , Kapczinski F. , Magalhaes P. V. S. 
Published: January 2016

ObjectiveTo assess the prevalence of childhood trauma and types of trauma on mood disorders among young adults in a population‐based sample. We further gathered data on family history of mood disorders to test the hypothesis that childhood trauma is a mediating factor for the association between family history of mood disorder and mood disorder in adulthood.MethodThis is a cross‐sectional study, including young adults with bipolar disorder, major depressive disorder, and matched controls without any mood disorder. Childhood trauma was assessed using the Childhood Trauma Questionnaire (CTQ). The Hicks and Tingley implementation was employed to assess whether trauma is a mediator of the effect of family history on diagnosis of any mood disorder.ResultsAll types of trauma were associated with both major depression and bipolar disorder, with the exception of sexual abuse, which was only associated with bipolar disorder. Moreover, family history of psychiatric illness was also associated with mood disorder in adulthood and with childhood trauma. Using the presence of any mood disorder as the outcome, a third of the effect of having any family history of mood disorder was mediated via childhood trauma.ConclusionThis investigation provides further support, in a population‐based sample of young adults, of the association between childhood trauma and mood disorders, with sexual abuse being specifically linked with bipolar disorder. The hypothesis that childhood trauma would function as a partial mediator of the association between family history of mood disorder and mood disorder in adulthood was also confirmed.