bluuebunny/crossref_metadata_2025_split huggingface dataset:
The TRANSPLANTA collection of Arabidopsis lines: a resource for functional analysis of transcription factors based on their conditional overexpression
Authors: Coego Alberto , Brizuela Esther , Castillejo Pablo , Ruíz Sandra , Koncz Csaba , del Pozo Juan C. , Piñeiro Manuel , Jarillo José A. , Paz‐Ares Javier , León José ,   The TRANSPLANTA Consortium
Published: January 2014

SummaryTranscription factors (TFs) are key regulators of gene expression in all organisms. In eukaryotes, TFs are often represented by functionally redundant members of large gene families. Overexpression might prove a means to unveil the biological functions of redundant TFs; however, constitutive overexpression of TFs frequently causes severe developmental defects, preventing their functional characterization. Conditional overexpression strategies help to overcome this problem. Here, we report on the TRANSPLANTA collection of Arabidopsis lines, each expressing one of 949 TFs under the control of a β–estradiol‐inducible promoter. Thus far, 1636 independent homozygous lines, representing an average of 2.6 lines for every TF, have been produced for the inducible expression of 634 TFs. Along with a GUS‐GFP reporter, randomly selected TRANSPLANTA lines were tested and confirmed for conditional transgene expression upon β–estradiol treatment. As a proof of concept for the exploitation of this resource, β–estradiol‐induced proliferation of root hairs, dark‐induced senescence, anthocyanin accumulation and dwarfism were observed in lines conditionally expressing full‐length cDNAs encoding RHD6, WRKY22, MYB123/TT2 and MYB26, respectively, in agreement with previously reported phenotypes conferred by these TFs. Further screening performed with other TRANSPLANTA lines allowed the identification of TFs involved in different plant biological processes, illustrating that the collection is a powerful resource for the functional characterization of TFs. For instance, ANAC058 and a TINY/AP2 TF were identified as modulators of ABA‐mediated germination potential, and RAP2.10/DEAR4 was identified as a regulator of cell death in the hypocotyl–root transition zone. Seeds of TRANSPLANTA lines have been deposited at the Nottingham Arabidopsis Stock Centre for further distribution.
FLOURY ENDOSPERM6 encodes a CBM48 domain‐containing protein involved in compound granule formation and starch synthesis in rice endosperm
Authors: Peng Cheng , Wang Yihua , Liu Feng , Ren Yulong , Zhou Kunneng , Lv Jia , Zheng Ming , Zhao Shaolu , Zhang Long , Wang Chunming , Jiang Ling , Zhang Xin , Guo Xiuping , Bao Yiqun , Wan Jianmin 
Published: January 2014

SummaryStarch is the most widespread form of energy storage in the plant kingdom. Although many enzymes and related factors have been identified for starch biosynthesis, unknown players remain to be identified, given that it is a complicated and sophisticated process. The endosperm of rice (Oryza sativa) has been used for the study of starch synthesis. Here, we report the cloning and characterization of the FLOURY ENDOSPERM6 (FLO6) gene in rice. In the flo6 mutant, the starch content is decreased and the normal physicochemical features of starch are changed. Significantly, flo6 mutant endosperm cells show obvious defects in compound granule formation. Map‐based cloning showed that FLO6 encodes a protein of unknown function. It harbors an N–terminal transit peptide that ensures its correct localization and functions in the plastid, and a C–terminal carbohydrate‐binding module 48 (CBM48) domain that binds to starch. Furthermore, FLO6 can interact with isoamylase1 (ISA1) both in vitro and in vivo, whereas ISA1 does not bind to starch directly. We thus propose that FLO6 may act as a starch‐binding protein involved in starch synthesis and compound granule formation through a direct interaction with ISA1 in developing rice seeds. Our data provide a novel insight into the role of proteins with the CBM48 domain in plant species.
Safety of a liberal policy for extended‐date preadmission testing samples
Authors: Le Nguyet , Harach Mary E. , Gould Joy M. , Herman Jay H. 
Published: January 2014

BackgroundRegulations governing pretransfusion testing allow specimen expiration to be extended past 3 days before the transfusion if a patient has not been transfused or pregnant in the preceding 3 months. Our hospital allows extension of the expiration of a presurgical specimen to 28 days if 1) the patient has neither been transfused nor pregnant in the past 3 months, 2) the patient does not have an antibody history, and 3) the current antibody screen (ABSC) is negative. Patients not meeting Criteria 2 and 3 are required to have specimens redrawn on the day of surgery (DOS). We evaluated the necessity of this policy.Study Design and MethodsFrom October 2009 to September 2010, there were 132 patients who did not meet the above criteria for specimen extension. Equivalent tests were performed on preadmission testing (PAT) and DOS specimens, and the results were compared.ResultsThe majority (113, 86%) of the samples redrawn on the DOS showed no change in antibody serology upon reinvestigation. Of the remaining patients, DOS specimens did not identify any new antibodies or change in blood product choices.ConclusionOf the PAT specimens rejected for antibody history or positive ABSC, none had new significant serologic findings on DOS. Based on these results, requiring a repeat specimen on the DOS may not be clinically necessary. Our facility changed the PAT policy to extend specimen acceptability to patients with red blood cell antibody history or positive ABSC at time of PAT. A 6‐month follow‐up period showed that this practice is safe.
On the interplay effects with proton scanning beams in stage III lung cancer
Authors: Li Yupeng , Kardar Laleh , Li Xiaoqiang , Li Heng , Cao Wenhua , Chang Joe Y. , Liao Li , Zhu Ronald X. , Sahoo Narayan , Gillin Michael , Liao Zhongxing , Komaki Ritsuko , Cox James D. , Lim Gino , Zhang Xiaodong 
Published: January 2014

Purpose:To assess the dosimetric impact of interplay between spot‐scanning proton beam and respiratory motion in intensity‐modulated proton therapy (IMPT) for stage III lung cancer.Methods:Eleven patients were sampled from 112 patients with stage III nonsmall cell lung cancer to well represent the distribution of 112 patients in terms of target size and motion. Clinical target volumes (CTVs) and planning target volumes (PTVs) were defined according to the authorsˈ clinical protocol. Uniform and realistic breathing patterns were considered along with regular‐ and hypofractionation scenarios. The dose contributed by a spot was fully calculated on the computed tomography (CT) images corresponding to the respiratory phase that the spot is delivered, and then accumulated to the reference phase of the 4DCT to generate the dynamic dose that provides an estimation of what might be delivered under the influence of interplay effect. The dynamic dose distributions at different numbers of fractions were compared with the corresponding 4D composite dose which is the equally weighted average of the doses, respectively, computed on respiratory phases of a 4DCT image set.Results:Under regular fractionation, the average and maximum differences in CTV coverage between the 4D composite and dynamic doses after delivery of all 35 fractions were no more than 0.2% and 0.9%, respectively. The maximum differences between the two dose distributions for the maximum dose to the spinal cord, heart V40, esophagus V55, and lung V20 were 1.2 Gy, 0.1%, 0.8%, and 0.4%, respectively. Although relatively large differences in single fraction, correlated with small CTVs relative to motions, were observed, the authorsˈ biological response calculations suggested that this interfractional dose variation may have limited biological impact. Assuming a hypofractionation scenario, the differences between the 4D composite and dynamic doses were well confined even for single fraction.Conclusions:Despite the presence of interplay effect, the delivered dose may be reliably estimated using the 4D composite dose. In general the interplay effect may not be a primary concern with IMPT for lung cancers for the authorsˈ institution. The described interplay analysis tool may be used to provide additional confidence in treatment delivery.
Comparison of flat cleaved and cylindrical diffusing fibers as treatment sources for interstitial photodynamic therapy
Authors: Baran Timothy M. , Foster Thomas H. 
Published: January 2014

Purpose:For interstitial photodynamic therapy (iPDT) of bulky tumors, careful treatment planning is required in order to ensure that a therapeutic dose is delivered to the tumor, while minimizing damage to surrounding normal tissue. In clinical contexts, iPDT has typically been performed with either flat cleaved or cylindrical diffusing optical fibers as light sources. Here, the authors directly compare these two source geometries in terms of the number of fibers and duration of treatment required to deliver a prescribed light dose to a tumor volume.Methods:Treatment planning software for iPDT was developed based on graphics processing unit enhanced Monte Carlo simulations. This software was used to optimize the number of fibers, total energy delivered by each fiber, and the position of individual fibers in order to deliver a target light dose (D90) to 90% of the tumor volume. Treatment plans were developed using both flat cleaved and cylindrical diffusing fibers, based on tissue volumes derived from CT data from a head and neck cancer patient. Plans were created for four cases: fixed energy per fiber, fixed number of fibers, and in cases where both or neither of these factors were fixed.Results:When the number of source fibers was fixed at eight, treatment plans based on flat cleaved fibers required each to deliver 7180–8080 J in order to deposit 90 J/cm2 in 90% of the tumor volume. For diffusers, each fiber was required to deliver 2270–2350 J (333–1178 J/cm) in order to achieve this same result. For the case of fibers delivering a fixed 900 J, 13 diffusers or 19 flat cleaved fibers at a spacing of 1 cm were required to deliver the desired dose. With energy per fiber fixed at 2400 J and the number of fibers fixed at eight, diffuser fibers delivered the desired dose to 93% of the tumor volume, while flat cleaved fibers delivered this dose to 79%. With both energy and number of fibers allowed to vary, six diffusers delivering 3485–3600 J were required, compared to ten flat cleaved fibers delivering 2780–3600 J.Conclusions:For the same number of fibers, cylindrical diffusers allow for a shorter treatment duration compared to flat cleaved fibers. For the same energy delivered per fiber, diffusers allow for the insertion of fewer fibers in order to deliver the same light dose to a target volume.
Dosimetric characterization and output verification for conical brachytherapy surface applicators. Part I. Electronic brachytherapy source
Authors: Fulkerson Regina K. , Micka John A. , DeWerd Larry A. 
Published: January 2014

Purpose:Historically, treatment of malignant surface lesions has been achieved with linear accelerator based electron beams or superficial x‐ray beams. Recent developments in the field of brachytherapy now allow for the treatment of surface lesions with specialized conical applicators placed directly on the lesion. Applicators are available for use with high dose rate (HDR)192Ir sources, as well as electronic brachytherapy sources. Part I of this paper will discuss the applicators used with electronic brachytherapy sources; Part II will discuss those used with HDR 192Ir sources. Although the use of these applicators has gained in popularity, the dosimetric characteristics including depth dose and surface dose distributions have not been independently verified. Additionally, there is no recognized method of output verification for quality assurance procedures with applicators like these. Existing dosimetry protocols available from the AAPM bookend the cross‐over characteristics of a traditional brachytherapy source (as described by Task Group 43) being implemented as a low‐energy superficial x‐ray beam (as described by Task Group 61) as observed with the surface applicators of interest.Methods:This work aims to create a cohesive method of output verification that can be used to determine the dose at the treatment surface as part of a quality assurance/commissioning process for surface applicators used with HDR electronic brachytherapy sources (Part I) and192Ir sources (Part II). Air‐kerma rate measurements for the electronic brachytherapy sources were completed with an Attix Free‐Air Chamber, as well as several models of small‐volume ionization chambers to obtain an air‐kerma rate at the treatment surface for each applicator. Correction factors were calculated using MCNP5 and EGSnrc Monte Carlo codes in order to determine an applicator‐specific absorbed dose to water at the treatment surface from the measured air‐kerma rate. Additionally, relative dose measurements of the surface dose distributions and characteristic depth dose curves were completed in‐phantom.Results:Theoretical dose distributions and depth dose curves were generated for each applicator and agreed well with the measured values. A method of output verification was created that allows users to determine the applicator‐specific dose to water at the treatment surface based on a measured air‐kerma rate.Conclusions:The novel output verification methods described in this work will reduce uncertainties in dose delivery for treatments with these kinds of surface applicators, ultimately improving patient care.
The Importance of a Normal Breathing Pattern for an Effective Abdominal-Hollowing Maneuver in Healthy People: An Experimental Study
Authors: Ha Sung-min , Kwon Oh-yun , Kim Su-jung , Choung Sung-dae 
Published: January 2014

Context:A normal breathing pattern while performing the abdominal-hollowing (AH) maneuver or spinal-stabilization exercise is essential for the success of rehabilitation programs and exercises. In previous studies, subjects were given standardized instructions to control the influence of respiration during the AH maneuver. However, the effect of breathing pattern on abdominal-muscle thickness during the AH maneuver has not been investigated.Objective:To compare abdominal-muscle thickness in subjects performing the AH maneuver under normal and abnormal breathing-pattern conditions and to investigate the effect of breathing pattern on the preferential contraction ratio (PCR) of the transverse abdominis.Design:Comparative, repeated-measures experimental study.Setting:University research laboratory.Participants:16 healthy subjects (8 male, 8 female) from a university population.Measurement:A real-time ultrasound scanner was used to measure abdominal-muscle thickness during normal and abnormal breathing patterns. A paired t test was used to assess the effect of breathing pattern on abdominal-muscle thickness and PCR.Results:Muscle thickness in the transverse abdominis and internal oblique muscles was significantly greater under the normal breathing pattern than under the abnormal pattern (P < .05). The PCR of the transverse abdominis was significantly higher under the normal breathing pattern compared with the abnormal pattern (P < .05).Conclusion:The results indicate that a normal breathing pattern is essential for performance of an effective AH maneuver. Thus, clinicians should ensure that patients adopt a normal breathing pattern before performing the AH maneuver and monitor transverse abdominis activation during the maneuver.
Succeed Together or Fail Alone: Going From Good to Great in Physical Education
Authors: Pennington Todd R. , Prusak Keven A. , Wilkinson Carol 
Published: January 2014

“What we have is a systemic failure —one that involves the relationship of physical education programs in public schools with teacher preparation in higher education.”(Siedentop & Locke, 1997). This assessment led Prusak, Pennington, Vincent-Graser, Beighle, and Morgan (2010) to an examination of a school district that seemed to have achieved Systemic Success in PE (SSPE). The authors sought to understand SSPE’s history from conception to institutionalization. This three-year, qualitative, follow-up study was conducted using Collins’ (2001) framework from Good to Great: Why Some Companies Make the Leap… and Others Don’t.Making this examination from a business sector perspective provides an insightful look into the making of SSPE. Results of this study provide evidence that while social sector organizations (such as education) share much in common with business sector companies, there are distinct and fascinating differences. Collins’ (2001) framework is both confirmed and extended in this study. Findings also provide a means for PE practitioners and PETE programs to accomplish what Siedentop and Locke (1997) hoped for—to succeed together.
Genome Sequences of Three Novel Bacillus cereus Bacteriophages
Authors: Grose Julianne H. , Jensen Jordan D. , Merrill Bryan D. , Fisher Joshua N. B. , Burnett Sandra H. , Breakwell Donald P. 
Published: January 2014

ABSTRACT

The
Bacillus cereus
group is an assemblage of highly related firmicute bacteria that cause a variety of diseases in animals, including insects and humans. We announce three high-quality, complete genome sequences of bacteriophages we isolated from soil samples taken at the bases of fruit trees in Utah County, Utah. While two of the phages (Shanette and JL) are highly related myoviruses, the bacteriophage Basilisk is a siphovirus.
Complete Genome Sequence of Pseudomonas aeruginosa MTB-1, Isolated from a Microbial Community Enriched by the Technical Formulation of Hexachlorocyclohexane
Authors: Ohtsubo Yoshiyuki , Sato Takuya , Kishida Kouhei , Tabata Michro , Ogura Yoshitoshi , Hayashi Tetsuya , Tsuda Masataka , Nagata Yuji 
Published: January 2014

ABSTRACT

Pseudomonas aeruginosa
MTB-1 does not degrade gamma-hexachlorocyclohexane (γ-HCH), but this bacterium persistently coexists with a γ-HCH-degrading strain,
Sphingomonas
sp. MM-1, in a microbial community enriched by the technical formulation of HCH. Here we report the complete MTB-1 genome sequence, with a 6.6-Mb circular chromosome.
Draft Genome Sequence of the Alkaliphilic and Xylanolytic
Paenibacillus
sp. Strain JCM 10914, Isolated from the Gut of a Soil-Feeding Termite
Authors: Ohkuma Moriya , Yuki Masahiro , Oshima Kenshiro , Suda Wataru , Oshida Yumi , Kitamura Keiko , Iida Toshiya , Hattori Masahira 
Published: January 2014

ABSTRACT

Panibacillus
sp. strain JCM 10914 is a xylanolytic alkaliphile isolated from the gut of a soil-feeding termite. Its draft genome sequence revealed various genes for hydrolytic enzymes and will facilitate studies on adaptation to the highly alkaline gut environment and its role in digesting soil organic matter in the gut.
Draft Genome Sequence of
Mortierella alpina
Isolate CDC-B6842
Authors: Etienne Kizee A. , Chibucos Marcus C. , Su Qi , Orvis Joshua , Daugherty Sean , Ott Sandra , Sengamalay Naomi A. , Fraser Claire M. , Lockhart Shawn R. , Bruno Vincent M. 
Published: January 2014

ABSTRACT

We report the draft genome sequence of
Mortierella alpina
isolate CDC-B6842.
M. alpina
is a nonpathogenic member of the
Mucoromycotina
subphylum of fungi that is an important model for understanding the molecular mechanisms of lipid production and metabolism.
Draft Genome Sequence of Enterococcus faecalis Strain PF3, Isolated from Adélie Penguin Feces from Antarctica
Authors: Spence Robert J. , Pavasovic Ana , Smith James J. , Prentis Peter J. 
Published: January 2014

ABSTRACT

Enterococcus faecalis
is one of the leading causes of nosocomial infections and is a common commensal organism in humans and other animals. In this study, we report a draft genome sequence for the
E. faecalis
strain PF3, isolated from Adélie penguin feces collected from Warriner Island, Antarctica.
Complete Genome Sequence of the Thermophilic Polychlorinated Biphenyl Degrader
Geobacillus
sp. Strain JF8 (NBRC 109937)
Authors: Shintani Masaki , Ohtsubo Yoshiyuki , Fukuda Kohei , Hosoyama Akira , Ohji Shoko , Yamazoe Atsushi , Fujita Nobuyuki , Nagata Yuji , Tsuda Masataka , Hatta Takashi , Kimbara Kazuhide 
Published: January 2014

ABSTRACT

Geobacillus
sp. strain JF8 (NBRC 109937) utilizes biphenyl and naphthalene as sole carbon sources and degrades polychlorinated biphenyl (PCB) at 60°C. Here, we report the complete nucleotide sequence of the JF8 genome (a 3,446,630-bp chromosome and a 39,678-bp plasmid). JF8 has the smallest genome among the known PCB degraders.
Complete Genome Sequence of Mycobacterium tuberculosis Strain MtURU-001, Isolated from a Rapidly Progressing Outbreak in Uruguay
Authors: Greif Gonzalo , Iraola Gregorio , Berná Luisa , Coitinho Cecilia , Rivas Carlos M. , Naya Hugo , Robello Carlos 
Published: January 2014

ABSTRACT

Despite efficient control programs, large clonal outbreaks of tuberculosis (TB) may arise in low-risk populations. Recently, an unusual TB outbreak was reported in Uruguay, reaching an elevated disease attack rate (53 to 69%). Here, we report the genome sequence of the
Mycobacterium tuberculosis
strain associated with this rapidly progressing outbreak, named MtURU-001.
Draft Genome Sequences of Fusobacterium nucleatum ChDC F145, ChDC F174, ChDC F206, and ChDC F300, Isolated from Human Subgingival Plaques in the Republic of Korea
Authors: Park Soon-Nang , Cho Eugene , Lim Yun Kyong , Kim Hwa-Sook , Kim Dae-Soo , Jung Jaeeun , Baek Jeong-Hun , Jo Eojin , Chang Young-Hyo , Shin Jeong Hwan , Choi Sang-Haeng , Kang Jihee , Choi YongUn , Park Hong-Seog , Kim Hongik , Kook Joong-Ki 
Published: January 2014

ABSTRACT

Recently, five strains were isolated from human subgingival plaques and were proposed as a novel subspecies of
Fusobacterium nucleatum
. Here, we report the draft genome sequences of the strains, except one for which the draft sequence was already introduced.
Recovery from sleep disturbance precedes that of depression and anxiety following mild traumatic brain injury: a 6-week follow-up study
Authors: Ma Hon-Ping , Ou Ju-Chi , Yeh Chun-Ting , Wu Dean , Tsai Shin-Han , Chiu Wen-Ta , Hu Chaur-Jong 
Published: January 2014

ObjectivesThe detailed course of mental disorders at the acute and subacute stages of mild traumatic brain injury (mTBI), especially with regard to recovery from sleep disturbances, has not been well characterised. The aim of this study was to determine the course of depression, anxiety and sleep disturbance, following an mTBI.SettingWe recruited patients with mTBI from three university hospitals in Taipei and healthy participants as control group for this study.Participants100 patients with mTBI (35 men) who were older than 20 years, with a Glasgow Coma Scale score of 13–15 and loss of consciousness for <30 min, completed the baseline and 6-week follow-up assessments. 137 controls (47 men) without TBI were recruited in the study. None of the participants had a history of cerebrovascular disease, mental retardation, previous TBI, epilepsy or severe systemic medical illness.Primary outcome measuresThe Beck Anxiety Inventory (BAI), the Beck Depression Inventory II (BDI), the Epworth Sleepiness Scale (ESS) and the Pittsburgh Sleep Quality Index (PSQI) were assessed for the patients with mTBI at baseline and 6 weeks after mTBI and for the controls.ResultsThe ESS scores were not significantly different between the mTBI at baseline or at 6 weeks after mTBI and controls. Although the BAI, BDI and PSQI scores of the mTBI group were significantly different than those of the control group at baseline, all had improved significantly 6 weeks later. However, only the PSQI score improved to a level that was not significantly different from that of the control group.ConclusionsDaytime sleepiness is not affected by mTBI. However, mTBI causes depression and anxiety and diminished sleep quality. Although all these conditions improve significantly within 6 weeks post-mTBI, only sleep quality improves to a pre-mTBI level. Thus, recovery from mTBI-induced sleep disturbance occurs more rapidly than that of mTBI-induced depression and anxiety.