bluuebunny/crossref_metadata_2025_split huggingface dataset:
First Report of Potato virus Y Strain N-Wilga Infecting Chrysanthemum in China
Authors: Liu X. L. , Wei Q. , Hong B. , Zhao X. T. 
Published: September 2014

Chrysanthemum (Chrysanthemum morifolium Ramat.) is a commercially important ornamental grown worldwide, and is also extensively used as an edible and medicinal plant. In the present work, viruses and viroids infecting chrysanthemum were investigated in China in 2012 and 2013. Typical viral symptoms were observed in field-grown chrysanthemum with leaf yellowing and mottled leaves in Wenjiang District, Sichuan Province, China. The incidence of these symptoms in the field was 12.3%. Chrysanthemum virus B (CVB), Tomato aspermy virus (TAV), Cucumber mosaic virus (CMV), Tobacoo mosaic virus (TMV), Chrysanthemum stunt viroid (CSVd), and Chrysanthemum chlorotic mottle viroid (CChMVd), which had previously been reported to infect chrysanthemum in China (2,3), were not detected by RT-PCR assay. Since these symptomatic chrysanthemum plants grew next to a tobacco field, viruses affecting tobacco were suspected as possible cause. Sixteen symptomatic leaves and 12 non-symptomatic leaves were collected and tested for Potato virus Y (PVY) presence using commercial PVY-specific DAS-ELISA kits (Catalog no. PSA20001, Agdia) Six samples were found positive for PVY. RT-PCR tests using specific primers for CP gene (CP-F 5′-ACTGTGATGAATGGGCTTATG-3′; CP-R 5′-GGCATATATGGTTCCTTTTTG-3′) (4) amplified a single, expected 218-bp DNA fragment from chrysanthemum extracts from all six samples positive for PVY in ELISA. These six PCR fragments were sequenced and found 100% identical to each other. The sequence (GenBank Accession No. KJ174515) shared 99% identity with corresponding sequences of several PVY isolates (NC_001616, EF026076, HM590407, and JQ924288). The same six positive samples were subjected to a multiplex RT-PCR assay (1) to identify the PVY strain type, and all six PVY samples from Sichuan were found to belong to the PVYN-Wi strain. To our knowledge, this is the first report of the PVYN-Wi strain infecting chrysanthemum in Sichuan, China. References: (1) M. Chikh Ali et al. Plant Dis. 10:1370, 2013. (2) E. A. Nassar et al. Int. J. Virol. 8:14, 2012. (3) H. Yamamoto et al. J. Gen. Plant Pathol. 71:156, 2005. (4) J. Q. Zhang et al. J. Phytopathol. 161:92, 2013.
Immediate Rescue Designs in Pediatric Analgesic Trials
Authors: Kossowsky Joe , Donado Carolina , Berde Charles B. 
Published: September 2014

Abstract

Background:
Designing analgesic clinical trials in pediatrics requires a balance between scientific, ethical, and practical concerns. A previous consensus group recommended immediate rescue designs using opioid sparing as a surrogate measure of analgesic efficacy. The authors summarize the performance of rescue analgesic designs in pediatric trials of four commonly used classes of analgesics: opioids, nonsteroidal antiinflammatory drugs, acetaminophen, and local anesthetics.

Methods:
MEDLINE, Embase, CINAHL, The Cochrane Library, and Web of science were searched in April 2013. The 85 studies selected were randomized or controlled clinical trials using immediate rescue paradigms in postoperative pain settings. A random-effects meta-analysis was used to synthesize predefined outcomes using Hedges’ g. Difference between the means of the treatment arms were also expressed as a percentage of the corresponding value in the placebo group (placebo-treatment/placebo). Distributions of pain scores in study and control groups and relationships between opioid sparing and pain scores were examined.

Results:
For each of the four study drug classes, significant opioid sparing was demonstrated in a majority of studies by one or more of the following endpoints: (1) total dose (milligram per kilogram per hour), (2) percentage of children requiring rescue medication, and (3) time to first rescue medication (minutes). Pain scores averaged 2.4/10 in study groups, 3.4/10 in control groups.

Conclusions:
Opioid sparing is a feasible pragmatic endpoint for pediatric pain analgesic trials. This review serves to guide future research in pediatric analgesia trials, which could test whether some specific design features may improve assay sensitivity while minimizing the risk of unrelieved pain.
Radiation Therapy for Very Elderly Patients Aged 80 Years and Older With Squamous Cell Carcinoma of the Uterine Cervix
Authors: Hata Masaharu , Koike Izumi , Miyagi Etsuko , Numazaki Reiko , Asai-Sato Mikiko , Kasuya Takeo , Kaizu Hisashi , Matsui Tonika , Hirahara Fumiki , Inoue Tomio 
Published: September 2014

Objectives:
We carried out a retrospective review to determine the role played by radiation therapy in the treatment of very elderly patients with uterine cervical cancer.

Materials and Methods:
Thirty elderly patients aged 80 years and older with squamous cell carcinoma of the uterine cervix, at clinical stages IB-IVA, underwent radiation therapy. Of these 30 patients, 6 received external irradiation alone and 24 received external irradiation and intracavitary brachytherapy. A total median dose of 69.0 Gy (range, 45.6 to 75.4 Gy) was delivered to the cervical tumors. No patients underwent chemotherapy.

Results:
At a median follow-up time of 24 months, 7 patients had developed recurrences, including local recurrences in 3 and distant metastases in 5. The local control and distant metastasis-free rates were 88% and 79%, respectively, at 2 years. The disease-free, cause-specific, and overall survival rates were 69%, 77%, and 75%, respectively, at 2 years. Primary tumor size, T category, and clinical stage were found to be significant prognostic factors for distant metastasis. Age and primary tumor size were considered as being significant variables that affected survival. With the exception of a transient hematologic reaction, there were no therapy-related toxicities of grade ≥3.

Conclusions:
Radiation therapy was safe and effective regarding local control of uterine cervical cancer in elderly patients aged 80 years and older, and appeared to contribute to their prolonged survival. Curative radiation therapy should be considered as a viable treatment option, even in very elderly patients.
Definitive Chemoradiation for Squamous Cell Carcinoma of the Rectum
Authors: Sturgeon Jared D. , Crane Christopher H. , Krishnan Sunil , Minsky Bruce D. , Skibber John M. , Rodriguez-Bigas Miguel A. , Chang George J. , You Y. Nancy , Eng Cathy , Das Prajnan 
Published: September 2014

Objectives:
Squamous cell carcinoma (SCC) of the rectum is a rare disease with <80 cases reported in the English literature. We reviewed outcomes in patients with SCC of the rectum treated with definitive chemoradiation at a single institution.

Materials and Methods:
We identified 14 patients treated definitively with chemoradiation for SCC of the rectum. All patients were female and the median age was 56 years at presentation. Patients were treated with external beam radiation therapy with a median dose of 54 Gy (range, 38 to 58.8 Gy). All patients received concurrent chemotherapy, with 5-flourouracil and cisplatin in 10 patients and capecitabine and cisplatin in 4 patients.

Results:
The median follow-up was 4.5 years (range, 1.8 to 16.3 y). Only 3 of the 14 patients had relapse or persistent disease, and 2 of these underwent successful salvage surgery. The remaining 11 patients had no evidence for local or distant relapse after chemoradiation. Only 1 patient died of SCC of the rectum, 1 died of a second primary, and 12 are alive with no evidence of disease. The 5-year actuarial overall survival, disease-free survival, and disease-specific survival rates were 81%, 72%, and 88% respectively.

Conclusions:
Chemoradiation is an ideal strategy for definitive therapy of SCC of the rectum with excellent disease-free survival and overall survival. In patients with local failure, salvage surgery can provide excellent outcomes.
Outcomes of Adults With Ewing Sarcoma Family of Tumors (ESFT) of the Kidney
Authors: Teegavarapu Purnima S. , Rao Priya , Matrana Marc R. , Cauley Diana H. , Wood Christopher G. , Patel Shreyaskumar , Tannir Nizar M. 
Published: September 2014

Background:
Ewing sarcoma family of tumors (ESFT) of the kidney are exceedingly rare. Given the rarity of this neoplasm and the complexity associated with its management, information regarding treatment and outcome is warranted.

Materials and Methods:
We conducted a retrospective study of patients with ESFT of the kidney who were treated at MDACC between January 1, 2001 and January 1, 2011. Descriptive statistics were used.

Results:
Thirteen patients were identified (median age, 33 y; male:female 11:2). Common presenting symptoms were back pain, flank pain, and hematuria. Six patients had metastatic disease at presentation. Initial diagnostic biopsy was performed in 6 patients. Immunohistochemistry showed strong positivity for CD99 (mic2) and cytogenetic analysis demonstrated evidence of EWSR1 fusion gene in 8 cases. Nine patients underwent nephrectomy. Frequently used chemotherapy regimens consisted of vincristine, doxorubicin, and ifosfamide. Median overall survival was 17.2 months. Three patients were alive at the time of analysis, at 2, 7, and 11 years from diagnosis (the latter without evidence of disease).

Conclusions:
Renal ESFT carry a guarded prognosis with limited response to therapy and short median overall survival. For patients with metastatic disease, diagnostic biopsy and sarcoma-based chemotherapy regimens are recommended as upfront therapeutic strategy. The role of nephrectomy in the metastatic setting is unclear. Future studies with novel therapies are needed.
Influence of Comorbidity on the Risk of Death
Authors: Elshaikh Mohamed A. , Vance Sean , Kamal Mona , Burmeister Charlotte , Hanna Rabbie K. , Rasool Nabila , Siddiqui Farzan 
Published: September 2014

Purpose/Objective(s):
The impact of competing medical comorbidity on survival endpoints in women with early stage endometrial carcinoma (EC) is not well studied. The study goal was to utilize a validated comorbidity scoring system to determine its impact on all-cause mortality as well as on recurrence-free survival (RFS), disease-specific survival (DSS), and overall survival (OS) in patients with early-stage EC.

Materials and Methods:
For this IRB-approved study, we reviewed our prospectively maintained uterine cancer database of 1720 patients. We identified 1132 patients with EC FIGO stages I-II who underwent hysterectomy from 1984 to 2011. Age-adjusted Charlson Comorbidity Index (AACCI) at time of hysterectomy was retrospectively calculated by physician chart review. The cause of death (uterine cancer-related and unrelated) was correlated with AACCI. Univariate and multivariate modeling with Cox regression analysis was used to determine significant predictors of OS, DSS, and RFS. The Kaplan-Meier and the log-rank test methods were used to evaluate survival outcomes.

Results:
After a median follow-up of 51 months, 262 deaths were recorded (42 from EC [16%], and 220 [84%] from other causes). Median AACCI score for the study cohort was 3 (range, 0 to 15). On the basis of AACCI, patients were grouped as follows: 0 to 2 (group 1, n=379), 3 to 4 (group 2, n=532), and ≥5 (group 3, n=221). By AACCI grouping, the 5-year RFS, DSS, and OS were 95%, 98%, and 97% for group 1, 89%, 95%, and 87% for group 2, and 86%, 95% and 72% for group 3 (P<0.0001). The cause of death in the first 10 years after hysterectomy in our study was mainly non-uterine cancer-related (78% vs. 22% for uterine cancer-related) causes. On multivariate analyses, higher AACCI, lymphovascular space invasion (LVSI), higher tumor grade, age, and involvement of the lower uterine segment were significant predictors of shorter OS. On multivariate analysis for DSS and RFS, only high tumor grade and LVSI were significant predictors.

Conclusions:
The cause of death for women with early stage EC is mainly nonuterine cancer-related. Comorbidity score is a significant predictor of OS in our study cohort. Comorbidity scores may be useful as a stratification factor in any prospective clinical trial for women with early-stage EC.
Intrinsic cortical dynamics dominate population responses to natural images across human visual cortex
Authors: Henriksson Linda , Khaligh-Razavi Seyed-Mahdi , Kay Kendrick , Kriegeskorte Nikolaus 
Published: September 2014

ABSTRACTIntrinsic cortical dynamics are thought to underlie trial-to-trial variability of visually evoked responses in animal models. Understanding their function in the context of sensory processing and representation is a major current challenge. Here we report that intrinsic cortical dynamics strongly affect the representational geometry of a brain region, as reflected in response-pattern dissimilarities, and exaggerate the similarity of representations between brain regions. We characterized the representations in several human visual areas by representational dissimilarity matrices (RDMs) constructed from fMRI response-patterns for natural image stimuli. The RDMs of different visual areas were highly similar when the response-patterns were estimated on the basis of the same trials (sharing intrinsic cortical dynamics), and quite distinct when patterns were estimated on the basis of separate trials (sharing only the stimulus-driven component). We show that the greater similarity of the representational geometries can be explained by the coherent fluctuations of regional-mean activation within visual cortex, reflecting intrinsic dynamics. Using separate trials to study stimulus-driven representations revealed clearer distinctions between the representational geometries: a Gabor wavelet pyramid model explained representational geometry in visual areas V1–3 and a categorical animate– inanimate model in the object-responsive lateral occipital cortex.
Structural Studies of Cinnamoyl-CoA Reductase and Cinnamyl-Alcohol Dehydrogenase, Key Enzymes of Monolignol Biosynthesis
Authors: Pan Haiyun , Zhou Rui , Louie Gordon V. , Mühlemann Joëlle K. , Bomati Erin K. , Bowman Marianne E. , Dudareva Natalia , Dixon Richard A. , Noel Joseph P. , Wang Xiaoqiang 
Published: September 2014

Abstract
The enzymes cinnamoyl-CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) catalyze the two key reduction reactions in the conversion of cinnamic acid derivatives into monolignol building blocks for lignin polymers in plant cell walls. Here, we describe detailed functional and structural analyses of CCRs from Medicago truncatula and Petunia hybrida and of an atypical CAD (CAD2) from M. truncatula. These enzymes are closely related members of the short-chain dehydrogenase/reductase (SDR) superfamily. Our structural studies support a reaction mechanism involving a canonical SDR catalytic triad in both CCR and CAD2 and an important role for an auxiliary cysteine unique to CCR. Site-directed mutants of CAD2 (Phe226Ala and Tyr136Phe) that enlarge the phenolic binding site result in a 4- to 10-fold increase in activity with sinapaldehyde, which in comparison to the smaller coumaraldehyde and coniferaldehyde substrates is disfavored by wild-type CAD2. This finding demonstrates the potential exploitation of rationally engineered forms of CCR and CAD2 for the targeted modification of monolignol composition in transgenic plants. Thermal denaturation measurements and structural comparisons of various liganded and unliganded forms of CCR and CAD2 highlight substantial conformational flexibility of these SDR enzymes, which plays an important role in the establishment of catalytically productive complexes of the enzymes with their NADPH and phenolic substrates.
ROP3 GTPase Contributes to Polar Auxin Transport and Auxin Responses and Is Important for Embryogenesis and Seedling Growth inArabidopsis
Authors: Huang Jia-bao , Liu Huili , Chen Min , Li Xiaojuan , Wang Mingyan , Yang Yali , Wang Chunling , Huang Jiaqing , Liu Guolan , Liu Yuting , Xu Jian , Cheung Alice Y. , Tao Li-zhen 
Published: September 2014

AbstractROP GTPases are crucial for the establishment of cell polarity and for controlling responses to hormones and environmental signals in plants. In this work, we show that ROP3 plays important roles in embryo development and auxin-dependent plant growth. Loss-of-function and dominant-negative (DN) mutations in ROP3 induced a spectrum of similar defects starting with altered cell division patterning during early embryogenesis to postembryonic auxin-regulated growth and developmental responses. These resulted in distorted embryo development, defective organ formation, retarded root gravitropism, and reduced auxin-dependent hypocotyl elongation. Our results showed that the expression of AUXIN RESPONSE FACTOR5/MONOPTEROS and root master regulators PLETHORA1 (PLT1) and PLT2 was reduced in DN-rop3 mutant embryos, accounting for some of the observed patterning defects. ROP3 mutations also altered polar localization of auxin efflux proteins (PINs) at the plasma membrane (PM), thus disrupting auxin maxima in the root. Notably, ROP3 is induced by auxin and prominently detected in root stele cells, an expression pattern similar to those of several stele-enriched PINs. Our results demonstrate that ROP3 is important for maintaining the polarity of PIN proteins at the PM, which in turn ensures polar auxin transport and distribution, thereby controlling plant patterning and auxin-regulated responses.
Arabidopsis thaliana RNase H2 Deficiency Counteracts the Needs for the WEE1 Checkpoint Kinase but Triggers Genome Instability
Authors: Kalhorzadeh Pooneh , Hu Zhubing , Cools Toon , Amiard Simon , Willing Eva-Maria , De Winne Nancy , Gevaert Kris , De Jaeger Geert , Schneeberger Korbinian , White Charles I. , De Veylder Lieven 
Published: September 2014

Abstract
The WEE1 kinase is an essential cell cycle checkpoint regulator in Arabidopsis thaliana plants experiencing replication defects. Whereas under non-stress conditions WEE1-deficient plants develop normally, they fail to adapt to replication inhibitory conditions, resulting in the accumulation of DNA damage and loss of cell division competence. We identified mutant alleles of the genes encoding subunits of the ribonuclease H2 (RNase H2) complex, known for its role in removing ribonucleotides from DNA-RNA duplexes, as suppressor mutants of WEE1 knockout plants. RNase H2 deficiency triggered an increase in homologous recombination (HR), correlated with the accumulation of γ-H2AX foci. However, as HR negatively impacts the growth of WEE1-deficient plants under replication stress, it cannot account for the rescue of the replication defects of the WEE1 knockout plants. Rather, the observed increase in ribonucleotide incorporation in DNA indicates that the substitution of deoxynucleotide with ribonucleotide abolishes the need for WEE1 under replication stress. Strikingly, increased ribonucleotide incorporation in DNA correlated with the occurrence of small base pair deletions, identifying the RNase H2 complex as an important suppressor of genome instability.
Adjustment of Host Cells for Accommodation of Symbiotic Bacteria: Vacuole Defunctionalization, HOPS Suppression, and TIP1g Retargeting in Medicago
Authors: Gavrin Aleksandr , Kaiser Brent N. , Geiger Dietmar , Tyerman Stephen D. , Wen Zhengyu , Bisseling Ton , Fedorova Elena E. 
Published: September 2014

Abstract
In legume–rhizobia symbioses, the bacteria in infected cells are enclosed in a plant membrane, forming organelle-like compartments called symbiosomes. Symbiosomes remain as individual units and avoid fusion with lytic vacuoles of host cells. We observed changes in the vacuole volume of infected cells and thus hypothesized that microsymbionts may cause modifications in vacuole formation or function. To examine this, we quantified the volumes and surface areas of plant cells, vacuoles, and symbiosomes in root nodules of Medicago truncatula and analyzed the expression and localization of VPS11 and VPS39, members of the HOPS vacuole-tethering complex. During the maturation of symbiosomes to become N2-fixing organelles, a developmental switch occurs and changes in vacuole features are induced. For example, we found that expression of VPS11 and VPS39 in infected cells is suppressed and host cell vacuoles contract, permitting the expansion of symbiosomes. Trafficking of tonoplast-targeted proteins in infected symbiotic cells is also altered, as shown by retargeting of the aquaporin TIP1g from the tonoplast membrane to the symbiosome membrane. This retargeting appears to be essential for the maturation of symbiosomes. We propose that these alterations in the function of the vacuole are key events in the adaptation of the plant cell to host intracellular symbiotic bacteria.
ABCG Transporters Are Required for Suberin and Pollen Wall Extracellular Barriers inArabidopsis
Authors: Yadav Vandana , Molina Isabel , Ranathunge Kosala , Castillo Indira Queralta , Rothstein Steven J. , Reed Jason W. 
Published: September 2014

AbstractEffective regulation of water balance in plants requires localized extracellular barriers that control water and solute movement. We describe a clade of five Arabidopsis thaliana ABCG half-transporters that are required for synthesis of an effective suberin barrier in roots and seed coats (ABCG2, ABCG6, and ABCG20) and for synthesis of an intact pollen wall (ABCG1 and ABCG16). Seed coats of abcg2 abcg6 abcg20 triple mutant plants had increased permeability to tetrazolium red and decreased suberin content. The root system of triple mutant plants was more permeable to water and salts in a zone complementary to that affected by the Casparian strip. Suberin of mutant roots and seed coats had distorted lamellar structure and reduced proportions of aliphatic components. Root wax from the mutant was deficient in alkylhydroxycinnamate esters. These mutant plants also had few lateral roots and precocious secondary growth in primary roots. abcg1 abcg16 double mutants defective in the other two members of the clade had pollen with defects in the nexine layer of the tapetum-derived exine pollen wall and in the pollen-derived intine layer. Mutant pollen collapsed at the time of anther desiccation. These mutants reveal transport requirements for barrier synthesis as well as physiological and developmental consequences of barrier deficiency.
Sterol Side Chain Reductase 2 Is a Key Enzyme in the Biosynthesis of Cholesterol, the Common Precursor of Toxic Steroidal Glycoalkaloids in Potato
Authors: Sawai Satoru , Ohyama Kiyoshi , Yasumoto Shuhei , Seki Hikaru , Sakuma Tetsushi , Yamamoto Takashi , Takebayashi Yumiko , Kojima Mikiko , Sakakibara Hitoshi , Aoki Toshio , Muranaka Toshiya , Saito Kazuki , Umemoto Naoyuki 
Published: September 2014

AbstractPotatoes (Solanum tuberosum) contain α-solanine and α-chaconine, two well-known toxic steroidal glycoalkaloids (SGAs). Sprouts and green tubers accumulate especially high levels of SGAs. Although SGAs were proposed to be biosynthesized from cholesterol, the biosynthetic pathway for plant cholesterol is poorly understood. Here, we identify sterol side chain reductase 2 (SSR2) from potato as a key enzyme in the biosynthesis of cholesterol and related SGAs. Using in vitro enzyme activity assays, we determined that potato SSR2 (St SSR2) reduces desmosterol and cycloartenol to cholesterol and cycloartanol, respectively. These reduction steps are branch points in the biosynthetic pathways between C-24 alkylsterols and cholesterol in potato. Similar enzymatic results were also obtained from tomato SSR2. St SSR2-silenced potatoes or St SSR2-disrupted potato generated by targeted genome editing had significantly lower levels of cholesterol and SGAs without affecting plant growth. Our results suggest that St SSR2 is a promising target gene for breeding potatoes with low SGA levels.