bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic and Metabolic Changes Associated with Photorespiratory Ammonium Accumulation in the Model Legume Lotus japonicus
Authors: Pérez-Delgado Carmen M. , García-Calderón Margarita , Sánchez Diego H. , Udvardi Michael K. , Kopka Joachim , Márquez Antonio J. , Betti Marco 
Published: June 2013

Abstract
The transcriptomic and metabolic consequences of the lack of plastidic glutamine (Gln) synthetase in the model legume Lotus japonicus were investigated. Wild-type and mutant plants lacking the plastidic isoform of Gln synthetase were grown in conditions that suppress photorespiration and then transferred for different lengths of time to photorespiratory conditions. Transcript and metabolite levels were determined at the different time points considered. Under photorespiratory active conditions, the mutant accumulated high levels of ammonium, followed by its subsequent decline. A coordinate repression of the photorespiratory genes was observed in the mutant background. This was part of a greater modulation of the transcriptome, especially in the mutant, that was paralleled by changes in the levels of several key metabolites. The data obtained for the mutant represent the first direct experimental evidence for a coordinate regulation of photorespiratory genes over time. Metabolomic analysis demonstrated that mutant plants under active photorespiratory conditions accumulated high levels of several amino acids and organic acids, including intermediates of the Krebs cycle. An increase in Gln levels was also detected in the mutant, which was paralleled by an increase in cytosolic Gln synthetase1 gene transcription and enzyme activity levels. The global panoramic of the transcripts and metabolites that changed in L. japonicus plants during the transfer from photorespiration-suppressed to photorespiration-active conditions highlighted the link between photorespiration and several other cellular processes, including central carbon metabolism, amino acid metabolism, and secondary metabolism.
A trait‐based ecosystem model suggests that long‐term responsiveness to rising atmospheric CO2 concentration is greater in slow‐growing than fast‐growing plants
Authors: Ali Ashehad A. , Medlyn Belinda E. , Crous Kristine Y. , Reich Peter B. 
Published: June 2013

Summary

Atmospheric carbon dioxide concentration (Ca) has a direct and measurable effect on plant growth. However, it does not affect all plant species equally, which could lead to shifts in competitive dominance of species in ecosystems.
We used a dynamic plant carbon–nitrogen model to systematically examine how species traits affect the long‐term Ca responsiveness of C3 plants when growing as established monocultures in the field. The model was tested against responses of 7 C3 herbaceous species growing in a free‐air Ca enrichment (FACE) experiment (BioCON) in Minnesota, USA.
Model simulations showed that several species traits affected the Ca response strongly, giving rise to a number of testable hypotheses about interspecific differences in responsiveness to Ca. The largest responses to rising Ca were obtained for species with low carbon‐use efficiency (net primary production: gross primary production ratio), low foliar carbon allocation, low stomatal conductance, low instantaneous photosynthetic nitrogen use efficiency and low specific leaf area.
In general, our model predicted that, for established plants growing in resource‐limited field conditions, species with slow growth rates would be most responsive to elevated Ca. This prediction was supported by data from the BioCON experiment.
Our model also predicts that, for young plants growing in non‐resource‐limited conditions, species with high growth rates will be most responsive to elevated Ca. This difference in species ranking under different resource availabilities is largely explained by the indirect effects of Ca on leaf area. Leaf‐area feedbacks favour fast‐growing species the most during leaf‐area expansion, but following stand maturation they favour slow‐growing species the most.

These results imply that species that respond strongly to elevated Ca in short‐term (non‐resource‐limited) glasshouse experiments are unlikely to also be the most responsive in resource‐limited field conditions, and therefore that we cannot directly extrapolate from glasshouse experiments to predict which species will be most responsive to elevated Ca in the long term.
Indirect effects and facilitation among native and non‐native species promote invasion success along an environmental stress gradient
Authors: Zarnetske Phoebe L. , Gouhier Tarik C. , Hacker Sally D. , Seabloom Eric W. , Bokil Vrushali A. 
Published: June 2013

Summary

The spatial distribution of species is mediated by a combination of biotic interactions and environmental conditions. Understanding the relative importance of these factors and how they interact is particularly important for predicting the spread of non‐native species and their impact on resident communities.

We used a 3‐species Lotka–Volterra model parameterized with field and experimental data to understand the potential for continued spread by an introduced, non‐native, dune‐building beach grass (Ammophila breviligulata) and whether this invasion will result in coexistence or displacement in the resident beach grass communities (native Elymus mollis and introduced, non‐native Ammophila arenaria) of the US Pacific Northwest.

We also used the model to investigate to what extent different rates of ocean‐driven sand supply mediate the outcomes of beach grass species interactions.

Our model suggests that A. breviligulata could invade and dominate dunes across the range of sand supply rates observed in the region. We found that sand supply influenced intra‐ vs. interspecific interactions, the strength of positive and indirect effects among beach grasses and the long‐term abundances of the beach grass species themselves.

Of the two non‐natives, A. breviligulata is the inferior dune‐building species. Thus, our results suggest that further invasions by A. breviligulata could reduce the coastal protection services afforded by tall dunes currently dominated by A. arenaria.

Synthesis: In systems with strong environmental forcing and stressful conditions such as coastal dunes, environmentally mediated positive and indirect species interactions can govern invasion success and long‐term native–non‐native coexistence. In doing so, these interactions ultimately shape community structure and ecosystem function. Understanding the joint effects of environmental forcing and species interactions on community assembly is particularly important in cases where species introductions can alter ecosystem services, such as coastal protection, which are vulnerable to the effects of climate change.
A genome‐wide association study to detect genetic variation for postpartum dysgalactia syndrome in five commercial pig breeding lines
Authors: Preissler Regine , Tetens Jens , Reiners Kerstin , Looft Holger , Kemper Nicole 
Published: June 2013

SummaryPostpartum dysgalactia syndrome (PDS) in sows is an important disease after parturition with a relevant economic impact, affecting the health and welfare of both sows and piglets. The genetic background of this disease has been discussed and its heritability estimated, but further genetic analyses are lacking in detail. The aim of the current study was to detect loci affecting the susceptibility to PDS through a genome‐wide association approach. The study was designed as a family‐based association study with matched sampling of affected sows and healthy half‐ or full‐sib control sows on six farms. For the study, 597 sows (322 affected vs. 275 healthy control sows) were genotyped on 62 163 single nucleotide polymorphisms (SNPs) using the Illumina PorcineSNP60 BeadChip. After quality control, 585 sows (314 affected vs. 271 healthy control sows) and 49 740 SNPs remained for further analysis. Statistics were performed mainly with the r package genabel and included a principal component analysis. A statistically significant genome‐wide associated SNP was identified on porcine chromosome (SSC) 17. Further promising results with moderate significance were detected on SSC 13 and on an unplaced scaffold with an older annotation on SSC 15. The PRICKLE2 and NRP2 genes were identified as candidate genes near associated SNPs. Several quantitative trait loci (QTL) have been previously described in these genomic regions, including QTL for mammary gland condition, as teat number and non‐functional nipples QTL, as well as QTL for body temperature and gestation length.
Fine mapping of the chicken congenital loco locus on chromosome 12
Authors: Okumura Y. , Ohtake T. , Uemoto Y. , Sato S. , Sato S. , Kobayashi E. 
Published: June 2013

SummaryCongenital loco in chicks is characterized by an apparent lack of control of the muscles of the neck. This disorder is inherited as a simple Mendelian recessive disease, caused by an autosomal recessive gene, lo. To date, there are no reports on the localization of this gene. The objective of this study was therefore to identify the genomic region of the lo locus. The experimental congenital loco population used here were selected from a Rhode Island Red (RIR) line and consisted of six generations, resulting in 124 chickens. A total of 113 DNA samples from offspring of four generations (G3, G4, G5, and G6) were used for genotyping. At first, genome‐wide linkage mapping was performed using 122 microsatellite markers on 22 autosomal chromosomes, and the lo locus was mapped to chromosome 12. We then performed fine mapping in two steps on chromosome 12. First, the lo locus was mapped to the interval between GGA12_5 and GGA12_11 using 13 new polymorphic markers. In the second step, fine mapping was performed by adding new families and 11 additional new polymorphic markers. Linkage mapping and haplotype information enabled the localization of the lo locus to a 1.1‐Mb region between GGA12_28 and GGA12_30. Genetic markers between GGA12_28 and GGA12_30 may be used to remove the carriers of congenital loco through this RIR line.
Agriculture and small towns in Africa
Authors: Dorosh Paul , Thurlow James 
Published: June 2013

AbstractAfrica is urbanizing rapidly. Yet most dual economy models focus on the sectoral rather than spatial dimensions of development. This article adopts a “dual–dual” approach to measuring rural/urban and farm/nonfarm linkages. We develop an economy‐wide model of Ethiopia that distinguishes between cities, towns, and rural areas. The model captures detailed sectoral and regional linkages, internal migration flows, and externalities from urban agglomeration. We find larger linkages between agricultural production and small towns and show that redirecting urban growth toward towns rather than cities leads to broader‐based economic growth and poverty reduction. In contrast, industry and services, particularly within cities, are far less effective in reaching rural areas and the poor. Africa's current urbanization pattern—toward major cities rather than towns—will weaken national growth–poverty linkages. Urbanization that takes advantage of the synergistic relationship between agriculture and small towns has the potential to result in a more inclusive growth trajectory.
Dry eye disease in French elderly subjects: the Alienor Study
Authors: Malet Florence , Le Goff Mélanie , Colin Joseph , Schweitzer Cédric , Delyfer Marie‐Noëlle , Korobelnik Jean‐François , Rougier Marie‐Bénédicte , Radeau Thierry , Dartigues Jean‐François , Delcourt Cécile 
Published: June 2013

Abstract.Purpose:  To describe dry eye disease in French elderly subjects.Methods:  The Alienor Study is a population‐based study on age‐related eye disease in 963 residents of Bordeaux (France), aged 73 years or more. Self‐reported dry eye disease and use of artificial tears were documented through face‐to‐face interview. Dry eye symptoms were assessed using the Ocular Surface Disease Index (OSDI) questionnaire and tear film stability by tear break‐up time measurements (TBUT). Definite dry eye disease was defined as self‐reported dry eye, confirmed by use of artificial tears and/or OSDI greater or equal to 22.Results:  Nine hundred and fifteen subjects, with mean age of 80 ± 4 years, returned the OSDI questionnaire. Of these, 271 (29.6%) subjects reported a dry eye disease and 135 (14.7%) were using artificial tears. An OSDI score > 22 was found in 359 (39.2%) subjects and a TBUT < 5 seconds in 335/746 (44.9%) subjects. Overall, definite dry eye affected 21.9% of subjects and was more frequent in women (27.1%) than in men (13.6%). After multivariate adjustment, dry eye disease was also significantly less frequent in subjects with high educational level (odds ratio (OR) = 0.49, 95% confidence interval (CI): 0.31–0.78 for long secondary school) and more frequent in subjects with ocular hypertension (OR = 1.61, 95% CI: 1.02–2.57) and those using anxiolytics (OR = 1.53, 95% CI: 1.02–2.29).Conclusions:  This large observational study confirmed the high prevalence of dry eye symptoms among elderly subjects and confirmed some of the previously identified risk factors (in particular female gender and use of anxiolytics).
Magnetic resonance imaging (MRI)‐guided transurethral ultrasound therapy of the prostate: a preclinical study with radiological and pathological correlation using customised MRI‐based moulds
Authors: Partanen Ari , Yerram Nitin K. , Trivedi Hari , Dreher Matthew R. , Oila Juha , Hoang Anthony N. , Volkin Dmitry , Nix Jeffrey , Turkbey Baris , Bernardo Marcelino , Haines Diana C. , Benjamin Compton J. , Linehan W. Marston , Choyke Peter , Wood Bradford J. , Ehnholm Gösta J. , Venkatesan Aradhana M. , Pinto Peter A. 
Published: June 2013

Objective
To characterise the feasibility and safety of a novel transurethral ultrasound (US)‐therapy device combined with real‐time multi‐plane magnetic resonance imaging (MRI)‐based temperature monitoring and temperature feedback control, to enable spatiotemporally precise regional ablation of simulated prostate gland lesions in a preclinical canine model.
To correlate ablation volumes measured with intra‐procedural cumulative thermal damage estimates, post‐procedural MRI, and histopathology.
Materials and Methods
Three dogs were treated with three targeted ablations each, using a prototype MRI‐guided transurethral US‐therapy system (Philips Healthcare, Vantaa, Finland).
MRI provided images for treatment planning, guidance, real‐time multi‐planar thermometry, as well as post‐treatment evaluation of efficacy.
After treatment, specimens underwent histopathological analysis to determine the extent of necrosis and cell viability.
Statistical analyses (Pearson's correlation, Student's t‐test) were used to evaluate the correlation between ablation volumes measured with intra‐procedural cumulative thermal damage estimates, post‐procedural MRI, and histopathology.
Results
MRI combined with a transurethral US‐therapy device enabled multi‐planar temperature monitoring at the target as well as in surrounding tissues, allowing for safe, targeted, and controlled ablations of prescribed lesions.
Ablated volumes measured by cumulative thermal dose positively correlated with volumes determined by histopathological analysis (r2 0.83, P < 0.001).
Post‐procedural contrast‐enhanced and diffusion‐weighted MRI showed a positive correlation with non‐viable areas on histopathological analysis (r2 0.89, P < 0.001, and r2 0.91, P = 0.003, respectively).
Additionally, there was a positive correlation between ablated volumes according to cumulative thermal dose and volumes identified on post‐procedural contrast‐enhanced MRI (r2 0.77, P < 0.01).
There was no difference in mean ablation volumes assessed with the various analysis methods (P > 0.05, Student's t‐test).
Conclusions
MRI‐guided transurethral US therapy enabled safe and targeted ablations of prescribed lesions in a preclinical canine prostate model.
Ablation volumes were reliably predicted by intra‐ and post‐procedural imaging.
Clinical studies are needed to confirm the feasibility, safety, oncological control, and functional outcomes of this therapy in patients in whom focal therapy is indicated.
Serum prostate‐specific antigen (PSA) concentration is positively associated with rate of disease reclassification on subsequent active surveillance prostate biopsy in men with low PSA density
Authors: Umbehr Martin H. , Platz Elizabeth A. , Peskoe Sarah B. , Bhavsar Nrupen A. , Epstein Jonathan I. , Landis Patricia , Partin Alan W. , Carter H. Ballentine 
Published: June 2013

Objective
To investigate the association between serum prostate‐specific antigen (PSA) concentration at active surveillance (AS) entry and disease reclassification on subsequent AS biopsy (‘biopsy reclassification’) in men with low PSA density (PSAD).
To investigate whether a clinically meaningful PSA threshold for AS eligibility/ineligibility for men with low PSAD can be identified based on risk of subsequent biopsy reclassification.
Patients and Methods
We included men enrolled in the Johns Hopkins AS Study (JHAS) who had a PSAD of <0.15 ng/mL/g (640 men).
We estimated the incidence rates (IRs; per 100 person years) and hazard ratios (HR) of biopsy reclassification (Gleason score ≥ 7, any Gleason pattern 4 or 5, ≥3 positive cores, or ≥50% cancer involvement/biopsy core) for categories of serum PSA concentration at the time of entry into AS.
We generated predicted IRs using Poisson regression to adjust for age and prostate volume, mean percentage free PSA (ratio of free to total PSA) and maximum percentage biopsy core involvement with cancer.
Results
The unadjusted IRs (per 100 person years) of biopsy reclassification across serum PSA concentration at entry into JHAS showed, in general, an increase; however, the pattern was not linear with higher IRs in the group ≥ 4 to <6 ng/mL (14.2, 95% confidence interval [CI] 11.8–17.2%) when compared with ≥6 to <8 ng/mL (8.4, 95% CI 5.7–12.3%) but almost similar IRs when compared with the group ≥ 8 to <10 ng/mL (14.8, 95% CI 8.4–26.1%).
The adjusted predicted IRs of reclassification showed a similar non‐linear increase in IRs, whereby the rates around 4 ng/mL were similar to the rates around 10 ng/mL.
ConclusionRisk for biopsy reclassification increased non‐linearly across PSA concentration in men with low PSAD, whereby no obvious clinically meaningful threshold could be identified. This information could be incorporated into decision‐making for AS. However, longer follow‐up times are needed to warrant final conclusions.
Histological inflammation and risk of subsequent prostate cancer among men with initially elevated serum prostate‐specific antigen (PSA) concentration in the Finnish prostate cancer screening trial
Authors: Yli‐Hemminki Tytti H. , Laurila Marita , Auvinen Anssi , Määttänen Liisa , Huhtala Heini , Tammela Teuvo L.J. , Kujala Paula M. 
Published: June 2013

Objective
To assess whether histological signs of inflammation are associated with an increased risk of subsequent prostate cancer (PCa) in men with elevated serum prostate‐specific antigen (PSA) concentrations and benign initial biopsy.
Materials and Methods
Study subjects were men aged 54–67 years with an elevated PSA (≥4 ng/mL or 3–4 ng/mL and free to total PSA ratio ≤0.16 or positive digital rectal examination), but a benign biopsy result within the Finnish population‐based randomised screening trial for PCa, which started in 1996.
A total of 293 prostate biopsies without PCa or suspicion of malignancy from the first screening round in the Tampere centre were re‐evaluated by a uropathologist to assess histological inflammation.
Results of the subsequent screening rounds were obtained from the trial database and PCa diagnoses made outside the screening were obtained from the Finnish Cancer Registry.
The median length of follow‐up was 10.5 years.
Cox regression analysis was used to assess PCa risk after the initial benign biopsy.
Results
Histological inflammation was found in 66% of the biopsies.
Subjects with inflammation at the biopsy had a slightly lower PCa risk in the second screening round (18 vs 27%, rate ratio 0.69, 95% confidence interval [CI] 0.35–1.34) relative to men without inflammation. In further follow‐up, the PCa risk remained nonsignificantly lower (hazard ratio [HR] 0.71, CI 0.46–1.10; P = 0.13). The risk was not appreciably affected by adjustment for age, PSA, prostate volume and family history of PCa (HR 0.67, CI 0.42–1.07; P = 0.092).
Conclusions
Histological inflammation in a prostate biopsy among men with an initial false‐positive screening test was not associated with an increased risk of subsequent PCa, but instead with a decreased risk which was of borderline significance.
Inflammation in prostate biopsy is not a useful risk indicator in PCa screening.
Receptor tyrosine kinases MET and RON as prognostic factors in diffuse large B‐cell lymphoma patients receiving R‐CHOP
Authors: Koh Young Wha , Hwang Hee Sang , Jung Se Jin , Park Chansik , Yoon Dok Hyun , Suh Cheolwon , Huh Jooryung 
Published: June 2013

Receptor tyrosine kinases MET and RON (MST1R) form non‐covalent complexes on the cell surface, a critical step in tumor progression. A recent study suggested a prognostic role for MET expression in diffuse large B‐cell lymphoma (DLBCL). The aim of this study was to examine the impact of MET and RON expression in uniformly treated DLBCL patients. The expression of MET and RON was retrospectively examined by immunohistochemistry in 120 DLBCL patients treated with rituximab combined with a CHOP regimen (cyclophosphamide, doxorubicin, vincristine, and prednisone). The median follow‐up time was 42.5 months (range, 1–89 months). Thirty‐two (26%) and 30 patients (25%) expressed MET or RON, respectively. Seventy‐five patients (62.5%) were negative for both MET and RON (MET−RON−). MET negativity was associated with worse overall survival (P = 0.029). In multivariate analysis, negativity for both MET and RON (MET−RON−) was strongly associated with inferior overall survival (P = 0.008). Interestingly, the MET−RON− phenotype retained its prognostic impact after subgroup analysis according to the international prognostic index or by the cell of origin by immunohistochemical algorithm by Choi et al. This study suggests that the MET−RON− phenotype is an independent prognostic factor in DLBCL patients receiving R‐CHOP, and may identify a subgroup of DLBCL patients who require more intensive therapy.
Sigma‐1 Receptor Knockout Impairs Neurogenesis in Dentate Gyrus of Adult Hippocampus Via Down‐Regulation of NMDA Receptors
Authors: Sha Sha , Qu Wei‐Jun , Li Lin , Lu Zi‐Hong , Chen Lei , Yu Wen‐Feng , Chen Ling 
Published: June 2013

SummaryAimsThis study investigated the influence of sigma‐1 receptor (σ1R) deficiency on adult neurogenesis.MethodsWe employed 8‐week‐old male σ1R knockout (σ1R−/−) mice to examine the proliferation and differentiation of progenitor cells, and the survival and neurite growth of newborn neurons in hippocampal dentate gyrus (DG).ResultsIn comparison with wild‐type (WT) littermates, the numbers of 24‐h‐old BrdU+ cells and Ki67+ cells in σ1R−/− mice increased, while the number of 28‐day‐old BrdU+ cells decreased without changes in proportion of BrdU+/NeuN+ cells and BrdU+/GFAP+ cells. The neurite density of newborn neurons was slightly reduced in σ1R−/− mice. In DG granular cells, N‐methyl‐d‐aspartate (NMDA)‐activated current (INMDA) and phosphorylation of NMDA receptor (NMDAr) NR2B were reduced in σ1R−/− mice without the alteration of NR2B expression and membrane properties compared to WT mice. The NR2B antagonist abolished the difference in INMDA between σ1R−/− mice and WT mice. The application of NMDAr agonist in σ1R−/− mice prevented the over‐proliferation of cells and reduction in newborn neurons, but it had no effects on the hypoplastic neurite. The administration of NMDAr antagonist in WT mice enhanced the cell proliferation and depressed the survival of newborn neurons.ConclusionThe σ1R deficiency impairs neurogenesis in DG through down‐regulation of NMDArs.