bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Dark Matter Crisis: Falsification of the Current Standard Model of Cosmology
Authors: Kroupa P. 
Published: March 2013

AbstractThe current standard model of cosmology (SMoC) requires The Dual Dwarf Galaxy Theorem to be true according to which two types of dwarf galaxies must exist: primordial dark-matter (DM) dominated (type A) dwarf galaxies, and tidal-dwarf and ram-pressure-dwarf (type B) galaxies void of DM. Type A dwarfs surround the host approximately spherically, while type B dwarfs are typically correlated in phasespace. Type B dwarfs must exist in any cosmological theory in which galaxies interact. Only one type of dwarf galaxy is observed to exist on the baryonic Tully-Fisher plot and in the radius-mass plane. The Milky Way satellite system forms a vast phase-space-correlated structure that includes globular clusters and stellar and gaseous streams. Other galaxies also have phase-space correlated satellite systems. Therefore, The Dual Dwarf Galaxy Theorem is falsified by observation and dynamically relevant cold or warm DM cannot exist. It is shown that the SMoC is incompatible with a large set of other extragalactic observations. Other theoretical solutions to cosmological observations exist. In particular, alone the empirical mass-discrepancy—acceleration correlation constitutes convincing evidence that galactic-scale dynamics must be Milgromian. Major problems with inflationary big bang cosmologies remain unresolved.
Stranding of Spawning Run Green Sturgeon in the Sacramento River: Post-Rescue Movements and Potential Population-Level Effects
Authors: Thomas Michael J. , Peterson Matthew L. , Friedenberg Nick , Van Eenennaam Joel P. , Johnson Joseph R. , Hoover Jan Jeffrey , Klimley A. Peter 
Published: March 2013

Abstract
The lower portion of the Sacramento River, California, has been highly engineered to protect low-lying surrounding communities from annual flood events. While engineered floodplains have provided adequate protection for the surrounding communities, there remain unintended consequences to migratory fish that become stranded during high flow events. In April 2011, we rescued 24 threatened Green Sturgeon Acipenser medirostris that were stranded in two flood diversions along the Sacramento River. We tagged these 24 Green Sturgeon with acoustic tags and analyzed their survival and migration success to their spawning grounds. Additionally, we provided a population viability analysis to show the potential impacts of stranding and the benefits of conducting rescues at the population level. We found that 17 of these 24 individuals continued their upstream migration to the spawning grounds. Modeling suggests that recurrent stranding of a similar magnitude without rescue could affect the long-term viability of Green Sturgeon in the Sacramento River. Population viability analyses of rescue predicted a 7% decrease below the population baseline model over 50 years as opposed to 33% without rescue. Despite the mitigated impact to the population with rescue, fish passage improvements should be considered as a long-term goal for preventing population risks at flood control diversions.
Received May 4, 2012; accepted December 6, 2012
Age at Maturity, Fork Length, and Sex Ratio of Upper Willamette River Hatchery Spring Chinook Salmon
Authors: Johnson Marc A. , Friesen Thomas A. 
Published: March 2013

Abstract
We used data from 17 brood years of coded-wire-tagged hatchery spring Chinook Salmon Oncorhynchus tshawytscha from the upper Willamette River to test for changes in mean age at maturity, fork length, and sex ratio. We found only limited evidence for any trend in age at maturity or sex ratio. However, Chinook Salmon sampled from tangle nets, recreational fisheries, spawning grounds, and hatcheries all presented trends of decline in mean fork length. Rates of change in fork length ranged from 0 to 5 mm per year in most sample collections, though fork length declined more rapidly for samples from tangle nets. We also observed a positive relationship between adult fork lengths and the median monthly Pacific Decadal Oscillation index in the year prior to juvenile liberation (the brood year). We suggest that future research should investigate the potential cause(s) for the decline in size of hatchery spring Chinook Salmon from the upper Willamette River, with attention to harvest, broad-scale environmental conditions, and hatchery spawning and rearing practices.
Received March 12, 2012; accepted December 11, 2012
Development of an Asian Carp Size Structure Index and Application through Demonstration
Authors: Phelps Quinton E. , Willis David W. 
Published: March 2013

Abstract
Asian carp (Cyprinidae) are among the most invasive fishes in North America, but assessment tools for evaluating stock structure have not been established. Thus, we used data from national and international published reports or manuscripts to develop standard length categories for four species of Asian carp. Due to the similarities in maximum reported size for Bighead Carp Hypophthalmichthys nobilis and Grass Carp Ctenopharyngodon idella, we propose the following standardized length categories for those two species: stock = 30 cm, quality = 54 cm, preferred = 68 cm, memorable = 89 cm, and trophy = 111 cm. Proposed Black Carp Mylopharyngodon piceus length categories are stock = 40 cm, quality = 72 cm, preferred = 90 cm, memorable = 118 cm, and trophy = 148 cm. Finally, we propose the following length categories for Silver Carp H. molitrix: stock = 25 cm, quality = 45 cm, preferred = 56 cm, memorable = 74 cm, and trophy = 93 cm. We then used existing data collected in the Illinois River and Mississippi River from 2003 to 2011 to evaluate Silver Carp proportional size distribution (PSD). Incremental PSD provided a temporal index of Silver Carp size structure in the Illinois River and strong cohorts could be followed through the incremental PSD values over time. Traditional PSD provided a quantifiable, comparative index of Silver Carp size structure among two locations in the Mississippi River and one location in the Illinois River. We believe this index provides an additional tool for fisheries managers to evaluate size structure of Asian carp and help assess overall population status.
Received September 19, 2012; accepted December 12, 2012
Channel Unit Use by Smallmouth Bass: Do Land-Use Constraints or Quantity of Habitat Matter?
Authors: Brewer Shannon K. 
Published: March 2013

Abstract
I examined how land use influenced the distribution of Smallmouth Bass Micropterus dolomieu in channel units (discrete morphological features—e.g., pools) of streams in the Midwestern USA. Stream segments (n = 36), from four clusters of different soil and runoff conditions, were identified that had the highest percent of forest (n = 12), pasture (n = 12), and urban land use (n = 12) within each cluster. Channel units within each stream were delineated and independently sampled once using multiple gears in summer 2006. Data were analyzed using a generalized linear mixed model procedure with a binomial distribution and odds ratio statistics. Land use and channel unit were strong predictors of age-0, age-1, and age-&gt;1 Smallmouth Bass presence. Each age-class was more likely to be present in streams within watersheds dominated by forest land use than in those with pasture or urban land uses. The interaction between land use and channel unit was not significant in any of the models, indicating channel unit use by Smallmouth Bass did not depend on watershed land use. Each of the three age-classes was more likely to use pools than other channel units. However, streams with high densities of Smallmouth Bass age &gt;1 had lower proportions of pools suggesting a variety of channel units is important even though habitat needs exist at the channel-unit scale. Management may benefit from future research addressing the significance of channel-unit quality as a possible mechanism for how land use impacts Smallmouth Bass populations. Further, management efforts aimed at improving stream habitat would likely be more beneficial if focused at the stream segment or landscape scale, where a variety of quality habitats might be supported.
Received September 10, 2012; accepted December 23, 2012
Brain and mood changes over 2 years in healthy controls and adults with heart failure and ischaemic heart disease
Authors: Almeida Osvaldo P. , Garrido Griselda J. , Etherton‐Beer Christopher , Lautenschlager Nicola T. , Arnolda Leonard , Alfonso Helman , Flicker Leon 
Published: March 2013

AimsHeart failure (HF) has been associated with cognitive dysfunction, a high prevalence of mood disorders, and a relative loss of grey matter in several brain regions. This study aimed to determine if, compared with controls with and without ischaemic heart disease (IHD), adults with HF show evidence of progressive loss of cerebral grey matter, and whether morphological changes are associated with changes in cognition, depression and anxiety symptoms over a follow‐up period of 2 years.Methods and resultsThis was a 24‐month longitudinal study of 19 participants with systolic HF, 43 with IHD, and 45 controls. Subjects were older than 45 years and free of cognitive impairment at the start of follow‐up. We acquired magnetic resonance images and used Statistical Parametric Mapping version 8 (SPM8) to investigate changes in the distribution of cerebral grey matter volume over time. We used the Cambridge Cognitive Examination of the Elderly (CAMCOG) and the Hospital Anxiety and Depression Scale (HADS) to assess 2‐year changes in cognitive function and mood. Changes in total grey matter volume and cognitive function were similar across the three study groups, but participants with HF showed evidence of increasing severity of anxiety and depressive symptoms. HF was associated with subtle regional loss of grey matter in the right and left thalamus, left caudate, left and right posterior cingulate, left and right parahippocampal gyri, left superior and middle temporal gyri, and right inferior parietal lobule compared with controls and, to a lesser extent, participants with IHD.ConclusionHF and IHD are not associated with a disproportional loss of cerebral grey matter or cognitive decline over 2 years compared with cardiologically healthy controls. Adults with HF experience increasing symptoms of anxiety and depression over 2 years compared with controls, and this increased vulnerability is associated with a relative loss of grey matter in brain regions that are important for the modulation of emotions.
Dehydrotriferulic and Dehydrodiferulic Acid Profiles of Cereal and Pseudocereal Flours
Authors: Jilek Margaret L. , Bunzel Mirko 
Published: March 2013

ABSTRACTDehydrooligomers of ferulic acid cross‐link polysaccharides such as arabinoxylans and pectic polysaccharides in cereal and certain pseudocereal grains, affecting physiological effects of these fiber components and their physicochemical properties during food processing. An HPLC‐MS method for the analysis of eight diferulic acids and five triferulic acids in low‐lignin samples such as cereal grains and pseudocereals was developed and validated. This method was applied to the analysis of ester‐linked diferulates and triferulates in maize, popcorn, wheat, rye, oats, barley, buckwheat, and amaranth, giving a complete profile of this set of diferulates and triferulates in cereals and pseudocereals. Triferulic acid contents of the cereal flours are roughly 1/10 of the diferulic acid contents, ranging between 23 (oats) and 161 (popcorn) μg/g of flour, with lower amounts for the pseudocereal flours (1–3 μg/g of flour). Dominating trimers are either the 5‐5/8‐O‐4‐ and/or the 8‐O‐4/8‐O‐4‐regioisomers with lower proportions of 8‐8cyclic/8‐O‐4‐, 8‐5noncyclic/8‐O‐4‐, and 8‐5noncyclic/5‐5‐triferulic acids. A unique diferulate pattern was found for buckwheat, with more than 90% of the dimers being 8‐5‐coupled. Amaranth contains an unusually high proportion of 8‐8cyclic‐diferulate, with 27% of the total dimers, whereas oats and barley show comparably high proportions (23%) of the 8‐8tetrahydrofuran diferulate.
Single‐Nucleotide Polymorphisms of IL‐10 and IL‐28B as Predictors of the Response of IFN Therapy in HCV Genotype 4–infected Children
Authors: Shaker Olfat G. , Nassar Yasser H. , Nour Zeinab A. , El Raziky Mona 
Published: March 2013

ABSTRACTBackground and Aims:Single‐nucleotide polymorphisms (SNPs) in the IL‐10 gene (−1082 [rs1800896], −819 [rs3021097], and −592 [rs1800872]) and the IL‐28B gene (rs12979860) in adults were shown to be associated with hepatitis C virus (HCV) clearance. The present study aimed to investigate the possible association of SNPs of IL‐10 and IL‐28B in predicting the treatment response of HCV genotype 4 in pediatric patients.Patients and Methods:A restriction fragment length polymorphism‐polymerase chain reaction and real‐time polymerase chain reaction techniques were used to genotype 34 pediatric patients with HCV genotype 4 for IL‐10 and IL‐28B SNPs, respectively. Patients received pegylated interferon‐α/ribavirin for 48 weeks subdivided according to their response to treatment into responders and nonresponders; also, 20 healthy individuals served as controls.Results:A significant difference (P < 0.005) was observed in SNP of IL‐28B rs12979860 frequencies between responders and nonresponders. In responders, CC genotype had greater frequency than CT and TT genotypes (60%, 30%, 10%), respectively, with C allele in its homozygous (CC) genotype more likely to respond to treatment than in its homozygous (TT) genotypes. SNPs of IL‐10 at −819 (rs3021097) showed significant differences in their genotype frequencies between responders and nonresponders to therapy, and TT genotype had greater frequency in responders than CT and CC (55%, 20%, 25%), respectively. Genotypes with T allele (CT/TT) showed higher rates of response than those with no T allele (CC).Conclusions:SNPs of the IL‐28B gene at (rs12979860) CC genotype as well as the IL‐10 gene SNPs at −819 (rs3021097)TT genotype can be used for predicting response to treatment before patients are prescribed the expensive pegylated interferon‐α/ribavirin therapy.
Exponentially accurate uniform asymptotic approximations for integrals and Bleistein's method revisited
Authors: Khwaja Sarah Farid , Olde Daalhuis Adri B. 
Published: March 2013

We obtain new uniform asymptotic approximations for integrals with a relatively exponentially small remainder. We illustrate how these results can be used to obtain remainder estimates in the Bleistein method. The method is created to deal with new types of integrals in which the usual methods for remainder estimates fail. As an application, we obtain an asymptotic expansion for

as

in |ph
λ
|≤
π
/2 uniformly for large |
z
|.
Thylakoid Terminal Oxidases Are Essential for the CyanobacteriumSynechocystissp. PCC 6803 to Survive Rapidly Changing Light Intensities
Authors: Lea-Smith David J. , Ross Nic , Zori Maria , Bendall Derek S. , Dennis John S. , Scott Stuart A. , Smith Alison G. , Howe Christopher J. 
Published: March 2013

AbstractCyanobacteria perform photosynthesis and respiration in the thylakoid membrane, suggesting that the two processes are interlinked. However, the role of the respiratory electron transfer chain under natural environmental conditions has not been established. Through targeted gene disruption, mutants of Synechocystis sp. PCC 6803 were generated that lacked combinations of the three terminal oxidases: the thylakoid membrane-localized cytochrome c oxidase (COX) and quinol oxidase (Cyd) and the cytoplasmic membrane-localized alternative respiratory terminal oxidase. All strains demonstrated similar growth under continuous moderate or high light or 12-h moderate-light/dark square-wave cycles. However, under 12-h high-light/dark square-wave cycles, the COX/Cyd mutant displayed impaired growth and was completely photobleached after approximately 2 d. In contrast, use of sinusoidal light/dark cycles to simulate natural diurnal conditions resulted in little photobleaching, although growth was slower. Under high-light/dark square-wave cycles, the COX/Cyd mutant suffered a significant loss of photosynthetic efficiency during dark periods, a greater level of oxidative stress, and reduced glycogen degradation compared with the wild type. The mutant was susceptible to photoinhibition under pulsing but not constant light. These findings confirm a role for thylakoid-localized terminal oxidases in efficient dark respiration, reduction of oxidative stress, and accommodation of sudden light changes, demonstrating the strong selective pressure to maintain linked photosynthetic and respiratory electron chains within the thylakoid membrane. To our knowledge, this study is the first to report a phenotypic difference in growth between terminal oxidase mutants and wild-type cells and highlights the need to examine mutant phenotypes under a range of conditions.
A Nostoc punctiforme Sugar Transporter Necessary to Establish a Cyanobacterium-Plant Symbiosis
Authors: Ekman Martin , Picossi Silvia , Campbell Elsie L. , Meeks John C. , Flores Enrique 
Published: March 2013

Abstract
In cyanobacteria-plant symbioses, the symbiotic nitrogen-fixing cyanobacterium has low photosynthetic activity and is supplemented by sugars provided by the plant partner. Which sugars and cyanobacterial sugar uptake mechanism(s) are involved in the symbiosis, however, is unknown. Mutants of the symbiotically competent, facultatively heterotrophic cyanobacterium Nostoc punctiforme were constructed bearing a neomycin resistance gene cassette replacing genes in a putative sugar transport gene cluster. Results of transport activity assays using 14C-labeled fructose and glucose and tests of heterotrophic growth with these sugars enabled the identification of an ATP-binding cassette-type transporter for fructose (Frt), a major facilitator permease for glucose (GlcP), and a porin needed for the optimal uptake of both fructose and glucose. Analysis of green fluorescent protein fluorescence in strains of N. punctiforme bearing frt::gfp fusions showed high expression in vegetative cells and akinetes, variable expression in hormogonia, and no expression in heterocysts. The symbiotic efficiency of N. punctiforme sugar transport mutants was investigated by testing their ability to infect a nonvascular plant partner, the hornwort Anthoceros punctatus. Strains that were specifically unable to transport glucose did not infect the plant. These results imply a role for GlcP in establishing symbiosis under the conditions used in this work.
Arabidopsis and Brachypodium distachyon Transgenic Plants Expressing Aspergillus nidulans Acetylesterases Have Decreased Degree of Polysaccharide Acetylation and Increased Resistance to Pathogens
Authors: Pogorelko Gennady , Lionetti Vincenzo , Fursova Oksana , Sundaram Raman M. , Qi Mingsheng , Whitham Steven A. , Bogdanove Adam J. , Bellincampi Daniela , Zabotina Olga A. 
Published: March 2013

Abstract
The plant cell wall has many significant structural and physiological roles, but the contributions of the various components to these roles remain unclear. Modification of cell wall properties can affect key agronomic traits such as disease resistance and plant growth. The plant cell wall is composed of diverse polysaccharides often decorated with methyl, acetyl, and feruloyl groups linked to the sugar subunits. In this study, we examined the effect of perturbing cell wall acetylation by making transgenic Arabidopsis (Arabidopsis thaliana) and Brachypodium (Brachypodium distachyon) plants expressing hemicellulose- and pectin-specific fungal acetylesterases. All transgenic plants carried highly expressed active Aspergillus nidulans acetylesterases localized to the apoplast and had significant reduction of cell wall acetylation compared with wild-type plants. Partial deacetylation of polysaccharides caused compensatory up-regulation of three known acetyltransferases and increased polysaccharide accessibility to glycosyl hydrolases. Transgenic plants showed increased resistance to the fungal pathogens Botrytis cinerea and Bipolaris sorokiniana but not to the bacterial pathogens Pseudomonas syringae and Xanthomonas oryzae. These results demonstrate a role, in both monocot and dicot plants, of hemicellulose and pectin acetylation in plant defense against fungal pathogens.
Empty Pericarp5Encodes a Pentatricopeptide Repeat Protein That Is Required for Mitochondrial RNA Editing and Seed Development in Maize
Authors: Liu Yu-Jun , Xiu Zhi-Hui , Meeley Robert , Tan Bao-Cai 
Published: March 2013

AbstractIn flowering plants, RNA editing is a posttranscriptional mechanism that converts specific cytidines to uridines in both mitochondrial and plastidial transcripts, altering the information encoded by these genes. Here, we report the molecular characterization of the empty pericarp5 (emp5) mutants in maize (Zea mays). Null mutation of Emp5 results in abortion of embryo and endosperm development at early stages. Emp5 encodes a mitochondrion-targeted DYW subgroup pentatricopeptide repeat (PPR) protein. Analysis of the mitochondrial transcripts revealed that loss of the EMP5 function abolishes the C-to-U editing of ribosomal protein L16 at the rpl16-458 site (100% edited in the wild type), decreases the editing at nine sites in NADH dehydrogenase9 (nad9), cytochrome c oxidase3 (cox3), and ribosomal protein S12 (rps12), and surprisingly increases the editing at five sites of ATP synthase F0 subunit a (atp6), apocytochrome b (cob), nad1, and rpl16. Mutant EMP5-4 lacking the E+ and DYW domains still retains the substrate specificity and editing function, only at reduced efficiency. This suggests that the E+ and DYW domains of EMP5 are not essential to the EMP5 editing function but are necessary for efficiency. Analysis of the ortholog in rice (Oryza sativa) indicates that rice EMP5 has a conserved function in C-to-U editing of the rice mitochondrial rpl16-458 site. EMP5 knockdown expression in transgenics resulted in slow growth and defective seeds. These results demonstrate that Emp5 encodes a PPR-DYW protein that is required for the editing of multiple transcripts in mitochondria, and the editing events, particularly the C-to-U editing at the rpl16-458 site, are critical to the mitochondrial functions and, hence, to seed development in maize.
Allosteric Regulation of Transport Activity by Heterotrimerization of Arabidopsis Ammonium Transporter Complexes in Vivo
Authors: Yuan Lixing , Gu Riliang , Xuan Yuanhu , Smith-Valle Erika , Loqué Dominique , Frommer Wolf B. , von Wirén Nicolaus 
Published: March 2013

Abstract
Ammonium acquisition by plant roots is mediated by AMMONIUM TRANSPORTERs (AMTs), ubiquitous membrane proteins with essential roles in nitrogen nutrition in all organisms. In microbial and plant cells, ammonium transport activity is controlled by ammonium-triggered feedback inhibition to prevent cellular ammonium toxicity. Data from heterologous expression in yeast indicate that oligomerization of plant AMTs is critical for allosteric regulation of transport activity, in which the conserved cytosolic C terminus functions as a trans-activator. Employing the coexpressed transporters AMT1;1 and AMT1;3 from Arabidopsis thaliana as a model, we show here that these two isoforms form functional homo- and heterotrimers in yeast and plant roots and that AMT1;3 carrying a phosphomimic residue in its C terminus regulates both homo- and heterotrimers in a dominant-negative fashion in vivo. 15NH4 + influx studies further indicate that allosteric inhibition represses ammonium transport activity in roots of transgenic Arabidopsis expressing a phosphomimic mutant together with functional AMT1;3 or AMT1;1. Our study demonstrates in planta a regulatory role in transport activity of heterooligomerization of transporter isoforms, which may enhance their versatility for signal exchange in response to environmental triggers.