bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alternative hypotheses to explain why biodiversity-ecosystem functioning relationships are concave-up in some natural ecosystems but concave-down in manipulative experiments
Authors: Mora Camilo , Danovaro Roberto , Loreau Michel 
Published: June 2014

AbstractRecent studies of the relationship between biodiversity and functioning in marine ecosystems have yielded non-saturating patterns that contrast sharply with the results of experimental studies, where ecosystem functioning rapidly saturates with increases in biodiversity. Here we provide a simple theoretical framework of three alternative hypotheses that, individually or combined, are likely to explain this contrast: i) the use of functional richness instead of species richness, ii) an increased production efficiency of species in producing biomass when more ecological interactions are present and iii) the fact that communities are likely assembled in an ordered succession of species from low to high ecological efficiency. Our results provide theoretical support for concave-up biodiversity-ecosystem functioning relationships in natural ecosystems and confirm that the loss of species can have substantially larger effects on the functioning of natural ecosystems than anticipated from controlled manipulative experiments.
Two distinct populations of Bovine IL-17+ T-cells can be induced and WC1+IL-17+γδ T-cells are effective killers of protozoan parasites
Authors: Peckham R. K. , Brill R. , Foster D. S. , Bowen A. L. , Leigh J. A. , Coffey T. J. , Flynn R. J. 
Published: June 2014

AbstractIL-17 has emerged as a key player in the immune system, exhibiting roles in protection from infectious diseases and promoting inflammation in autoimmunity. Initially thought to be CD4 T-cell-derived, the sources of IL-17 are now known to be varied and belong to both the innate and adaptive arms of the immune system. Mechanisms for inducing IL-17 production in lymphoid cells are thought to rely on appropriate antigenic stimulation in the context of TGF-β1, IL-6 and/or IL-1β. Using culture protocols adapted from human studies, we have effectively induced both bovine CD4+ and WC1+ γδ T-cells to produce IL-17 termed Th17 and γδ17 cells, respectively. The negative regulatory effect of IFN-γ on mouse and human IL-17 production can be extended to the bovine model, as addition of IFN-γ decreases IL-17 production in both cell types. Furthermore we show that infection with the protozoan Neospora caninum will induce fibroblasts to secrete pro-IL-17 factors thereby inducing a γδ17 phenotype that preferentially kills infected target cells. Our study identifies two T-cell sources of IL-17 and is the first to demonstrate a protective effect of IL-17+ T-cells in ruminants. Our findings offer further opportunities for future adjuvants or vaccines which could benefit from inducing these responses.
The consensus-based approach for gene/enzyme replacement therapies and crystallization strategies: the case of human alanine–glyoxylate aminotransferase
Authors: Mesa-Torres Noel , Yunta Cristina , Fabelo-Rosa Israel , Gonzalez-Rubio Juana María , Sánchez-Ruiz José M. , Salido Eduardo , Albert Armando , Pey Angel L. 
Published: June 2014

Protein stability is a fundamental issue in biomedical and biotechnological applications of proteins. Among these applications, gene- and enzyme-replacement strategies are promising approaches to treat inherited diseases that may benefit from protein engineering techniques, even though these beneficial effects have been largely unexplored. In the present study we apply a sequence-alignment statistics procedure (consensus-based approach) to improve the activity and stability of the human AGT (alanine–glyoxylate aminotransferase) protein, an enzyme which causes PH1 (primary hyperoxaluria type I) upon mutation. By combining only five consensus mutations, we obtain a variant (AGT-RHEAM) with largely enhanced in vitro thermal and kinetic stability, increased activity, and with no side effects on foldability and peroxisomal targeting in mammalian cells. The structure of AGT-RHEAM reveals changes at the dimer interface and improved electrostatic interactions responsible for increased kinetic stability. Consensus-based variants maintained the overall protein fold, crystallized more easily and improved the expression as soluble proteins in two different systems [AGT and CIPK24 (CBL-interacting serine/threonine-protein kinase) SOS2 (salt-overly-sensitive 2)]. Thus the consensus-based approach also emerges as a simple and generic strategy to increase the crystallization success for hard-to-get protein targets as well as to enhance protein stability and function for biomedical applications.
Ultrasound-triggered disruption and self-healing of reversibly cross-linked hydrogels for drug delivery and enhanced chemotherapy
Authors: Huebsch Nathaniel , Kearney Cathal J. , Zhao Xuanhe , Kim Jaeyun , Cezar Christine A. , Suo Zhigang , Mooney David J. 
Published: June 2014

Significance
Drug-releasing polymers give clinicians the ability to deliver chemotherapy directly to tumors, sparing the rest of the body from toxic side effects. Most devices deliver a constant, unchangeable drug dose over time. However, we found that cancer cells are more sensitive to short-term, high-dose “bursts” of the chemotherapeutic mitoxantrone than to constant doses over longer periods, suggesting a benefit for implantable devices that allow external control over dose and timing. Biocompatible, injectable alginate hydrogels displayed the ability to self-heal damage induced by ultrasound pulses, enabling on-demand delivery of mitoxantrone, in vitro and in vivo, and mitoxantrone-loaded gels implanted near tumors were more effective at eliminating tumor growth when a daily pulse of ultrasound was applied.
Effects of Age at Treatment on Oxytetracycline Mark Formation in Larval Northern Pike
Authors: Rhoten Jason C. , Fisher Shannon J. , Logsdon Dale E. , Pittman Bruce J. 
Published: June 2014

Abstract
Oxytetracycline (OTC) immersion treatments were evaluated at the Waterville State Fish Hatchery (Waterville, Minnesota) for producing fluorescent marks on larval Northern Pike Esox lucius otoliths. A pilot marking trial conducted with 7-d-posthatch (dph) larvae resulted in poor mark efficacy and prompted further investigation on the treatment of younger larvae and modification of the treatment by use of osmotic induction to promote better mark formation. Northern Pike treated within 24 h post-hatch had significantly higher mark efficacies and marked otolith intensities than did Northern Pike treated at later life stages. Similar to the pilot marking trial, immersion of 7-dph fry in OTC solution resulted in poor mark efficacy, in which only 38% of the inspected fry possessed visible marks and most of the marks that were visible appeared faint. Simple immersion of newly hatched fry in OTC solution resulted in 91% marking success, and 65% of the visible marks appeared either clear or intense. The poorer mark efficacy on 7-dph fry suggests that differences in mark formation were more dependent on contemporaneous physiological processes than on otolith size. Osmotic induction prior to OTC immersion had a much weaker effect on mark intensity than did age-class of treatment in the study.
Received November 12, 2013; accepted March 30, 2014
A Semi-Automated Method for Monitoring Dam Passage of Upstream Migrant Yellow-Phase American Eels
Authors: Welsh Stuart A. , Aldinger Joni L. 
Published: June 2014

Abstract
Fish passage facilities at dams have become an important focus of fishery management in riverine systems. Given the personnel and travel costs associated with physical monitoring programs, automated or semi-automated systems are an attractive alternative for monitoring fish passage facilities. We designed and tested a semi-automated system for eel ladder monitoring at Millville Dam on the lower Shenandoah River, West Virginia. A motion-activated eel ladder camera (ELC) photographed each yellow-phase American Eel Anguilla rostrata that passed through the ladder. Digital images (with date and time stamps) of American Eels allowed for total daily counts and measurements of eel TL using photogrammetric methods with digital imaging software. We compared physical counts of American Eels with camera-based counts; TLs obtained with a measuring board were compared with TLs derived from photogrammetric methods. Data from the ELC were consistent with data obtained by physical methods, thus supporting the semi-automated camera system as a viable option for monitoring American Eel passage. Time stamps on digital images allowed for the documentation of eel passage time—data that were not obtainable from physical monitoring efforts. The ELC has application to eel ladder facilities but can also be used to monitor dam passage of other taxa, such as crayfishes, lampreys, and water snakes.
Received December 31, 2013; accepted March 11, 2014
Relationships between lower‐limb kinematics and block phase performance in a cross section of sprinters
Authors: Bezodis Neil Edward , Salo Aki Ilkka Tapio , Trewartha Grant 
Published: June 2014

AbstractThis study investigated lower‐limb kinematics to explain the techniques used to achieve high levels of sprint start performance. A cross‐sectional design was used to examine relationships between specific technique variables and horizontal external power production during the block phase. Video data were collected (200 Hz) at the training sessions of 16 sprinters who ranged in 100 m personal best times from 9.98 to 11.6 s. Each sprinter performed three 30 m sprints and reliable (all intraclass correlation coefficients, ICC(2,3) ≥ 0.89) lower‐limb kinematic data were obtained through manual digitising. The front leg joints extended in a proximal‐to‐distal pattern for 15 sprinters, and a moderate positive relationship existed between peak front hip angular velocity and block power (r = 0.49, 90% confidence limits = 0.08–0.76). In the rear leg, there was a high positive relationship between relative push duration and block power (r = 0.53, 90% confidence limits = 0.13–0.78). The rear hip appeared to be important; rear hip angle at block exit was highly related to block power (r = 0.60, 90% confidence limits = 0.23–0.82), and there were moderate positive relationships with block power for its range of motion and peak angular velocity (both r = 0.49, 90% confidence limits = 0.08–0.76). As increased block power production was not associated with any negative aspects of technique in the subsequent stance phase, sprinters should be encouraged to maximise extension at both hips during the block phase.
L2 vs. L1 Use of Synonymy: An Empirical Study of Synonym Use/Acquisition
Authors: Liu Dilin , Zhong Shouman 
Published: June 2014

AbstractSynonymy is important but difficult for language learners to grasp. Using a forced-choice question instrument, along with corpus data as reference, this study examines the use of four sets of synonyms by intermediate/advanced Chinese EFL/ESL learners and native English speakers. The data analyses reveal several key findings, including a general synonym acquisition trajectory. First, synonyms are often differentiated by their typical collocates; hence, the acquisition of synonyms is largely the learning of their salient collocates. Secondly, construal of the communicative purpose/context at hand also plays an important role in synonym selection. Thirdly, EFL/ESL learners begin to show some grasp of the salient usages/meanings of synonyms, and their grasp of synonyms advances significantly as their English proficiency increases to advanced level, but advanced learners still exhibit difficulties in synonym use, including an inadequate ability in forming context-called-for unique construals. Fourthly, frequency plays a crucial role in synonym acquisition, as low-frequency synonyms and salient synonym collocation usages with a low raw frequency are especially difficult for L2 learners. Implications for pedagogy and future research are also discussed.
First Report of Bean common mosaic virus Infecting Mungbean (Vigna radiata) in China
Authors: Cui X. Y. , Shen L. , Yuan X. X. , Gu H. P. , Chen X. 
Published: June 2014

Bean common mosaic virus (BCMV) is a member of the genus Potyvirus and one of the numerous viruses that can infect Phaseolus vulgaris. In May of 2013, we planted more than 100 varieties of mungbean in fields and a greenhouse of Nanjing. Mungbean (Vigna radiata (Linn.) Wilczek.) with leaves displaying mosaic and shrinkage typical of viral infection was observed in a greenhouse and a field in Nanjing. About 60% of the varieties can be infected. The symptoms in some sources from Southeast Asian countries and wild germplasm are heavier, while the symptoms are lighter on the local varieties. It can be transmitted to mungbean via aphid or mechanical inoculation, or by seeds. The infected leaves were collected for electron micrograph analysis. Pinwheel inclusion and filamentous virus particles were observed, indicating a Potyvirus infection. To confirm the presence of Potyvirus infection, total RNA was extracted from plants from the greenhouse and field, and RT-PCR was performed using universal Potyvirus primers (Sprimer (+) 5′-GGXAAYAAYAGYGGXCAZCC-3′; X=A, G, C or T, Y=T or C, Z=A or G); M4T (5′-GTTTTCCCAGTCACGAC(T)-3′), which amplify a region of the 3′ fragment of the RNA-dependent RNA polymerase of potyviruses (1). The 596-bp sequence was found to be 95% identical to the BCMV isolate HB (GenBank Accession No. KC478389.1). To confirm the presence of BCMV, three leaf samples were randomly collected and all were determined to be positive when subjected to ELISA using BCMV-specific antibodies. The virus infecting mungbean was identified as BCMV and the strain was named BCMV-JAAS (KJ866945). Using gene-specific primers (BCMV-cp-F: 5′-CAAAAGGACAAGGATTGAGGA, BCMV-cp-R: 3′-ACAACAAACATTGCCGTAGC) for the reported coat protein gene in BCMV, a 1,080-bp gene fragment was amplified from the total RNA of the isolate, and subsequent sequence analysis indicated that an 862-bp region contained the complete cp gene that encodes a 228 amino acid protein. The nucleotide sequences of the cp gene from the isolate shared 96% homology with the reported BCMV-HB. The phylogenetic trees based on the CP gene show that BCMV-JAAS (KJ866945) was most closely related to other Chinese BCMV isolates (KF439722.1 and AJ132145.1) followed by Azuki mosaic virus (AB012663.1) and Peanut stripe virus (U34972.1). These results indicate that the virus associated with the mosaic disease in mungbean is an isolate of BCMV. To our knowledge, this is the first report of BCMV infecting mungbean in China. BCMV affects a wide range of legume crops and can spread rapidly, causing serious harm. The discovery could effectively control BCMV and characterize the prevalent BCMV strains. Research utilizing whole-genome sequencing of the mungbean isolate is continuing and is currently being expanded to characterize the genetic diversity of the virus, assisting in the study of the evolution of the virus. Reference: (1) J. Chen and J. P. Chen. Chin. J. Virol. 18:372, 2002.
Are phylogenetic patterns the same in anthropology and biology?
Authors: Morrison David A. 
Published: June 2014

AbstractThe use of phylogenetic methods in anthropological fields such as archaeology, linguistics and stemmatology (involving what are often called “culture data”) is based on an analogy between human cultural evolution and biological evolution. We need to understand this analogy thoroughly, including how well anthropology data fit the model of a phylogenetic tree, as used in biology. I provide a direct comparison of anthropology datasets with both phenotype and genotype datasets from biology. The anthropology datasets fit the tree model approximately as well as do the genotype data, which is detectably worse than the fit of the phenotype data. This is true for datasets with <500 parsimony-informative characters, as well as for larger datasets. This implies that cross-cultural (horizontal) processes have been important in the evolution of cultural artifacts, as well as branching historical (vertical) processes, and thus a phylogenetic network will be a more appropriate model than a phylogenetic tree.
Compression of short-read sequences using path encoding
Authors: Kingsford Carl , Patro Rob 
Published: June 2014

AbstractStoring, transmitting, and archiving the amount of data produced by next generation sequencing is becoming a significant computational burden. For example, large-scale RNA-seq meta-analyses may now routinely process tens of terabytes of sequence. We present here an approach to biological sequence compression that reduces the difficulty associated with managing the data produced by large-scale transcriptome sequencing. Our approach offers a new direction by sitting between pure reference-based compression and reference-free compression and combines much of the benefit of reference-based approaches with the flexibility ofde novoencoding. Our method, called path encoding, draws a connection between storing paths in de Bruijn graphs — a common task in genome assembly — and context-dependent arithmetic coding. Supporting this method is a system, called a bit tree, to compactly store sets of kmers that is of independent interest. Using these techniques, we are able to encode RNA-seq reads using 3% – 11% of the space of the sequence in raw FASTA files, which is on average more than 34% smaller than recent competing approaches. We also show that even if the reference is very poorly matched to the reads that are being encoded, good compression can still be achieved.
Environmental History Modulates Arabidopsis Pattern-Triggered Immunity in a HISTONE ACETYLTRANSFERASE1–Dependent Manner
Authors: Singh Prashant , Yekondi Shweta , Chen Po-Wen , Tsai Chia-Hong , Yu Chun-Wei , Wu Keqiang , Zimmerli Laurent 
Published: June 2014

Abstract
In nature, plants are exposed to a fluctuating environment, and individuals exposed to contrasting environmental factors develop different environmental histories. Whether different environmental histories alter plant responses to a current stress remains elusive. Here, we show that environmental history modulates the plant response to microbial pathogens. Arabidopsis thaliana plants exposed to repetitive heat, cold, or salt stress were more resistant to virulent bacteria than Arabidopsis grown in a more stable environment. By contrast, long-term exposure to heat, cold, or exposure to high concentrations of NaCl did not provide enhanced protection against bacteria. Enhanced resistance occurred with priming of Arabidopsis pattern-triggered immunity (PTI)–responsive genes and the potentiation of PTI-mediated callose deposition. In repetitively stress-challenged Arabidopsis, PTI-responsive genes showed enrichment for epigenetic marks associated with transcriptional activation. Upon bacterial infection, enrichment of RNA polymerase II at primed PTI marker genes was observed in environmentally challenged Arabidopsis. Finally, repetitively stress-challenged histone acetyltransferase1-1 (hac1-1) mutants failed to demonstrate enhanced resistance to bacteria, priming of PTI, and increased open chromatin states. These findings reveal that environmental history shapes the plant response to bacteria through the development of a HAC1-dependent epigenetic mark characteristic of a primed PTI response, demonstrating a mechanistic link between the primed state in plants and epigenetics.
The Cyclin-Dependent Kinase Inhibitor KRP6 Induces Mitosis and Impairs Cytokinesis in Giant Cells Induced by Plant-Parasitic Nematodes in Arabidopsis
Authors: Vieira Paulo , De Clercq Annelies , Stals Hilde , Van Leene Jelle , Van De Slijke Eveline , Van Isterdael Gert , Eeckhout Dominique , Persiau Geert , Van Damme Daniël , Verkest Aurine , Antonino de Souza José Dijair , Júnior  , Glab Nathalie , Abad Pierre , Engler Gilbert , Inzé Dirk , De Veylder Lieven , De Jaeger Geert , Engler Janice de Almeida 
Published: June 2014

Abstract
In Arabidopsis thaliana, seven cyclin-dependent kinase (CDK) inhibitors have been identified, designated interactors of CDKs or Kip-related proteins (KRPs). Here, the function of KRP6 was investigated during cell cycle progression in roots infected by plant-parasitic root-knot nematodes. Contrary to expectations, analysis of Meloidogyne incognita–induced galls of KRP6-overexpressing lines revealed a role for this particular KRP as an activator of the mitotic cell cycle. In accordance, KRP6-overexpressing suspension cultures displayed accelerated entry into mitosis, but delayed mitotic progression. Likewise, phenotypic analysis of cultured cells and nematode-induced giant cells revealed a failure in mitotic exit, with the appearance of multinucleated cells as a consequence. Strong KRP6 expression upon nematode infection and the phenotypic resemblance between KRP6 overexpression cell cultures and root-knot morphology point toward the involvement of KRP6 in the multinucleate and acytokinetic state of giant cells. Along these lines, the parasite might have evolved to manipulate plant KRP6 transcription to the benefit of gall establishment.
How to assess Drosophila cold tolerance: chill coma temperature and lower lethal temperature are the best predictors of cold distribution limits
Authors: Andersen Jonas L. , Manenti Tommaso , Sørensen Jesper G. , MacMillan Heath A. , Loeschcke Volker , Overgaard Johannes 
Published: June 2014

Summary

Thermal tolerance may limit and therefore predict ectotherm geographic distributions. However, which of the many metrics of thermal tolerance best predict distribution is often unclear, even for drosophilids, which constitute a popular and well‐described animal model.

Five metrics of cold tolerance were measured for 14 Drosophila species to determine which metrics most strongly correlate with geographic distribution. The species represent tropical to temperate regions but all were reared under similar (common garden) conditions (20 °C). The traits measured were: chill coma temperature (CTmin), lethal temperature (LTe50), lethal time at low temperature (LTi50), chill coma recovery time (CCRT) and supercooling point (SCP).

Measures of CTmin, LTe50 and LTi50 proved to be the best predictors to describe the variation in realized latitudinal distributions (R2 = 0·699, R2 = 0·741 and 0·550, respectively) and estimated environmental cold exposure (R2 = 0·633, R2 = 0·641 and 0·511, respectively). Measures of CCRT also correlated significantly with estimated minimum temperature (R2 = 0·373), while the SCP did not. These results remained consistent after phylogenetically independent analysis or when applying nonlinear regression. Moreover, our findings were supported by a similar analysis based on existing data compiled from the Drosophila cold tolerance literature.

Trait correlations were strong between LTe50, LTi50 and CTmin, respectively (0·83 > R2 > 0·55). However, surprisingly, there was only a weak correlation between the entrance into coma (CTmin) and the recovery from chill coma (CCRT) (R2 = 0·256).

Considering the findings of the present study, data from previous studies and the logistical constraints of each measure of cold tolerance, we conclude that CTmin and LTe50 are superior measures when estimating the ecologically relevant cold tolerance of drosophilids. Of these two traits, CTmin requires less equipment, time and animals and thereby presents a relatively fast, simple and dynamic measure of cold tolerance.