bluuebunny/crossref_metadata_2025_split huggingface dataset:
A fully traits-based approach to modeling global vegetation distribution
Authors: van Bodegom Peter M. , Douma Jacob C. , Verheijen Lieneke M. 
Published: September 2014

SignificanceModels on vegetation dynamics are indispensable for our understanding of climate change impacts. These models contain variables describing vegetation attributes, so-called traits. However, the direct impacts of trait variation on global vegetation distribution are unknown. We derived global trait maps based on information on environmental drivers. Subsequently, we characterized nine globally representative vegetation types based on their trait combinations and could make valid predictions of their global occurrence probabilities based on trait maps. This study provides a proof of concept for the link between plant traits and vegetation types, stimulating enhanced application of trait-based approaches in vegetation modeling. We envision that our approach, our observation-driven trait maps, and vegetation maps may inspire a new generation of powerful traits-based vegetation models.
Functional trait space and the latitudinal diversity gradient
Authors: Lamanna Christine , Blonder Benjamin , Violle Cyrille , Kraft Nathan J. B. , Sandel Brody , Šímová Irena , Donoghue John C. , Svenning Jens-Christian , McGill Brian J. , Boyle Brad , Buzzard Vanessa , Dolins Steven , Jørgensen Peter M. , Marcuse-Kubitza Aaron , Morueta-Holme Naia , Peet Robert K. , Piel William H. , Regetz James , Schildhauer Mark , Spencer Nick , Thiers Barbara , Wiser Susan K. , Enquist Brian J. 
Published: September 2014

SignificanceWe present a conceptual framework for testing theories for the latitudinal gradient of species richness in terms of variation in functional diversity at the alpha, beta, and gamma scales. We compared ecological community theory with large-scale observational data of tree species richness and functional diversity. We found that the patterns of functional trait diversity are not consistent with any one theory of species diversity. These conflicting results indicate that none of the broad classes of biodiversity theory considered here is alone able to explain the latitudinal gradient of species diversity in terms of functional trait space.
Hypothesized link between Neoproterozoic greening of the land surface and the establishment of an oxygen-rich atmosphere
Authors: Kump Lee R. 
Published: September 2014

Significance
The evolution of the biota and of atmospheric composition have been tightly coupled throughout Earth history. Of key importance has been the establishment of an oxygen-rich atmosphere, and this has apparently occurred in two major steps. The second step occurred during the Neoproterozoic, at the time when various lines of evidence suggest a significant expansion of terrestrial life and soil development. The present paper links these two events in a unique way, not through increased oxygen production on land, but through increased consumption in biotic soils that until compensated by higher atmospheric oxygen levels, restricted the supply of oxygen to the weathering environment.
Ethnolinguistic structuring of sorghum genetic diversity in Africa and the role of local seed systems
Authors: Westengen Ola T. , Okongo Mark Atam , Onek Leo , Berg Trygve , Upadhyaya Hari , Birkeland Siri , Kaur Khalsa Siri Dharma , Ring Kristoffer H. , Stenseth Nils C. , Brysting Anne K. 
Published: September 2014

Significance
This paper shows that cultural factors play a key role in shaping the genetic structure in sorghum. We present molecular evidence of close associations between sorghum population structure and the distribution of ethnolinguistic groups in Africa. We show that traditional seed-management practices, which have played an important role for survival and expansion of agropastoral groups in the past, still are remarkably resilient to threats to human security. We argue that efforts to strengthen African sorghum seed systems are more likely to be successful when building on, rather than seeking to replace, existing traditional seed systems and landraces.
Pulque production from fermented agave sap as a dietary supplement in Prehispanic Mesoamerica
Authors: Correa-Ascencio Marisol , Robertson Ian G. , Cabrera-Cortés Oralia , Cabrera-Castro Rubén , Evershed Richard P. 
Published: September 2014

Significance
This research provides the earliest direct chemical evidence for the production of alcoholic beverage pulque in Mesoamerica, based on organic residues recovered from pottery vessels from Teotihuacan. A novel bacterial lipid biomarker approach is reported, which provides a new means of documenting the consumption of bacterially fermented alcoholic beverages in antiquity worldwide. At Teotihuacan, we have evidence that pulque was stored in distinctive amphorae vessels sealed with pine resin, as well as in other, less specialized vessels. Direct evidence of pulque production provides new insights into how the nutritional requirements of Teotihuacanos were sustained in a region in which the diet was largely based on plants and crop failures, due to drought and frost damage, which resulted in frequent shortfalls in staples.
Ultradian corticosterone pulses balance glutamatergic transmission and synaptic plasticity
Authors: Sarabdjitsingh Ratna Angela , Jezequel Julie , Pasricha Natasha , Mikasova Lenka , Kerkhofs Amber , Karst Henk , Groc Laurent , Joëls Marian 
Published: September 2014

Significance
A pulse of the adrenal hormone corticosterone (CORT) changes hippocampal glutamate transmission for many hours. CORT is normally released in hourly pulses, with a steeply rising amplitude just before awakening. How organisms can be prepared for imminent danger if the first high-amplitude pulse of CORT would lastingly change glutamate transmission—thus potentially deadlocking the system—has remained an enigma. We show that exposure of hippocampal cells to a second high-amplitude CORT pulse completely normalizes all aspects of glutamate transmission (including synaptic plasticity), thus lifting the potential deadlock caused by a first pulse. This ensures that the system remains fully responsive to any stressful event that requires encoding of information, an important principle that promotes survival of individuals.
Early origin of parental care in Mesozoic carrion beetles
Authors: Cai Chen-Yang , Thayer Margaret K. , Engel Michael S. , Newton Alfred F. , Ortega-Blanco Jaime , Wang Bo , Wang Xiang-Dong , Huang Di-Ying 
Published: September 2014

Significance
We report on the unique discovery of Jurassic and Cretaceous carrion beetles (Silphidae) from China and Myanmar, early relatives of one of the most protected of beetle species in North America, and which clearly preserve evidence indicative of complex parental care. This finding represents the earliest evidence of parental care, a behavioral repertoire that is the first step in the development of truly social behavior and one that is intensely studied by ecologists, ethologists, and evolutionary biologists alike. Our fossils clearly span the origins of parent–offspring communication and allow us to provide a robust estimate of the time of origin for this complex behavior.
Mathematical model of renal interstitial fibrosis
Authors: Hao Wenrui , Rovin Brad H. , Friedman Avner 
Published: September 2014

Significance
This paper deals with fibrosis of the kidney, a disease caused by inflammation, and so far there has been no way to diagnose and monitor the disease’s progression with noninvasive methods (the only way to determine the disease state is by biopsy, which cannot be frequently repeated). For this reason we developed a mathematical model of progression of renal fibrosis and validated it with biomarkers that were obtained from patients’ urine samples. We then used the model to show how antifibrosis drugs that are currently being developed for nonrenal fibrosis can be used to treat renal fibrosis.
Cellular redox regulation, signaling, and stress response in plants
Authors: Shigeoka Shigeru , Maruta Takanori 
Published: September 2014

AbstractCellular and organellar redox states, which are characterized by the balance between oxidant and antioxidant pool sizes, play signaling roles in the regulation of gene expression and protein function in a wide variety of plant physiological processes including stress acclimation. Reactive oxygen species (ROS) and ascorbic acid (AsA) are the most abundant oxidants and antioxidants, respectively, in plant cells; therefore, the metabolism of these redox compounds must be strictly and spatiotemporally controlled. In this review, we provided an overview of our previous studies as well as recent advances in (1) the molecular mechanisms and regulation of AsA biosynthesis, (2) the molecular and genetic properties of ascorbate peroxidases, and (3) stress acclimation via ROS-derived oxidative/redox signaling pathways, and discussed future perspectives in this field.
Transcriptional response machineries of Bacillus subtilis conducive to plant growth promotion
Authors: Hirooka Kazutake 
Published: September 2014

Abstract
Bacillus subtilis collectively inhabits the rhizosphere, where it contributes to the promotion of plant growth, although it does not have a direct symbiotic relationship to plants as observed in the case of rhizobia between leguminous plants. As rhizobia sense the flavonoids released from their host roots through the NodD transcriptional factor, which triggers transcription of the nod genes involved in the symbiotic processes, we supposed that B. subtilis utilizes certain flavonoids as signaling molecules to perceive and adapt to the rhizospheric environment that it is in. Our approaches to identify the flavonoid-responsive transcriptional regulatory system from B. subtilis resulted in the findings that three transcriptional factors (LmrA/QdoR, YetL, and Fur) are responsive to flavonoids, with the modes of action being different from each other. We also revealed a unique regulatory system by two transcriptional factors, YcnK and CsoR, for copper homeostasis in B. subtilis. In this review, we summarize the molecular mechanisms of these regulatory systems with the relevant information and discuss their physiological significances in the mutually beneficial interaction between B. subtilis and plants, considering the possibility of their application for plant cultivation.
Fish protein intake induces fast-muscle hypertrophy and reduces liver lipids and serum glucose levels in rats
Authors: Kawabata Fuminori , Mizushige Takafumi , Uozumi Keisuke , Hayamizu Kohsuke , Han Li , Tsuji Tomoko , Kishida Taro 
Published: September 2014

Abstract
In our previous study, fish protein was proven to reduce serum lipids and body fat accumulation by skeletal muscle hypertrophy and enhancing basal energy expenditure in rats. In the present study, we examined the precise effects of fish protein intake on different skeletal muscle fiber types and metabolic gene expression of the muscle. Fish protein increased fast-twitch muscle weight, reduced liver triglycerides and serum glucose levels, compared with the casein diet after 6 or 8 weeks of feeding. Furthermore, fish protein upregulated the gene expressions of a fast-twitch muscle-type marker and a glucose transporter in the muscle. These results suggest that fish protein induces fast-muscle hypertrophy, and the enhancement of basal energy expenditure by muscle hypertrophy and the increase in muscle glucose uptake reduced liver lipids and serum glucose levels. The present results also imply that fish protein intake causes a slow-to-fast shift in muscle fiber type.
The female human heart at rest and during exercise: A review
Authors: Nio Amanda Q. X. , Stöhr Eric J. , Shave Rob 
Published: September 2014

AbstractSexual dimorphism exists in numerous aspects of exercise physiology. One area that has long been debated is the potential of sex differences in cardiac structure and function. Anthropometric differences exist between males and females, and the relationship between absolute body size and cardiac structure dictate that men typically have larger hearts than women. However, increasing evidence suggests that males and females may also demonstrate different cardiac structure and function independent of body size, and it is likely that female sex hormones play a role in these differences. The purpose of this review is to draw together and examine the literature that has compared cardiac structure and function in men and women at rest and during exercise. We make specific reference to the influence of female sex hormones, and discuss the confounding effects of age and training status. Wherever possible, we provide conclusive remarks. Due to the paucity of data in this field, and general lack of consensus, the review concludes by making recommendations for future work.
GALAXY EMISSION LINE CLASSIFICATION USING THREE-DIMENSIONAL LINE RATIO DIAGRAMS
Authors: Vogt Frédéric P. A. , Dopita Michael A. , Kewley Lisa J. , Sutherland Ralph S. , Scharwächter Julia , Basurah Hassan M. , Ali Alaa , Amer Morsi A. 
Published: September 2014

ABSTRACT
Two-dimensional (2D) line ratio diagnostic diagrams have become a key tool in understanding the excitation mechanisms of galaxies. The curves used to separate the different regions—H ii-like or excited by an active galactic nucleus (AGN)—have been refined over time but the core technique has not evolved significantly. However, the classification of galaxies based on their emission line ratios really is a multi-dimensional problem. Here we exploit recent software developments to explore the potential of three-dimensional (3D) line ratio diagnostic diagrams. We introduce the

diagrams, which are a specific set of 3D diagrams that separate the oxygen abundance and the ionization parameter of H ii region-like spectra and also enable us to probe the excitation mechanism of the gas. By examining these new 3D spaces interactively, we define the

diagnostics, a new set of 2D diagnostics that can provide the metallicity of objects excited by hot young stars and that cleanly separate H ii region-like objects from the different classes of AGNs. We show that these

diagnostics are consistent with the key log [N ii]/Hα versus log [O iii]/Hβ diagnostic currently used by the community. They also have the advantage of attaching a probability that a given object belongs to one class or the other. Finally, we discuss briefly why

diagrams can provide a new way to differentiate and study the different classes of AGNs in anticipation of a dedicated follow-up study.
Primary brain tumors and posterior reversible encephalopathy syndrome
Authors: Kamiya-Matsuoka Carlos , Cachia David , Olar Adriana , Armstrong Terri S. , Gilbert Mark R. 
Published: September 2014

Abstract

Background
Posterior reversible encephalopathy syndrome (PRES) is a neurotoxic encephalopathic state associated with reversible cerebral vasogenic edema. It is an increasingly recognized occurrence in the oncology population. However, it is very uncommon in patients with primary brain tumors (PBTs). The aim of this study was to analyze the clinicoradiological features and report the clinical outcomes of PRES in PBT patients.

Methods
We identified 4 cases with PBT who developed PRES at MD Anderson Cancer Center (MDACC) between 2012 and 2014. Clinical and radiological data were abstracted from their records. In addition, we also solicited 8 cases from the literature.

Results
The median age at PRES onset was 19 years, male-to-female ratio was 1:1, and the syndrome occurred in patients with ependymoma (n = 4), glioblastoma (n = 3), diffuse intrinsic pontine glioma (DIPG; n = 3), juvenile pilocytic astrocytoma (n = 1), and atypical meningioma (n = 1). Two glioblastomas and 2 DIPG cases received bevacizumab and vandetanib before the onset of symptoms, respectively. The most common clinical presentation was seizures (n = 7). Three MDACC patients recovered completely in 3–4 weeks after the onset of symptoms. One patient died due to active cancer and several comorbidities including PRES.

Conclusions
Hypertension seems to be the most important coexisting risk factor for development of PRES; however, the potential effects of chemotherapeutic agents in the pathogenesis of PRES should also be examined. The clinicoradiological course of PRES in PBT patients did not vary from the classical descriptions of PRES found in other causes. PRES must be considered as part of the differential diagnosis in patients with PBTs presenting with seizures or acute encephalopathy.
First Report of Bacterial Blight of Pomegranate Caused by Xanthomonas axonopodis pv. punicae in Turkey
Authors: Icoz S. M. , Polat I. , Sulu G. , Yilmaz M. , Unlu A. , Soylu S. , Bozkurt I. A. , Baysal Ö. 
Published: September 2014

Pomegranate (Punica granatum L.) is an increasingly important fruit crop that is widely cultivated in Turkey. Typical bacterial blight symptoms were observed since spring of 2011 in pomegranate orchards located in Antalya Province. Symptoms were characterized by dark brown, angular to irregularly shaped spots on leaves and fruit; cankers on stems, branches, and trunks; and split trunks. The pathogen was isolated from leaf spots on naturally infected plants showing typical symptoms onto yeast dextrose chalk agar. Bright yellow bacterial colonies were consistently isolated. Bacterial strains were characterized as gram negative, oxidase negative, catalase positive, tobacco hypersensitivity positive, and able to produce acid from L-arabinose, D-galactose, D-glucose, and D-mannitol but not from D-xylose. Pathogenicity of the representative bacterial strain Serik-4 was performed on 2-year-old pomegranate plants cv. Hicaz. Leaves were sprayed until runoff with bacterial cell suspensions containing 107 CFU/ml. Inoculated plants were covered with transparent plastic bags to maintain moisture for 48 h. Negative control plants were inoculated with sterile distilled water. Plants were then incubated in a greenhouse at 30°C for 14 days. Symptoms on leaves included dark brown, angular to irregularly shaped water soaked lesions along the veins of the inoculated plants 10 days after inoculation. No lesions developed on the control plants. The symptoms on inoculated plants were similar to those on naturally infected plants. Yellow bacterial colonies were re-isolated from the inoculated plants and identified as the same as the original strain by conventional tests and FAME analysis, thus fulfilling Koch's postulates. Fatty acid methyl ester profiling of the representative strain Serik-4 using GC-MIDI (Microbial Identification Inc, Newark, DE) identified the genus of the bacterium as Xanthomonas. The identity of Serik-4 was further confirmed by amplifying the 16S rRNA gene with the universal primers 27F and 1492R (3) and sequence analysis (GenBank Accession No. KM007073). The 16S rRNA gene sequences of Serik-4 was 99% identical to the corresponding gene sequences of the Xanthomonas axonopodis pv. punicae strain present in the NCBI database (JQ067629.1). High incidence of bacterial blight caused by X. axonopodis pv. punicae on pomegranate has been previously reported in India (2), Pakistan (1), and South Africa (4). To our knowledge, this is the first report of bacterial blight on pomegranate caused by X. axonopodis pv. punicae in Turkey. References: (1) M. A. Akhtar and M. H. R. Bhatti. Pakistan J. Agric. Res. 13:95, 1992. (2) R. Chand and R. Kishun. Indian Phytopathol. 44:370, 1991. (3) D. J. Lane. Page 115 in: Nucleic Acid Techniques in Bacterial Systematics, 1991. (4) Y. Petersen et al. Australas. Plant Pathol. 39:544, 2010.
Interpretable per Case Weighted Ensemble Method for Cancer Associations
Authors: Jalali Adrin , Pfeifer Nico 
Published: September 2014

AbstractMotivationMolecular measurements from cancer patients such as gene expression and DNA methylation are usually very noisy. Further-more, cancer types can be very heterogeneous. Therefore, one of the main assumptions for machine learning, that the underlying unknown distribution is the same for all samples, might not be completely fullfilled. We introduce a method, that can estimate this bias on a per-feature level and incorporate calculated feature confidences into a weighted combination of classifiers with disjoint feature sets.ResultsThe new method achieves state-of-the-art performance on many different cancer data sets with measured DNA methylation or gene expression. Moreover, we show how to visualize the learned classifiers to find interesting associations with the target label. Applied to a leukemia data set we find several ribosomal proteins associated with leukemia's risk group that might be interesting targets for follow-up studies and support the hypothesis that the ribosomes are a new frontier in gene regulation.Availability:The method is available under GPLv3+ License athttps://github.com/adrinjalali/Network-Classifier.
Crystal structure of anhydrous poly[bis(μ2-sarcosinato-κ3O,N:O′)copper(II)]
Authors: Butcher Ray J. , Brewer Greg , Zemba Matthew 
Published: September 2014

The title compound, [Cu(C3H6NO2)2]n, is a bis-complex of the anion of sarcosine (N-methylglycine). The asymmetric unit consists of a copper(II) ion, located on a center of inversion, and one molecule of the uninegative sarcosinate anion. The copper(II) ion exhibits a typical Jahn–Teller distorted [4 + 2] coordination geometry. The four shorter equatorial bonds are to the nitrogen and carboxylate O atoms of two sarcosinate anions, and the longer axial bonds are to carboxylate O atoms of neighboring complexes. The overall structure is made up from two chains formed by these longer axial Cu—O bonds, one extending parallel to [011] and the other parallel to [0-11]. Each one-dimensional array is connected by the equatorial bridging moieties to the chains on either side, creating an extended two-dimensional framework parallel to (100). There is a single intermolecular hydrogen-bonding interaction within the sheets between the amino NH group and an O atom of an adjacent molecule.
An imported case of cutaneous leishmaniasis caused by Leishmania (Leishmania) donovani in Japan
Authors: Ito Kotaro , Takahara Masakazu , Ito Makoto , Oshiro Minoru , Takahashi Kenzo , Uezato Hiroshi , Imafuku Shinichi 
Published: September 2014

AbstractLeishmaniasis is a major world health problem, and 12 million people are estimated to be infected in 88 countries. There have been few reports of leishmaniasis in Japan and all were of foreign origin; therefore diagnosis is difficult for Japanese physicians. There are 21 different pathogenic Leishmania species, and identification is obtained by polymerase chain reaction (PCR). Here we report an imported case of leishmaniasis by Leishmania (Leishmania) donovani infection from Sri Lanka. L. (L.) donovani usually causes visceral leishmaniasis, but in this case, the patient manifested cutaneous leishmaniasis. The identification of Leishmania species by PCR and investigation of the patient's background such as nationality and disease endemicity are important for diagnosis and treatment. This is the first report of cutaneous leishmaniasis by L. (L.) donovani in Japan.