bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multi-proxy approach to assessing isolation basin stratigraphy from the Lofoten Islands, Norway
Authors: Balascio Nicholas L. , Zhang Zhaohui , Bradley Raymond S. , Perren Bianca , Dahl Svein Olaf , Bakke Jostein 
Published: September 2010

AbstractThis study takes a comprehensive approach to characterizing the isolation sequence of Heimerdalsvatnet, a coastal lake in the Lofoten Islands, northern Norway. We use established methods and explore new techniques to assess changes in marine influence. Bathymetric and sub-bottom profiles were acquired to examine basin-wide sedimentation and a 5.8 m sediment core spanning the last 7800 cal yr BP was analyzed. We measured magnetic susceptibility, bulk organic matter properties, molecular biomarkers, diatom assemblages, and elemental profiles acquired by scanning X-ray fluorescence. These characteristics of the sediment reflect detailed changes in salinity and water column conditions as the lake was progressively isolated. Three distinct litho/chemo-stratigraphic units represent a restricted marine phase (7800–6500 cal yr BP), a transitional phase characterized by intermittent marine influence (6500–4900 cal yr BP), and complete isolation and freshwater sedimentation (4900 cal yr BP to present). Although there are uncertainties in the estimate of the threshold elevation of the lake, the timing of these phases generally corresponds with previous interpretations of the local relative sea-level history. This record captures sea-level regression following the Tapes transgression and supports the interpretation of a subsequent sea-level stillstand, dated in Heimerdalsvatnet from 6500 to 4900 cal yr BP.
Gross-Hopkins duality and the Gorenstein condition
Authors: Dwyer W. G. , Greenlees J. P. C. , Iyengar S. B. 
Published: September 2010

AbstractGross and Hopkins have proved that in chromatic stable homotopy, Spanier-Whitehead duality nearly coincides with Brown-Comenetz duality. We give a conceptual interpretation of this phenomenon in terms of a Gorenstein condition [8] for maps of ring spectra.
Middle ear structures in fossorial mammals: a comparison with non‐fossorial species
Authors: Mason M. J. 
Published: September 2010

AbstractA large data set, comprising certain measurements of middle ear structures in mammals, was compiled both from measurements made by the author and from the literature. Parameters of the middle ear apparatus believed to be important to audition were compared between fossorial and non‐fossorial species, in an attempt to identify general trends among fossorial groups. Although their tympanic membranes are not of unusual size, many fossorial mammals possess enlarged stapes footplate areas, resulting in low anatomical area ratios. Low anatomical lever ratios are also common, and the reduction or loss of middle ear muscles seems to be a consistent trend. These characteristics might be associated with poor sensitivity to airborne sound. Other features of the middle ear apparatus are more variable both between and within fossorial families. The middle ear ossicles of fossorial rodents, talpid moles and some golden moles were not found to differ in mass from those of non‐fossorial mammals of similar body size. The similar ossicular morphologies of these animals suggest convergent adaptation towards a subterranean environment, but the middle ear structure alone does not seem to explain the restricted hearing range observed in certain of these species. Some genera of golden moles possess extraordinarily hypertrophied auditory ossicles, which, relative to body mass, are the largest of all mammals for which data are available. These ossicles seem to be adaptations towards a form of inertial bone conduction, used for the detection of substrate vibrations. In stark contrast, the marsupial mole Notoryctes has particularly small ossicles. The unusual middle ear structures of this animal may well be degenerate.
The reproductive biology of Ptomascopus morio, a brood parasite of Nicrophorus
Authors: Trumbo Stephen T. , Kon Masahiro , Sikes Derek 
Published: September 2010

AbstractNicrophorine beetles (Nicrophorus and Ptomascopus spp.) use small carcasses as a food source for young, a breeding ecology distinct from other silphid beetles. While adaptations to the use of small carcasses are well known for Nicrophorus (emitting sex pheromone, burying, rounding and removing hair from carcasses, regulating brood size, regurgitating to young, and preventing predation), there is little information regarding its sister group, Ptomascopus. Like Nicrophorus, Ptomascopus morio males emit pheromone to attract females. In the absence of carrion competitors Ptomascopus morio parents were found to stay with a carcass and their brood for up to 10 days. We tested six hypotheses to examine whether young benefit from this long period of parent–offspring contact. (1) There was no evidence that parents buried or otherwise pre‐empted carcasses to reduce competitive pressure. (2) We found no evidence that parents influenced the decomposition of the carcass. This was supported by experimental manipulations in which brood production (number of larvae and total brood mass) was no greater on carcasses on which parents were present than on carcasses not ‘prepared’ by parents. In addition, the carcass was not rounded and little hair was removed by the adults. (3) The presence of parents benefited the brood by reducing the negative effects of competition with carrion fly larvae. This likely resulted from predatory feeding by adult beetles. (4) Females adjusted clutch size to the size of the carcass. Parents, however, did not make a second adjustment in brood size after young reached the larval stage (filial cannibalism), as occurs in Nicrophorus. (5) Although parents were observed to open feeding holes in the carcass, this was not necessary for normal larval growth and survival. Parents were not observed to feed young directly by regurgitation. (6) Lastly, parents did not reduce predation on their brood when a conspecific intruder was present. These findings suggest that after the female parent adjusts clutch size to the size of the resource, the only parental benefit is clearing the carcass of fly larvae. Other differences with Nicrophorus include an extended period of oviposition (5 days) and less pronounced changes in ovarian mass and juvenile hormone titers in response to discovery of a carcass. In a field experiment in Kyoto, Japan, 17 of 21 broods of N. concolor during August contained larvae of P. morio. Mixed Nicrophorus–Ptomascopus broods were less common at other times of the year and when N. quadripunctatus occupied carcasses. In the laboratory, P. morio was able to parasitize 19 of 20 broods of N. concolor. The pattern of oviposition, the absence of explicit parental behaviours, and the interactions with N. concolor in the field suggest that Ptomascopus morio is a brood parasite of Nicrophorus.
Functional anatomy of the ovaries of wild brush‐tailed porcupines (Atherurus africanus, Gray 1842) from Gabon
Authors: Jori Ferran , López‐Béjar Manel , Mayor Pedro , López Carlos 
Published: September 2010

AbstractThe brush‐tailed porcupine Atherurus africanus is an important source of meat for local people in tropical forested areas of Central Africa. Information on the biology of this species in free‐ranging conditions is scarce. Data on its reproduction and productivity are essential to establish accurate management practices in the exploitation of this rodent. In order to provide data on the reproductive physiology and to assess the prolificacy of the brush‐tailed porcupine in the wild, the structural and functional anatomy of the ovaries of free‐ranging females were studied. Twenty‐two female carcasses were obtained from various markets in Libreville, Gabon, between August 1995 and February 1997. Reproductive tracts were macroscopically examined for the presence of embryos or foetuses. The ovaries were embedded in paraffin wax or plastic and examined by light microscopy. The morphology and constituent cell types of the ovaries were similar to those described for other hystricognath rodents. All pregnant females had only one embryo or foetus and the number of corpora lutea (CL) per female was 19.9 ± 5.4 (mean diameter ±sd, 1709 ± 421 μm), including one CL of pregnancy (diameter, 4821 ± 1364 μm). Also, 8.9 ± 6.8 accessory CL per female in the pre‐implantation and embryonic stages of pregnancy (diameter, 1629 ± 463 μm) were observed. The average active luteal volume was high (115.6 ± 73.5 mm3). The mean number of antral follicles in the adult females was 24.6 ± 9.9. The study confirms that the brush‐tailed porcupine is a mono‐embryonic species, as observed in captive breeding experiences, but polyovular, suggesting important ovum mortality. This unusual reproductive feature in a mammalian species gives this rodent a low reproductive productivity. Therefore, A. africanus could be more susceptible to the effects of hunting than generally thought.
Breeding biology of high‐latitude Antarctic fulmarine petrels (Procellariidae)
Authors: Hodum Peter J. 
Published: September 2010

AbstractThis paper provides basic information about the breeding biology of four species of Antarctic fulmarine petrels breeding in the Rauer Islands, East Antarctica: Antarctic fulmar Fulmarus glacialoides, Antarctic petrel Thalassoica antarctica, Cape petrel Daption capense, and snow petrel Pagodroma nivea. Timing and duration of the nesting cycle, incubation and nestling periods, and timing of breeding were determined over three consecutive breeding cycles. Comparing these data with those of other populations revealed that the duration of breeding showed little interannual and spatial variation within the four species. The length of the breeding period varied between the species, with incubation period and nesting cycle length positively related to adult body mass. Nestling period length also differed between the species but was unrelated to adult body mass. Breeding period lengths for these fulmarine petrels were shorter than those for other procellarids and albatrosses. Compressed and invariant breeding cycles of Antarctic fulmarine petrels may have evolved in response to a short season which limits breeding and to opportunities presented by highly abundant food sources.
Sand‐dwellers in rocky habitats: a new species of Gerbillus (Mammalia: Rodentia) from Mali
Authors: Granjon L. , Aniskin V. M. , Volobouev V. , Sicard B. 
Published: September 2010

AbstractThe genus Gerbillus (Mammalia: Rodentia) is characterized by an important morphological homogeneity associated with an extensive karyotypic diversity. Here we describe a new species of Gerbillus from the Inner Delta of the Niger River in Mali, on the basis of morphological and chromosomal data. This new species seems to be morphologically very similar to G. campestris, another bare‐footed species known from northern Africa. Nevertheless, it can be distinguished from the latter species by a different molar pattern and a specific karyotype. The three specimens on which this description is based were caught in a rocky outcrop, and behavioural observations in captivity suggest an adaptation to life in rocky habitats. This finding is unusual as rodents of the genus Gerbillus are generally sand‐dwellers. Moreover, this new species enriches the gerbil community of this Sahelian region, in which at least nine species of the genus can be found. Finally, this description highlights the importance of chromosomal studies for the characterization of biological diversity in tropical rodents, where morphological sibling species are numerous.
Life in the slow lane? Demography and life histories of male and female sifaka (Propithecus verreauxi verreauxi)
Authors: Richard Alison F. , Dewar Robert E. , Schwartz Marion , Ratsirarson Joelisoa 
Published: September 2010

AbstractA 16‐year study of wild, unprovisioned sifaka Propithecus verreauxi verreauxi at Beza Mahafaly in south‐west Madagascar provides estimates of age‐specific fertility, mortality, and dispersal in a population of 426 marked animals, and longitudinal records of individual life histories. Sifaka females give birth for the first time later and live longer, for their size, than mammals in other orders; they also give birth later and continue reproducing longer, for their size, than other primates. Theory postulates that these features, commonly referred to as bet‐hedging, evolve in unpredictable environments in association with widely varying infant survival and a trade‐off between reproductive effort and adult survival. The climate of south‐west Madagascar is highly unpredictable compared to almost all other regions in the tropics with similar average rainfall, and we argue that sifaka females are bet‐hedgers par excellence. Male sifaka, in contrast, become reproductively active at an earlier age than females, and are less likely to have long lives than females. The atypical direction of this asymmetry between males and females reflects a ‘slowing down’ of female life histories rather than a ‘speeding up’ of male life histories. Two other unusual features of sifaka biology and behaviour may be linked to the unpredictability of Madagascar's climate: intense local competition between females, and a sex ratio at birth strongly biased in favour of males in most years. In drought years, reproductive females must cope with suddenly intensified resource constraints. This, in turn, may strongly limit the number of ‘breeding slots’ available over the long‐term for females.
Rainfall, dispersal and reproductive inhibition in eusocial Damaraland mole‐rats (Cryptomys damarensis)
Authors: Molteno A. J. , Bennett N. C. 
Published: September 2010

AbstractNon‐reproductive female Damaraland mole‐rats Cryptomys damarensis that were caught before a period of good rainfall (during which 90% of the average annual fell) (Group 1), exhibited a significantly lower pituitary sensitivity to gonadotrophin‐releasing hormone compared to non‐reproductive females (Group 2) caught in the same area, close to the end of the wet period. Group 2 were also significantly heavier than Group 1. Pituitary sensitivity was not significantly correlated to body mass within either group of females, nor within groups of reproductive males and non‐reproductive males from a laboratory held colony. This suggests that rainfall may have resulted in the simultaneous, but unrelated, increase in pituitary sensitivity and body mass. Larger size and reduced sexual inhibition assist dispersal and the probability of successful independent reproduction, during periods when environmental constraints on dispersal are relaxed. These findings support the hypothesis that low rainfall may be an important constraint on dispersal and an important factor promoting the evolution of reproductive inhibition, and consequently eusociality, in this species.
Metric learning for enzyme active-site search
Authors: Kato Tsuyoshi , Nagano Nozomi 
Published: September 2010

Abstract
Motivation: Finding functionally analogous enzymes based on the local structures of active sites is an important problem. Conventional methods use templates of local structures to search for analogous sites, but their performance depends on the selection of atoms for inclusion in the templates.
Results: The automatic selection of atoms so that site matches can be discriminated from mismatches. The algorithm provides not only good predictions, but also some insights into which atoms are important for the prediction. Our experimental results suggest that the metric learning automatically provides more effective templates than those whose atoms are selected manually.
Availability: Online software is available at http://www.net-machine.net/∼kato/lpmetric1/
Contact: kato-tsuyoshi@k.u-tokyo.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Statistical considerations for digital approaches to non-invasive fetal genotyping
Authors: Chu Tianjiao , Bunce Kimberly , Hogge W. Allen , Peters David G. 
Published: September 2010

Abstract
Motivation: A growing body of literature has demonstrated the potential for non-invasive diagnosis of a variety of human genetic diseases using cell-free DNA extracted from maternal plasma samples in early gestation. Such methods are of great significance to the obstetrics community because of their potential use as clinical standard of care. Proof of concept for such approaches has been established for aneuploidy and paternally inherited dominant traits. Although significant progress has recently been made, the non-invasive diagnosis of monogenic diseases that segregate in a recessive mendelian fashion is more problematic. Recent developments in microfluidic digital PCR and DNA sequencing have resulted in a number of recent advances in this field. These have largely, although not exclusively, been used for the development of diagnostic methods for aneuploidy. However, given their prevalence, it is likely that such methods will be utilized towards the development of non-invasive methods for diagnosing monogenetic disorders.
Results: With this in mind, we have undertaken a statistical modeling of three contemporary (digital) analytical methods in the context of prenatal diagnosis using cell free DNA for monogenic diseases that segregate in a recessive mendelian fashion. We provide an experimental framework for the future development of diagnostic methods in this context that should be considered when designing molecular assays that seek to establish proof of concept in this field.
Contact: dgp6@pitt.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Identification of Context-Dependent Motifs by Contrasting ChIP Binding Data
Authors: Mason Mike J. , Plath Kathrin , Zhou Qing 
Published: September 2010

AbstractMotivation: DNA binding proteins play crucial roles in the regulation of gene expression. Transcription factors (TFs) activate or repress genes directly while other proteins influence chromatin structure for transcription. Binding sites of a TF exhibit a similar sequence pattern called a motif. However, a one-to-one map does not exist between each TF and motif. Many TFs in a protein family may recognize the same motif with subtle nucleotide differences leading to different binding affinities. Additionally, a particular TF may bind different motifs under certain conditions, for example in the presence of different co-regulators. The availability of genome-wide binding data of multiple collaborative TFs makes it possible to detect such context-dependent motifs.Results: We developed a contrast motif finder (CMF) for the de novo identification of motifs that are differentially enriched in two sets of sequences. Applying this method to a number of TF binding datasets from mouse embryonic stem cells, we demonstrate that CMF achieves substantially higher accuracy than several well-known motif finding methods. By contrasting sequences bound by distinct sets of TFs, CMF identified two different motifs that may be recognized by Oct4 dependent on the presence of another co-regulator and detected subtle motif signals that may be associated with potential competitive binding between Sox2 and Tcf3.Availability: The software CMF is freely available for academic use at www.stat.ucla.edu/∼zhou/CMFContact: zhou@stat.ucla.eduSupplementary information: Supplementary data are available at Bioinformatics online and the CMF website.
The cardiac renin–angiotensin system is responsible for high‐salt diet‐induced left ventricular hypertrophy in mice
Authors: Le Corvoisier Philippe , Adamy Christophe , Sambin Lucien , Crozatier Bertrand , Berdeaux Alain , Michel Jean‐Baptiste , Hittinger Luc , Su JinBo 
Published: September 2010

AimsThis study aimed to determine the role of the renin–angiotensin system (RAS) in high‐salt (HS) diet‐induced left ventricular hypertrophy (LVH).Methods and resultsSwiss mice were subjected to regular salt (RS) diet (0.6% NaCl), HS diet (4% NaCl), and HS plus irbesartan (50 mg/kg/day) or ramipril (1 mg/kg/day). After 8 weeks, arterial pressure was similar in all groups and similar to baseline, whereas left ventricle/body weight ratio was higher in HS mice than in RS mice (P < 0.005). There were also significant increases in collagen density, angiotensin‐converting enzyme activity, angiotensin II type 1 receptor (AT1 receptor) density, and extracellular signal‐regulated kinase (ERK1/2) phosphorylation in the left ventricle. Interestingly, increases in wall thickness and ERK1 phosphorylation were more marked in the septum than in the rest of the left ventricle. Irbesartan or ramipril treatment prevented LVH and the increase in ERK phosphorylation and reduced collagen content and AT1 up‐regulation but up‐regulated AT2 receptors.ConclusionIn normal mice, HS diet induces septum‐predominant LVH and fibrosis through activation of the cardiac RAS–ERK pathway, which can be blocked by irbesartan or ramipril, indicating a key role of the cardiac RAS in HS diet‐induced LVH.
Arsenic Speciation in Phloem and Xylem Exudates of Castor Bean
Authors: Ye Wen-Ling , Wood B. Alan , Stroud Jacqueline L. , Andralojc P. John , Raab Andrea , McGrath Steve P. , Feldmann Jörg , Zhao Fang-Jie 
Published: September 2010

Abstract
How arsenic (As) is transported in phloem remains unknown. To help answer this question, we quantified the chemical species of As in phloem and xylem exudates of castor bean (Ricinus communis) exposed to arsenate [As(V)], arsenite [As(III)], monomethylarsonic acid [MMA(V)], or dimethylarsinic acid. In the As(V)- and As(III)-exposed plants, As(V) was the main species in xylem exudate (55%–83%) whereas As(III) predominated in phloem exudate (70%–94%). The ratio of As concentrations in phloem to xylem exudate varied from 0.7 to 3.9. Analyses of phloem exudate using high-resolution inductively coupled plasma-mass spectrometry and accurate mass electrospray mass spectrometry coupled to high-performance liquid chromatography identified high concentrations of reduced and oxidized glutathione and some oxidized phytochelatin, but no As(III)-thiol complexes. It is thought that As(III)-thiol complexes would not be stable in the alkaline conditions of phloem sap. Small concentrations of oxidized glutathione and oxidized phytochelatin were found in xylem exudate, where there was also no evidence of As(III)-thiol complexes. MMA(V) was partially reduced to MMA(III) in roots, but only MMA(V) was found in xylem and phloem exudate. Despite the smallest uptake among the four As species supplied to plants, dimethylarsinic acid was most efficiently transported in both xylem and phloem, and its phloem concentration was 3.2 times that in xylem. Our results show that free inorganic As, mainly As(III), was transported in the phloem of castor bean exposed to either As(V) or As(III), and that methylated As species were more mobile than inorganic As in the phloem.