bluuebunny/crossref_metadata_2025_split huggingface dataset:
A general method for accurate estimation of false discovery rates in identification of differentially expressed genes
Authors: Tan Yuan-De , Xu Hongyan 
Published: March 2014

AbstractSummary: The ‘omic’ data such as genomic data, transcriptomic data, proteomic data and single nucleotide polymorphism data have been rapidly growing. The omic data are large-scale and high-throughput data. Such data challenge traditional statistical methodologies and require multiple tests. Several multiple-testing procedures such as Bonferroni procedure, Benjamini–Hochberg (BH) procedure and Westfall–Young procedure have been developed, among which some control family-wise error rate and the others control false discovery rate (FDR). These procedures are valid in some cases and cannot be applied to all types of large-scale data. To address this statistically challenging problem in the analysis of the omic data, we propose a general method for generating a set of multiple-testing procedures. This method is based on the BH theorems. By choosing a C-value, one can realize a specific multiple-testing procedure. For example, by setting C = 1.22, our method produces the BH procedure. With C &lt; 1.22, our method generates procedures of weakly controlling FDR, and with C &gt; 1.22, the procedures strongly control FDR. Those with C = G (number of genes or tests) and C = 0 are, respectively, the Bonferroni procedure and the single-testing procedure. These are the two extreme procedures in this family. To let one choose an appropriate multiple-testing procedure in practice, we develop an algorithm by which FDR can be correctly and reliably estimated. Simulated results show that our method works well for an accurate estimation of FDR in various scenarios, and we illustrate the applications of our method with three real datasets.Availability and implementation: Our program is implemented in Matlab and is available upon request.Contact : hxu@gru.eduSupplementary information: Supplementary data are available at Bioinformatics online.
comTAR: a web tool for the prediction and characterization of conserved microRNA targets in plants
Authors: Chorostecki Uciel , Palatnik Javier F. 
Published: March 2014

Abstract
Motivation: MicroRNAs (miRNAs) are major regulators of gene expression in plants and animals. They recognize their target messenger RNAs (mRNAs) by sequence complementarity and guide them to cleavage or translational arrest. So far, the prediction of plant miRNA–target pairs generally relies on the use of empirical parameters deduced from known miRNA–target interactions.
Results: We developed comTAR, a web tool for the prediction of miRNA targets that is mainly based on the conservation of the potential regulation in different species. We used data generated from a pipeline applied to transcript datasets of 33 angiosperms that was used to build a database of potential miRNA targets of different plant species. The database contains information describing each miRNA–target pair, their function and evolutionary conservation, while the results are displayed in a user-friendly interface. The tool also allows the search using new miRNAs.
Availability and implementation: The Web site is free to all users, with no login requirements, at http://rnabiology.ibr-conicet.gov.ar/comtar .
Contact: palatnik@ibr-conicet.gov.ar or chorostecki@ibr-conicet.gov.ar
FSuite: exploiting inbreeding in dense SNP chip and exome data
Authors: Gazal Steven , Sahbatou Mourad , Babron Marie-Claude , Génin Emmanuelle , Leutenegger Anne-Louise 
Published: March 2014

Abstract
Summary: FSuite is a user-friendly pipeline developed for exploiting inbreeding information derived from human genomic data. It can make use of single nucleotide polymorphism chip or exome data. Compared with other software, the advantage of FSuite is that it provides a complete suite of scripts to describe and use the inbreeding information. It includes a module to detect inbred individuals and estimate their inbreeding coefficient, a module to describe the proportion of different mating types in the population and the individual probability to be offspring of different mating types that can be useful for population genetic studies. It also allows the identification of shared regions of homozygosity between affected individuals (homozygosity mapping) that can be used to identify rare recessive mutations involved in monogenic or multifactorial diseases.
Availability and implementation: FSuite is developed in Perl and uses R functions to generate graphical outputs. This pipeline is freely available under GNU GPL license at: http://genestat.cephb.fr/software/index.php/FSuite .
Contact: fsuite.software@gmail.com or steven.gazal@inserm.fr
Supplementary information: Supplementary data is available at Bioinformatics online.
Reflections on the success of traditional fisheries management
Authors: Hilborn Ray , Ovando Daniel 
Published: March 2014

Abstract
The argument persists that the continued overexploitation by many fisheries around the world is evidence that current approaches to fisheries management are failing, and that more precautionary management approaches are needed. We review the available estimates of the status of fish stocks from three sources: the FAO's “State of Marine Resources”, a database on scientific stock assessments, and recent estimates from statistical models designed to determine the status of unassessed fish stocks. The two key results are (i) that stocks that are scientifically assessed are in better shape and indeed are not typically declining but rebuilding, and (ii) that large stocks appear to be in better shape than small stocks. These results support the view that stocks that are managed are improving, while stocks that are not managed are not. Large stocks receive far more management attention than small stocks in jurisdictions that have active fisheries management systems, and most unassessed stocks are simply not managed. We assert that fisheries management as currently practised can (and often does) lead to sustainable fisheries, and what is needed is to actively manage the unassessed fisheries of the world. More precautionary management is not necessarily needed to ensure the sustainability of managed fisheries.
Using correlations between cosmic microwave background lensing and large-scale structure to measure primordial non-Gaussianity
Authors: Giannantonio Tommaso , Percival Will J. 
Published: March 2014

Abstract
We apply a new method to measure primordial non-Gaussianity, using the cross-correlation between galaxy surveys and the cosmic microwave background (CMB) lensing signal to measure galaxy bias on very large scales, where local-type primordial non-Gaussianity predicts a k2 divergence. We use the CMB lensing map recently published by the Planck Collaboration, and measure its external correlations with a suite of six galaxy catalogues spanning a broad redshift range. We then consistently combine correlation functions to extend the recent analysis by Giannantonio et al., where the density–density and the density–CMB temperature correlations were used. Due to the intrinsic noise of the Planck lensing map, which affects the largest scales most severely, we find that the constraints on the galaxy bias are similar to the constraints from density–CMB temperature correlations. Including lensing constraints only improves the previous statistical measurement errors marginally, and we obtain fNL = 12 ± 21 (1σ) from the combined data set. However, the lensing measurements serve as an excellent test of systematic errors: we now have three methods to measure the large-scale, scale-dependent bias from a galaxy survey: auto-correlation, and cross-correlation with both CMB temperature and lensing. As the publicly available Planck lensing maps have had their largest scale modes at multipoles l &lt; 10 removed, which are the most sensitive to the scale-dependent bias, we consider mock CMB lensing data covering all multipoles. We find that, while the effect of fNL indeed increases significantly on the largest scales, so do the contributions of both cosmic variance and the intrinsic lensing noise, so that the improvement is small.
Large-scale gas sloshing out to half the virial radius in the strongest cool core REXCESS galaxy cluster, RXJ2014.8-2430
Authors: Walker S. A. , Fabian A. C. , Sanders J. S. 
Published: March 2014

Abstract
We search the cool core galaxy clusters in the REXCESS sample for evidence of large-scale gas sloshing, and find clear evidence for sloshing in RXJ2014.8-2430, the strongest cool core cluster in the REXCESS cluster sample. The residuals of the surface brightness distribution from the azimuthal average for RXJ2014 show a prominent swirling excess feature extending out to an abrupt surface brightness discontinuity at 800 kpc from the cluster core (half the virial radius) to the south, which the XMM–Newton observations confirm to be cold, low-entropy gas. The gas temperature is significantly higher outside this southern surface brightness discontinuity, indicating that this is a cold front 800 kpc from the cluster core. Chandra observations of the central 200 kpc show two clear younger cold fronts on opposite sides of the cluster. The scenario appears qualitatively consistent with simulations of gas sloshing due to minor mergers which raise cold, low-entropy gas from the core to higher radius, resulting in a swirling distribution of opposing cold fronts at increasing radii. However, the scale of the observed sloshing is much larger than that which has been simulated at present, and is similar to the large-scale sloshing recently observed in the Perseus cluster and Abell 2142.
Systems Analysis of Auxin Transport in the Arabidopsis Root Apex
Authors: Band Leah R. , Wells Darren M. , Fozard John A. , Ghetiu Teodor , French Andrew P. , Pound Michael P. , Wilson Michael H. , Yu Lei , Li Wenda , Hijazi Hussein I. , Oh Jaesung , Pearce Simon P. , Perez-Amador Miguel A. , Yun Jeonga , Kramer Eric , Alonso Jose M. , Godin Christophe , Vernoux Teva , Hodgman T. Charlie , Pridmore Tony P. , Swarup Ranjan , King John R. , Bennett Malcolm J. 
Published: March 2014

Abstract
Auxin is a key regulator of plant growth and development. Within the root tip, auxin distribution plays a crucial role specifying developmental zones and coordinating tropic responses. Determining how the organ-scale auxin pattern is regulated at the cellular scale is essential to understanding how these processes are controlled. In this study, we developed an auxin transport model based on actual root cell geometries and carrier subcellular localizations. We tested model predictions using the DII-VENUS auxin sensor in conjunction with state-of-the-art segmentation tools. Our study revealed that auxin efflux carriers alone cannot create the pattern of auxin distribution at the root tip and that AUX1/LAX influx carriers are also required. We observed that AUX1 in lateral root cap (LRC) and elongating epidermal cells greatly enhance auxin's shootward flux, with this flux being predominantly through the LRC, entering the epidermal cells only as they enter the elongation zone. We conclude that the nonpolar AUX1/LAX influx carriers control which tissues have high auxin levels, whereas the polar PIN carriers control the direction of auxin transport within these tissues.
The life and times of a senior scholar: an interview with Jane Dutton
Authors: Moore Karl 
Published: March 2014

Purpose
– The aim of this paper was to interview a senior scholar in the field of management.

Design/methodology/approach
– A structured interview method was used.

Findings
– Jane discussed her life and times, a fascinating recounting of history.

Originality/value
– The paper provides a unique perspective on the career of a management scholar.
Persistent pruritic papules and plaques associated with adult‐onset Still's disease: Report of six cases
Authors: Kikuchi Nobuyuki , Satoh Masataka , Ohtsuka Mikio , Yamamoto Toshiyuki 
Published: March 2014

AbstractTypical skin rash, which appears and disappears along with respective rise and fall of fever, is well‐known, and included as one of the major criteria of adult‐onset Still's disease (AOSD) (Yamaguchi's criteria). In addition, various skin lesions are occasionally observed in association with AOSD. Persistent pruritic eruptions present with some clinical features, such as urticarial erythema, flagellate erythema, erythematous, slightly scaly or crusted papules, and/or plaques on the trunk and extremities. These lesions show unique histological features such as dyskeratosis with a peculiar, distinctive distribution in the upper epidermis and cornified layers with focal hyperkeratosis. We describe herein six cases of AOSD, which presented with skin lesions of persistent pruritic papules and plaques. All six cases were female, and three of them were elderly women. The patients presented with linear erythematous streaks, scaly erythema, keratotic papules, infiltrative plaques and irregular coalesced erythemas. By contrast, histological features were characteristic, and dyskeratotic cells were found in the horny layers as well as in the upper layers of the epidermis. Persistent pruritic eruption is an important cutaneous sign for the diagnosis of AOSD.
Case of giant basal cell carcinoma around the base of the penis in an elderly patient
Authors: Suyama Takayuki , Teramoto Yukiko , Yamamoto Akifumi , Kuroda Isao , Yoshikawa Shusuke , Kiyohara Yoshio 
Published: March 2014

AbstractWe report a case of an 85‐year‐old man with a doughnut‐shaped basal cell carcinoma around the base of the penis invading the cavernosum urethra. In cases in which curative resection is planned, the penis is resected, cystostomy is performed, and postoperative self‐management is required. In line with the patient's wishes and the fact that he was an elderly person living alone without family support, we decided to perform penis‐conserving surgery. Relapse occurred once, for which additional resection was conducted. Two years after the resection, there was no evidence of tumor recurrence. The therapeutic plan for elderly patients should be modified after considering the patient's social background, wishes, activity and life expectancy.
Cases with a spontaneous regression of an infiltrating non‐crateriform keratoacanthoma and squamous cell carcinoma with a keratoacanthoma‐like component
Authors: Misago Noriyuki , Takai Toshihiro , Murata Yozo , Nagase Kotaro , Narisawa Yutaka 
Published: March 2014

AbstractWe herein report the natural course of an early/proliferative stage keratoacanthoma (KA) with infiltrating islands of cytological malignancy (case 1) and a squamous cell carcinoma (SCC) with a KA‐like component (case 2), which were observed until their complete regression. The presented case 1 suggests that one of the histopathological forms of KA includes this unusual, infiltrating, non‐crateriform architecture, and also indicates the possibility of complete remission in the KA associated with infiltrating islands of cytological malignancy. In the presented case 2, the peripherally‐associated KA‐like focus was histopathologically considered to be either a remnant of KA focus or verrucous keratosis (hyperplasia). Therefore, the complete spontaneous regression of case 2 suggests that SCC arising in KA still has the potential of spontaneous regression, or that an extremely rare event, namely, the spontaneous regression of (traditional) SCC occurred in the present case.
Efficacious treatment of psoriasis with low‐dose and intermittent cyclosporin microemulsion therapy
Authors: Ito Taisuke , Furukawa Fukumi , Iwatsuki Keiji , Matsue Hiroyuki , Shimada Shinji , Takigawa Masahiro , Tokura Yoshiki 
Published: March 2014

AbstractCyclosporin is used for moderate to severe psoriasis and improves not only the skin lesions but also quality of life of the patients. To improve its safe use, we evaluated a low‐dose, intermittent regimen of cyclosporin in the treatment of psoriasis vulgaris. Seventy‐three patients received approximately 2.5 mg/kg per day of cyclosporin microemulsion twice daily before breakfast and dinner for 2–12 weeks until 75% reduction was achieved in Psoriasis Area and Severity Index (PASI) score. When the skin lesions relapsed after cessation of cyclosporin and showed less than 50% reduction from baseline in PASI score, cyclosporin was restarted. This cessation and restart cycle was repeated if necessary. Treatment outcomes were assessed at 12, 48 and 96 weeks after initiation of the therapy. The initial dose of cyclosporin was 2.32 ± 0.27 (standard deviation [SD]) mg/kg per day. At baseline, the mean PASI score was 11.3 ± 5.3 (SD). An average of 49.8 ± 23.8 (SD) days of the therapy achieved PASI 75% reduction. In 20 of 73 patients, the second course of cyclosporin was required. The mean interval between the first and second course was 94 days. An average of 60.8 ± 26.9 days was required to achieve PASI 75% reduction in the second course, which was not significantly longer than that in the first course. Only six patients required cyclosporin for 96 weeks. The adverse effects included one case of hypertension. Our study suggests that low‐dose, intermittent cyclosporin microemulsion is efficacious for the treatment of moderate to severe psoriasis.
Heterostyly promotes disassortative pollination and reduces sexual interference in Darwin's primroses: evidence from experimental studies
Authors: Keller Barbara , Thomson James D. , Conti Elena 
Published: March 2014

Summary

Different strategies to reduce selfing and promote outcrossing have evolved in hermaphroditic flowers. Heterostyly, a complex floral polymorphism that occurs in at least 27 families of angiosperms, is hypothesized to achieve both goals by optimizing cross‐pollination (via disassortative pollen transfer) and restricting gamete wastage to autogamy (via the reduction in sexual interference between male and female organs).

In heterostylous flowers, the reciprocal positioning of sexual organs in different morphs and the pollen incompatibility system within flower or between flowers of the same morph are thought to optimize both male and female functions, reducing the conflicts inherent to the occurrence of both sexual organs in the same reproductive unit. Specific elements of the disassortative‐pollination and sexual‐interference hypotheses have been tested individually before. However, despite the long‐standing interest in heterostyly – ever since Darwin's seminal work on primroses – the predictions derived from these two hypotheses have never been experimentally and systematically examined in the same system.

Using distylous primroses (Primula elatior, P. vulgaris), we compare pollen transfer (i) between reciprocal and non‐reciprocal flowers; (ii) from anthers onto different parts of the pollinator's body; and (iii) within flower and between flowers of the same morph. We further test whether (iv) anther–stigma distance correlates with self‐pollen transfer and whether (v) seed set differs after pollinations with compatible, incompatible and both pollen types.

Reciprocal herkogamy promotes differential placement of pollen onto different parts of the pollinator's body, thus effecting transfer of more pollen to reciprocal than to non‐reciprocal stigmas and realizing the key predictions of the disassortative‐pollination hypothesis. However, short‐styled flowers transfer pollen more disassortatively than long‐styled flowers in both species, whereas long‐styled flowers export more pollen to non‐reciprocal than to reciprocal stigmas in P. vulgaris, thus compromising male function in this species. Furthermore, larger distance between sexual organs lowers self‐ and intra‐morph pollination and the pollen incompatibility system decreases seed production after self‐pollination, thus diminishing sexual interference.

Our results help us understand how the morphological and physiological components of heterostyly contribute to optimizing pollen transfer and minimizing self‐ and intra‐morph pollination, thus promoting more efficient outcrossing in species with this floral polymorphism.
Does body mass convey a digestive advantage for large herbivores?
Authors: Steuer Patrick , Südekum Karl‐Heinz , Tütken Thomas , Müller Dennis W. H. , Kaandorp Jacques , Bucher Martin , Clauss Marcus , Hummel Jürgen 
Published: March 2014

Summary

A key concept of body mass (BM) in niche separation of large herbivores assumes that the decrease in diet quality inherent to increasing BM (due to less selective feeding behaviour) is balanced by a simultaneous increase in digestive ability (due to longer retention times), resulting in no or less‐than‐expected reduction in digestibility (as measured in the animal as a result of diet quality and digestive ability). However, the second part of this concept has been challenged recently due to theoretical problems and mismatch with empirical data.

A proxy for digestibility, such as metabolic faecal nitrogen (MFN), will comprise both information on diet quality and digestive ability in free‐ranging animals. In captive animals, if diet is kept constant, such a proxy can exclusively indicate digestive ability. Comparing free‐ranging and captive animals under such conditions, one would expect an increase in MFN with BM in captive animals and no relationship between these measures in free‐ranging animals if BM was related to digestive ability.

We compared captive ungulates on a consistent grass hay diet (17 species; 30–4000 kg BM) to a sample of free‐ranging East African ungulates (19 species; 12–4000 kg BM). MFN was used as the major proxy for digestibility.

In captive animals, there was no influence of BM on MFN (P = 0·466); for free‐ranging animals, a significant decreasing effect of body mass on MFN (P = 0·002) and therefore diet quality was found at a scaling of BM−0·15.

In conclusion, scenarios that assume a compensation of the evident decrease in diet quality with BM via an increased digestive ability are not supported by this study. This does not rule out other feeding‐related factors in facilitating large BM, such as compensation by an increased diet intake.
Spatial networks of fleshy‐fruited trees drive the flow of avian seed dispersal through a landscape
Authors: Rodríguez‐Pérez Javier , García Daniel , Martínez Daniel 
Published: March 2014

Summary

Seed dispersal by animals leads to plant genes, individuals and species flowing across the landscape, but this process has been seldom seen as the explicit result of structural or landscape connectivity.

For two years, we studied avian seed dispersal of fleshy‐fruited trees in a secondary forest of the northern Iberian Peninsula, considering the areas under the canopies of fruiting trees as hubs of seed deposition.

Using graph‐theory models, we set a spatially explicit network in a continuous landscape, with individual fruiting trees as nodes and expected frugivore movements as links between nodes. We calculated the contribution of each tree to network connectivity, finding strong inter‐annual variability derived from tree properties (position, fruit crop and species).

Trees contributing the most to connectivity accumulated larger seed clumps under their canopies, demonstrating agreement between a network structural connectivity and the functional connectivity of seed dispersal flow. This pattern, however, is accentuated when the large‐scale distribution of fruiting crops closely matches that of individual trees, suggesting between‐year variation in resource tracking by avian frugivores.

Our findings reveal connectivity to be an emerging property of plant‐disperser systems, operating at the scale of individual fruiting plants, but contingent on the yearly, large‐scale templates of fruiting crops.