bluuebunny/crossref_metadata_2025_split huggingface dataset:
1.0 T open-configuration magnetic resonance-guided microwave ablation of pig livers in real time
Authors: Dong Jun , Zhang Liang , Li Wang , Mao Siyue , Wang Yiqi , Wang Deling , Shen Lujun , Dong Annan , Wu Peihong 
Published: August 2015

AbstractThe current fastest frame rate of each single image slice in MR-guided ablation is 1.3 seconds, which means delayed imaging for human at an average reaction time: 0.33 seconds. The delayed imaging greatly limits the accuracy of puncture and ablation and results in puncture injury or incomplete ablation. To overcome delayed imaging and obtain real-time imaging, the study was performed using a 1.0-T whole-body open configuration MR scanner in the livers of 10 Wuzhishan pigs. A respiratory-triggered liver matrix array was explored to guide and monitor microwave ablation in real-time. We successfully performed the entire ablation procedure under MR real-time guidance at 0.202 s, the fastest frame rate for each single image slice. The puncture time ranged from 23 min to 3 min. For the pigs, the mean puncture time was shorted to 4.75 minutes and the mean ablation time was 11.25 minutes at power 70 W. The mean length and widths were 4.62 ± 0.24 cm and 2.64 ± 0.13 cm, respectively. No complications or ablation related deaths during or after ablation were observed. In the current study, MR is able to guide microwave ablation like ultrasound in real-time guidance showing great potential for the treatment of liver tumors.
Stability analysis of a model gene network links aging, stress resistance and negligible senescence
Authors: Kogan Valeria , Molodtsov Ivan , Menshikov Leonid I. , Reis Robert J. Shmookler , Fedichev Peter 
Published: August 2015

AbstractSeveral animal species are considered to exhibit what is called negligible senescence, i.e. they do not show signs of functional decline or any increase of mortality with age. Recent studies in naked mole rat and long-lived sea urchins showed that these species do not alter their gene-expression profiles with age as much as other organisms do. This is consistent with exceptional endurance of naked mole rat tissues to various genotoxic stresses. We conjectured, therefore, that the lifelong transcriptional stability of an organism may be a key determinant of longevity. We analyzed the stability of a simple genetic-network model and found that under most common circumstances, such a gene network is inherently unstable. Over a time it undergoes an exponential accumulation of gene-regulation deviations leading to death. However, should the repair systems be sufficiently effective, the gene network can stabilize so that gene damage remains constrained along with mortality of the organism. We investigate the relationship between stress-resistance and aging and suggest that the unstable regime may provide a mathematical basis for the Gompertz “law” of aging in many species. At the same time, this model accounts for the apparently age-independent mortality observed in some exceptionally long-lived animals.
Towards coherent infinitival patterns in the history of German
Authors: Demske Ulrike 
Published: August 2015

According to Haider (2010), we have to distinguish three types of infinitival complements in Present-Day German: (i) CP complements, (ii) VP complements and (iii) verbal clusters. While CP complements give rise to biclausal structures, VP complements and verbal clusters indicate a monoclausal structure. Non-finite verbs in verbal clusters build a syntactic unit with the governing verb. It is only the last infinitival pattern that we address as a so-called coherent infinitival pattern, a notion introduced in the influential work of Bech (1955/57). Verbal clusters are bound to languages with an OV grammar, hence the well-known differences regarding infinitival syntax in German and English (Haider 2003, Bobaljik 2004). On the widespread assumption that German has been an OV language throughout its history (Axel 2007), we expect all three types of infinitival complements to be present from the earliest attestions of German.This expectation, however, is not borne out. In the present article, I show that we find infinitival complements projecting either CPs or VPs in older stages of German, while verbal clusters turn out to be a quite recent phenomenon in the history of German, as already suggested in work by Askedal (1998), Demske (2008) and Maché & Abraham (2011). In line with current beliefs that German is underspecified regarding the direction of government in earlier stages of its historical development, I argue that the rise of verbal clusters is motivated by the increasing stabilization of an OV grammar since the 16th century.
Energy self-sufficient sustainable integrated farming systems for livelihood security under a changing climate scenario in an Indian context: a case-study approach.
Authors: Behera U. K. , Amjath Babu Amjath Babu , Kaechele H. , France J. 
Published: August 2015

Abstract
The farming systems of the world have to meet multiple demands, e.g. supporting livelihood, conserving biodiversity, off-setting emissions and adapting to climate change. As a traditional way of farming in India, an integrated farming system (IFS) represents multiple crops (cereals, legumes, tree crops, vegetables, etc.) and multiple enterprises (livestock production, fish farming, bee keeping, etc.) on a single farm. Taking a case-study approach, we analyse the economics, calculate energy balances and describe the resource flows within such an integrated farm. Additionally, the concept of an IFS that makes these farms energy self-sufficient (or even in surplus), especially in modern forms of energy, is discussed. We argue for integrating renewable energy production possibilities, i.e. wind energy, solar energy, biofuels and biogas production, within these farms. Such farms can mitigate carbon emissions and offer resilience to probable climatic changes. Owing to the presence of diverse environments and various trophic levels, it can also support multiple species and hence have a role in biodiversity conservation. The study is a novel attempt to bring energy security to rural India while addressing climate change and biodiversity concerns. It should lead to ensuring sustainable livelihood options for small-holder farmers in India and potentially has global relevance. A number of policy options that may facilitate the transition are also briefly discussed.
LncRNA-ID: Long non-coding RNA IDentification using balanced random forests
Authors: Achawanantakun Rujira , Chen Jiao , Sun Yanni , Zhang Yuan 
Published: August 2015

Abstract
Motivation: Long non-coding RNAs (lncRNAs), which are non-coding RNAs of length above 200 nucleotides, play important biological functions such as gene expression regulation. To fully reveal the functions of lncRNAs, a fundamental step is to annotate them in various species. However, as lncRNAs tend to encode one or multiple open reading frames, it is not trivial to distinguish these long non-coding transcripts from protein-coding genes in transcriptomic data.
Results: In this work, we design a new tool that calculates the coding potential of a transcript using a machine learning model (random forest) based on multiple features including sequence characteristics of putative open reading frames, translation scores based on ribosomal coverage, and conservation against characterized protein families. The experimental results show that our tool competes favorably with existing coding potential computation tools in lncRNA identification.
Availability and implementation: The scripts and data can be downloaded at https://github.com/zhangy72/LncRNA-ID
Contact: yannisun@msu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
HapCol: accurate and memory-efficient haplotype assembly from long reads
Authors: Pirola Yuri , Zaccaria Simone , Dondi Riccardo , Klau Gunnar W. , Pisanti Nadia , Bonizzoni Paola 
Published: August 2015

Abstract
Motivation: Haplotype assembly is the computational problem of reconstructing haplotypes in diploid organisms and is of fundamental importance for characterizing the effects of single-nucleotide polymorphisms on the expression of phenotypic traits. Haplotype assembly highly benefits from the advent of ‘future-generation’ sequencing technologies and their capability to produce long reads at increasing coverage. Existing methods are not able to deal with such data in a fully satisfactory way, either because accuracy or performances degrade as read length and sequencing coverage increase or because they are based on restrictive assumptions.
Results: By exploiting a feature of future-generation technologies—the uniform distribution of sequencing errors—we designed an exact algorithm, called HapCol, that is exponential in the maximum number of corrections for each single-nucleotide polymorphism position and that minimizes the overall error-correction score. We performed an experimental analysis, comparing HapCol with the current state-of-the-art combinatorial methods both on real and simulated data. On a standard benchmark of real data, we show that HapCol is competitive with state-of-the-art methods, improving the accuracy and the number of phased positions. Furthermore, experiments on realistically simulated datasets revealed that HapCol requires significantly less computing resources, especially memory. Thanks to its computational efficiency, HapCol can overcome the limits of previous approaches, allowing to phase datasets with higher coverage and without the traditional all-heterozygous assumption.
Availability and implementation: Our source code is available under the terms of the GNU General Public License at http://hapcol.algolab.eu/.
Contact: bonizzoni@disco.unimib.it
Supplementary information: Supplementary data are available at Bioinformatics online.
glmgraph: an R package for variable selection and predictive modeling of structured genomic data
Authors: Chen Li , Liu Han , Kocher Jean-Pierre A. , Li Hongzhe , Chen Jun 
Published: August 2015

Abstract
Summary: One central theme of modern high-throughput genomic data analysis is to identify relevant genomic features as well as build up a predictive model based on selected features for various tasks such as personalized medicine. Correlating the large number of ‘omics’ features with a certain phenotype is particularly challenging due to small sample size (n) and high dimensionality (p). To address this small n, large p problem, various forms of sparse regression models have been proposed by exploiting the sparsity assumption. Among these, network-constrained sparse regression model is of particular interest due to its ability to utilize the prior graph/network structure in the omics data. Despite its potential usefulness for omics data analysis, no efficient R implementation is publicly available. Here we present an R software package ‘glmgraph’ that implements the graph-constrained regularization for both sparse linear regression and sparse logistic regression. We implement both the L1 penalty and minimax concave penalty for variable selection and Laplacian penalty for coefficient smoothing. Efficient coordinate descent algorithm is used to solve the optimization problem. We demonstrate the use of the package by applying it to a human microbiome dataset, where phylogeny structure among bacterial taxa is available.
Availability and implementation: ‘glmgraph’ is implemented in R and C++ Armadillo and publicly available under CRAN.
Contact: chen.jun2@mayo.edu or hongzhe@upenn.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
CoD: inferring immune-cell quantities related to disease states
Authors: Frishberg Amit , Steuerman Yael , Gat-Viks Irit 
Published: August 2015

Abstract
Motivation: The immune system comprises a complex network of genes, cells and tissues, coordinated through signaling pathways and cell−cell communications. However, the orchestrated role of the multiple immunological components in disease is still poorly understood. Classifications based on gene-expression data have revealed immune-related signaling pathways in various diseases, but how such pathways describe the immune cellular physiology remains largely unknown.
Results: We identify alterations in cell quantities discriminating between disease states using ‘ Cell type of Disease’ (CoD), a classification-based approach that relies on computational immune-cell decomposition in gene-expression datasets. CoD attains significantly higher accuracy than alternative state-of-the-art methods. Our approach is shown to recapitulate and extend previous knowledge acquired with experimental cell-quantification technologies.
Conclusions: The results suggest that CoD can reveal disease-relevant cell types in an unbiased manner, potentially heralding improved diagnostics and treatment.
Availability and implementation: The software described in this article is available at http://www.csgi.tau.ac.il/CoD/.
Contact: iritgv@post.tau.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
A rapid assessment of trends in the multispecies small-scale fishery of Palamós (Catalonia, Spain)
Authors: Dimitriadis Caterina , Carranza Alvar , Vilela Raúl , Casadevall Margarida 
Published: August 2015

Abstract
Monitoring small-scale fisheries (SSFs) is challenging due to the limited information available and their underlying socioeconomic characteristics. This constitutes a serious impediment to assess the compliance level of Aichi Biodiversity Targets (ABT). The European Union has committed itself to include an Ecosystem Approach to Fisheries Management (EAFM) in its Common Fisheries Policy. EAFM depends on suites of indicators that track the pressure exercised, the state of the ecosystem, and the socio-economic consequences of management objectives. Therefore, The Living Planet Index (LPI) is proposed here for describing the performance of SSF towards the ABT. We show that the LPI can be reformulated to track trends in Fishing Effort (LPIFE), trends in Fish Populations (LPIFP), and both the state and trends related to the contribution of fisheries to broader society (LPIDEB). The implementation of the LPI in SSF applies several principles of the EAFM, including decentralization, fishers participation, and consideration of local knowledge. In this paper, we used 10-year daily data from the Cofradía at Palamós port, Catalonia - Spain. This is a multi-species SSF landing ca. 130 species, from which 10.9% are of special interest, being listed by the IUCN or in agreements by regional conventions. We observe a decreasing trend in the LPIFP, the LPIFE, and in the LPIDEB, including 36 species or groups, accounting for 90% of total landings, suggesting an overall decrease in the sustainability of this SSF. We conclude that use of the LPIFP is especially well suited to standardize the reporting of information for multispecies fisheries using a wide array of fishing strategies, and results strongly suggest the feasibility of using the LPI methodology to standardize reporting of any given agreed fisheries indicator in order enhance management towards the ABTs.
Heat-induced Epitope Retrieval for Immunohistochemistry at High Altitude: A Quality Assurance Study
Authors: Stevens Keith A. , Kovach Charles K. , Tompkins Michael , Ruegg Patsy , Cohen Cynthia 
Published: August 2015

Introduction:
Heat-induced epitope retrieval (HIER) of formalin-fixed paraffin-embedded tissues is now a standard practice in immunohistochemistry (IHC). In this study, we aimed to test the effect of altering HIER temperature on IHC staining quality at high altitude, the hypothesis being that lower HIER temperatures would result in improved staining patterns.

Materials and Methods:
In a laboratory at high altitude (Aurora, CO), we used a platform with automated onboard epitope retrieval, and systematically tested 3 different HIER temperatures (100°C, 95°C, 90°C) with 4 IHC stains that are commonly used in routine practice: CD3, Ki67, CK20, and Melan A (n=10 for each antibody/epitope retrieval temperature combination). A scoring system was devised, the slides were scored in a blinded manner, and statistical analysis was performed. For comparison, the same study was performed in a laboratory near sea level (Atlanta, GA).

Results:
At high altitude, lower HIER temperatures resulted in improved staining patterns, as quantified by stronger staining intensity and greater area of the slides stained. The scores obtained with HIER temperatures of 95°C and 90°C were higher than those obtained with HIER of 100°C, and the difference was found to be statistically significantly for some antibody/epitope retrieval temperature combinations (P<0.05). This effect was not seen in the laboratory near sea level.

Conclusions:
We show that alternate epitope retrieval recommendations are warranted for laboratories at high altitude. Furthermore, we suggest that manufactures should consider how their instruments will perform at high altitude as they further automate the process of IHC.
The role of mentoring relationships in counseling programs
Authors: Boswell Jennifer N. , Wilson Angie D. , Stark Marcella D. , Onwuegbuzie Anthony J 
Published: August 2015

Purpose
– The goals of a mentoring relationship are important to the development of mentees. The purpose of this paper is to focus on the specific needs of students and junior faculty in counseling programs.

Design/methodology/approach
– The authors used a psychological phenomenological research approach to understand the role and significance of a mentor and the mentoring relationship. In this qualitative research study, pre-tenured faculty, doctoral- and master’s-level students in counselor education programs in the USA were interviewed (n=30), to explore the mentorship needs.

Findings
– In the study, the authors identified 28 codes that emerged from the participants’ lived experiences, which then were organized into seven meta-codes. The seven meta-codes were: relationship between mentor and mentee; communication style or patterns; preferred gender of mentor; introduction to the relationship; mentee needs; mentee benefits; and experiences as a mentee.

Originality/value
– In the paper, the authors sought to explore the mentoring needs of students and junior faculty in counselor education programs and how these needs can begin to be addressed effectively.
STEM mentoring and the use of the principles of Adult Mentoring Inventory
Authors: Feldhaus Charles , Bentrem Kristin 
Published: August 2015

Purpose– The purpose of this convergent parallel mixed methods paper is to explore the mentoring experience within the context of a science, technology, engineering and math (STEM) specific mentoring program for urban, at risk, high school youth, using the Principles of Adult Mentoring Inventory (PAMI) as an instrument that modeled effective mentoring behavior. The study took place at a large, urban, Midwestern university in the USA.Design/methodology/approach– A research design was developed and both quantitative and qualitative data were collected in parallel, analyzed separately and then merged to determine results. The PAMI instrument that measures six constructs of mentor effectiveness was administered to STEM mentors as a pre/post-test and enabled researchers to collect quantitative data. Researchers used focus groups to collect qualitative data in the form of transcribed interviews. This study sought to inform STEM mentoring program development by collecting both qualitative and quantitative data independently and simultaneously in order to confirm findings. Researchers used a convergent parallel mixed methods design to first, reinforce and corroborate the findings given the small sample size (n=8); second, minimize alternative interpretations from data gathering and analysis, third, make clear various factors contributing to the effectiveness of STEM mentoring.Findings– Throughout the mentoring experience, mentor perceptions of their mentoring abilities increased to be in the “more highly effective” range within PAMI. In five of the six constructs the results indicated mentors scored lower on the pre-test than they did on the post-test of the PAMI, meaning mentor perceptions of mentoring abilities improved overall during the course and the mentoring experience. Common themes from both quantitative and qualitative results were developed, are discussed using the PAMI constructs as organizers, and include communication, information, and gender differences.Originality/value– This study added to the dearth of literature and investigations surrounding STEM mentoring. Many studies have concentrated primarily on mentoring but few have investigated the concept of STEM mentoring program best practices. The results of this study provided a multidimensional look at STEM mentoring programs that impact urban, at risk, high school youth.
Healthcare succession management: are we ready?
Authors: VanVactor Jerry D. 
Published: August 2015

Purpose– The purpose of this paper is to present practicing management professionals with a model related to succession management and planning.Design/methodology/approach– Using a review of existent literature, this work examines and expounds upon the impact of succession management and planning as a potential genesis of, and an opportunity to mitigate, organizational problems related to senior executive turnover.Findings– This manuscript presents a succession management and planning model for practicing professionals that is based on three key tenets: first, a plan (of some sort) is necessary for corporate resilience and sustainability; second, an organization has in inherent responsibility and need to plan for replacements and prioritize allocation of resources; and third, succession management planning aids in the establishment of organizational resilience and stability amid contingencies.Practical implications– This work examines how, ultimately, succession management and planning is a means to risk/crisis management aimed at reducing gaps and associated problems related to changes among human capital distribution.Social implications– While this work is written with emphasis placed upon managing transition among healthcare organizations and personnel, the information is equally relevant and applicable to a broader audience. In an applied sense, this model provides management professionals with concepts related to orchestrating change at both the individual and organizational levels.Originality/value– While there is a dearth of literature examining succession management in a variety of industries, little information is directed specifically toward healthcare. This manuscript provides concepts related to effective risk mitigation via defined succession management and planning.