bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhancement of an anti-tumor immune response by transient blockade of central T cell tolerance
Authors: Khan Imran S. , Mouchess Maria L. , Zhu Meng-Lei , Conley Bridget , Fasano Kayla J. , Hou Yafei , Fong Lawrence , Su Maureen A. , Anderson Mark S.
Published: April 2014

Thymic central tolerance is a critical process that prevents autoimmunity but also presents a challenge to the generation of anti-tumor immune responses. Medullary thymic epithelial cells (mTECs) eliminate self-reactive T cells by displaying a diverse repertoire of tissue-specific antigens (TSAs) that are also shared by tumors. Therefore, while protecting against autoimmunity, mTECs simultaneously limit the generation of tumor-specific effector T cells by expressing tumor self-antigens. This ectopic expression of TSAs largely depends on autoimmune regulator (Aire), which is expressed in mature mTECs. Thus, therapies to deplete Aire-expressing mTECs represent an attractive strategy to increase the pool of tumor-specific effector T cells. Recent work has implicated the TNF family members RANK and RANK-Ligand (RANKL) in the development of Aire-expressing mTECs. We show that in vivo RANKL blockade selectively and transiently depletes Aire and TSA expression in the thymus to create a window of defective negative selection. Furthermore, we demonstrate that RANKL blockade can rescue melanoma-specific T cells from thymic deletion and that persistence of these tumor-specific effector T cells promoted increased host survival in response to tumor challenge. These results indicate that modulating central tolerance through RANKL can alter thymic output and potentially provide therapeutic benefit by enhancing anti-tumor immunity.
Constant term of Eisenstein integrals on a reductive 𝑝-adic symmetric space
Authors: Carmona Jacques , Delorme Patrick
Published: April 2014

Let

H
H

be the fixed point group of a rational involution

σ
\sigma

of a reductive

p
p

-adic group on a field of characteristic different from 2. Let

P
P

be a

σ
\sigma

-parabolic subgroup of

G
G

, i.e. such that

σ
(
P
)

\sigma (P)

is opposite

P
P

. We denote the intersection

P
∩
σ
(
P
)

P\cap \sigma (P)

by

M
M

.

Kato and Takano on one hand and Lagier on the other associated canonically to an

H
H

-form, i.e. an

H
H

-fixed linear form,

ξ
\xi

, on a smooth admissible

G
G

-module,

V
V

, a linear form on the Jacquet module

j
P

(
V
)

j_P(V)

of

V
V

along

P
P

which is fixed by

M
∩
H

M\cap H

. We call this operation the constant term of

H
H

-forms. This constant term is linked to the asymptotic behaviour of the generalized coefficients with respect to

ξ
\xi

.

P. Blanc and the second author defined a family of

H
H

-forms on certain parabolically induced representations, associated to an

M
∩
H

M\cap H

-form,

η
\eta

, on the space of the inducing representation.

The purpose of this article is to describe the constant term of these

H
H

-forms.

Also it is shown that when

η
\eta

is discrete, i.e. when the generalized coefficients of

η
\eta

are square integrable modulo the center, the corresponding family of

H
H

-forms on the induced representations is a family of tempered, in a suitable sense,

H
H

-forms. A formula for the constant term of Eisenstein integrals is given.
Multiscale DNA partitioning: statistical evidence for segments
Authors: Futschik Andreas , Hotz Thomas , Munk Axel , Sieling Hannes
Published: April 2014

Motivation: DNA segmentation, i.e. the partitioning of DNA in compositionally homogeneous segments, is a basic task in bioinformatics. Different algorithms have been proposed for various partitioning criteria such as Guanine/Cytosine (GC) content, local ancestry in population genetics or copy number variation. A critical component of any such method is the choice of an appropriate number of segments. Some methods use model selection criteria and do not provide a suitable error control. Other methods that are based on simulating a statistic under a null model provide suitable error control only if the correct null model is chosen.

Results: Here, we focus on partitioning with respect to GC content and propose a new approach that provides statistical error control: as in statistical hypothesis testing, it guarantees with a user-specified probability that the number of identified segments does not exceed the number of actually present segments. The method is based on a statistical multiscale criterion, rendering this as a segmentation method that searches segments of any length (on all scales) simultaneously. It is also accurate in localizing segments: under benchmark scenarios, our approach leads to a segmentation that is more accurate than the approaches discussed in the comparative review of Elhaik et al. In our real data examples, we find segments that often correspond well to features taken from standard University of California at Santa Cruz (UCSC) genome annotation tracks.

Availability and implementation: Our method is implemented in function smuceR of the R-package stepR available at http://www.stochastik.math.uni-goettingen.de/smuce.

Contact:  andreas.futschik@jku.at or thomas.hotz@tu-ilmenau.de

Supplementary information:  Supplementary Data are available at Bioinformatics online.
aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data
Authors: Rosenberger George , Ludwig Christina , Röst Hannes L. , Aebersold Ruedi , Malmström Lars
Published: April 2014

Motivation: The determination of absolute quantities of proteins in biological samples is necessary for multiple types of scientific inquiry. While relative quantification has been commonly used in proteomics, few proteomic datasets measuring absolute protein quantities have been reported to date. Various technologies have been applied using different types of input data, e.g. ion intensities or spectral counts, as well as different absolute normalization strategies. To date, a user-friendly and transparent software supporting large-scale absolute protein quantification has been lacking.

Results: We present a bioinformatics tool, termed aLFQ, which supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/MS proteomics data, together with validation algorithms enabling automated data analysis and error estimation.

Availability and implementation:  aLFQ is written in R and freely available under the GPLv3 from CRAN (http://www.cran.r-project.org). Instructions and example data are provided in the R-package. The raw data can be obtained from the PeptideAtlas raw data repository (PASS00321).

Contact:  lars.malmstroem@imsb.biol.ethz.ch

Supplementary information:  Supplementary Data are available at Bioinformatics online.
MRMPROBS suite for metabolomics using large-scale MRM assays
Authors: Tsugawa Hiroshi , Kanazawa Mitsuhiro , Ogiwara Atsushi , Arita Masanori
Published: April 2014

Summary: We developed new software environment for the metabolome analysis of large-scale multiple reaction monitoring (MRM) assays. It supports the data format of four major mass spectrometer vendors and mzML common data format. This program provides a process pipeline from the raw-format import to high-dimensional statistical analyses. The novel aspect is graphical user interface-based visualization to perform peak quantification, to interpolate missing values and to normalize peaks interactively based on quality control samples. Together with the software platform, the MRM standard library of 301 metabolites with 775 transitions is also available, which contributes to the reliable peak identification by using retention time and ion abundances.

Availability and implementation: MRMPROBS is available for Windows OS under the creative-commons by-attribution license at http://prime.psc.riken.jp.

Contact:  hiroshi.tsugawa@riken.jp

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Prognostic Significance of Nodal Ratio in Patients Undergoing Adjuvant Chemoradiotherapy After Curative Resection for Ampullary Cancer
Authors: Kim Kyubo , Chie Eui Kyu , Jang Jin-Young , Kim Sun Whe , Han Sae-Won , Oh Do-Youn , Im Seock-Ah , Kim Tae-You , Bang Yung-Jue , Ha Sung W.
Published: April 2014

Objectives:

To analyze the outcome of patients with ampullary cancer who had undergone curative surgery followed by adjuvant chemoradiotherapy and to identify the prognostic factors for these patients

Methods:

Between January 1991 and August 2006, 71 patients with ampullary cancer underwent curative resection followed by adjuvant radiotherapy. There were 38 males and 33 females, and median age was 56 years (range, 28 to 77 y). Postoperative radiotherapy was delivered to tumor bed and regional lymph nodes up to 40 to 50 Gy at 2 Gy/fraction; 67 patients also received intravenous 5-fluorouracil as a radiosensitizer. Median follow-up duration was 72 months for survivors.

Results:

There were 5 isolated locoregional recurrences, 20 isolated distant metastases, and 11 combined locoregional and distant relapses. The 5-year locoregional relapse-free and overall survival rates were 76.2% and 64.5%, respectively. On multivariate analysis, nodal ratio and histologic differentiation were significant prognostic factors for overall survival (P=0.0382 and 0.0331, respectively).

Conclusions:

Adjuvant chemoradiotherapy after curative resection can achieve a long-term survival rate in patients with ampullary cancer. Nodal ratio and histologic differentiation are independent prognostic factors for these patients.
Comparison of Strength, Consistency, and Speed of COR-KNOT versus Manually Hand-Tied Knots in an Ex Vivo Minimally Invasive Model
Authors: Lee Candice Y. , Sauer Jude S. , Gorea Heather R. , Martellaro Angelo J. , Knight Peter A.
Published: April 2014

Objective

This study compared the strength, consistency, and speed of prosthetic attachment sutures secured with automated fasteners with those of manual knots using an ex vivo porcine mitral valve annuloplasty model. A novel miniature pressure transducer system was developed to quantify pressures between sutured prosthetic rings and underlying cardiac tissue.

Methods

Sixteen mitral annuloplasty rings were sewn into ex vivo pig hearts. Eight rings were secured with the COR-KNOT device; and eight rings, with hand-tied knots using a knot pusher. A cardiac surgeon and a surgery resident each completed four manually tied rings and four COR-KNOT rings via a thoracotomy trainer. The total time to knot and cut each ring's sutures was recorded. Suture attachment pressures were measured within (intrasuture) and between (extrasuture) each suture loop using a 0.5 × 2.0-mm microtransducer probe system.

Results

The suture holding pressures for the COR-KNOT fasteners were significantly greater than for the manually tied knots (median, 1008.9 vs 415.8 mm Hg, P < 0.001). All automated fasteners measured greater than 500 mm Hg, whereas 56% of the hand-tied knots were less than 500 mm Hg, and 14% were less than 75 mm Hg. There was less variation in attachment pressures for the COR-KNOT fasteners than for the hand-tied knots (SD, 401.6 vs 499.3 mm Hg, P = 0.04). Significant time savings occurred with the use of the COR-KNOT compared with manual tying (12.4 vs 71.1 seconds perknot, P = 0.001).

Conclusions

The novel microtransducer technology provided an innovative means of evaluating cardiac prosthetic anchoring sutures. In this model, mitral annuloplasty ring sutures secured with the COR-KNOT device were stronger, more consistent, and faster than with manually tied knots.
Encoding range minima and range top-2 queries
Authors: Davoodi Pooya , Navarro Gonzalo , Raman Rajeev , Rao S. Srinivasa
Published: April 2014

We consider the problem of
encoding range minimum queries
(RMQs): given an array
A
[1..
n
] of distinct totally ordered values, to pre-process
A
and create a data structure that can answer the query RMQ(
i
,
j
), which returns the index containing the smallest element in
A
[
i
..
j
],
without
access to the array
A
at query time. We give a data structure whose space usage is 2
n
+
o
(
n
) bits, which is asymptotically optimal for worst-case data, and answers RMQs in
O
(1) worst-case time. This matches the previous result of Fischer and Heun, but is obtained in a more natural way. Furthermore, our result can encode the RMQs of a random array
A
in 1.919
n
+
o
(
n
) bits in expectation, which is not known to hold for Fischer and Heun’s result. We then generalize our result to the encoding
range top-2 query
(RT2Q) problem, which is like the encoding RMQ problem except that the query RT2Q(
i
,
j
) returns the indices of both the smallest and second smallest elements of
A
[
i
..
j
]. We introduce a data structure using 3.272
n
+
o
(
n
) bits that answers RT2Qs in constant time, and also give lower bounds on the
effective entropy
of the RT2Q problem.
A new graph model and algorithms for consistent superstring problems
Authors: Na Joong Chae , Cho Sukhyeun , Choi Siwon , Kim Jin Wook , Park Kunsoo , Sim Jeong Seop
Published: April 2014

Problems related to string inclusion and non-inclusion have been vigorously studied in diverse fields such as data compression, molecular biology and computer security. Given a finite set of positive strings

and a finite set of negative strings

, a string
α
is a consistent superstring if every positive string is a substring of
α
and no negative string is a substring of
α
. The shortest (resp. longest) consistent superstring problem is to find a string
α
that is the shortest (resp. longest) among all the consistent superstrings for the given sets of strings. In this paper, we first propose a new graph model for consistent superstrings for given

and

. In our graph model, the set of strings represented by paths satisfying some conditions is the same as the set of consistent superstrings for

and

. We also present algorithms for the shortest and the longest consistent superstring problems. Our algorithms solve the consistent superstring problems for all cases, including cases that are not considered in previous work. Moreover, our algorithms solve in polynomial time the consistent superstring problems for more cases than the previous algorithms. For the polynomially solvable cases, our algorithms are more efficient than the previous ones.
Large-scale detection of repetitions
Authors: Smyth W. F.
Published: April 2014

Combinatorics on words began more than a century ago with a demonstration that an infinitely long string with
no
repetitions could be constructed on an alphabet of only three letters. Computing
all
the repetitions (such as ⋯
TTT
⋯ or ⋯
CGACGA
⋯ ) in a given string

x

of length
n
is one of the oldest and most important problems of computational stringology, requiring

time in the worst case. About a dozen years ago, it was discovered that repetitions can be computed as a by-product of the
Θ
(
n
)-time computation of all the
maximal periodicities
or
runs
in

x

. However, even though the computation is linear, it is also brute force: global data structures, such as the
suffix array
, the
longest common prefix array
and the
Lempel–Ziv factorization
, need to be computed in a preprocessing phase. Furthermore, all of this effort is required despite the fact that the expected number of runs in a string is generally a small fraction of the string length. In this paper, I explore the possibility that repetitions (perhaps also other regularities in strings) can be computed in a manner commensurate with the size of the output.
Indexing a sequence for mapping reads with a single mismatch
Authors: Crochemore Maxime , Langiu Alessio , Rahman M. Sohel
Published: April 2014

Mapping reads against a genome sequence is an interesting and useful problem in computational molecular biology and bioinformatics. In this paper, we focus on the problem of indexing a sequence for mapping reads with a single mismatch. We first focus on a simpler problem where the length of the pattern is given beforehand during the data structure construction. This version of the problem is interesting in its own right in the context of the next generation sequencing. In the sequel, we show how to solve the more general problem. In both cases, our algorithm can construct an efficient data structure intime and space and can answer subsequent queries intime. Here,nis the length of the sequence,mis the length of the read, 0<ε<1 andis the optimal output size.
Resistotype of Helicobacter pylori isolates: the impact on eradication outcome
Authors: Alfizah Hanafiah , Norazah Ahmad , Hamizah Razlan , Ramelah Mohamed
Published: April 2014

Antibiotic resistance is increasing worldwide, and it has been regarded as the main factor reducing the efficacy ofHelicobacter pyloritherapy. The aim of this study was to determine the phenotype and genotype of antibiotic-resistant strains ofH. pyloriin the Malaysian population and to evaluate the impact of antibiotic resistance to eradication outcome. One hundred and sixty-oneH. pyloriisolates were analysed in this study. Metronidazole, clarithromycin, fluoroquinolone, amoxicillin and tetracycline susceptibilities were determined by Etest. PCR followed by DNA sequencing was carried out to determine mutations. The medical records of the patients infected with resistant strains were reviewed to determine the eradication outcome. Metronidazole resistance was encountered in 36.6 % ofH. pyloriisolates, whereas clarithromycin and fluoroquinolone resistance was observed in 1.2  and 1.9 % of isolates, respectively. All strains tested were susceptible to amoxicillin and tetracycline. Frameshift and nonsense mutations inrdxAandfrxAgenes resulting in stop codons contributed to metronidazole resistance, which leads to reduced eradication efficacy. A2142G and A2143G mutations of 23S rRNA were identified as causing failure of the eradication therapy. Mutation at either codon 87 or 91 of thegyrAgene was identified in fluoroquinolone-resistant strains. However, the effect of resistance could not be assessed. This study showed that frameshift and nonsense mutations inrdxAorfrxAgenes and point mutations in the 23S rRNA affected the efficacy ofH. pylorieradication therapy.
Regulatory variants explain much more heritability than coding variants across 11 common diseases
Authors: Gusev Alexander , Lee S Hong , Neale Benjamin M , Trynka Gosia , Vilhjalmsson Bjarni J , Finucane Hilary , Xu Han , Zang Chongzhi , Ripke Stephan , Stahl Eli , Schizophrenia Working Group of the PGC n/a , SWE-SCZ Consortium n/a , Kahler Anna K , Hultman Christina M , Purcell Shaun M , McCarroll Steven A , Daly Mark , Pasaniuc Bogdan , Sullivan Patrick F , Wray Naomi R , Raychaudhuri Soumya , Price Alkes L
Published: April 2014

Common variants implicated by genome-wide association studies (GWAS) of complex diseases are known to be enriched for coding and regulatory variants. We applied methods to partition the heritability explained by genotyped SNPs (h2g) across functional categories (while accounting for shared variance due to linkage disequilibrium) to genotype and imputed data for 11 common diseases. DNaseI Hypersensitivity Sites (DHS) from 218 cell-types, spanning 16% of the genome, explained an average of 79% of h2g (5.1× enrichment; P < 10−20); further enrichment was observed at enhancer and cell-type specific DHS elements. The enrichments were much smaller in analyses that did not use imputed data or were restricted to GWAS- associated SNPs. In contrast, coding variants, spanning 1% of the genome, explained only 8% of h2g (13.8× enrichment; P = 5 × 10−4). We replicated these findings but found no significant contribution from rare coding variants in an independent schizophrenia cohort genotyped on GWAS and exome chips.
Notorious Novel Avian Influenza Viruses H10N8 and H7N9 in China in 2013 Co-originated from H9N2
Authors: Chen Liang , Zhu Feng , Xiong Chenglong , Zhang Zhijie , Jiang Lufang , Li Rui , Zhao Genming , Chen Yue , Jiang Qingwu
Published: April 2014

In 2013, two new avian influenza viruses (AIVs) H7N9 and H10N8 emerged in China caused worldwide concerns. Previous studies have studied their originations independently; this study is the first time to investigate their co-originating characteristics. Gene segments of assorted subtype influenza A viruses, as well as H10N8 and H7N9, were collected from public database. With the help of series software, small and large-scale phylogenetic trees, mean evolutionary rates, and divergence years were obtained successionally. The results demonstrated the two AIVs co-originated from H9N2, and shared a spectrum of mutations in common on many key sites related to pathogenic, tropism and epidemiological characteristics. For a long time, H9N2 viruses had been circulated in eastern and southern China; poultry was the stable and lasting maintenance reservoir. High carrying rate of AIVs H9N2 in poultry had an extremely high risk of co-infections with other influenza viruses, which increased the risk of virus reassortment. It implied that novel AIVs reassortants based on H9N2 might appear and prevail at any time in China; therefore, surveillance of H9N2 AIVs should be given a high priority.
Critical success factors for implementation of risk assessment and management practices within the Tanzanian construction industry
Authors: Chileshe Nicholas , John Kikwasi Geraldine
Published: April 2014

Purpose

– Despite the extensive research on critical success factors (CSFs), there is a paucity of studies that examine CSFs for the deployment of risk assessment and management processes in developing countries, particularly, Africa. The purpose of this paper is to investigate the perception of construction professionals on CSFs appertaining to the deployment of risk assessment and management practices (RAMP) in Tanzania with the aim of filling the knowledge gap.

Design/methodology/approach

– The primary data were collected from 67 construction professionals working with clients (private and public), consultants, and contractor organisations (foreign and local) within the Tanzanian construction. Response data was subjected to descriptive and inferential statistics with one-way analysis of variance to examine the differences in the perception of the identified CSFs.

Findings

– The descriptive and empirical analysis demonstrated a disparity of the ranking of the ten CSFs among the groups; however, the differences were not significant. Based on the overall sample, the results of the mean score ranking indicate that “awareness of risk management processes”; “team work and communications”; and “management style” were the three highly ranked CSFs whereas “co-operative culture”; “customer requirement”; and “positive human dynamics” were considered to be the least important.

Research limitations/implications

– The study did not differentiate the perceptions of the CSFs according to the ownership (local or foreign), and the sample consisted of organisations in one industry operating in Tanzania. Consequently, the findings may not generalise to other industries or to organisations operating in other countries.

Practical implications

– For RAMP to be implemented effectively, Tanzanian constructional-related organisations should consider the identified CSFs as a vehicle for improving project success through reduction of risk uncertainty. Furthermore, regardless of the type of organisation, “management style”, “team work and communication” are necessary for the successful deployment of RAMP.

Originality/value

– This study makes a contribution to the body of knowledge on the subject within a previously unexplored context. The study provides insights on the drivers and enablers (CSFs) of risk assessment implementation across the Tanzania construction sector.
The effect of construction demand on contract auctions: an experiment
Authors: Soo Alexander , Lan Oo Bee
Published: April 2014

Purpose

– The purpose of this paper is to present an experiment to test the effect of construction demand on the mark-up price level in construction contract auctions.

Design/methodology/approach

– An experimental approach was adopted for this study. In a controlled laboratory environment, a first-price sealed bid auction was simulated with varying number of projects available over ten rounds to simulate changing construction demand. Two experimental treatments were run in parallel, one exhibiting a “booming” demand over time, and the other group with a “recession” scenario. The experiment involved student (inexperienced) bidders with a construction project management background.

Findings

– The results show that inexperienced bidders do behave differently when subjected to varying levels of construction demand. Variations in the bid price level are affected by varying levels of construction demand and the general mark-up level for the bidders experiencing a booming scenario was higher on average compared to bidders subjected to the recession scenario.

Research limitations/implications

– An identified limitation of this study is the use of student subjects in the experiment, thus the experiment results are limited in generalisation to inexperienced bidders. Further studies may be able to replicate the experiment with experienced industry practitioners to observe the results.

Practical implications

– The results allow for industry practitioners to gain a stronger understanding of the effects of varying levels of construction demand and the need to consider construction demand in construction contracting. For construction clients, the level of construction demand may be used as an indicator to assist in the timing to call tenders to achieve a desirable price. For contractors, increased awareness of how demand affects competition and the price level will allow additional optimisations to be achieved in the bid price.

Originality/value

– Construction demand has been widely known to be one of the key factors affecting contractors’ bidding decisions. However, there has been little empirical investigation of the changes in bidders’ behaviour due to varying levels of construction demand. This paper attempts to add to the empirical research knowledgebase through an experimental setting.
Sexual differences in Lobelia spicata populations: floral morphometrics, stigma pollen loads, and pollen tube growth
Authors: Molano‐Flores Brenda , Faivre Amy E.
Published: April 2014

In many gynodioecious species, gender differences have been documented. Previous studies on populations of Lobelia spicata consistently documented hermaphrodites having larger corollas than females, but inconsistencies as to whether females had higher fruit set or not. In this study we expanded the data set on floral morphology, and to relate morphological differences to potential reproductive output we recorded stigma pollen loads and pollen tube growth to the ovary for both genders from four populations. Also, individuals were bagged to determine if and how much self‐pollen deposition occurred on stigmas. Because this species is self‐compatible but protandrous, it was thought unlikely to be able to self‐fertilize through autogamy. Hermaphroditic flowers were larger than female flowers in four out of the six flower traits analyzed. Overall, hermaphroditic flowers had larger corollas and stigma–nectary distance, but female flowers had longer and wider stigmas and more ovules. Open‐pollinated hermaphroditic flowers received more pollen grains on the stigma than female flowers. Positive correlations were found between floral morphological traits and stigma pollen load, but only for hermaphrodites. Pollen was found on the stigmas of all hermaphroditic bagged individuals and on a few female bagged individuals, though pollen tube growth was quite limited. Lastly, population differences were found. This study has identified several floral morphological traits and pollen grain/tube differences between genders and among populations for Lobelia spicata, supporting overall patterns identified in other gynodioecious species and adding a more detailed description of differences between the reproductive biology of each gender for this particular species.
Whose illness is it anyway? On facing illness as a couple
Authors: Altschuler Jenny
Published: April 2014

This article explores current trends in research and clinical practice regarding life‐limiting illness and couple relationships; focusing on intimacy, gender, coping strategies and congruence in perceptions. A case example is used to illustrate how systemic ideas and techniques can help couples address the challenges they face and rethink what they want and need from each other.

Practitioner points

In all clinical work it is important to bear witness to partners' shared and different experiences.

It is also important to reflect on resonances with one's own experiences of loss and illness.

Where couples are struggling, systemic techniques offer a way of increasing relational awareness, authenticity and mutuality.
Agglomeration Economies and Productivity Growth in Manufacturing Industry: Empirical Evidence from Indonesia
Authors: Widodo Wahyu , Salim Ruhul , Bloch Harry
Published: April 2014

This study examines the effect of agglomeration economies on productivity growth in Indonesian manufacturing industries during the first decade of this century. Productivity growth is measured at the firm level using the Färe‐Primont Productivity Index. Each firm's productivity growth is then regressed against a set of firm and industry characteristics, including three measures of agglomeration representing the effects of specialisation, diversity and competition. The results show evidence of a positive specialisation effect and a negative diversity effect for aggregate manufacturing and sub‐sectors. Furthermore, there are mixed effects across industries, suggesting that Porter's competition externalities stimulate firm productivity growth under some conditions but not others.
Solubility of Fructose in Water–Ethanol and Water–Methanol Mixtures by Using H‐Bonding Models
Authors: Alavi Tahereh , Pazuki Gholamreza , Raisi Ahmadreza
Published: April 2014

The solubility of fructose in water–ethanol and water–methanol mixtures and the saturated density of each solution at 20, 30, and 40 °C over a range of water mass percentage have been measured. Also, a new modification of the Wilson model has been proposed to describe solubility data satisfactorily. The H‐UNIQUAC and H‐NRTL models were applied and a comparison between these 3 models was carried out. These 3 models were used to estimate the experimental data which was reported in this study. The comparison of the results showed that the H‐Wilson model has the lowest AAD% between these 3 models in correlating the solubility data and the saturated density.
Application of Oxidized Starch in Bake‐Only Chicken Nuggets
Authors: Purcell Sarah , Wang Ya‐Jane , Seo Han‐Seok
Published: April 2014

There is a need to reduce the fat content in fried foods because of increasing health concerns from consumers. Oxidized starches have been utilized in many coating applications for their adhesion ability. However, it is not known if they perform similarly in bake‐only products. This study investigated the application of oxidized starch in bake‐only chicken nuggets. Oxidized starches were prepared from 7 starches and analyzed for gelatinization and pasting properties. Chicken nuggets were prepared using batter containing wheat flour, oxidized starch, salt, and leavening agents prior to steaming, oven baking, freezing, and final oven baking for sensory evaluation. All nuggets were analyzed for hardness by a textural analyzer, crispness by an acoustic sound, and sensory characteristics by a trained panel. The oxidation level used in the study did not alter the gelatinization temperature of most starches, but increased the peak pasting viscosity of both types of corn and rice starches and decreased that of tapioca and potato starches. There were slight differences in peak force and acoustic reading between some treatments; however, the differences were not consistent with starch type or amylose content. There was no difference among the treatments as well as between the control with wheat flour and the treatments partially replaced with oxidized starches in all sensory attributes of bake‐only nuggets evaluated by the trained panel.

Practical Application

There is a need to reduce the fat content in fried food, such as chicken nuggets, because of increasing childhood obesity. Oxidized starches are widely used in coating applications for their adhesion ability. This study investigated the source of oxidized starches in steam‐baked coated nuggets for their textural and sensorial properties. The findings from this research will provide an understanding of the contributions of starch source and oxidation to the texture and sensory attributes of bake‐only nuggets, and future directions to improve the batter formulation for bake‐only nuggets.
Characterization of White Mahlab (Prunus mahaleb L.) Seed Oil: A Rich Source of α‐Eleostearic Acid
Authors: Sbihi Hassen Mohamed , Nehdi Imededdine Arbi , Al‐Resayes Saud Ibrahim
Published: April 2014

Seed oils with high polyunsaturated fatty acid content are used in various industries including the food and pharmaceutical industries. White mahlab (Prunus mahaleb L.) seed was found to contain 31% oil. The oil was highly polyunsaturated and abundant in α‐eleostearic (38.32%), oleic (31.29%), and linoleic (22.96%) acids, which together comprised 93.91% of the total fatty acids. The α‐eleostearic acid was identified and characterized based on 1H‐NMR, UV, and FTIR spectroscopy. The oil was characterized by a relatively high quantity of tocopherols with γ‐tocopherol as the major tocopherol isomer. The physicochemical characteristics of the white mahlab seed and seed oil were also determined. The thermogravimetric analysis indicated that the oil was thermally stable up to 350 °C and began to decompose at 520 °C. This study demonstrated that these seeds may be reused and their oil incorporated into other food products, a beneficial practice considering that the compounds present in the seeds and oils have positive effects on human health.

Practical Application

In this study, mahlab seed oil was found to have potentials to become a new edible oil source as it contained a high level of polyunsaturated fatty acids especially, α‐eleostearic acid, which is a conjugated fatty acid rarely found in vegetable oils and has a beneficial effects on human health.
Predictive Modeling for Growth of Non‐ and Cold‐adapted Listeria monocytogenes on Fresh‐cut Cantaloupe at Different Storage Temperatures
Authors: Hong Yoon‐Ki , Yoon Won Byong , Huang Lihan , Yuk Hyun‐Gyun
Published: April 2014

The aim of this study was to determine the growth kinetics of Listeria monocytogenes, with and without cold‐adaption, on fresh‐cut cantaloupe under different storage temperatures. Fresh‐cut samples, spot inoculated with a 4‐strain cocktail of L. monocytogenes (∼3.2 log CFU/g), were exposed to constant storage temperatures held at 10, 15, 20, 25, or 30 °C. All growth curves of L. monocytogenes were fitted to the Baranyi, modified Gompertz, and Huang models. Regardless of conditions under which cells grew, the time needed to reach 5 log CFU/g decreased with the elevated storage temperature. Experimental results showed that there were no significant differences (P > 0.05) in the maximum growth rate k (log CFU/g h−1) and lag phase duration λ (h) between the cultures of L. monocytogenes with or without previous cold‐adaption treatments. No distinct difference was observed in the growth pattern among 3 primary models at various storage temperatures. The growth curves of secondary modeling were fitted on an Arrhenius‐type model for describing the relationship between k and temperature of the L. monocytogenes on fresh‐cut cantaloupe from 10 to 30 °C. The root mean square error values of secondary models for non‐ and cold‐adapted cells were 0.018, 0.021, and 0.024, and 0.039, 0.026, and 0.017 at the modified Gompertz, Baranyi, and Huang model, respectively, indicating that these 3 models presented the good statistical fit. This study may provide valuable information to predict the growth of L. monocytogenes on fresh‐cut cantaloupes at different storage conditions.
exonsampler: a computer program for genome‐wide and candidate gene exon sampling for targeted next‐generation sequencing
Authors: Cosart Ted , Beja‐Pereira Albano , Luikart Gordon
Published: April 2014

The computer program exonsampler automates the sampling of thousands of exon sequences from publicly available reference genome sequences and gene annotation databases. It was designed to provide exon sequences for the efficient, next‐generation gene sequencing method called exon capture. The exon sequences can be sampled by a list of gene name abbreviations (e.g. IFNG, TLR1), or by sampling exons from genes spaced evenly across chromosomes. It provides a list of genomic coordinates (a bed file), as well as a set of sequences in fasta format. User‐adjustable parameters for collecting exon sequences include a minimum and maximum acceptable exon length, maximum number of exonic base pairs (bp) to sample per gene, and maximum total bp for the entire collection. It allows for partial sampling of very large exons. It can preferentially sample upstream (5 prime) exons, downstream (3 prime) exons, both external exons, or all internal exons. It is written in the Python programming language using its free libraries. We describe the use of exonsampler to collect exon sequences from the domestic cow (Bos taurus) genome for the design of an exon‐capture microarray to sequence exons from related species, including the zebu cow and wild bison. We collected ~10% of the exome (~3 million bp), including 155 candidate genes, and ~16 000 exons evenly spaced genomewide. We prioritized the collection of 5 prime exons to facilitate discovery and genotyping of SNPs near upstream gene regulatory DNA sequences, which control gene expression and are often under natural selection.
DNA barcoding provides support for a cryptic species complex within the globally distributed and fishery important opah (Lampris guttatus)
Authors: Hyde John R. , Underkoffler Karen E. , Sundberg Meagan A.
Published: April 2014

The cornerstone of fisheries management relies on a solid taxonomic base and an understanding of how animals can be grouped into coherent management units. Surprisingly, little is known about the basic biology and ecology of opah (Lampris guttatus), a globally distributed species that is commercially exploited and regionally common in the North Pacific. Recent efforts to collect life history data on this species uncovered evidence of two North Pacific morphotypes. Sequencing of the mitochondrial cytochrome c oxidase I gene (655 bp) for these morphotypes and other specimens collected worldwide (n = 480) produced five strongly diverged and well‐supported clades. Additional sequence data from the cytochrome b gene (1141 bp) as well as the nuclear recombination activating gene 1 (1323 bp) corroborated these results, suggesting these five clades probably represent separate species. Our conclusion that opah is a complex of five separate species has implications for management and indicates a need to gather additional data on these poorly understood fishes.
Seasonal and interannual variation in vegetation composition: Implications for survey design and data interpretation
Authors: Schultz Nick L. , Reid Nick , Lodge Greg , Hunter John T.
Published: April 2014

Understanding how vegetation composition varies with season and interannual climate variability is important for any ecological research that uses vegetation data derived from surveys for the basis of inference. Misunderstanding this variation can influence land management and planning decisions, leading to poor implementation of biodiversity offsetting mechanisms, for example. We monitored plots (400 m2) grazed by livestock paired with adjacent ungrazed plots in derived native pastures four times a year over 2.5 years on the North‐West Slopes of New South Wales. Species density in plots varied greatly with season and interannual rainfall. Highest species density was recorded in spring, though species density in summer was not significantly lower, nor was a spring–summer peak in species density evident in the 2009 drought. Surveys in spring 2008 had the highest species density, and recorded only 60–72% of the total species recorded at each site over 2.5 years. Variation in the proportion of total site diversity represented in combinations of two or three surveys was large, though the best combinations comprised surveys from spring and summer in years of above‐average rainfall, either from the same spring‐summer, or from different years. Compositional differences among sites were much greater than within sites, showing that differences among sites related to broad environmental gradients were not overwhelmed by seasonal and interannual variability in site composition. When grazing was excluded, there was no evidence of competitive exclusion by the dominant grasses, and no directional shift in composition. The implications of these findings for ecological research depend on the question being addressed: if capturing a large proportion of site diversity is important, then surveys must be carefully timed, or repeat surveys must be conducted. Single surveys did not effectively capture site diversity for use in biodiversity offsetting, and the timing of repeat surveys was critical.
New gall midges (Diptera: Cecidomyiidae) from Papua New Guinea
Authors: Kolesik Peter , Butterill Philip T
Published: April 2014

Two new species of gall midges that feed on trees in Papua New Guinea are described. The larvae of Schizomyia novoguineensis Kolesik sp. nov. transform the flowers of Macaranga aleuritoides (Euphorbiaceae) into spherical galls preventing sexual reproduction of the host tree. The larvae of Rhopalomyia psychotriae Kolesik sp. nov. induce pustulate leaf galls on Psychotria ramuensis (Rubiaceae). Descriptions of adults and immature stages, and DNA sequences of the cytochrome oxidase unit I mitochondrial gene segment, are given for each of the new species.
Assessment of children's digital courseware in light of developmentally appropriate courseware criteria
Authors: Ihmeideh Fathi Mahmoud
Published: April 2014

Developmentally appropriate courseware can play a crucial role in enhancing children's learning and development. Research studies have demonstrated that early childhood educators face major challenges in selecting and updating developmental courseware that supports young children's development. The primary purpose of this study was to assess children's digital courseware employed in Jordanian kindergartens in accordance with developmentally appropriate courseware criteria. A random sample of 57 courseware programs employed in both public and private kindergartens was assessed using 10 criteria for developmentally appropriate courseware. The findings suggest that the courseware implemented in Jordanian kindergartens exhibited a moderate degree of appropriateness. The courseware was the most developmentally appropriate in the areas of “technical features” and “clear instruction,” while the real‐work model and transformations were the least appropriate. Moreover, the findings revealed that children's courseware implemented in public kindergartens was more developmentally appropriate than those in private kindergartens. These findings and their implications were discussed.
Crucial role of androgen receptor in vascular H2S biosynthesis induced by testosterone
Authors: Brancaleone V , Vellecco V , Matassa D S , d'Emmanuele di Villa Bianca R , Sorrentino R , Ianaro A , Bucci M , Esposito F , Cirino G
Published: April 2014

Background and Purpose

Hydrogen sulphide (H2S) is a gaseous mediator strongly involved in cardiovascular homeostasis, where it provokes vasodilatation. Having previously shown that H2S contributes to testosterone‐induced vasorelaxation, here we aim to uncover the mechanisms underlying this effect.

Experimental Approach

H2S biosynthesis was evaluated in rat isolated aortic rings following androgen receptor (NR3C4) stimulation. Co‐immunoprecipitation and surface plasmon resonance analysis were performed to investigate mechanisms involved in NR3C4 activation.

Key Results

Pretreatment with NR3C4 antagonist nilutamide prevented testosterone‐induced increase in H2S and reduced its vasodilator effect. Androgen agonist mesterolone also increased H2S and induced vasodilatation; effects attenuated by the selective cystathionine‐γ lyase (CSE) inhibitor propargylglycine. The NR3C4‐multicomplex‐derived heat shock protein 90 (hsp90) was also involved in this effect; its specific inhibitor geldanamycin strongly reduced testosterone‐induced H2S production. Neither progesterone nor 17‐β‐oestradiol induced H2S release. Furthermore, we demonstrated that CSE, the main vascular H2S‐synthesizing enzyme, is physically associated with the NR3C4/hsp90 complex and the generation of such a ternary system represents a key event leading to CSE activation. Finally, H2S levels in human blood collected from male healthy volunteers were higher than those in female samples.

Conclusions and Implications

We demonstrated that selective activation of the NR3C4 is essential for H2S biosynthesis within vascular tissue, and this event is based on the formation of a ternary complex between cystathionine‐γ lyase, NR3C4and hsp90. This novel molecular mechanism operating in the vasculature, corroborated by higher H2S levels in males, suggests that the L‐cysteine/CSE/H2S pathway may be preferentially activated in males leading to gender‐specific H2S biosynthesis.

Linked Articles

This article is part of a themed section on Pharmacology of the Gasotransmitters. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2015.172.issue-6
Novel therapeutic targets in myeloma bone disease
Authors: Webb S L , Edwards C M
Published: April 2014

Multiple myeloma is a neoplastic disorder of plasma cells characterized by clonal proliferation within the bone marrow. One of the major clinical features of multiple myeloma is the destructive osteolytic bone disease that occurs in the majority of patients. Myeloma bone disease is associated with increased osteoclast activity and suppression of osteoblastogenesis. Bisphosphonates have been the mainstay of treatment for many years; however, their use is limited by their inability to repair existing bone loss. Therefore, research into novel approaches for the treatment of myeloma bone disease is of the utmost importance. This review will discuss the current advances in our understanding of osteoclast stimulation and osteoblast suppression mechanisms in myeloma bone disease and the treatments that are under development to target this destructive and debilitating feature of myeloma.
Foster care assessment: an exploratory study of the placement assessment process in Flanders and the Netherlands
Authors: Vanderfaeillie Johan , Damen Harm , Pijnenburg Huub , van den Bergh Peter , Van Holen Frank
Published: April 2014

Family foster care placement decision‐making has a weak scientific underpinning. The identification of clusters of foster children (groups of foster children with similar characteristics) can help improve decision quality. In this study, we investigated if foster children could indeed be clustered, which problems were identified at the time of placement and what might be the influence of placement history. Two clusters of foster children were found: (i) young children with coinciding parental child‐rearing incapacity and familial problems, and (ii) older children with child problems. At the time of placement, familial problems were more often identified in younger children with a placement history. These findings stress the importance of approaching foster care assessment as part of a dynamic decision‐making process. It is key to finding the most appropriate situation for the child. At the same time, it must be decided how the desired situation can be realized, wherein placement decisions are based on an appraisal of whether or not a foster placement is an appropriate solution. In conjunction with this, it needs to be decided how the parents can be supported towards reunification, or whether or not long‐term foster care is the best option for the child, and if so what conditions need to be met.