bluuebunny/crossref_metadata_2025 huggingface dataset:
Mesoporous silica nanoparticles (MSNs) as an efficient and reusable nanocatalyst for synthesis of β-amino ketones through one-pot three-component Mannich reactions
Authors: Nasresfahani Zahra , Kassaee Mohammad Zaman , Nejati-Shendi Mohammad , Eidi Esmaiel , Taheri Qazale
Published: March 2016

In this paper, mesoporous silica nanoparticles (MSNs) are introduced as an efficient nanocatalyst for synthesis of β-amino ketones.
Highly oriented poly(vinylidene fluoride-co-trifluoroethylene) ultrathin films with improved ferroelectricity
Authors: Zhu Huie , Yamamoto Shunsuke , Matsui Jun , Miyashita Tokuji , Mitsuishi Masaya
Published: March 2016

Fabrication of poly(vinylidene fluoride) copolymer monolayer (3.5 nm thick) was succeeded, exhibiting superior ferroelectricity and potential applications as non-volatile memories.
‘Breathing-crystals’ the origin of electrochemical activity of mesoporous Li–MnO2
Authors: Sayle Thi X. T. , Kgatwane Kenneth , Ngoepe Phuti E. , Sayle Dean C.
Published: March 2016

Akin to Le Chatalier's principle, we show that a mesoporous material can mitigate the effect of stress by expanding or contracting elastically into the pore space; we simulate this ‘breathing-crystal’ phenomenon using MD simulation.
Silica core–shell particles for the dual delivery of gentamicin and rifamycin antibiotics
Authors: Mebert Andrea M. , Aimé Carole , Alvarez Gisela S. , Shi Yupeng , Flor Sabrina A. , Lucangioli Silvia E. , Desimone Martin F. , Coradin Thibaud
Published: March 2016

Increasing bacterial resistance calls for the simultaneous delivery of multiple antibiotics.
Study on color-tunable phosphor-coated white light-emitting diodes with high S/P ratios
Authors: Guo Ziquan , Shih Tienmo , Xiao Jingjing , Lu Hongli , Lu Yijun , Wu Tingzhu , Lin Yue , Gao Yulin , Xiao Hua , Chen Zhong
Published: March 2016

In this study, we have investigated the trade-off between the color rendering index (CRI, Ra) and the scotopic/photopic ratio (S/P) for color-tunable phosphor-coated white light-emitting diodes (LEDs) at two CRI limitations (Ra ≥ 70 and Ra ≥ 96). First, luminescent spectra measurements have been conducted to determine experimental results of Ra and S/P under various correlated color temperatures (CCTs). Then, a nonlinear programming method has been adopted for the optimization of Ra and S/P by varying spectral shapes through adjusting spectral parameters, such as peak wavelengths, full-width at half-maxima, and relative intensities. Therefore, polynomial curves of optimal S/P versus CCT at two Ra limitations have been discovered, enabling users to obtain optimal S/P under arbitrary CCTs within [2700 K, 6500 K]. In addition, a comparison study between the present work and our previous work has also been conducted at Ra = 70, and a fair agreement of optimal S/P has been observed.
Dopamine synapse is a neuroligin-2–mediated contact between dopaminergic presynaptic and GABAergic postsynaptic structures
Authors: Uchigashima Motokazu , Ohtsuka Toshihisa , Kobayashi Kazuto , Watanabe Masahiko
Published: March 2016

Significance

Nigrostriatal dopaminergic projections form a number of dopamine synapses onto medium spiny neurons in the striatum, and have strong influence on emotion, motivation, voluntary movement, and cognition. Despite the functional importance, the molecular composition at dopamine synapses remains unknown. Here we demonstrate that dopamine synapses are neurochemically mismatched contacts formed between dopaminergic presynaptic and GABAergic postsynaptic structures. Intriguingly, neuroligin-2 expressed at the GABAergic postsynaptic structure controls striatal synapse formation by giving competitive advantage to heterologous dopamine synapses over conventional GABAergic synapses. Therefore, our findings suggest that neuroligin-mediated formation of such neurochemically mismatched synapses could be a novel strategy to increase the target selectivity and potency of modulation by anchoring release sites of neuromodulators to their receptive targets.
A note on non-ordinary primes
Authors: Jin Seokho , Ma Wenjun , Ono Ken
Published: March 2016

Suppose that

O
L

O_L

is the ring of integers of a number field

L
L

, and suppose that
\[
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="f left-parenthesis z right-parenthesis equals sigma-summation Underscript n equals 1 Overscript normal infinity Endscripts a Subscript f Baseline left-parenthesis n right-parenthesis q Superscript n Baseline element-of upper S Subscript k Baseline intersection upper O Subscript upper L Baseline left-bracket left-bracket q right-bracket right-bracket">

f
(
z
)
=

∑

n
=
1

∞

a
f

(
n
)

q
n

∈

S
k

∩

O
L

[
[
q
]
]

f(z)=\sum _{n=1}^{\infty }a_f(n)q^n\in S_k\cap O_L[[q]]

\]
(note:

q
:=

e

2
π
i
z

q:=e^{2\pi i z}

) is a normalized Hecke eigenform for

S
L

2

(

Z

)

\mathrm {SL}_2(\mathbb {Z})

. We say that

f
f

is non-ordinary at a prime

p
p

if there is a prime ideal

p

⊂

O
L

\frak {p}\subset O_L

above

p
p

for which
\[

a
f

(
p
)
≡
0

(
mod

p

)
.

a_f(p)\equiv 0\pmod {\frak {p}}.

\]
For any finite set of primes

S
S

, we prove that there are normalized Hecke eigenforms which are non-ordinary for each

p
∈
S

p\in S

. The proof is elementary and follows from a generalization of work of Choie, Kohnen and the third author.
NSimScan: DNA comparison tool with increased speed, sensitivity and accuracy
Authors: Novichkov Vladimir , Kaznadzey Anna , Alexandrova Natalia , Kaznadzey Denis
Published: March 2016

Summary: Nucleotide Similarity Scanner (NSimScan) is specialized for searching massive DNA databases for distant similarities. Its targeted applications include phylogenomics, comparative and functional studies of non-coding sequences, contamination detection, etc. NSimScan outperforms industry standard tools in combined sensitivity, accuracy and speed, operating at sensitivity similar to BLAST, accuracy of ssearch and speed of MegaBLAST.

Availability and implementation: NSimScan is available at https://github.com/abadona/qsimscan as a part of QSimScan package. It is implemented in C ++, distributed under MIT license and supported on Linux, OS X and Windows (with cygwin).

Contact:  dkaznadzey@yahoo.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
SNPhood: investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data
Authors: Arnold Christian , Bhat Pooja , Zaugg Judith B.
Published: March 2016

Motivation: The vast majority of the many thousands of disease-associated single nucleotide polymorphisms (SNPs) lie in the non-coding part of the genome. They are likely to affect regulatory elements, such as enhancers and promoters, rather than the function of a protein. To understand the molecular mechanisms underlying genetic diseases, it is therefore increasingly important to study the effect of a SNP on nearby molecular traits such as chromatin or transcription factor binding.

Results: We developed SNPhood, a user-friendly Bioconductor R package to investigate, quantify and visualise the local epigenetic neighbourhood of a set of SNPs in terms of chromatin marks or TF binding sites using data from NGS experiments.

Availability and implementation: SNPhood is publicly available and maintained as an R Bioconductor package at http://bioconductor.org/packages/SNPhood/.

Contact:  judith.zaugg@embl.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
BLESS 2: accurate, memory-efficient and fast error correction method
Authors: Heo Yun , Ramachandran Anand , Hwu Wen-Mei , Ma Jian , Chen Deming
Published: March 2016

Summary: The most important features of error correction tools for sequencing data are accuracy, memory efficiency and fast runtime. The previous version of BLESS was highly memory-efficient and accurate, but it was too slow to handle reads from large genomes. We have developed a new version of BLESS to improve runtime and accuracy while maintaining a small memory usage. The new version, called BLESS 2, has an error correction algorithm that is more accurate than BLESS, and the algorithm has been parallelized using hybrid MPI and OpenMP programming. BLESS 2 was compared with five top-performing tools, and it was found to be the fastest when it was executed on two computing nodes using MPI, with each node containing twelve cores. Also, BLESS 2 showed at least 11% higher gain while retaining the memory efficiency of the previous version for large genomes.

Availability and implementation: Freely available at https://sourceforge.net/projects/bless-ec

Contact:  dchen@illinois.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
CellMiner Companion: an interactive web application to explore CellMiner NCI-60 data
Authors: Wang Sufang , Gribskov Michael , Hazbun Tony R. , Pascuzzi Pete E.
Published: March 2016

Summary: The NCI-60 human tumor cell line panel is an invaluable resource for cancer researchers, providing drug sensitivity, molecular and phenotypic data for a range of cancer types. CellMiner is a web resource that provides tools for the acquisition and analysis of quality-controlled NCI-60 data. CellMiner supports queries of up to 150 drugs or genes, but the output is an Excel file for each drug or gene. This output format makes it difficult for researchers to explore the data from large queries. CellMiner Companion is a web application that facilitates the exploration and visualization of output from CellMiner, further increasing the accessibility of NCI-60 data.

Availability and Implementation: The web application is freely accessible at https://pul-bioinformatics.shinyapps.io/CellMinerCompanion. The R source code can be downloaded at https://github.com/pepascuzzi/CellMinerCompanion.git.

Contact:  ppascuzz@purdue.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Genome-scale prediction of moonlighting proteins using diverse protein association information
Authors: Khan Ishita K. , Kihara Daisuke
Published: March 2016

Motivation: Moonlighting proteins (MPs) show multiple cellular functions within a single polypeptide chain. To understand the overall landscape of their functional diversity, it is important to establish a computational method that can identify MPs on a genome scale. Previously, we have systematically characterized MPs using functional and omics-scale information. In this work, we develop a computational prediction model for automatic identification of MPs using a diverse range of protein association information.

Results: We incorporated a diverse range of protein association information to extract characteristic features of MPs, which range from gene ontology (GO), protein–protein interactions, gene expression, phylogenetic profiles, genetic interactions and network-based graph properties to protein structural properties, i.e. intrinsically disordered regions in the protein chain. Then, we used machine learning classifiers using the broad feature space for predicting MPs. Because many known MPs lack some proteomic features, we developed an imputation technique to fill such missing features. Results on the control dataset show that MPs can be predicted with over 98% accuracy when GO terms are available. Furthermore, using only the omics-based features the method can still identify MPs with over 75% accuracy. Last, we applied the method on three genomes: Saccharomyces cerevisiae, Caenorhabditis elegans and Homo sapiens, and found that about 2–10% of proteins in the genomes are potential MPs.

Availability and Implementation: Code available at http://kiharalab.org/MPprediction

Contact:  dkihara@purdue.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Automated eligibility screening and monitoring for genotype-driven precision oncology trials
Authors: Eubank Michael H , Hyman David M , Kanakamedala Amritha D , Gardos Stuart M , Wills Jonathan M , Stetson Peter D
Published: March 2016

The Information Systems Department at Memorial Sloan Kettering Cancer Center developed the DARWIN Cohort Management System (DCMS). The DCMS identifies and tracks cohorts of patients based on genotypic and clinical data. It assists researchers and treating physicians in enrolling patients to genotype-matched IRB-approved clinical trials. The DCMS sends automated, actionable, and secure email notifications to users with information about eligible or enrolled patients before their upcoming appointments. The system also captures investigators input via annotations on patient eligibility and preferences on future status updates. As of August 2015, the DCMS is tracking 159,893 patients on both clinical operations and research cohorts. 134 research cohorts have been established and track 64,473 patients. 51,192 of these have had one or more genomic tests including MSK-IMPACT, comprising the pool eligible for genotype-matched studies. This paper describes the design and evolution of this Informatics solution.
Modeling Preferences Using Roll Call Votes in Parliamentary Systems
Authors: Bräuninger Thomas , Müller Jochen , Stecker Christian
Published: March 2016

Models of ideal point estimation usually build on the assumption of spatial preferences. This ignores legislators' non-policy incentives and is thus likely to produce implausible results for many legislatures. We study this problem in parliamentary systems and develop a model of roll call voting that considers both thepolicyand the non-policy,tacticalincentives of legislators. We go on to show how the relative weight of these policy and tactical incentives is influenced by the identity of the mover and characteristics of the motion. Analyses of two data sets of 2174 roll call votes in German state legislatures and 3295 roll call votes in the British House of Commons result in three main findings. First, we show that tactical incentives may be more important than policy incentives, and second, that the importance of tactical incentives varies with the importance of motions. Third, there are interesting twists: backbench private members' bills may reverse tactical incentives whereas proposals from anti-system parties are virtually always rejected by moderate parties, rendering these votes uninformative. Our findings have implications for ideal point estimation in parliamentary systems, as well as for research on separation of power systems.
Treatment of in-transit and metastatic melanoma in two patients treated with ipilimumab and topical imiquimod
Authors: Joseph Richard W. , Cappel Mark , Tzou Katherine , Bagaria Sanjay , Gilstrap Cheryl , Swaika Abhisek , Jambusaria-Pahlajani Anokhi
Published: March 2016

Checkpoint blockade inhibitors have revolutionized the treatment of metastatic melanoma. Despite the success of these agents in improving the overall survival of patients with metastatic melanoma, not all patients achieve clinical benefit, leaving room for improvement. The presence of cutaneous metastases in patients with metastatic melanoma provides the unique opportunity to treat the cutaneous lesions with a local modality while simultaneously treating systemic disease with systemic therapy. Herein, we describe the treatment of two patients with both in-transit and metastatic melanoma with the combination of the topical toll-like receptor 7 agonist imiquimod with systemic ipilimumab. Both patients appeared to have progressed and developed new cutaneous and systemic metastases while on single agent ipilimumab only to respond when started on topical imiquimod. Both patients tolerated the combination of imiquimod and ipilimumab without serious adverse events, and both patients had excellent clinical responses. These cases provide a proof of principle of the possibility of the combination of toll-like receptor 7 agonists with immune checkpoint blockade inhibitors.
Therapeutic potential of RQ-00311651, a novel T-type Ca2+ channel blocker, in distinct rodent models for neuropathic and visceral pain
Authors: Sekiguchi Fumiko , Kawara Yuma , Tsubota Maho , Kawakami Eri , Ozaki Tomoka , Kawaishi Yudai , Tomita Shiori , Kanaoka Daiki , Yoshida Shigeru , Ohkubo Tsuyako , Kawabata Atsufumi
Published: March 2016

T-type Ca2+ channels (T channels), particularly Cav3.2 among the 3 isoforms, play a role in neuropathic and visceral pain. We thus characterized the effects of RQ-00311651 (RQ), a novel T-channel blocker, in HEK293 cells transfected with human Cav3.1 or Cav3.2 by electrophysiological and fluorescent Ca2+ signaling assays, and also evaluated the antiallodynic/antihyperalgesic activity of RQ in somatic, visceral, and neuropathic pain models in rodents. RQ-00311651 strongly suppressed T currents when tested at holding potentials of −65 ∼ −60 mV, but not −80 mV, in the Cav3.1- or Cav3.2-expressing cells. RQ-00311651 also inhibited high K+-induced Ca2+ signaling in those cells. In mice, RQ, administered intraperitoneally (i.p.) at 5 to 20 mg/kg or orally at 20 to 40 mg/kg, significantly suppressed the somatic hyperalgesia and visceral pain-like nociceptive behavior/referred hyperalgesia caused by intraplantar and intracolonic administration of NaHS or Na2S, H2S donors, respectively, which involve the enhanced activity of Cav3.2 channels. RQ-00311651, given i.p. at 5 to 20 mg/kg, exhibited antiallodynic or antihyperalgesic activity in rats with spinal nerve injury–induced neuropathy or in rats and mice with paclitaxel-induced neuropathy. Oral and i.p. RQ at 10 to 20 mg/kg also suppressed the visceral nociceptive behavior and/or referred hyperalgesia accompanying cerulein-induced acute pancreatitis and cyclophosphamide-induced cystitis in mice. The analgesic and antihyperalgesic/antiallodynic doses of oral and i.p. RQ did not significantly affect the locomotor activity and motor coordination. Together, RQ is considered a state-dependent blocker of Cav3.1/Cav3.2 T channels and may serve as an orally available analgesic for treatment of neuropathic and inflammatory pain including distinct visceral pain with minimum central side effects.
The effect of local vs remote experimental pain on motor learning and sensorimotor integration using a complex typing task
Authors: Dancey Erin , Murphy Bernadette A. , Andrew Danielle , Yielder Paul
Published: March 2016

Recent work demonstrated that capsaicin-induced acute pain improved motor learning performance; however, baseline accuracy was very high, making it impossible to discern the impact of acute pain on motor learning and retention. In addition, the effects of the spatial location of capsaicin application were not explored. Two experiments were conducted to determine the interactive effects of acute pain vs control (experiment 1) and local vs remote acute pain (experiment 2) on motor learning and sensorimotor processing. For both experiments, somatosensory evoked potential (SEP) amplitudes and motor learning acquisition and retention (accuracy and response time) data were collected at baseline, after application, and after motor learning. Experiment 1: N11 (P < 0.05), N13 (P < 0.05), and N30 (P < 0.05) SEP peak amplitudes increased after motor learning in both groups, whereas the N20 SEP peak increased in the control group (P < 0.05). At baseline, the intervention group outperformed the control group in accuracy (P < 0.001). Response time improved after motor learning (P < 0.001) and at retention (P < 0.001). Experiment 2: The P25 SEP peak decreased in the local group after application of capsaicin cream (P < 0.01), whereas the N30 SEP peaks increased after motor learning in both groups (P < 0.05). Accuracy improved in the local group at retention (P < 0.005), and response time improved after motor learning (P < 0.005) and at retention (P < 0.001). This study suggests that acute pain may increase focal attention to the body part used in motor learning, contributing to our understanding of how the location of pain impacts somatosensory processing and the associated motor learning.
Prognosis of patients with syncope seen in the emergency room department: an evaluation of four different risk scores recommended by the European Society of Cardiology guidelines
Authors: Barón-Esquivias Gonzalo , Fernández-Cisnal Agustín , Arce-León Álvaro , Toro Rocio , Cantero-Pérez Eva , Parejo-Matos Juan , Romero-Rodriguez Nieves , Montero Emilio , Martinez Angel
Published: March 2016

Aim

To apply, analyze, and evaluate the four syncope risk scores recommended by the 2009 European guidelines and the different parameters that they use to predict death, syncope recurrence, and hospital readmission in the population seen in the emergency room department (ERD) for syncope.

Methods and results

A total of 323 patients aged older than 14 years [mean age 59 (32–75) years] and seen in ERD for syncope over a 2-month period were included in the study; 50.7% were women. Patients were evaluated using the four risk scores and were followed up for at least 2 years. In all, 275 patients (85.2%) were discharged directly from ERD after evaluation. During 28±5 months of follow-up, 8% died, 18.3% presented a further syncopal episode, and 18.6% were readmitted to hospital. Only two of the four risk scores were useful in risk discrimination, but no statistically significant differences were detected between predicted risk and observed risk. Multivariate analysis indicated relationships between age and death, a history of cardiovascular disease and syncope recurrence, and between presyncopal palpitations and hospital readmission.

Conclusion

Although a large number of events occur after syncope, the risk scores recommended by guidelines overestimate risk, but there were no statistically significant differences between observed and predicted risk.
HPV-16 Detected in One-Fourth Eyes With Retinoblastoma: A Prospective Case-control Study From North India
Authors: Naru Jasmine , Aggarwal Ritu , Singh Usha , Kakkar Nandita , Bansal Deepak
Published: March 2016

The incidence of nonfamilial retinoblastoma (RB) is believed to be higher in developing countries. The reports on association of human papillomavirus (HPV) with RB are limited and contradictory. The aim was to investigate the prevalence of HPV in RB tumor tissue. In the prospective study, consecutive eyes enucleated for RB from patients lacking a family history of RB were enrolled as cases over a 3-year period. Controls included donor eyes obtained from the eye bank. Normal retinal tissue from the donor eyes and tumor tissue from eyes with RB was subjected to DNA isolation. Polymerase chain reaction followed by dot-blot hybridization was performed to detect 21 HPV genotypes. The study cohort included 39 RB and 42 normal retinal tissues. A positive result for HPV-polymerase chain reaction was obtained in 10 (25.6%) tumor tissues and none of the control eyes. HPV-16 was the only subtype detected. Socioeconomic status (P=0.58) or maternal age (P=0.58) was not associated with presence of HPV. All HPV-positive patients had undergone a vaginal delivery (P=0.60). HPV-16 was detected in one-fourth cases of nonfamilial RB. None of the control cases (donor eyes) tested positive. Implication of the presence of HPV in RB tissue and role in carcinogenesis needs further elucidation.
Bortezomib, Dexamethasone, Mitoxantrone, and Vinorelbine (BDMV): An Active Reinduction Regimen for Children With Relapsed Acute Lymphoblastic Leukemia and Asparaginase Intolerance
Authors: Yeo Kee K. , Gaynon Paul S. , Fu Cecilia H. , Wayne Alan S. , Sun Weili
Published: March 2016

Background:

Children with relapsed acute lymphoblastic leukemia (ALL) typically receive vincristine-prednisone-l-asparaginase-doxorubicin reinduction chemotherapy similar to contemporary induction regimens. However, up to 20% of patients are unable to receive vincristine-prednisone-l-asparaginase-doxorubicin secondary to asparaginase intolerance. We report our experience with a promising reinduction regimen for children with relapsed ALL who are unable to receive asparaginase.

Patients and Methods:

This is a single institution, retrospective review of the safety and activity of bortezomib, dexamethasone, mitoxantrone, and vinorelbine (BDMV) in patients with relapsed ALL. Complete remission and adverse events after reinduction were study endpoints. Patients treated with BDMV between 2012 and 2015 were identified. Response and adverse events (AEs) were assessed by review of medical records. Standard response criteria were used and AEs were graded based on NCI CTCAEv4.0.

Results:

Seven of 10 patients achieved complete remission after 1 cycle of BDMV, with 4 achieving minimal residual disease negativity. The most common ≥grade 3 nonhematological toxicities were infection (91%), gastrointestinal (45%), metabolic (45%), and cardiovascular (9%).

Conclusions:

BDMV is an active reinduction regimen for children with relapsed ALL who cannot receive asparaginase. The toxicity profile is as expected for this patient population. Further prospective clinical trials are warranted to evaluate the safety and efficacy of BDMV.
The Pransky interview: Aldo Zini, President and CEO of Aethon, Inc.
Authors: Pransky Joanne
Published: March 2016

Purpose

– The following paper is a “Q
&
A interview” conducted by Joanne Pransky of Industrial Robot Journal as a method to impart the combined technological, business and personal experience of a prominent, robotic industry engineer-turned successful business leader, regarding the commercialization and challenges of bringing technological inventions to market while overseeing a company. This paper aims to discuss these issues.

Design/methodology/approach

– The interviewee is Aldo Zini, President and CEO of Aethon, Inc., a robotics and software company that has developed an innovative automated platform to improve internal supply logistics. In this interview, Zini shares some of the technical and business details that have led up to the latest version of Aethon’s core product, the TUG, a mobile autonomous robot with more than 450 installs worldwide.

Findings

– Zini received a BS in Industrial Engineering from the University of Pittsburgh and a master’s in Public Management (Health Systems IT) from Carnegie Mellon University. While obtaining his BS degree, Zini did an internship in hospital consulting and became immediately interested in healthcare automation as a way to solve hospital inefficiencies. Zini went on to become the Vice President of Sales and Marketing for Automated Healthcare, which developed the first robotic medication dispensing system for hospitals (ROBOT-Rx) and was acquired by McKesson for $67 million. Before joining and investing in Aethon, Zini was Senior Vice President of sales and marketing for TechRx, one of the largest providers of software solutions to the pharmacy industry, which was sold to NDC Corporation for over $200 million.

Originality/value

– Zini has been leading the technology revolution in hospital automation for more than 25 years. His contributions to technology-driven companies have led to acquisitions worth more than a quarter of a billion dollars. Zini owns several patents in medication-dispensing technology, and is credited with the development of key methodologies in quantifying the value proposition for several technology platforms deployed in hundreds of hospitals across the country.
Ranking of finance journals: a stochastic dominance analysis
Authors: Kao Erin H. , Hsu Chuan-Hao , Lu Yunlin , Fung Hung-Gay
Published: March 2016

Purpose

– Prior studies in citation-based journal rankings tend to be static to compare across journals. One journal may be judged better in citations than other journals at some points in time but not at the others. The assumption that the citation distribution is normally distributed and that the citation observations are independent and identically distributed (i.i.d.) may not be appropriate. The paper aims to discuss these issues.

Design/methodology/approach

– This study uses a stochastic dominance (SD) analysis, which overcomes the dynamic nature of changes in citation over time. The SD method proposed by Linton, Maasoumi, and Whang (hereafter LMW, 2005) does not require the data to be i.i.d. We use the LMW method to compare the relative ranking of 23 finance journals using citations for all articles from them during 1990-2010.

Findings

– The study indicates that the citation distribution changes over time. Thus a SD analysis is a better approach for a comparison of journal ranking. The findings unambiguously place JF, JFE, RFS, JFQA, and JFI in the top five spots of the finance journal ranking. The “near-top” journals, such as JBF, JCF, and FM, are not clear cut in the SD analysis.

Research limitations/implications

– The results confirm that ranking for the lower ranked journals may change over time especially, but the top three journals appear to be robust across methods and over time.

Originality/value

– The results of SD analysis provides more convincing evidence on finance journal ranking and could be useful to rank academic institutions, faculty research quality, and help the authors to decide what to read and which journals are influential.
High Medieval Monasteries as Communities of Practice: Approaching Monastic Learning Through Letters
Authors: Long Micol
Published: March 2016

The theme of learning in high medieval monasteries can be approached by analysing such contexts as “communities of practice” on the basis of preserved monastic letters and letter‐collections. The letters' propagandistic function makes it extremely interesting to analyse the ways in which they represent learning in order to serve different purposes: to attract people to a monastery, to offer advice to members of monastic communities, and even to intervene in the debate that opposed monastic to secular and scholastic modes of study. Moreover, epistolary sources offer insights into the complex dynamics of social interactions within the monastery, in particular the plurality of learning agents and the reciprocal nature of learning exchanges. Therefore, this approach can offer a valuable contribution to the study of learning as a shared and dialectical process, which takes place through social interaction within a heterogeneous community. In addition, it helps to understand the way in which learning is linked to the shaping of identities, both individual and communal, because it affects and transforms the reciprocal social roles of the members of a monastic community.
Developmental and behavioural effects of the endophytic Fusarium moniliforme Fe14 towards Meloidogyne graminicola in rice
Authors: Le H.T.T. , Padgham J.L. , Hagemann M.H. , Sikora R.A. , Schouten A.
Published: March 2016

The root‐knot nematode, Meloidogyne graminicola, is an important pest of rice in many rice production areas worldwide. The endophyte Fusarium moniliforme strain Fe14, isolated from a disinfected root of rice, has previously shown potential antagonistic activity against M. graminicola. This study shows the effects of Fe14 on M. graminicola behaviour, infection, development and reproduction. The endophyte Fe14 colonisation significantly reduced M. graminicola penetration into rice roots by 55% and increased the male to female ratio nine times. The endophyte also delayed juvenile development into female inside the rice root. These results suggest a suboptimal performance of the giant cell and a cumulative effect of the endophyte on the long‐term root‐knot nematode population development. In split‐root assays, the application of Fe14 at the inducer side significantly reduced nematode invasion at the responder side by 38% and 60% in two independent trials. This result suggests a systemic effect of the endophyte on rice plants. The root exudates from Fe14‐treated plants were either less attractive or had repellent effect on nematode movement. The results, when compared to what was described for other endophytic Fusarium against other nematode species, may indicate a basal response mechanism initiated in the plant by endophytic Fusarium spp. The present study may give leads for unravelling the molecular mechanisms responsible for the induced systemic defence responses in plants.
Creating a critical mass eliminates the effects of stereotype threat on women's mathematical performance
Authors: Pennington Charlotte R. , Heim Derek
Published: March 2016

Background

Women in mathematical domains may become attuned to situational cues that signal a discredited social identity, contributing to their lower achievement and underrepresentation.

Aim

This study examined whether heightened in‐group representation alleviates the effects of stereotype threat on women's mathematical performance. It further investigated whether single‐sex testing environments and stereotype threat influenced participants to believe that their ability was fixed (fixed mindset) rather than a trait that could be developed (growth mindset).

Sample and method

One hundred and forty‐four female participants were assigned randomly to a self‐as‐target or group‐as‐target stereotype threat condition or to a control condition. They completed a modular arithmetic maths test and a mindset questionnaire either alone or in same‐sex groups of 3–5 individuals.

Results

Participants solved fewer mathematical problems under self‐as‐target and group‐as‐target stereotype threat when they were tested alone, but these performance deficits were eliminated when they were tested in single‐sex groups. Participants reported a weaker growth mindset when they were tested under stereotype threat and in single‐sex groups. Moreover, evidence of inconsistent mediation indicated that single‐sex testing environments negatively predicted mindset but positively predicted mathematical performance.

Conclusions

These findings suggest that single‐sex testing environments may represent a practical intervention to alleviate stereotype threat effects but may have a paradoxical effect on mindset.
Processing Conversational Implicatures: Alternatives and Counterfactual Reasoning
Authors: van Tiel Bob , Schaeken Walter
Published: March 2016

In a series of experiments, Bott and Noveck (2004) found that the computation of scalar inferences, a variety of conversational implicature, caused a delay in response times. In order to determine what aspect of the inferential process that underlies scalar inferences caused this delay, we extended their paradigm to three other kinds of inferences: free choice inferences, conditional perfection, and exhaustivity in “it”‐clefts. In contrast to scalar inferences, the computation of these three kinds of inferences facilitated response times. Following a suggestion made by Chemla and Bott (2014), we propose that the time it takes to compute a conversational implicature depends on the structural characteristics of the required alternatives.
Sequestration of cellular interacting partners by protein aggregates: implication in a loss‐of‐function pathology
Authors: Yang Hui , Hu Hong‐Yu
Published: March 2016

Protein misfolding and aggregation are a hallmark of several neurodegenerative diseases (NDs). However, how protein aggregation leads to cytotoxicity and neurodegeneration is still controversial. Emerging evidence demonstrates that sequestration of cellular‐interacting partners by protein aggregates contributes to the pathogenesis of these diseases. Here, we review current research on sequestration of cellular proteins by protein aggregates and its relation to proteinopathies. Based on different interaction modes, we classify these protein sequestrations into four types: protein coaggregation, domain/motif‐mediated sequestration, RNA‐assisted sequestration, and sequestration of molecular chaperones. Thus, the cellular essential proteins and/or RNA hijacked by protein aggregates may lose their biological functions, consequently resulting in cytotoxicity and neurodegeneration. We have proposed a hijacking model recapitulating the sequestration process and the loss‐of‐function pathology of ND.
Association of Migraine Headaches With Suicidal Ideation Among Pregnant Women in Lima, Peru
Authors: Friedman Lauren E. , Gelaye Bizu , Rondon Marta B. , Sanchez Sixto E. , Peterlin B. Lee , Williams Michelle A.
Published: March 2016

Background

Suicide is a leading cause of maternal death globally, and suicide prevalence rates have been shown to be increased in those with migraine. No previous study has examined the association between migraine and suicidal ideation during pregnancy.

Objective

To examine the association between migraine and suicidal ideation among a cohort of pregnant women.

Methods

A cross‐sectional study was conducted among 3372 pregnant women attending prenatal care clinics in Lima, Peru. Suicidal ideation and depression were assessed using the Patient Health Questionnaire‐9 (PHQ‐9) scale during early pregnancy. Migraine classification (including migraine and probable migraine) was based on International Classification of Headache Disorders‐III beta criteria. Multivariable logistic regression analyses were performed to estimate odds ratios (OR) and 95% confidence intervals (95%CI).

Results

Suicidal ideation was more common among those with migraine (25.6%) as compared to those with probable migraine (22.1%, P < .001) or non‐migraineurs (12.3%, P < .001). After adjusting for confounders, including depression, those with migraine or probable migraine had a 78% increased odds of suicidal ideation (OR = 1.78; 95% CI: 1.46‐2.17), as compared with non‐migraineurs. Women with both migraine and depression had a 4.14‐fold increased odds of suicidal ideation (OR = 4.14; 95% CI: 3.17‐5.42) compared to those with neither condition.

Conclusion

Migraine is associated with increased odds of suicidal ideation in pregnant women even when controlling for depression. These findings support the consideration of screening women with comorbid migraine and depression for suicidal behavior during pregnancy.
The Link Between Migraine, Reversible Cerebral Vasoconstriction Syndrome and Cervical Artery Dissection
Authors: Mawet Jérôme , Debette Stéphanie , Bousser Marie‐Germaine , Ducros Anne
Published: March 2016

Headache is the common thread of migraine, reversible cerebral vasoconstriction syndrome (RCVS) and cervical artery dissection (CeAD), three medical conditions that otherwise appear to be very different. However, epidemiological, clinical and genetic data suggest that these conditions share common and complex features and are, at least partly, linked. The purpose of this manuscript is to review existing evidence for an association between migraine, RCVS and CeAD and discuss the potential underlying mechanisms.
HLA‐B allele dropout in PCR sequence‐specific oligonucleotide probe typing due to intronic polymorphism in the novel B*58:01:01:02 allele
Authors: He Y. , Wang W. , Han Z. , He J. , Chen N. , Dong L. , Tao S. , Zhang W. , He J. , Zhu F. , Lv H.
Published: March 2016

Currently, Luminex technology based on the PCR sequence‐specific oligonucleotide (SSO) probe method has been widely used for HLA genotyping in the immunogenetics laboratories. Here, we reported a case with HLA‐B allele dropout by Luminex technology. The initial HLA‐B result of the Luminex method with a commercial agent kit was inconclusive, and then, the result of PCR‐SBT technology indicated the dropout as a HLA‐B*58 allele. Subsequently, the full‐length sequence of HLA‐B allele was determined by TOPO‐TA cloning, and a novel allele B*58:01:01:02 was identified in the individual. Compared with HLA‐B*58:01:01:01, the novel allele showed some nucleotides difference at 509 C>T, 521 T>G and CCC insertion in position 503 of intron 2. According to the full‐length sequence, the new mutations of intron 2 were contributed to HLA‐B locus allele dropout in the sample. Our results indicated multiplatform should be used to improve the HLA typing accuracy when a conclusive HLA genotype cannot be determined.
Insights into the pathogenic mechanisms of Chromosome 9 open reading frame 72 (C9orf72) repeat expansions
Authors: Todd Tiffany W. , Petrucelli Leonard
Published: March 2016

The identification of a hexanucleotide repeat expansion in a non‐coding region of C9orf72 as a major cause of both frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) drastically changed the field of research on both of these conditions. Yet, despite the vast amount of work aimed at elucidating the molecular mechanisms underlying the role of this repeat in disease, the exact pathomechanisms are still unclear. A reduction in the expression of the C9orf72 gene is observed in patients, but a gain‐of‐function model is now preferred. The hexanucleotide repeat expansion forms RNA foci in the central nervous system (CNS) of repeat‐positive FTD and ALS patients, and these foci are believed to sequester RNA‐binding proteins (RBPs) and impair their function in RNA processing. At the same time, the repeat undergoes repeat‐associated non‐ATG translation to produce dipeptide repeat proteins that also form inclusions in the patient CNS. Studies from cells and flies suggest that these proteins may also be an important factor in the disease. Finally, the hexanucleotide repeat also induces the mislocalization and aggregation of TAR DNA‐binding protein 43 (TDP‐43) through an as yet unknown mechanism. This review covers the different potential pathogenic factors that have been put forth for C9orf72‐repeat‐associated FTD and ALS (C9‐FTD/ALS), while highlighting some remaining questions.

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A repeat expansion in C9orf72 is a common cause of both frontal temporal dementia and amyotrophic lateral sclerosis. Although there is a decrease in C9orf72 expression in patients, this repeat is believed to induce disease primarily through an unknown gain‐of‐function mechanism involving the RNA, repeat‐associated non‐AUG translation, or both. This review summarizes and discusses current knowledge on C9orf72 repeat‐associated pathophysiology.

This article is part of the Frontotemporal Dementia special issue.
Improving Practices of Risk Assessment and Intervention Planning for Persons with Intellectual Disabilities Who Sexually Offend
Authors: Keller Jason
Published: March 2016

Proactive assessment and intervention planning should be undertaken in cases of sexual behavior by persons with intellectual disability (ID) that is outside of acceptable norms. Although best practices in risk assessment for the general offender population are somewhat established, sexually inappropriate behavior among individuals with ID is distinct. Research in effective specialized risk assessment and intervention planning for this client group is an emerging area of focus. This article reviews contemporary academic research on this subject and highlights opportunities for improvement. First, research on risk factors for this client group was reviewed, observing the differences between empirically validated common factors and factors that are specific to the individual. Second, existing actuarial and structured clinical judgment approaches were evaluated. Third, the person‐centered planning approach to service planning for persons with ID was examined, highlighting how the principles of this approach may be used to enhance current practices in risk assessment and intervention planning. The author concludes that effective collaboration between support teams and clinical professionals, with focus maximized on individual risk factors and strengths, should lead to improved outcomes of risk assessment and intervention planning for persons with ID whose sexual behavior is inappropriate. A call to action is presented for the development of an enhanced, fourth‐generation, approach that embodies a collaborative framework.
Odontochilus napoensis sp. nov. (Orchidoideae: Orchidaceae) from southwestern Guangxi, China
Authors: Tang Huan , Feng Hui‐Zhe , Huang Yun‐Feng
Published: March 2016

Odontochilus napoensis, a new species from southwestern Guangxi, China, is described and illustrated. It is close to Odontochilus inabae (Hayata) T. P. Lin, but can be distinguished by its glabrous ovary, solitary flower, and 2.0–3.5 mm long filaments of flanges. It is also similar to O. nanlingensis (L. P. Siu & K. Y. Lang) Ormerod, but differs by the solitary, not resupinate flower, and light greenish–brown lateral sepals.
Predictors of motivation to comply with social referents regarding one's romantic relationship
Authors: ETCHEVERRY PAUL E. , AGNEW CHRISTOPHER R.
Published: March 2016

This research examined predictors of motivation to comply with social referents regarding one's romantic relationship. Two variables are argued to predict motivation to comply with the opinions of social network members: (a) social consequences of compliance and (b) perceived relationship expertise. Three studies examined the association of these variables with motivation to comply. Study 1 used survey research to demonstrate that these variables predict motivation to comply. Studies 2 and 3 experimentally manipulated social consequences of compliance and perceived relationship expertise, respectively, providing evidence of a causal connection between these variables and motivation to comply. Across three studies, the results support the role of social consequences of compliance and perceived relationship expertise in understanding social influences on romantic decision making.
A case of adenocarcinoma with enteroblastic differentiation of the ampulla of Vater
Authors: Mitsuma Koko , Taniguchi Hirokazu , Kishi Yoji , Hiraoka Nobuyoshi
Published: March 2016

Cancer of the ampulla of Vater is rare, though it has various histological types and its histogenesis is fascinating in view of the anatomically complex nature of the ampulla. Fetal gut‐like adenocarcinoma, usually found in the stomach, can also develop in the ampullary region in extremely rare cases. Here we present a case of ampullary adenocarcinoma with enteroblastic and neuroendocrine differentiation. A 55‐year‐old woman presented with an epigastric pain. Endoscopic examination revealed a 2‐cm submucosal tumor‐like lesion in the ampulla. The surgical specimen showed that an exposed protruding type of tumor appeared as a well‐demarcated whitish‐yellow solid mass. Microscopically, the tumor had proliferated in the common channel and invaded the duodenal submucosa with mucosal lesion of intestinal‐type adenocarcinoma. The main tumor consisted of three different histological types showing transitional areas: adenocarcinoma with enteroblastic differentiation (ENT), neuroendocrine carcinoma (NEC), and well differentiated adenocarcinoma (WEL). Morphologically the ENT resembled fetal gut and immunohistochemically expressed SALL4 and glypican 3. The WEL was positive for CK20 and CDX2, revealing an intestinal‐type phenotype. AFP and HepPar1 were not evident in any part of the lesion. We speculated this tumor had arisen from intestinal‐type adenocarcinoma of the common channel and acquired enteroblastic and neuroendocrine differentiation during growth.
Relation between hyaluronan synthesis and cell morphology in ovarian clear cell carcinomas
Authors: Kato Noriko , Shibata Kasumi , Uchigasaki Shinya , Kurose Akira
Published: March 2016

Ovarian clear cell carcinomas often show a spherule‐like mucoid stroma. In ascitic fluid, they form spheroids with a hollow acellular space. In spite of the absence of stromal cells, both the mucoid stroma and hollow spheroids contain abundant extracellular matrix, and one of the major components is hyaluronan. It has been suggested that tumor‐derived hyaluronan plays a significant role in the formation of these structures. To clarify this, a hyaluronan inhibition assay was performed on HAC‐2, a clear cell carcinoma cell line, in vitro. When hyaluronan synthesis was inhibited by 4‐methylumbelliferone, HAC‐2 failed to show the spherule‐like accumulation of hyaluronan or hollow spheroids. Inhibition of hyaluronan synthesis was associated with the reduction of cell growth. Analysis of 28 archival ascites cytology specimens showed that clear cell carcinomas expressed hyaluronan more frequently than serous carcinomas (11 of 14 vs 3 of 14, respectively, P < 0.05). All of these facts indicate that tumor‐derived hyaluronan is essential for the formation of the mucoid stroma or hollow spheroids, and that hyaluronan is also involved in the regulation of cell growth in ovarian clear cell carcinomas. The inhibition of hyaluronan synthesis could be a potential adjunctive therapy for refractory clear cell carcinomas outside the ovary.