bluuebunny/crossref_metadata_2025 huggingface dataset:
Spectroscopic and energy transfer properties of Dy3+-doped, Tb3+/Dy3+-codoped dense oxyfluoride borogermanate scintillating glasses
Authors: Sun Xin-Yuan , Yu Xiao-Guang , Jiang Da-Guo , Wang Wen-Feng , Li Yu-Nong , Chen Zhi-Quan , Zhou Yun-Zhi , Yang Qing-Mei , Kang Zhitao
Published: June 2016

Dy3+-, Tb3+-activated, and Tb3+/Dy3+-coactivated oxyfluoride borogermanate scintillating glasses with the density of about 6.50 g/cm3 were successfully synthesized by a melt-quenching method. The structure and optical properties including transmittance, photoluminescence (excitation and emission spectra), photoluminescence decay, and X-ray excited luminescence (XEL) behaviors were studied in detail. Our results reveal that the energy transfer efficiency from Dy3+ to Tb3+ ions increases with an increase of Tb3+ concentration. The energy transfer mechanism is determined to be electric dipole–dipole interaction. However, the XEL intensity of Tb3+ decreases with the incorporation of sensitizer Dy3+ into borogermanate scintillating glass, which may result from the different mechanisms under ultraviolet light and X-ray excitation.
Nano-crystallization in ZnO-doped In2O3 thin films via excimer laser annealing for thin-film transistors
Authors: Fujii Mami N. , Ishikawa Yasuaki , Ishihara Ryoichi , van der Cingel Johan , Mofrad Mohammad R. T. , Bermundo Juan Paolo Soria , Kawashima Emi , Tomai Shigekazu , Yano Koki , Uraoka Yukiharu
Published: June 2016

In a previous work, we reported the high field effect mobility of ZnO-doped In2O3 (IZO) thin film transistors (TFTs) irradiated by excimer laser annealing (ELA) [M. Fujii et al., Appl. Phys. Lett. 102, 122107 (2013)]. However, a deeper understanding of the effect of ELA on the IZO film characteristics based on crystallinity, carrier concentrations, and optical properties is needed to control localized carrier concentrations for fabricating self-aligned structures in the same oxide film and to adequately explain the physical characteristics. In the case of as-deposited IZO film used as the channel, a high carrier concentration due to a high density of oxygen vacancies was observed; such a film does not show the required TFT characteristics but can act as a conductive film. We achieved a decrease in the carrier concentration of IZO films by crystallization using ELA. This means that ELA can form localized conductive or semi-conductive areas on the IZO film. We confirmed that the reason for the carrier concentration decrease was the decrease of oxygen-deficient regions and film crystallization. The annealed IZO films showed nano-crystalline phase, and the temperature at the substrate was substantially less than the temperature limit for flexible films such as plastic, which is 50°C. This paves the way for the formation of self-aligned structures and separately formed conductive and semi-conductive regions in the same oxide film.
Effect of parity on changes in udder traits, milk yield and composition of West African dwarf sheep during lactation
Authors: Adegoke E. O. , Machebe N. S. , Ezekwe A. G. , Agaviezor O. B.
Published: June 2016

Twelve West African Dwarf sheep, comprising four ewes in each of the Parities 1, 2 and 3, were used to determine the effect of parity on udder traits during lactation, milk yield and composition. Udder length, udder width, udder circumference, udder volume, teat length, teat width, teat circumference, distance between the teats and teat height from the ground of sheep were measured in centimetres (cm) weekly for 12 weeks of lactation, commencing from Day 4 postpartum. Parity highly influenced (P < 0.05) udder traits, except udder volume (P > 0.05). The udder length, width and circumference were higher (P < 0.05) in Parity-3 ewes than Parity-1 and -2 ewes. A similar trend was shown for teat length, width and circumference. Parity had no effect (P > 0.05) on udder volume, but significantly (P > 0.05) affected distance between the teats and teat height from the ground. With the exception of udder volume, all traits peaked by the 3rd week of lactation, and gradually declined thereafter. Milk yield and milk weight peaked by the 3rd week postpartum and these were higher for ewes in Parity 3. Milk yield and milk weight declined faster in ewes in Parities 1 and 2 than they did in Parity-3 ewes (P < 0.05) as lactation length increased. In regard to milk composition, moisture, protein and fat, but not total solid, solid-not-fat and lactose, were greater (P < 0.05) in Parity-3 ewes both at peak milk yield (3rd week of lactation) and end of lactation. From these findings, we conclude that parity type plays a significant role in influencing udder traits, milk yield and milk quality in ewes.
Fodder quality and intake by dairy cows. 1. Preference for oaten hays
Authors: Dynes R. A. , Purser D. B. , Baker S. K.
Published: June 2016

This work was undertaken to determine whether measurement of preference 30 min after alternative hays are offered to lactating dairy cows adequately predicts preference over a 3-day period and to determine the influence of the concentrations of water-soluble carbon (WSC) and neutral detergent fibre (NDF) of hays on preference. Eleven test hays were chosen to provide an NDF concentration of between 45% and 60% and a WSC concentration of between 10% and 30%. The test hays were each offered to lactating dairy cows as an alternative choice, with two control hays with NDF concentrations of 49% and 54%. A replicated Latin-square design was used to determine the preference of cows for the test hays, using three cows for each test hay versus control-hay comparison. Preference measured 30 min after hays were offered to cows was highly correlated with measures of preference made after 24 h and again for the same measures on the third day of the hays being offered. However, preference measures with the two different control hays were not well related, thus indicating that preference values are control-hay specific. Total hay intake was unchanged with the low-NDF control hay but declined with increasing NDF concentration of the test hays with the higher-NDF control hay. WSC did not influence preference at any one level of NDF of the test hays when the control hay had a low NDF concentration, but there was a small rise in preference at each NDF level when the control hay had a higher NDF concentration. This may have been a result of a contribution of WSC to digestibility as much as to taste response. With the low-NDF control hay, drivers of preference were the NDF concentration and the digestibility of the hay, but with the higher-NDF control hay, the drivers were the NDF concentration and fibre characteristics (shear and potential fibre digestibility). Calculation of the NDF concentration of the total hay consumed, test plus control hays, suggested that a change in drivers of selection is likely at the point where the NDF concentration of the test hay equals that of the control hay. Unless models identifying selection drivers handle non-linear data, misleading results may be obtained.
Self-Assembly of an Amphiphilic OEG-Linked Glutamide Lipid
Authors: Wang Shuo , Zhang Youguo , Li Qiang , Sun Rongqin , Ma Lin , Li Liangchun
Published: June 2016

Amphiphilic peptides with or without oligoethylene glycol (OEG) chains based on 3,4-bis(benzyloxy)benzoic-linked glutamide were designed and their self-assembly was investigated. It was found that the amphiphilic peptide 3 with OEG chains could not only form stable gels in a wide range of solvents, but also showed better solubility in solvents than those without OEG chains. Fibrillar and nanotube structures were found in the gels formed and the width of the fibres could be tuned with added water content. The UV-vis and XRD results suggested that the driving forces for the peptide self-assembly were mainly intermolecular π–π and hydrogen-bonding interactions. These results provide a deeper understanding of the self-assembly mechanism and size control of nanofibrils formed by an OEG-based amphiphilic peptide.
The imperative need for nationally coordinated bioassessment of rivers and streams
Authors: Nichols Susan J. , Barmuta Leon A. , Chessman Bruce C. , Davies Peter E. , Dyer Fiona J. , Harrison Evan T. , Hawkins Charles P. , Jones Iwan , Kefford Ben J. , Linke Simon , Marchant Richard , Metzeling Leon , Moon Katie , Ogden Ralph , Peat Michael , Reynoldson Trefor B. , Thompson Ross M.
Published: June 2016

Declining water quality and ecological condition is a typical trend for rivers and streams worldwide as human demands for water resources increase. Managing these natural resources sustainably is a key responsibility of governments. Effective water management policies require information derived from long-term monitoring and evaluation. Biological monitoring and assessment are critical for management because bioassessment integrates the biological, physical and chemical features of a waterbody. Investment in nationally coordinated riverine bioassessment in Australia has almost ceased and the foci of management questions are on more localised assessments. However, rivers often span political and administrative boundaries, and their condition may be best protected and managed under national policies, supported by a coordinated national bioassessment framework. We argue that a nationally coordinated program for the bioassessment of riverine health is an essential element of sustainable management of a nation’s water resources. We outline new techniques and research needed to streamline current arrangements to meet present-day and emerging challenges for coordinating and integrating local, regional and national bioassessment activities. This paper draws on international experience in riverine bioassessment to identify attributes of successful broad-scale bioassessment programs and strategies needed to modernise freshwater bioassessment in Australia and re-establish national broad-scale focus.
Spatiotemporal variation among demersal ichthyofauna in a subtropical estuary bordering World Heritage-listed and marine protected areas: implications for resource management
Authors: Possatto Fernanda E. , Broadhurst Matt K. , Gray Charles A. , Spach Henry L. , Lamour Marcelo R.
Published: June 2016

Benthic trawl surveys were performed to quantify the spatiotemporal distributions of teleosts and key abiotic associations throughout an ecologically important estuary within Brazil’s Atlantic Forest biosphere. Approximately 52000 fish (51% juveniles) representing 75 species were sampled, with residents accounting for 36 and 61% of total species and individuals respectively. Five artisanally important species comprised 77 and 81% of individuals and biomass respectively. Cathorops spixii was most abundant (>40% of total), whereas Stellifer rastrifer, Aspistor luniscutis, Sphoeroides greeleyi and S. testudineus collectively contributed towards 37 and 34% of individuals and biomass respectively. The abundance of A. luniscutis, C. spixii and S. rastrifer was negatively associated with salinity, whereas the presence of the latter two species was also positively associated with temperature, and S. greeleyi and S. testudineus (mostly adults) were more abundant in deeper areas. These relationships seemed to be affected by species-specific reproductive (S. rastrifer, C. spixii and A. luniscutis), habitat (S. greeleyi and S. testudineus) and prey preferences (juvenile C. spixii and A. luniscutis). Protection for these various species may be achieved via immediate fishing effort regulations, but more research is required to manage other anthropogenic effects. Such work should be a priority to ultimately preserve what is one of the most important South American biodiversity areas.
Do body size, diet type or residence time explain habitat use in a vertebrate herbivore community?
Authors: Garnick S. , Di Stefano J. , Elgar M. A. , Coulson G.
Published: June 2016

Many theories attempt to explain patterns of community organisation among large herbivores. We explored the role of body size, diet type and residence time on habitat use in a community comprising four metatherians (western grey kangaroo, Macropus fuliginosus; eastern grey kangaroo, M. giganteus; red-necked wallaby, Notamacropus rufogriseus; swamp wallaby, Wallabia bicolor) and two eutherians (red deer, Cervus elaphus; European rabbit, Oryctolagus cuniculus) in south-eastern Australia. We used camera traps to estimate habitat occupancy, quantified habitat specialisation using relative entropy, and ran regressions using percentage grass consumed, log(mass) and log(time at site) as predictor variables and relative entropy as the response. If body size influenced habitat use, we predicted smaller species would occupy fewer habitats. If diet type influenced habitat use, we predicted intermediate feeders would use more habitats. If the time that a species had been present at a site predicted community organisation, newer species would use more habitats. None of these theories explained habitat use in our community. Red deer used a narrower range of habitats than expected, perhaps due to the poor suitability of habitats available in the Grampians. While interactions between our hypotheses are likely to be important, the body size model deserves further attention in this community.
Deletion of the gene
Pip4k2c
, a novel phosphatidylinositol kinase, results in hyperactivation of the immune system
Authors: Shim Hyeseok , Wu Chuan , Ramsamooj Shivan , Bosch Kaitlyn N. , Chen Zuojia , Emerling Brooke M. , Yun Jihye , Liu Hui , Choo-Wing Rayman , Yang Zhiwei , Wulf Gerburg M. , Kuchroo Vijay Kumar , Cantley Lewis C.
Published: June 2016

Significance

The mammalian target of rapamycin complex 1 (mTORC1) signaling pathway is an important facet of the immune system, including that it regulates T-cell differentiation and activation. Here, we report that type 2 phosphatidylinositol-5-phosphate 4-kinase gamma (protein, PI5P4Kγ; gene,
PIP4K2C
) plays a role in the regulation of the immune system by manipulating mTORC1 signaling. These results suggest that the SNP at the
PIP4K2C
locus (rs1678542) in human patients with autoimmunity might cause a decrease in PI5P4Kγ expression and thereby an increase in mTORC1 signaling. In addition, these results imply that inhibition of mTORC1 would be beneficial to these patients. These studies also suggest that agents that inhibit PIP4K2C function could be useful to enhance cancer immunotherapy.
A Virtue Analysis of Recreational Marijuana Use
Authors: Sullivan Ezra , Austriaco Nicanor
Published: June 2016

Several empirical studies suggest that recreational marijuana is popularly perceived as an essentially harmless rite of passage that ends as young people settle into their careers and their adult intimate relationships. Is this perception accurate? To answer this question, we evaluate the morality of recreational marijuana use from a virtue perspective guided by the theological synthesis of St. Thomas Aquinas. Since the medical data reveals that recreational marijuana use is detrimental to the well-being of the user, we conclude that it is a vicious activity, an instance of the vice of intoxication, and as such would be morally illicit.

Lay summary: In contrast to its medical use, the recreational use of marijuana cannot be justified for at least three reasons. First, as scientists have amply documented, it harms the organic functioning of the human body. Second, it impedes our ability to reason and in so doing does harm to us. Finally, it has lasting detrimental effects on the user and his neighbor, even when it occurs in a casual setting. Intoxication is always contrary to the integral good of the person. Thus, the use of marijuana is never warranted even for good, non-medical reasons.
Sonnet XXX: Love, Dignity, and Dying
Authors: Ely E. Wesley
Published: June 2016

All of us in medicine who care for patients who are chronically critically ill, dying of incurable illnesses, will be faced with discussions about the value of their lives and about the appropriateness of ongoing supportive care. Such discussions are good and true, and they must always be done within the context of the sanctity of every human life and the promise of God that we are His children, each and every one of us. In this article, I explore the end-of-life path of a patient with amyotrophic lateral sclerosis (ALS) and the courageous faith that she demonstrated in the face of her illness. I explore with you, the reader, the hard-core conversations that took place at her bedside and their meaning in light of Catholic moral teaching. This story is not meant to indicate that we should always do all interventions at all times for all patients. That would be a teaching counter to Evangelium vitae. This story is meant to help you think through the path of your patients and of you as a physician or other type of healthcare professional in serving your patients. Primum non nocere. Ad majorem Dei gloriam.
A Philosophical Assessment of TK's Autopsy Report: Implications for the Debate over the Brain Death Criteria
Authors: Austriaco Nicanor Pier Giorgio
Published: June 2016

In recent years, there has been increasing evidence that the totally brain-dead patient is able to continue to live and to maintain some integrated functions, albeit with the necessary assistance of mechanical ventilation. Several years ago, the autopsy report of a totally brain-dead patient named TK who was kept on life support for nearly twenty years was published in the Journal of Child Neurology. He remains the individual kept on life support the longest after suffering total brain failure. In this essay, I argue that the clinical data described in the autopsy report demonstrate that TK's long-term survival after total brain failure supports the claim acknowledged by the President's Council on Bioethics that the brain-dead patient retains his bodily integrity. As such, he is not dead. He is still a living, though severely disabled, human organism, a human person made in the image and likeness of God.

Lay summary: Traditionally, the presence or absence of bodily integration has been used to definitively discern the presence or absence of life in the human being where decomposition of the body is the surest sign of death. The autopsy report of a patient named TK who was brain-dead for nearly twenty years demonstrates that brain-dead patients retain their bodily integrity. As such, TK and other brain-dead patients are not dead. They are living, though severely disabled, human organisms, who are human persons made in the image and likeness of God.
Permanent versus determinant: Not via saturations
Authors: Bürgisser Peter , Ikenmeyer Christian , Hüttenhain Jesko
Published: June 2016

Let

D
e

t
n

Det_n

denote the closure of the

G
l

n
2

(

C

)

\mathrm {Gl}_{n^2}(\mathbb {C})

-orbit of the determinant polynomial

d
e
t

n

\mathrm {det}_n

with respect to linear substitution. The highest weights (partitions) of irreducible

G
l

n
2

(

C

)

\mathrm {Gl}_{n^2}(\mathbb {C})

-representations occurring in the coordinate ring of

D
e

t
n

Det_n

form a finitely generated monoid

S
(
D
e

t
n

)

S(Det_n)

. We prove that the saturation of

S
(
D
e

t
n

)

S(Det_n)

contains all partitions

λ
\lambda

with length at most 

n
n

and size divisible by 

n
n

. This implies that representation theoretic obstructions for the permanent versus determinant problem must be holes of the monoid

S
(
D
e

t
n

)

S(Det_n)

.
Ramsey’s theorem for singletons and strong computable reducibility
Authors: Dzhafarov Damir , Patey Ludovic , Solomon Reed , Westrick Linda
Published: June 2016

We answer a question posed by Hirschfeldt and Jockusch by showing that whenever

k
>
ℓ

k > \ell

, Ramsey’s theorem for singletons and

k
k

-colorings,

R
T

k
1

\mathsf {RT}^1_k

, is not strongly computably reducible to the stable Ramsey’s theorem for

ℓ
\ell

-colorings,

S
R
T

ℓ
2

\mathsf {SRT}^2_\ell

. Our proof actually establishes the following considerably stronger fact: given

k
>
ℓ

k > \ell

, there is a coloring

c
:
ω
→
k

c : \omega \to k

such that for every stable coloring

d
:
[
ω

]
2

→
ℓ

d : [\omega ]^2 \to \ell

(computable from

c
c

or not), there is an infinite homogeneous set

H
H

for

d
d

that computes no infinite homogeneous set for

c
c

. This also answers a separate question of Dzhafarov, as it follows that the cohesive principle,

C
O
H

\mathsf {COH}

, is not strongly computably reducible to the stable Ramsey’s theorem for all colorings,

S
R
T

>
∞

2

\mathsf {SRT}^2_{>\infty }

. The latter is the strongest partial result to date in the direction of giving a negative answer to the longstanding open question of whether

C
O
H

\mathsf {COH}

is implied by the stable Ramsey’s theorem in

ω
\omega

-models of

R
C
A

0

\mathsf {RCA}_0

.
Spectra of definite type in waveguide models
Authors: Lotoreichik Vladimir , Siegl Petr
Published: June 2016

We develop an abstract method to identify spectral points of definite type in the spectrum of the operator

T
1

⊗

I
2

+

I
1

⊗

T
2

T_1\otimes I_2 + I_1\otimes T_2

, applicable in particular for non-self-adjoint waveguide type operators with symmetries. Using the remarkable properties of the spectral points of definite type, we obtain new results on realness of weakly coupled bound states and of low lying essential spectrum in the

P

T

\mathcal {P}\mathcal {T}

-symmetric waveguide. Moreover, we show that the pseudospectrum has a tame behavior near the low lying essential spectrum and exclude the accumulation of non-real eigenvalues from this part of the essential spectrum. The advantage of our approach is particularly visible when the resolvent of the unperturbed operator cannot be explicitly expressed and most of the mentioned conclusions are extremely hard to prove by direct methods.
Biharmonic hypersurfaces in a sphere
Authors: Luo Yong , Maeta Shun
Published: June 2016

In this short paper we will survey some recent developments in the geometric theory of biharmonic submanifolds, with an emphasis on the newly discovered Liouville type theorems and applications of known Liouville type theorems in the research of the nonexistence of biharmonic submanifolds. A new Liouville type theorem for superharmonic functions on complete manifolds is proved and its applications in a kind of nonexistence of biharmonic hypersurfaces in a sphere is provided.
On the distribution of the coefficients of modular forms modulo 𝑝^{𝑗}
Authors: Dai Haobo , Fang Xianwen
Published: June 2016

We investigate the distribution of the coefficients of a modular form modulo

p
j

p^j

where

p
≥
3

p\geq 3

is a prime and

j
j

is a positive integer. Our work heavily relies on the result of Bellaïche and Soundararajan.
Novel applications of multitask learning and multiple output regression to multiple genetic trait prediction
Authors: He Dan , Kuhn David , Parida Laxmi
Published: June 2016

Given a set of biallelic molecular markers, such as SNPs, with genotype values encoded numerically on a collection of plant, animal or human samples, the goal of genetic trait prediction is to predict the quantitative trait values by simultaneously modeling all marker effects. Genetic trait prediction is usually represented as linear regression models. In many cases, for the same set of samples and markers, multiple traits are observed. Some of these traits might be correlated with each other. Therefore, modeling all the multiple traits together may improve the prediction accuracy. In this work, we view the multitrait prediction problem from a machine learning angle: as either a multitask learning problem or a multiple output regression problem, depending on whether different traits share the same genotype matrix or not. We then adapted multitask learning algorithms and multiple output regression algorithms to solve the multitrait prediction problem. We proposed a few strategies to improve the least square error of the prediction from these algorithms. Our experiments show that modeling multiple traits together could improve the prediction accuracy for correlated traits.

Availability and implementation: The programs we used are either public or directly from the referred authors, such as MALSAR ( http://www.public.asu.edu/~jye02/Software/MALSAR/ ) package. The Avocado data set has not been published yet and is available upon request.

Contact:  dhe@us.ibm.com
Simultaneous prediction of enzyme orthologs from chemical transformation patterns for
de novo
metabolic pathway reconstruction
Authors: Tabei Yasuo , Yamanishi Yoshihiro , Kotera Masaaki
Published: June 2016

Motivation : Metabolic pathways are an important class of molecular networks consisting of compounds, enzymes and their interactions. The understanding of global metabolic pathways is extremely important for various applications in ecology and pharmacology. However, large parts of metabolic pathways remain unknown, and most organism-specific pathways contain many missing enzymes. Results: In this study we propose a novel method to predict the enzyme orthologs that catalyze the putative reactions to facilitate the de novo reconstruction of metabolic pathways from metabolome-scale compound sets. The algorithm detects the chemical transformation patterns of substrate–product pairs using chemical graph alignments, and constructs a set of enzyme-specific classifiers to simultaneously predict all the enzyme orthologs that could catalyze the putative reactions of the substrate–product pairs in the joint learning framework. The originality of the method lies in its ability to make predictions for thousands of enzyme orthologs simultaneously, as well as its extraction of enzyme-specific chemical transformation patterns of substrate–product pairs. We demonstrate the usefulness of the proposed method by applying it to some ten thousands of metabolic compounds, and analyze the extracted chemical transformation patterns that provide insights into the characteristics and specificities of enzymes. The proposed method will open the door to both primary (central) and secondary metabolism in genomics research, increasing research productivity to tackle a wide variety of environmental and public health matters.

Availability and Implementation :

Contact : maskot@bio.titech.ac.jp
RNAiFold2T: Constraint Programming design of thermo-IRES switches
Authors: Garcia-Martin Juan Antonio , Dotu Ivan , Fernandez-Chamorro Javier , Lozano Gloria , Ramajo Jorge , Martinez-Salas Encarnacion , Clote Peter
Published: June 2016

Motivation: RNA thermometers (RNATs) are cis -regulatory elements that change secondary structure upon temperature shift. Often involved in the regulation of heat shock, cold shock and virulence genes, RNATs constitute an interesting potential resource in synthetic biology, where engineered RNATs could prove to be useful tools in biosensors and conditional gene regulation.

Results: Solving the 2-temperature inverse folding problem is critical for RNAT engineering. Here we introduce RNAiFold2T, the first Constraint Programming (CP) and Large Neighborhood Search (LNS) algorithms to solve this problem. Benchmarking tests of RNAiFold2T against existent programs (adaptive walk and genetic algorithm) inverse folding show that our software generates two orders of magnitude more solutions, thus allowing ample exploration of the space of solutions. Subsequently, solutions can be prioritized by computing various measures, including probability of target structure in the ensemble, melting temperature, etc. Using this strategy, we rationally designed two thermosensor internal ribosome entry site ( thermo -IRES) elements, whose normalized cap-independent translation efficiency is approximately 50% greater at 42 °C than 30 °C, when tested in reticulocyte lysates. Translation efficiency is lower than that of the wild-type IRES element, which on the other hand is fully resistant to temperature shift-up. This appears to be the first purely computational design of functional RNA thermoswitches, and certainly the first purely computational design of functional thermo-IRES elements.

Availability: RNAiFold2T is publicly available as part of the new release RNAiFold3.0 at https://github.com/clotelab/RNAiFold and http://bioinformatics.bc.edu/clotelab/RNAiFold , which latter has a web server as well. The software is written in C ++ and uses OR-Tools CP search engine.

Contact:  clote@bc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction
Authors: Cui Xuefeng , Lu Zhiwu , Wang Sheng , Jing-Yan Wang Jim , Gao Xin
Published: June 2016

Motivation : Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment, threading and alignment-free methods, protein homology detection remains a challenging open problem. Recently, network methods that try to find transitive paths in the protein structure space demonstrate the importance of incorporating network information of the structure space. Yet, current methods merge the sequence space and the structure space into a single space, and thus introduce inconsistency in combining different sources of information.

Method : We present a novel network-based protein homology detection method, CMsearch, based on cross-modal learning. Instead of exploring a single network built from the mixture of sequence and structure space information, CMsearch builds two separate networks to represent the sequence space and the structure space. It then learns sequence–structure correlation by simultaneously taking sequence information, structure information, sequence space information and structure space information into consideration.

Results: We tested CMsearch on two challenging tasks, protein homology detection and protein structure prediction, by querying all 8332 PDB40 proteins. Our results demonstrate that CMsearch is insensitive to the similarity metrics used to define the sequence and the structure spaces. By using HMM–HMM alignment as the sequence similarity metric, CMsearch clearly outperforms state-of-the-art homology detection methods and the CASP-winning template-based protein structure prediction methods.

Availability and implementation: Our program is freely available for download from http://sfb.kaust.edu.sa/Pages/Software.aspx .

Contact : xin.gao@kaust.edu.sa

Supplementary information : Supplementary data are available at Bioinformatics online.
Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks
Authors: Glicksberg Benjamin S. , Li Li , Badgeley Marcus A. , Shameer Khader , Kosoy Roman , Beckmann Noam D. , Pho Nam , Hakenberg Jörg , Ma Meng , Ayers Kristin L. , Hoffman Gabriel E. , Dan Li Shuyu , Schadt Eric E. , Patel Chirag J. , Chen Rong , Dudley Joel T.
Published: June 2016

Motivation: Underrepresentation of racial groups represents an important challenge and major gap in phenomics research. Most of the current human phenomics research is based primarily on European populations; hence it is an important challenge to expand it to consider other population groups. One approach is to utilize data from EMR databases that contain patient data from diverse demographics and ancestries. The implications of this racial underrepresentation of data can be profound regarding effects on the healthcare delivery and actionability. To the best of our knowledge, our work is the first attempt to perform comparative, population-scale analyses of disease networks across three different populations, namely Caucasian (EA), African American (AA) and Hispanic/Latino (HL).

Results: We compared susceptibility profiles and temporal connectivity patterns for 1988 diseases and 37 282 disease pairs represented in a clinical population of 1 025 573 patients. Accordingly, we revealed appreciable differences in disease susceptibility, temporal patterns, network structure and underlying disease connections between EA, AA and HL populations. We found 2158 significantly comorbid diseases for the EA cohort, 3265 for AA and 672 for HL. We further outlined key disease pair associations unique to each population as well as categorical enrichments of these pairs. Finally, we identified 51 key ‘hub’ diseases that are the focal points in the race-centric networks and of particular clinical importance. Incorporating race-specific disease comorbidity patterns will produce a more accurate and complete picture of the disease landscape overall and could support more precise understanding of disease relationships and patient management towards improved clinical outcomes.

Contacts : rong.chen@mssm.edu or joel.dudley@mssm.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
RADIS:analysis ofRAD-seq data for interspecific phylogeny
Authors: Cruaud Astrid , Gautier Mathieu , Rossi Jean-Pierre , Rasplus Jean-Yves , Gouzy Jérôme
Published: June 2016

In an attempt to make the processing of RAD-seq data easier and allow rapid and automated exploration of parameters/data for phylogenetic inference, we introduce the perl pipeline RADIS. Users of RADIS can let their raw Illumina data be processed up to phylogenetic tree inference, or stop (and restart) the process at some point. Different values for key parameters can be explored in a single analysis (e.g. loci building, sample/loci selection), making possible a thorough exploration of data. RADIS relies on Stacks for demultiplexing of data, removing PCR duplicates and building individual and catalog loci. Scripts have been specifically written for trimming of reads and loci/sample selection. Finally, RAxML is used for phylogenetic inferences, though other software may be utilized.

Availability and implementation: RADIS is written in perl, designed to run on Linux and Unix platforms. RADIS and its manual are freely available from http://www1.montpellier.inra.fr/CBGP/software/RADIS/.

Contact:  astrid.cruaud@supagro.inra.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
@MInter: automated text-mining of microbial interactions
Authors: Lim Kun Ming Kenneth , Li Chenhao , Chng Kern Rei , Nagarajan Niranjan
Published: June 2016

Motivation: Microbial consortia are frequently defined by numerous interactions within the community that are key to understanding their function. While microbial interactions have been extensively studied experimentally, information regarding them is dispersed in the scientific literature. As manual collation is an infeasible option, automated data processing tools are needed to make this information easily accessible.

Results: We present @MInter, an automated information extraction system based on Support Vector Machines to analyze paper abstracts and infer microbial interactions. @MInter was trained and tested on a manually curated gold standard dataset of 735 species interactions and 3917 annotated abstracts, constructed as part of this study. Cross-validation analysis showed that @MInter was able to detect abstracts pertaining to one or more microbial interactions with high specificity (specificity = 95%, AUC = 0.97). Despite challenges in identifying specific microbial interactions in an abstract (interaction level recall = 95%, precision = 25%), @MInter was shown to reduce annotator workload 13-fold compared to alternate approaches. Applying @MInter to 175 bacterial species abundant on human skin, we identified a network of 357 literature-reported microbial interactions, demonstrating its utility for the study of microbial communities.

Availability and implementation: @MInter is freely available at https://github.com/CSB5/atminter.

Contact:  nagarajann@gis.a-star.edu.sg

Supplementary information:  Supplementary data are available at Bioinformatics online.
Disseminated Mycobacterium chimaera Infection After Cardiothoracic Surgery
Authors: Tan Nicholas , Sampath Rahul , Abu Saleh Omar M. , Tweet Marysia S. , Jevremovic Dragan , Alniemi Saba , Wengenack Nancy L. , Sampathkumar Priya , Badley Andrew D.
Published: June 2016

Ten case reports of disseminated Mycobacterium chimaera infections associated with cardiovascular surgery were published from Europe. We report 3 cases of disseminated M chimaera infections with histories of aortic graft and/or valvular surgery within the United States. Two of 3 patients demonstrated ocular involvement, a potentially important clinical finding.
The far distance to G7.47+0.06 from proper motion measurement of H2O masers
Authors: Yamauchi Aya , Yamashita Kazuyoshi , Honma Mareki , Sunada Kazuyoshi , Nakagawa Akiharu , Ueno Yuji
Published: June 2016

We report on a distance measurement of 22 GHz H2O maser features associated with an ultra-compact H ii region G7.47+0.06 using VERA (VLBI Exploration of Radio Astrometry). Since the source is located farther away than 10 kpc, it turned out to be difficult to derive the distance from annual parallax measurement. Meanwhile, we clearly detected the source's proper motion parallel to the Galactic plane. The proper motion is μ = −5.03 ± 0.07 mas yr−1 and is approaching the Galactic center. We applied a new method to determine the source distance based on absolute proper motions. Considering uncertainties of the Galactic rotation curve and the solar peculiar motion, the detected proper motion leads to a source distance of D = 20 ± 2 kpc, demonstrating that astrometric observation can provide an accurate distance measurement at a 10% level even for sources too distant to measure the annual parallax. Lastly, we scale the physical parameters of the H ii region estimated in a previous paper to be 20 kpc, and show that the H2O maser features are associated with a massive star-forming region corresponding to the spectral type of O5.5.
Out-of-School Suspensions of Black Youths: Culture, Ability, Disability, Gender, and Perspective
Authors: Haight Wendy , Kayama Misa , Gibson Priscilla Ann
Published: June 2016

Racial disproportionality in out-of-school suspensions is a persistent social justice issue in public schools. This article examines out-of-school suspensions of four black youths from the perspectives of the youths, their caregivers, and educators. The case involving David, a 14-year-old African American with a learning disability, illustrates the challenges of students experiencing the intersection of disability and race. The case involving George, a 14-year-old Liberian immigrant, illustrates how parents and teachers may form alliances around shared goals and values despite profound cultural differences in understanding of youths’ misbehavior. The case involving Nina, a 12-year-old African American, illustrates how educators’ failure to consider the context of her misbehaviors as responses to sexual harassment, along with their subsequent harsh punishment and failure to protect her, led to her disengagement from school. The case involving Craig, a 16-year-old African American, provides a glimpse into how the use of criminal justice language to refer to youths’ misbehaviors can support the development of a criminalized self- and social identity. These cases illustrate the diversity of black students—including ability, disability, culture, and gender—and how events surrounding suspensions are interpreted by students, caregivers, and educators. Understanding such diversity will undergird implementation of effective alternatives to suspensions.
The Relationship Between Academic Motivation and Lifelong Learning During Residency: A Study of Psychiatry Residents
Authors: Sockalingam Sanjeev , Wiljer David , Yufe Shira , Knox Matthew K. , Fefergrad Mark , Silver Ivan , Harris Ilene , Tekian Ara
Published: June 2016

Purpose

To examine the relationship between lifelong learning (LLL) and academic motivation for residents in a psychiatry residency program, trainee factors that influence LLL, and psychiatry residents’ LLL practices.

Method

Between December 2014 and February 2015, 105 of 173 (61%) eligible psychiatry residents from the Department of Psychiatry, University of Toronto, completed a questionnaire with three study instruments: an LLL needs assessment survey, the Jefferson Scale of Physician Lifelong Learning (JeffSPLL), and the Academic Motivation Scale (AMS). The AMS included a relative autonomy motivation score (AMS-RAM) measuring the overall level of intrinsic motivation (IM).

Results

A significant correlation was observed between JeffSPLL and AMS-RAM scores (r = 0.39, P < .001). Although there was no significant difference in JeffSPLL and AMS-RAM scores based on respondents’ level of training (senior vs. junior resident), gender, or age, analysis of AMS subdomains showed that junior residents had a significantly higher score on the extrinsic motivation identification domain (mean difference [M] = 0.38; 95% confidence interval [CI] [0.01, 0.75]; P = .045; d = 0.44) compared with senior residents. Clinician scientist stream (CSS) residents had significantly higher JeffSPLL scores compared with non-CSS residents (M = 3.15; 95% CI [0.52, 5.78]; P = .020; d = 0.57).

Conclusions

The use of rigorous measures to study LLL and academic motivation confirmed prior research documenting the positive association between IM and LLL. The results suggest that postgraduate curricula aimed at enhancing IM, for example, through support for learning autonomously, could be beneficial to cultivating LLL in learners.
The Effect of Different Carbapenem Antibiotics (Ertapenem, Imipenem/Cilastatin, and Meropenem) on Serum Valproic Acid Concentrations
Authors: Wu Chien-Chih , Pai Tsung-Yu , Hsiao Fei-Yuan , Shen Li-Jiuan , Wu Fe-Lin Lin
Published: June 2016

Background:

Carbapenem antibiotics (CBPMs) may significantly reduce the serum concentration of valproic acid (VPA), but the extent of this effect among various CBPMs is unknown. This study compared the extent and onset of the interactions among ertapenem, imipenem/cilastatin, and meropenem.

Methods:

A 5-year retrospective study was performed. Hospitalized patients over 18 years old who received VPA and a CBPM concurrently were enrolled via the pharmacy computer system. Patients who lacked VPA serum concentration measurements before or during CBPMs' use, had concurrent medication(s) that might interfere with VPA metabolism, or had a history of liver cirrhosis were excluded. Total VPA serum concentrations before and during CBPMs' use and after its discontinuation were recorded, and differences among various CBPMs were analyzed.

Results:

Fifty-two patients were included in this analysis. Irrespective of the route of administration, VPA serum concentrations were subtherapeutic in 90% of the subjects during CBPMs' use. There was a significant decrease (P < 0.001) in VPA serum concentrations during the use of CBPMs: 72% ± 17%, 42% ± 22%, and 67% ± 19% in the ertapenem (N = 9), imipenem/cilastatin (N = 17), and meropenem (N = 26) groups, respectively. The effect of ertapenem and meropenem on VPA was significantly more expressed than that of imipenem/cilastatin (P < 0.005). The onset of this drug interaction occurred within 24 hours of CBPMs' administration, and VPA serum concentrations returned to 90% of baseline within 7 days of CBPMs' discontinuation along with a 20% increase in VPA dose. Increasing VPA dose during the use of ertapenem or meropenem did not result in elevating VPA serum concentrations to therapeutic levels during the combined therapy period.

Conclusions:

CBPMs reduced VPA serum concentration within 24 hours of administration by approximately 60%. Ertapenem and meropenem had a greater effect on VPA serum concentration than imipenem/cilastatin. Because of the dramatic reduction of VPA serum concentration during CBPMs' use, concomitant use of VPA and CBPMs should be avoided.
Evidence that electronic health records can promote physician counseling for healthy behaviors
Authors: Bae Jaeyong , Hockenberry Jason M. , Rask Kimberly J. , Becker Edmund R.
Published: June 2016

Background:

Health behavior counseling services may help patients manage chronic conditions effectively and slow disease progression. Studies show, however, that many providers fail to provide these services because of time constraints and inability to tailor counseling to individual patient needs. Electronic health records (EHRs) have the potential to increase appropriate counseling by providing pertinent patient information at the point of care and clinical decision support.

Purpose:

This study estimates the impact of select EHR functionalities on the rate of health behavior counseling provided during primary care visits.

Methodology:

Multivariable regression analyses of the 2007–2010 National Ambulatory Medical Care Survey were conducted to examine whether eight EHR components representing four core functionalities of EHR systems were correlated with the rate of health behavior counseling services. Propensity score matching was used to control for confounding factors given the use of observational data. To address concerns that EHR may only lead to improved documentation of counseling services and not necessarily improved care, the association of EHR functionalities with prescriptions for smoking cessation medications was also estimated.

Findings:

The use of an EHR system with health information and data, order entry and management, result management, decision support, and a notification system for abnormal test results was associated with an approximately 25% increase in the probability of health behavior counseling delivered. Clinical reminders were associated with more health behavior counseling services when available in combination with patient problem lists. The laboratory results viewer was also associated with more counseling services when implemented with a notification system for abnormal results.

Practice Implication:

An EHR system with key supportive functionalities can enhance delivery of preventive health behavior counseling services in primary care settings. Meaningful use criteria should be evaluated to ensure that they encourage the adoption of EHR systems with those functionalities shown to improve clinical care.
STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF BENIGN FLECK RETINA USING MULTIMODAL IMAGING
Authors: Neriyanuri Srividya , Rao Chetan , Raman Rajiv
Published: June 2016

Purpose:

To report structural and functional features in a case series of benign fleck retina using multimodal imaging.

Methods:

Four cases with benign fleck retina underwent complete ophthalmic examination that included detailed history, visual acuity, and refractive error testing, FM-100 hue test, dilated fundus evaluation, full field electroretinogram, fundus photography with autofluorescence, fundus fluorescein angiography, and swept-source optical coherence tomography.

Results:

Age group of the cases ranged from 19 years to 35 years (3 males and 1 female). Parental consanguinity was reported in two cases. All of them were visually asymptomatic with best-corrected visual acuity of 20/20 (moderate astigmatism) in both the eyes. Low color discrimination was seen in two cases. Fundus photography showed pisciform flecks which were compactly placed on posterior pole and were discrete, diverging towards periphery. Lesions were seen as smaller dots within 1500 microns from fovea and were hyperfluorescent on autofluorescence. Palisading retinal pigment epithelium defects were seen in posterior pole on fundus fluorescein angiography imaging; irregular hyper fluorescence was also noted. One case had reduced cone responses on full field electroretinogram; the other three cases had normal electroretinogram. On optical coherence tomography, level of lesions varied from retinal pigment epithelium, inner segment to outer segment extending till external limiting membrane.

Conclusion:

Functional and structural deficits in benign fleck retina were picked up using multimodal imaging.