bluuebunny/crossref_metadata_2025 huggingface dataset:
Visual processing of connected and unconnected letters and words in Arabic
Authors: Ganayim Deia
Published: February 2016

A letter-reading task (Experiments 1) and a word-reading task of regular words (Experiments 2) and of visually distorted words (Experiments 3) were used to examine the reciprocal interaction between phonological encoding strategies and visual factors, such as the global word shape, local letters shape, and inter-letter spacing. Our participants comprised Arabic readers familiar with different letter and word forms (connected vs. unconnected: without inter-letter spaces vs. with inter-letter spaces). In addition, this study is the first instance of the word length effect being studied in an Arabic context using different word lengths (3 vs. 5 letters). The average reading times for Arabic words are affected by the word connectivity, since the average reading time is shorter for connected than unconnected words of all word lengths (3 and 5 letters) reflecting the activation of lexical route, which processes letters in letter strings in parallel. As well, the average reading times for Arabic words are affected by the word length, since the average reading time is shorter for 3-letter words than 5-letter words reflecting the activation of non-lexical route, which processes letters in letter strings sequentially. Length effect is the signature of the non-lexical route due to its seriality caused by assembled phonology.
Thinking-for-translating
Authors: Cifuentes Férez Paula
Published: February 2016

The present paper examines the acquisition of English physical motion constructions by Spanish translators in training. Drawing from Talmy’s (1985, 1991, 2000) typological framework for motion event descriptions and Slobin’s (1996, 2003) thinking-for-speaking hypothesis, the main aim of this research is to study whether the acquisition of English lexicalization patterns by Spanish translators in training could be facilitated by instructing them to think-for-translating into English. To this end, first, participants in the experimental and control group were told to translate some narrative fragments from Spanish into English. Then, once they completed the task, participants in the experimental group were instructed on the typological differences between English and Spanish with regard to the domain of physical motion and on how to render typical Spanish motion descriptions into English motion constructions. Finally, after a one week delay they were told to translate new fragments from Spanish into English. We observed that participants in the experimental group produced a higher number of manner verbs plus path expressions than the control group which, in turn, favoured the use of non-manner verbs plus path expressions. The results show that, overall, instruction contributes to better performance in the production of satellite-framed constructions but translators in training still have problems with the use of satellites and prepositional phrases.
Legal metaphors in translation
Authors: Vegara Fabregat Laura
Published: February 2016

There is wide literature on metaphor and legal language (e.g., Henly 1987; Twardzisz 2008, amongst many others). Certainly, metaphor is a part of legal language (Alcaraz and Hughes 2002: 43), but not just an ornamental part. Metaphors may play a very important role in legal texts, a cognitive role. They can convey intricate legal notions and may also communicate certain opinions and perspectives (Dickerson 1996: 374; Joo 2002: 23). Another interesting aspect connected with metaphors in the language of law is translation. We must bear in mind that legal translation has its own special difficulties, such as complex terminology and usually two very dissimilar legal systems as background (Soriano 2002: 53; Gémar 2002: 167). Metaphorical expressions constitute an additional hindrance for legal translators since they transfer a metaphorical image together with a legal concept. In the present study we aim at analysing some metaphorical expressions found in the United States Supreme Court opinions and their translation. We will focus on the scrutiny of some English–Spanish translation strategies in order to comment on the solutions adopted. Our hope is to shed some light on the field of legal translation regarding metaphors.
Thermal and mechanical stability of retained austenite in 1%C bearing steels with varying Si contents
Authors: Sourmail T. , Millot-Méheux M.
Published: February 2016

The present study is concerned with thermal and mechanical stability of retained austenite (RA) obtained in high-carbon, high-silicon steels after quenching and tempering. Through the investigation of three different alloy compositions with Si content of ∼0.3, 0.6 and 1.2 wt-%, it is shown that increasing silicon dramatically increases thermal stability. Compression tests on quenched and tempered specimens indicate that RA was also mechanically more stable when present in higher silicon steels.

This paper is part of a Themed Issue on Recent developments in bearing steels.
Effects of alloy 718 microstructure on hydrogen embrittlement susceptibility for oil and gas environments
Authors: Kagay B. , Findley K. , Coryell S. , Nissan A. B.
Published: February 2016

The effects of alloy 718 microstructure on hydrogen embrittlement susceptibility and tensile fracture mode were assessed through slow strain rate tensile testing and fracture surface analysis. Alloy 718 was annealed and aged to produce microstructures with variations in grain size and amount of grain boundary precipitates. Furthermore, the different ageing conditions likely resulted in differences in volume fractions and sizes of γ′ and γ′′ precipitates. The extent of grain boundary precipitation had the strongest effect on hydrogen embrittlement susceptibility, while grain size did not have any significant effect. Hydrogen embrittlement susceptibility was also correlated with differences in strength level, which was primarily controlled by the γ′ and γ′′ precipitate populations.
Force response characteristics and mechanical properties of friction stir welded AA2024 sheets
Authors: Ji L. , Zuo D. W. , Wang M.
Published: February 2016

Process force and tensile properties in friction stir welding of AA2024 sheets were studied. Results show that the forces present a periodic variation with the same periodicity which is nearly equal to the time of one tool rotation, and thus it only depends on rotation speed. With increasing welding speed the forces increase gradually, while with increasing rotation speed the forces first decrease and then increase. Joints with superior strength-ductility synergy are produced at 900 rev min−1–300 mm min−1 and 1000 rev min−1–350 mm min−1. These joints experience nearly the same peak temperature and axial force. As heat input increases the failure initiates from the interface between nugget zone (NZ) and thermo-mechanically affected zone to heat-affected zone continuing to NZ.
Physical and functional interaction between the α- and γ-secretases: A new model of regulated intramembrane proteolysis
Authors: Chen Allen C. , Kim Sumin , Shepardson Nina , Patel Sarvagna , Hong Soyon , Selkoe Dennis J.
Published: February 2016

Many single-transmembrane proteins are sequentially cleaved by ectodomain-shedding α-secretases and the γ-secretase complex, a process called regulated intramembrane proteolysis (RIP). These cleavages are thought to be spatially and temporally separate. In contrast, we provide evidence for a hitherto unrecognized multiprotease complex containing both α- and γ-secretase. ADAM10 (A10), the principal neuronal α-secretase, interacted and cofractionated with γ-secretase endogenously in cells and mouse brain. A10 immunoprecipitation yielded γ-secretase proteolytic activity and vice versa. In agreement, superresolution microscopy showed that portions of A10 and γ-secretase colocalize. Moreover, multiple γ-secretase inhibitors significantly increased α-secretase processing (r = −0.86) and decreased β-secretase processing of β-amyloid precursor protein. Select members of the tetraspanin web were important both in the association between A10 and γ-secretase and the γ→α feedback mechanism. Portions of endogenous BACE1 coimmunoprecipitated with γ-secretase but not A10, suggesting that β- and α-secretases can form distinct complexes with γ-secretase. Thus, cells possess large multiprotease complexes capable of sequentially and efficiently processing transmembrane substrates through a spatially coordinated RIP mechanism.
In vivo single-particle imaging of nuclear mRNA export in budding yeast demonstrates an essential role for Mex67p
Authors: Smith Carlas , Lari Azra , Derrer Carina Patrizia , Ouwehand Anette , Rossouw Ammeret , Huisman Maximiliaan , Dange Thomas , Hopman Mark , Joseph Aviva , Zenklusen Daniel , Weis Karsten , Grunwald David , Montpetit Ben
Published: February 2016

Many messenger RNA export proteins have been identified; yet the spatial and temporal activities of these proteins and how they determine directionality of messenger ribonucleoprotein (mRNP) complex export from the nucleus remain largely undefined. Here, the bacteriophage PP7 RNA-labeling system was used in Saccharomyces cerevisiae to follow single-particle mRNP export events with high spatial precision and temporal resolution. These data reveal that mRNP export, consisting of nuclear docking, transport, and cytoplasmic release from a nuclear pore complex (NPC), is fast (∼200 ms) and that upon arrival in the cytoplasm, mRNPs are frequently confined near the nuclear envelope. Mex67p functions as the principal mRNP export receptor in budding yeast. In a mex67-5 mutant, delayed cytoplasmic release from NPCs and retrograde transport of mRNPs was observed. This proves an essential role for Mex67p in cytoplasmic mRNP release and directionality of transport.
MRN, CtIP, and BRCA1 mediate repair of topoisomerase II–DNA adducts
Authors: Aparicio Tomas , Baer Richard , Gottesman Max , Gautier Jean
Published: February 2016

Repair of DNA double-strand breaks (DSBs) with complex ends poses a special challenge, as additional processing is required before DNA ligation. For example, protein–DNA adducts must be removed to allow repair by either nonhomologous end joining or homology-directed repair. Here, we investigated the processing of topoisomerase II (Top2)–DNA adducts induced by treatment with the chemotherapeutic agent etoposide. Through biochemical analysis in Xenopus laevis egg extracts, we establish that the MRN (Mre11, Rad50, and Nbs1) complex, CtIP, and BRCA1 are required for both the removal of Top2–DNA adducts and the subsequent resection of Top2-adducted DSB ends. Moreover, the interaction between CtIP and BRCA1, although dispensable for resection of endonuclease-generated DSB ends, is required for resection of Top2-adducted DSBs, as well as for cellular resistance to etoposide during genomic DNA replication.
Lipid raft–dependent plasma membrane repair interferes with the activation of B lymphocytes
Authors: Miller Heather , Castro-Gomes Thiago , Corrotte Matthias , Tam Christina , Maugel Timothy K. , Andrews Norma W. , Song Wenxia
Published: February 2016

Cells rapidly repair plasma membrane (PM) damage by a process requiring Ca2+-dependent lysosome exocytosis. Acid sphingomyelinase (ASM) released from lysosomes induces endocytosis of injured membrane through caveolae, membrane invaginations from lipid rafts. How B lymphocytes, lacking any known form of caveolin, repair membrane injury is unknown. Here we show that B lymphocytes repair PM wounds in a Ca2+-dependent manner. Wounding induces lysosome exocytosis and endocytosis of dextran and the raft-binding cholera toxin subunit B (CTB). Resealing is reduced by ASM inhibitors and ASM deficiency and enhanced or restored by extracellular exposure to sphingomyelinase. B cell activation via B cell receptors (BCRs), a process requiring lipid rafts, interferes with PM repair. Conversely, wounding inhibits BCR signaling and internalization by disrupting BCR–lipid raft coclustering and by inducing the endocytosis of raft-bound CTB separately from BCR into tubular invaginations. Thus, PM repair and B cell activation interfere with one another because of competition for lipid rafts, revealing how frequent membrane injury and repair can impair B lymphocyte–mediated immune responses.
P-cadherin promotes collective cell migration via a Cdc42-mediated increase in mechanical forces
Authors: Plutoni Cédric , Bazellieres Elsa , Le Borgne-Rochet Maïlys , Comunale Franck , Brugues Agusti , Séveno Martial , Planchon Damien , Thuault Sylvie , Morin Nathalie , Bodin Stéphane , Trepat Xavier , Gauthier-Rouvière Cécile
Published: February 2016

Collective cell migration (CCM) is essential for organism development, wound healing, and metastatic transition, the primary cause of cancer-related death, and it involves cell–cell adhesion molecules of the cadherin family. Increased P-cadherin expression levels are correlated with tumor aggressiveness in carcinoma and aggressive sarcoma; however, how P-cadherin promotes tumor malignancy remains unknown. Here, using integrated cell biology and biophysical approaches, we determined that P-cadherin specifically induces polarization and CCM through an increase in the strength and anisotropy of mechanical forces. We show that this mechanical regulation is mediated by the P-cadherin/β-PIX/Cdc42 axis; P-cadherin specifically activates Cdc42 through β-PIX, which is specifically recruited at cell–cell contacts upon CCM. This mechanism of cell polarization and migration is absent in cells expressing E- or R-cadherin. Thus, we identify a specific role of P-cadherin through β-PIX–mediated Cdc42 activation in the regulation of cell polarity and force anisotropy that drives CCM.
Biophysical changes reduce energetic demand in growth factor–deprived lymphocytes
Authors: Hecht Vivian C. , Sullivan Lucas B. , Kimmerling Robert J. , Kim Dong-Hwee , Hosios Aaron M. , Stockslager Max A. , Stevens Mark M. , Kang Joon Ho , Wirtz Denis , Vander Heiden Matthew G. , Manalis Scott R.
Published: February 2016

Cytokine regulation of lymphocyte growth and proliferation is essential for matching nutrient consumption with cell state. Here, we examine how cellular biophysical changes that occur immediately after growth factor depletion promote adaptation to reduced nutrient uptake. After growth factor withdrawal, nutrient uptake decreases, leading to apoptosis. Bcl-xL expression prevents cell death, with autophagy facilitating long-term cell survival. However, autophagy induction is slow relative to the reduction of nutrient uptake, suggesting that cells must engage additional adaptive mechanisms to respond initially to growth factor depletion. We describe an acute biophysical response to growth factor withdrawal, characterized by a simultaneous decrease in cell volume and increase in cell density, which occurs before autophagy initiation and is observed in both FL5.12 Bcl-xL cells depleted of IL-3 and primary CD8+ T cells depleted of IL-2 that are differentiating toward memory cells. The response reduces cell surface area to minimize energy expenditure while conserving biomass, suggesting that the biophysical properties of cells can be regulated to promote survival under conditions of nutrient stress.
Loss of OMA1 delays neurodegeneration by preventing stress-induced OPA1 processing in mitochondria
Authors: Korwitz Anne , Merkwirth Carsten , Richter-Dennerlein Ricarda , Tröder Simon E. , Sprenger Hans-Georg , Quirós Pedro M. , López-Otín Carlos , Rugarli Elena I. , Langer Thomas
Published: February 2016

Proteolytic cleavage of the dynamin-like guanosine triphosphatase OPA1 in mitochondria is emerging as a central regulatory hub that determines mitochondrial morphology under stress and in disease. Stress-induced OPA1 processing by OMA1 triggersmitochondrial fragmentation, which is associated with mitophagy and apoptosis in vitro. Here, we identify OMA1 as a critical regulator of neuronal survival in vivo and demonstrate that stress-induced OPA1 processing by OMA1 promotes neuronal death and neuroinflammatory responses. Using mice lacking prohibitin membrane scaffolds as a model of neurodegeneration, we demonstrate that additional ablation of Oma1 delays neuronal loss and prolongs lifespan. This is accompanied by the accumulation of fusion-active, long OPA1 forms, which stabilize the mitochondrial genome but do not preserve mitochondrial cristae or respiratory chain supercomplex assembly in prohibitin-depleted neurons. Thus, long OPA1 forms can promote neuronal survival independently of cristae shape, whereas stress-induced OMA1 activation and OPA1 cleavage limit mitochondrial fusion and promote neuronal death.
Collective cell migration in development
Authors: Scarpa Elena , Mayor Roberto
Published: February 2016

During embryonic development, tissues undergo major rearrangements that lead to germ layer positioning, patterning, and organ morphogenesis. Often these morphogenetic movements are accomplished by the coordinated and cooperative migration of the constituent cells, referred to as collective cell migration. The molecular and biomechanical mechanisms underlying collective migration of developing tissues have been investigated in a variety of models, including border cell migration, tracheal branching, blood vessel sprouting, and the migration of the lateral line primordium, neural crest cells, or head mesendoderm. Here we review recent advances in understanding collective migration in these developmental models, focusing on the interaction between cells and guidance cues presented by the microenvironment and on the role of cell–cell adhesion in mechanical and behavioral coupling of cells within the collective.
Breaking down to build up: Neuroligin’s C-terminal domain strengthens the synapse
Authors: Newell-Litwa Karen A.
Published: February 2016

The mechanisms by which neuroligin adhesion molecules modulate synaptic plasticity remain unclear. In this issue, Liu et al. (2016. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201509023) demonstrate that neuroligin 1 promotes actin assembly associated with synaptic strengthening independent of adhesion, suggesting additional ways for neuroligins to contribute to neuronal development and disease pathology.
Making sure late endosomes are on time
Authors: Leslie Mitch
Published: February 2016

Researchers discover two proteins that help maturing endosomes shed phosphatidylinositide.
Majority Digraphs
Authors: Lai Tri , Endrullis Jörg , Moss Lawrence S.
Published: February 2016

A majority digraph is a finite simple digraph

G
=
(
V
,
→
)

G=(V,\to )

such that there exist finite sets

A
v

A_v

for the vertices

v
∈
V

v\in V

with the following property:

u
→
v

u\to v

if and only if “more than half of the

A
u

A_u

are

A
v

A_v

”. That is,

u
→
v

u\to v

if and only if

|

A
u

∩

A
v

|

>

1
2

⋅

|

A
u

|

|A_u \cap A_v | > \frac {1}{2} \cdot |A_u|

. We characterize the majority digraphs as the digraphs with the property that every directed cycle has a reversal. If we change

1
2

\frac {1}{2}

to any real number

α
∈
(
0
,
1
)

\alpha \in (0,1)

, we obtain the same class of digraphs. We apply the characterization result to obtain a result on the logic of assertions “most

X
X

are

Y
Y

” and the standard connectives of propositional logic.
Completely bounded Λ_{𝑝} sets that are not Sidon
Authors: Hare Kathryn , Mohanty Parasar
Published: February 2016

In this paper we construct examples of completely bounded

Λ
p

\Lambda _p

sets, which are not Sidon, on any compact abelian group. As a consequence, we have a new proof of the classical result for the existence of non-Sidon,

Λ
p

\Lambda _p

sets on any compact abelian group.
Minimal sets for group actions on dendrites
Authors: Marzougui Habib , Naghmouchi Issam
Published: February 2016

Let

G
G

be a group acting by homeomorphisms on a dendrite

X
X

. First, we show that any minimal set

M
M

of

G
G

is either a finite orbit or a Cantor set (resp. a finite orbit) when the set of endpoints of

X
X

is closed (resp. countable). Furthermore, we prove, regardless of the type of the dendrite

X
X

, that if the action of

G
G

on

X
X

has at least two minimal sets, then necessarily it has a finite orbit (and even an orbit consisting of one or two points). Second, we explore the topological and geometrical properties of infinite minimal sets when the action of

G
G

has a finite orbit. We show in this case that any infinite minimal set

M
M

is a Cantor set which is the set of endpoints of its convex hull

[
M
]

[M]

and there is no other infinite minimal set in

[
M
]

[M]

. On the other hand, we consider the family

M

\mathcal {M}

of all minimal sets in the hyperspace

2

X

2^{X}

(endowed with the Hausdorff metric). We prove that

M

\mathcal {M}

is closed in

2

X

2^{X}

and that the family

F

\mathcal {F}

of all finite orbits (when it is non-empty) is dense in

M

\mathcal {M}

. As a consequence, the union of all minimal sets of

G
G

is closed in

X
X

.
Classification of trisections and the Generalized Property R Conjecture
Authors: Meier Jeffrey , Schirmer Trent , Zupan Alexander
Published: February 2016

We show that the members of a large class of unbalanced four-manifold trisections are standard, and we present a family of trisections that is likely to include non-standard trisections of the four-sphere. As an application, we prove a stable version of the Generalized Property R Conjecture for

c
c

–component links with tunnel number at most

c
c

.
Notes on the subspace perturbation problem for off-diagonal perturbations
Authors: Seelmann Albrecht
Published: February 2016

The variation of spectral subspaces for linear self-adjoint operators under an additive bounded off-diagonal perturbation is studied. To this end, the optimization approach for general perturbations in [J. Anal. Math., to appear; arXiv:1310.4360 (2013)] is adapted. It is shown that, in contrast to the case of general perturbations, the corresponding optimization problem cannot be reduced to a finite-dimensional problem. A suitable choice of the involved parameters provides an upper bound for the solution of the optimization problem. In particular, this yields a rotation bound on the subspaces that is stronger than the previously known one from [J. Reine Angew. Math. 708 (2015), 1-15].
Host trait combinations drive abundance and canopy distribution of atmospheric bromeliad assemblages
Authors: Chaves Cleber Juliano Neves , Dyonisio Júlio César , Rossatto Davi Rodrigo
Published: February 2016

Epiphytes are strongly dependent on the conditions created by their host's traits and a certain degree of specificity is expected between them, even if these species are largely abundant in a series of tree hosts of a given environment, as in the case of atmospheric bromeliads. Despite their considerable abundance in these environments, we hypothesize that stochasticity alone cannot explain the presence and abundance of atmospheric bromeliads on host trees, since host traits could have a greater influence on the establishment of these bromeliads. We used secondary and reforested seasonal forests and three distinct silvicultures to test whether species richness, phylogenetic diversity and functional diversity of trees can predict the differential presence, abundance and distribution of atmospheric bromeliads on hosts. We compared the observed parameters of their assemblage with null models and performed successive variance hierarchic partitions of abundance and distribution of the assemblage to detect the influence of multiple traits of the tree hosts. Our results do not indicate direct relationships between the abundance of atmospheric bromeliads and phylogenetic or functional diversity of trees, but instead indicate that bromeliads occurred on fewer tree species than expected by chance. We distinguished functional tree patterns that can improve or reduce the abundance of atmospheric bromeliads, and change their distribution on branches and trunk. While individual tree traits are related to increased abundance, species traits are related to the canopy distribution of atmospheric bromeliad assemblages. A balance among these tree functional patterns drives the atmospheric bromeliad assemblage of the forest patches.
SMART on FHIR: a standards-based, interoperable apps platform for electronic health records
Authors: Mandel Joshua C , Kreda David A , Mandl Kenneth D , Kohane Isaac S , Ramoni Rachel B
Published: February 2016

Objective In early 2010, Harvard Medical School and Boston Children’s Hospital began an interoperability project with the distinctive goal of developing a platform to enable medical applications to be written once and run unmodified across different healthcare IT systems. The project was called Substitutable Medical Applications and Reusable Technologies (SMART).

Methods We adopted contemporary web standards for application programming interface transport, authorization, and user interface, and standard medical terminologies for coded data. In our initial design, we created our own openly licensed clinical data models to enforce consistency and simplicity. During the second half of 2013, we updated SMART to take advantage of the clinical data models and the application-programming interface described in a new, openly licensed Health Level Seven draft standard called Fast Health Interoperability Resources (FHIR). Signaling our adoption of the emerging FHIR standard, we called the new platform SMART on FHIR.

Results We introduced the SMART on FHIR platform with a demonstration that included several commercial healthcare IT vendors and app developers showcasing prototypes at the Health Information Management Systems Society conference in February 2014. This established the feasibility of SMART on FHIR, while highlighting the need for commonly accepted pragmatic constraints on the base FHIR specification.

Conclusion In this paper, we describe the creation of SMART on FHIR, relate the experience of the vendors and developers who built SMART on FHIR prototypes, and discuss some challenges in going from early industry prototyping to industry-wide production use.
Effects of an e-Prescribing interface redesign on rates of generic drug prescribing: exploiting default options
Authors: Malhotra Sameer , Cheriff Adam D , Gossey J Travis , Cole Curtis L , Kaushal Rainu , Ancker Jessica S
Published: February 2016

Objective Increasing the use of generic medications could help control medical costs. However, educational interventions have limited impact on prescriber behavior, and e-prescribing alerts are associated with high override rates and alert fatigue. Our objective was to evaluate the effect of a less intrusive intervention, a redesign of an e-prescribing interface that provides default options intended to “nudge” prescribers towards prescribing generic drugs.

Methods This retrospective cohort study in an academic ambulatory multispecialty practice assessed the effects of customizing an e-prescribing interface to substitute generic equivalents for brand-name medications during order entry and allow a one-click override to order the brand-name medication.

Results Among drugs with generic equivalents, the proportion of generic drugs prescribed more than doubled after the interface redesign, rising abruptly from 39.7% to 95.9% (a 56.2% increase; 95% confidence interval, 56.0–56.4%; P  < .001). Before the redesign, generic drug prescribing rates varied by therapeutic class, with rates as low as 8.6% for genitourinary products and 15.7% for neuromuscular drugs. After the redesign, generic drug prescribing rates for all but four therapeutic classes were above 90%: endocrine drugs, neuromuscular drugs, nutritional products, and miscellaneous products.

Discussion Changing the default option in an e-prescribing interface in an ambulatory care setting was followed by large and sustained increases in the proportion of generic drugs prescribed at the practice.

Conclusions Default options in health information technology exert a powerful effect on user behavior, an effect that can be leveraged to optimize decision making.
Automated identification and predictive tools to help identify high-risk heart failure patients: pilot evaluation
Authors: Evans R Scott , Benuzillo Jose , Horne Benjamin D , Lloyd James F , Bradshaw Alejandra , Budge Deborah , Rasmusson Kismet D , Roberts Colleen , Buckway Jason , Geer Norma , Garrett Teresa , Lappé Donald L
Published: February 2016

Objective Develop and evaluate an automated identification and predictive risk report for hospitalized heart failure (HF) patients.

Methods Dictated free-text reports from the previous 24 h were analyzed each day with natural language processing (NLP), to help improve the early identification of hospitalized patients with HF. A second application that uses an Intermountain Healthcare-developed predictive score to determine each HF patient’s risk for 30-day hospital readmission and 30-day mortality was also developed. That information was included in an identification and predictive risk report, which was evaluated at a 354-bed hospital that treats high-risk HF patients.

Results The addition of NLP-identified HF patients increased the identification score’s sensitivity from 82.6% to 95.3% and its specificity from 82.7% to 97.5%, and the model’s positive predictive value is 97.45%. Daily multidisciplinary discharge planning meetings are now based on the information provided by the HF identification and predictive report, and clinician’s review of potential HF admissions takes less time compared to the previously used manual methodology (10 vs 40 min). An evaluation of the use of the HF predictive report identified a significant reduction in 30-day mortality and a significant increase in patient discharges to home care instead of to a specialized nursing facility.

Conclusions Using clinical decision support to help identify HF patients and automatically calculating their 30-day all-cause readmission and 30-day mortality risks, coupled with a multidisciplinary care process pathway, was found to be an effective process to improve HF patient identification, significantly reduce 30-day mortality, and significantly increase patient discharges to home care.
A method for modeling co-occurrence propensity of clinical codes with application to ICD-10-PCS auto-coding
Authors: Subotin Michael , Davis Anthony R
Published: February 2016

Objective Natural language processing methods for medical auto-coding, or automatic generation of medical billing codes from electronic health records, generally assign each code independently of the others. They may thus assign codes for closely related procedures or diagnoses to the same document, even when they do not tend to occur together in practice, simply because the right choice can be difficult to infer from the clinical narrative.

Methods We propose a method that injects awareness of the propensities for code co-occurrence into this process. First, a model is trained to estimate the conditional probability that one code is assigned by a human coder, given than another code is known to have been assigned to the same document. Then, at runtime, an iterative algorithm is used to apply this model to the output of an existing statistical auto-coder to modify the confidence scores of the codes.

Results We tested this method in combination with a primary auto-coder for International Statistical Classification of Diseases-10 procedure codes, achieving a 12% relative improvement in F -score over the primary auto-coder baseline. The proposed method can be used, with appropriate features, in combination with any auto-coder that generates codes with different levels of confidence.

Conclusions The promising results obtained for International Statistical Classification of Diseases-10 procedure codes suggest that the proposed method may have wider applications in auto-coding.
The Association Between Chronic Pain and Cardiac Disease
Authors: Fayaz Alan , Watt Hilary C. , Langford Richard M. , Donaldson Liam J.
Published: February 2016

Objectives:

Chronic pain may increase the risk of cardiac disease, but the extent to which confounding variables account for this association has yet to be satisfactorily established. This study aims to examine the possibility of an independent association between these 2 variables.

Methods:

We applied logistic regression analysis to data from 8596 adults surveyed in a population study of the health of the population of England. The association between cardiac disease (angina and/or myocardial infarction) and chronic pain (pain lasting >3 months) was explored, taking account of 10 potentially confounding variables including the regular use of nonsteroidal anti-inflammatory drugs.

Results:

Participants reporting chronic pain (n=3023) were more likely to experience cardiac disease than those without pain: odds ratio (OR), 1.55; 95% confidence interval (CI), 1.15-2.07. Subsets of participants fulfilling various criteria for high-intensity chronic pain demonstrated stronger associations with cardiac disease suggesting a “dose-response” element to the relationship: chronic widespread pain (OR, 3.3; 95% CI, 1.42-7.68); higher-disability chronic pain (OR, 2.35; 95% CI, 1.71-3.23); and higher average chronic pain score (OR, 1.95; 95% CI, 1.40-2.71). Adjustment for regular prescription of nonsteroidal anti-inflammatory drugs did not reduce the association of chronic pain with cardiac disease.

Discussion:

Patients reporting chronic pain, in particular those most severely affected, may be at significantly increased risk of cardiac disease. Future studies should focus on determining whether reducing the impact of chronic pain can improve cardiac health.
Multiple Levels of Suffering
Authors: Mathur Vani A. , Kiley Kasey B. , Haywood Carlton , Bediako Shawn M. , Lanzkron Sophie , Carroll C. Patrick , Buenaver Luis F. , Pejsa Megan , Edwards Robert R. , Haythornthwaite Jennifer A. , Campbell Claudia M.
Published: February 2016

Objective:

People living with sickle cell disease (SCD) experience severe episodic and chronic pain and frequently report poor interpersonal treatment within health-care settings. In this particularly relevant context, we examined the relationship between perceived discrimination and both clinical and laboratory pain.

Methods:

Seventy-one individuals with SCD provided self-reports of experiences with discrimination in health-care settings and clinical pain severity, and completed a psychophysical pain testing battery in the laboratory.

Results:

Discrimination in health-care settings was correlated with greater clinical pain severity and enhanced sensitivity to multiple laboratory-induced pain measures, as well as stress, depression, and sleep. After controlling for relevant covariates, discrimination remained a significant predictor of mechanical temporal summation (a marker of central pain facilitation), but not clinical pain severity or suprathreshold heat pain response. Furthermore, a significant interaction between experience with discrimination and clinical pain severity was associated with mechanical temporal summation; increased experience with discrimination was associated with an increased correlation between clinical pain severity and temporal summation of pain.

Discussion:

Perceived discrimination within health-care settings was associated with pain facilitation. These findings suggest that discrimination may be related to increased central sensitization among SCD patients, and more broadly that health-care social environments may interact with pain pathophysiology.
Transhydrogenase and growth substrate influence lipid hydrogen isotope ratios inDesulfovibrio alaskensis G20
Authors: Leavitt William D. , Flynn Theodore M , Suess Melanie K , Bradley Alexander S
Published: February 2016

Microbial fatty acids preserve metabolic and environmental information in their hydrogen isotope ratios (2H/1H). This ratio is influenced by parameters that include the 2H/1H of water in the microbial growth environment, and biosynthetic fractionations between water and lipid. In some microbes, this biosynthetic fractionation has been shown to vary systematically with central energy metabolism, and controls on fatty acid2H/1H may be linked to the intracellular production of NADPH. We examined the apparent fractionation between media water and the fatty acids produced byDesulfovibrio alaskensisG20. Growth was in batch culture with malate as an electron donor for sulfate respiration, and with pyruvate and fumarate as substrates for fermentation and for sulfate respiration. A larger fractionation was observed as a consequence of respiratory or fermentative growth on pyruvate than growth on fumarate or malate. This difference correlates with opposite apparent flows of electrons through the electron bifurcating/confurcating transhydrogenase NfnAB. When grown on malate or fumarate, mutant strains ofD. alaskensis G20containing transposon disruptions in a copy ofnfnABshow different fractionations than the wild type strain. This phenotype is muted during fermentative growth on pyruvate, and it is absent when pyruvate is a substrate for sulfate reduction. All strains and conditions produced similar fatty acid profiles, and the2H/1H of individual lipids changed in concert with the mass-weighted average. Unsaturated fatty acids were generally depleted in2H relative to their saturated homologues, and anteiso- branched fatty acids were generally depleted in2H relative to straight-chain fatty acids. Fractionation correlated with growth rate, a pattern that has also been observed in the fractionation of sulfur isotopes during dissimilatory sulfate reduction by sulfate reducing bacteria.
16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife: the importance of cleaning post-sequencing data before estimating positivity, prevalence and co-infection
Authors: Galan Maxime , Razzauti Maria , Bard Emilie , Bernard Maria , Brouat Carine , Charbonnel Nathalie , Dehne-Garcia Alexandre , Loiseau Anne , Tatard Caroline , Tamisier Lucie , Vayssier-Taussat Muriel , Vignes Helene , Cosson Jean François
Published: February 2016

Human impact on natural habitats is increasing the complexity of human-wildlife interfaces and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. We investigated the potential for recent developments in 16S rRNA amplicon sequencing to facilitate the multiplexing of large numbers of samples needed to improve our understanding of the risk of zoonotic disease transmission posed by urban rodents in West Africa. In addition to listing pathogenic bacteria in wild populations, as in other high-throughput sequencing (HTS) studies, our approach can estimate essential parameters for studies of zoonotic risk, such as prevalence and patterns of coinfection within individual hosts. However, the estimation of these parameters requires cleaning of the raw data to mitigate the biases generated by HTS methods. We present here an extensive review of these biases and of their consequences, and we propose a comprehensive trimming strategy for managing these biases. We demonstrated the application of this strategy using 711 commensal rodents collected from 24 villages in Senegal, including 208Mus musculus domesticus, 189Rattus rattus, 93Mastomys natalensisand 221Mastomys erythroleucus.Seven major genera of pathogenic bacteria were detected in their spleens:Borrelia, Bartonella, Mycoplasma, Ehrlichia, Rickettsia, StreptobacillusandOrientia. The last five of these genera have never before been detected in West African rodents. Bacterial prevalence ranged from 0% to 90% of individuals per site, depending on the bacterial taxon, rodent species and site considered, and 26% of rodents displayed coinfection. The 16S rRNA amplicon sequencing strategy presented here has the advantage over other molecular surveillance tools of dealing with a large spectrum of bacterial pathogens without requiring assumptions about their presence in the samples. This approach is therefore particularly suitable for continuous pathogen surveillance in the context of disease monitoring programs.
Validation of a habitat suitability index for oyster restoration
Authors: Theuerkauf Seth J. , Lipcius Romuald N.
Published: February 2016

Habitat suitability index (HSI) models provide spatially explicit information on the capacity of a given habitat to support a species of interest, and their prevalence has increased dramatically in recent years. Despite caution that the reliability of HSIs must be validated using independent, quantitative data, most HSIs intended to inform terrestrial and marine species management remain unvalidated. Furthermore, of the eight HSI models developed for eastern oyster (Crassostrea virginica) restoration and fishery production, none has been validated. Consequently, we developed, calibrated, and validated an HSI for the eastern oyster to identify optimal habitat for restoration in a tributary of Chesapeake Bay, the Great Wicomico River (GWR). The GWR harbors an unparalleled, restored oyster population, and therefore serves as an excellent model system for assessing the validity of the HSI. The HSI was derived from GIS layers of bottom type, salinity, and water depth (surrogate for dissolved oxygen), and was tested using live adult oyster density data from a survey of high vertical relief reefs (HRR) and low vertical relief reefs (LRR) in the sanctuary network. Live adult oyster density was a statistically significant sigmoid function of the HSI, which validates the HSI as a robust predictor of suitable oyster reef habitat for rehabilitation or restoration. In addition, HRR had on average 103-116 more adults m-2than LRR at a given level of the HSI. For HRR, HSI values ≥0.3 exceeded the accepted restoration target of 50 live adult oysters m−2. For LRR, the HSI was generally able to predict live adult oyster densities that meet or exceed the target at HSI values ≥0.3. The HSI indicated that there remain large areas of suitable habitat for restoration in the GWR. This study provides a robust framework for HSI model development and validation, which can be refined and applied to other systems and previously developed HSIs to improve the efficacy of native oyster restoration.
Aging shapes the population-mean and ‐dispersion of gene expression in human brains
Authors: Brinkmeyer-Langford Candice L. , Guan Jinting , Ji Guoli , Cai James J.
Published: February 2016

Human aging is associated with cognitive decline and an increased risk of neurodegenerative disease. Our objective for this study was to evaluate potential relationships between age and variation in gene expression across different regions of the brain. We analyzed the Genotype-Tissue Expression (GTEx) data from 54 and 101 tissue samples across 13 brain regions in post-mortem donors of European descent aged between 20 and 70 years at death. After accounting for the effects of covariates and hidden confounding factors, we identified 1,446 protein-coding genes whose expression in one or more brain regions is correlated with chronological age at a false discovery rate of 5%. These genes are involved in various biological processes including apoptosis, mRNA splicing, amino acid biosynthesis, and neurotransmitter transport. The distribution of these genes among brain regions is uneven, suggesting variable regional responses to aging. We also found that the aging response of many genes, e.g.,TP37andC1QA, depends on individuals’ genotypic backgrounds. Finally, using dispersion-specific analysis, we identified genes such asIL7R,MS4A4E, andTERF1/TERF2whose expressions are differentially dispersed by aging, i.e., variances differ between age groups. Our results demonstrate that age-related gene expression is brain region-specific, genotype-dependent, and associated with both mean and dispersion changes. Our findings provide a foundation for more sophisticated gene expression modeling in the studies of age-related neurodegenerative diseases.
Cell Segmentation with Random Ferns and Graph-cuts
Authors: Browet A. , De Vleeschouwer C. , Jacques L. , Mathiah N. , Saykali B. , Migeotte I.
Published: February 2016

The progress in imaging techniques have allowed the study of various aspect of cellular mechanisms. To isolate individual cells in live imaging data, we introduce an elegant image segmentation framework that effectively extracts cell boundaries, even in the presence of poor edge details. Our approach works in two stages. First, we estimate pixel interior/border/exterior class probabilities using random ferns. Then, we use an energy minimization framework to compute boundaries whose localization is compliant with the pixel class probabilities. We validate our approach on a manually annotated dataset.
Analysis of reverse logistics implementation practices by South Australian construction organisations
Authors: Chileshe Nicholas , Rameezdeen Raufdeen , Hosseini M. Reza , Lehmann Steffen , Udeaja Chika
Published: February 2016

Purpose

– A large number of benefits have been reported when reverse logistics (RL) is fully implemented in the construction industry. However, RL is yet to become common place in the construction sector, particularly in Australia. The particular sub-sector in which RL operates is small and weak and the remainder of the sector must embrace and accommodate it comfortably. Research is lacking on how to promoting RL in the construction industry. Very little has been done to identify the current practices that have the potential to promote RL industry-wide. The purpose of this paper is to identify the practices that work well in the sector, a strategy could be mapped out to promote RL to all stakeholders.

Design/methodology/approach

– In order to fill the above gap, the present study used a mixed method approach to gather and evaluate current practices and their potential to promote RL in South Australia’s construction industry. Practices that were identified using a comprehensive literature review were evaluated with a questionnaire survey and series of interviews involving construction professionals.

Findings

– The findings are that practices facilitating deconstruction is the most important, followed by practices facilitating the use of salvaged materials in new construction to promote RL in South Australia. Awareness of deconstruction benefits, challenges and procedures at the organisation level and facilities and services at industry level were associated with RL implementation. Availability of salvaged materials in the market was found to influence its use in new construction and as a consequence its demand. Designing for reverse logistics is another practice that could facilitate deconstruction and the onus of its promotion lies mainly with the designers.

Research limitations/implications

– This research was confined to one state in Australia. As such the generalisation to other states and other countries should be treated cautiously.

Practical implications

– The findings of this study can help inform the industry and its stakeholders on areas that they need to concentrate more on to make the South Australian construction industry a fully RL integrated one. To that end the authors propose some recommendations arising from the findings reported here.

Originality/value

– This study makes a contribution to the body of knowledge on reserve logistics within a previously unexplored South Australian context. In addition, the study provides valuable insights into the contribution of RL practices to the construction industry.