bluuebunny/crossref_metadata_2025 huggingface dataset:
Adipogenesis and epicardial adipose tissue: A novel fate of the epicardium induced by mesenchymal transformation and PPARγ activation
Authors: Yamaguchi Yukiko , Cavallero Susana , Patterson Michaela , Shen Hua , Xu Jian , Kumar S. Ram , Sucov Henry M.
Published: February 2015

Significance

A layer of fat surrounds the heart in most mammals, including humans. The biology of this tissue has been speculated for centuries, but never subjected to experimental analysis because common experimental model species are thought to not have this tissue. In this study, we show that rodents have cardiac fat, albeit in a very specific location in the heart. We implicate the origin of this tissue from the epicardium (the outer epithelium of the heart) and the underlying mechanisms that account for its derivation. By comparing human and mouse epicardial cells, we provide an explanation for the prominent species differences in the presence and amount of cardiac adipose tissue.
Adverse childhood experiences and physiological wear-and-tear in midlife: Findings from the 1958 British birth cohort
Authors: Barboza Solís Cristina , Kelly-Irving Michelle , Fantin Romain , Darnaudéry Muriel , Torrisani Jérôme , Lang Thierry , Delpierre Cyrille
Published: February 2015

Significance

The role of early life experiences on health is of major concern to research. Recent studies have shown that chronic stress may “get under the skin” to alter human developmental processes and impact later health. Our findings suggest that early negative circumstances during childhood, collected prospectively in a British birth cohort, could be associated with physiological wear-and-tear in midlife as measured by allostatic load. This relationship was largely explained by health behaviors, body mass index, and socioeconomic status in adulthood, but not entirely. These results suggest that a biological link between adverse childhood exposures and adult health may be plausible. Our findings contribute to the development of more adapted public health interventions, both at a societal and individual level.
NADPH oxidase 4 is a critical mediator in Ataxia telangiectasia disease
Authors: Weyemi Urbain , Redon Christophe E. , Aziz Towqir , Choudhuri Rohini , Maeda Daisuke , Parekh Palak R. , Bonner Michael Y. , Arbiser Jack L. , Bonner William M.
Published: February 2015

Significance

Ataxia telangiectasia (A-T) is a rare, autosomal recessive disorder characterized by progressive cerebellar degeneration. Oxidative stress is one cause of the symptoms of A-T disease. We report that inactivation of NADPH oxidase 4 (NOX4) reduced ROS, oxidative DNA damage, DNA double-strand breaks and replicative senescence in A-T primary cells. Analyses of A-T patients revealed elevated levels of NOX4 in the cerebellum that also correlated with increased levels of DNA damage and apoptosis. These observations were substantiated by the absence of abnormal NOX4 cerebellar expression in mouse models of A-T disease which do not display cerebellar degeneration. However, injecting A-T mice with NOX4 inhibitor decreased their elevated cancer incidence. Therefore, NOX4 appears as a critical mediator in A-T disease.
Absence of knots in known RNA structures
Authors: Micheletti Cristian , Di Stefano Marco , Orland Henri
Published: February 2015

Significance

Biopolymers have arguably evolved to be free of entanglements that could impair their folding or function. This selection mechanism is, however, opposed by the general physical principle that sufficiently long and densely packed polymers are inevitably entangled. This competition is nowadays well-documented for proteins and viral DNA, which can be knotted and yet, functionally viable. By contrast, the incidence of knots in RNA is still virtually unexplored. To fill this gap, we topologically profiled thousands of RNA structures, finding only three deeply knotted chains. Comparison with higher-resolution homologs further suggests that these instances may actually be unknotted as well. The practical absence of knots indicates that thermodynamic or kinetic mechanisms are likely at play for minimizing the entanglement of biologically viable structured RNAs.
The spontaneous emergence of conventions: An experimental study of cultural evolution
Authors: Centola Damon , Baronchelli Andrea
Published: February 2015

Significance

Social conventions shape every aspect of our lives, from how we greet each other to the languages we speak. Yet their origins have been a topic of theoretical speculation since the time of Aristotle. Most approaches assume that institutions are necessary to organize large populations, but the simplest explanation is that universally accepted conventions are the unintended consequence of individuals’ efforts to coordinate locally with one another. Although this hypothesis is compelling, it lacks conclusive empirical support. Here, we present results from controlled experiments demonstrating that changes in network connectivity can cause global social conventions to spontaneously emerge from local interactions, even though people have no knowledge about the population, or that they are coordinating at a global scale.
Rate of language evolution is affected by population size
Authors: Bromham Lindell , Hua Xia , Fitzpatrick Thomas G. , Greenhill Simon J.
Published: February 2015

Significance

Evolutionary methods are increasingly being applied to investigating linguistic change. But does language change conform to the predictions of evolutionary theory? Here, we use data from closely related pairs of languages to show that a key prediction of evolutionary theory is met: rates of gain of new words are higher in larger populations whereas rates of word loss are greater in small populations. Our analysis provides, to our knowledge, the first statistically robust evidence of an influence of population size on rate of language change. These results demonstrate the potential for demographic factors to influence language evolution.
Magnetic nanopantograph in the SrCu
2
(BO
3
)
2
Shastry–Sutherland lattice
Authors: Radtke Guillaume , Saúl Andrés , Dabkowska Hanna A. , Salamon Myron B. , Jaime Marcelo
Published: February 2015

Significance

The spins of the unpaired electrons in a solid tend to align along an applied magnetic field. In the case of antiferromagnetic materials having competing interactions (frustration) it is common to observe that the magnetization increases, exhibiting complicated structures with discrete jumps and plateaus. SrCu
2
(BO
3
)
2
is one of these materials, for which we find experimentally that its macroscopic physical dimensions also change with the magnetic field, mimicking the behavior in the magnetization. Using quantum mechanics, we show quantitatively that due to the orthogonal arrangement of the magnetic Cu
2+
dimers acting as pantographs, minute deformations allow significant reduction in the effective interactions responsible for the antiferromagnetism. This drop is sufficient to compensate the elastic energy loss in the lattice deformation.
Dynamic phototuning of 3D hydrogel stiffness
Authors: Stowers Ryan S. , Allen Shane C. , Suggs Laura J.
Published: February 2015

Significance

Extracellular matrix (ECM) stiffness is an influential factor in many biological processes. Temporal changes in ECM stiffness are observed in cancer, cardiovascular disease, and wound healing, and are likely involved in disease progression. However, no cell culture systems exist to appropriately model temporal changes in ECM stiffness to determine the biological relevance and mechanisms involved. Here, we present a 3D hydrogel cell culture system in which the matrix stiffness can be tuned by light. Our approach offers both spatial and temporal control of stiffness, is compatible with cell culture, and can be used transdermally for in vivo applications. This system is amenable to many applications to investigate the influence of matrix stiffness on cell behavior and fate.
Network-based metaanalysis identifies HNF4A and PTBP1 as longitudinally dynamic biomarkers for Parkinson’s disease
Authors: Santiago Jose A. , Potashkin Judith A.
Published: February 2015

Significance

Development of therapeutic strategies for Parkinson’s disease (PD) is hampered by the lack of reliable biomarkers to identify patients at early stages of the disease and track the therapeutic effect of potential drugs and neuroprotective agents. Readily accessible biomarkers capable of providing information about disease status are expected to accelerate this progress. We identified hepatocyte nuclear factor (
HNF4A
) and polypyrimidine tract binding protein 1 (
PTBP1
) mRNAs as promising blood biomarkers for identifying early stage PD patients with high diagnostic accuracy. Furthermore,
HNF4A
was identified as a potential biomarker to monitor disease severity. Longitudinal analysis demonstrated that
HNF4A
and
PTBP1
are longitudinally dynamic biomarkers that provide insights into the molecular mechanisms underlying the altered insulin signaling in PD patients and may enable novel therapeutic strategies.
Thioredoxin, a master regulator of the tricarboxylic acid cycle in plant mitochondria
Authors: Daloso Danilo M. , Müller Karolin , Obata Toshihiro , Florian Alexandra , Tohge Takayuki , Bottcher Alexandra , Riondet Christophe , Bariat Laetitia , Carrari Fernando , Nunes-Nesi Adriano , Buchanan Bob B. , Reichheld Jean-Philippe , Araújo Wagner L. , Fernie Alisdair R.
Published: February 2015

Significance

The present work extends redox-based change in enzyme activity to the TCA cycle of plant mitochondria. Thioredoxin (TRX) was found to regulate the activity of enzymes of the mitochondrial cycle (succinate dehydrogenase and fumarase) and of an enzyme associated with it (ATP-citrate lyase) by modulating thiol redox status. A combination of experiments based on mutant and carbon isotope labeling analyses provides evidence that flux through this pathway is coordinately modulated by TRX at the enzyme level of both mitochondria and cytosol. The results provide in vivo confirmation of earlier in vitro results and further show that mitochondria resemble plastids in using TRX and redox status to regulate the main carbon flux pathway of the organelle.
TCL1
targeting
miR-3676
is codeleted with tumor protein p53 in chronic lymphocytic leukemia
Authors: Balatti Veronica , Rizzotto Lara , Miller Cecelia , Palamarchuk Alexey , Fadda Paolo , Pandolfo Rosantony , Rassenti Laura Z. , Hertlein Erin , Ruppert Amy S. , Lozanski Arletta , Lozanski Gerard , Kipps Thomas J. , Byrd John C. , Croce Carlo M. , Pekarsky Yuri
Published: February 2015

Significance

B-cell chronic lymphocytic leukemia (CLL) is the most common adult leukemia. We previously found that dysregulation of the T-cell leukemia/lymphoma 1 (
TCL1
) oncogene is a critical contributing event in the pathogenesis of this disease. In this study we investigated molecular causes of
TCL1
overexpression in CLL. We identified
miR-3676
as a powerful regulator of
TCL1
expression. We found that
miR-3676
is down-regulated on all groups of CLLs and mutated in 1% of CLLs. Interestingly,
miR-3676
is located at 17p13, only 500-kb centromeric of tumor protein p53 (
Tp53
), and is codeleted with
Tp53
in 17p-deleted CLL. Loss of
miR-3676
causes high levels of
TCL1
expression contributing to CLL progression. Thus, this study uncovers a major mechanism in the pathogenesis of CLL.
Auxin binding protein 1 (ABP1) is not required for either auxin signaling or
Arabidopsis
development
Authors: Gao Yangbin , Zhang Yi , Zhang Da , Dai Xinhua , Estelle Mark , Zhao Yunde
Published: February 2015

Significance

The plant hormone auxin is a key regulator of plant growth. It has been hypothesized that some auxin responses are mediated by a candidate auxin receptor called auxin binding protein 1 (ABP1). Support for this hypothesis mainly comes from the analyses of
Arabidopsis ABP1
knockdown lines generated by cellular immunization or antisense approaches. However, these approaches are subject to off-target effects. As an alternative, we have recovered two new null alleles of
abp1
. Surprisingly, neither of the mutants exhibits defects in growth and development, or auxin response, indicating that ABP1 does not have a major role in these responses under normal growth conditions. These results require that the role of ABP1 in plant growth and auxin response be reexamined.
Quorum sensing and policing of
Pseudomonas aeruginosa
social cheaters
Authors: Wang Meizhen , Schaefer Amy L. , Dandekar Ajai A. , Greenberg E. Peter
Published: February 2015

Significance

Cooperation is subject to social cheating. Cheats benefit from the activity of cooperators and gain a fitness advantage. One way higher organisms prevent infiltration by cheats is policing: Cooperators penalize cheats at some cost to themselves. Cooperating groups of bacteria are susceptible to social cheating, but little is known about bacterial policing. We have built on an understanding a quorum-sensing regulated cooperative activity in
Pseudomonas aeruginosa
to show that quorum sensing control of and resistance to cyanide production serves as a cheater policing mechanism. Understanding how bacteria cooperate and how they control social cheats has evolutionary implications, provides important insights about ways to control bacterial populations, and has ramifications with respect to synthetic system design.
Geometry of the 𝐿_{𝑞}-centroid bodies of an isotropic log-concave measure
Authors: Giannopoulos Apostolos , Stavrakakis Pantelis , Tsolomitis Antonis , Vritsiou Beatrice-Helen
Published: February 2015

We study some geometric properties of the

L
q

L_q

-centroid bodies

Z
q

(
μ
)

Z_q(\mu )

of an isotropic log-concave measure

μ
\mu

on

R

n

{\mathbb R}^n

. For any

2
⩽
q
⩽

n

2\leqslant q\leqslant \sqrt {n}

and for

ε
∈
(

ε
0

(
q
,
n
)
,
1
)

\varepsilon \in (\varepsilon _0(q,n),1)

we determine the inradius of a random

(
1
−
ε
)
n

(1-\varepsilon )n

-dimensional projection of

Z
q

(
μ
)

Z_q(\mu )

up to a constant depending polynomially on

ε
\varepsilon

. Using this fact we obtain estimates for the covering numbers

N
(

[
b
]

q

B
2
n

,
t

Z
q

(
μ
)
)

N(\sqrt {[b]{q}}B_2^n,tZ_q(\mu ))

,

t
⩾
1

t\geqslant 1

, thus showing that

Z
q

(
μ
)

Z_q(\mu )

is a

β
\beta

-regular convex body. As a consequence, we also get an upper bound for

M
(

Z
q

(
μ
)
)

M(Z_q(\mu ))

.
The topological complexity of Cantor attractors for unimodal interval maps
Authors: Li Simin , Shen Weixiao
Published: February 2015

For a non-flat

C
3

C^3

unimodal map with a Cantor attractor, we show that for any open cover

U

\mathcal U

of this attractor, the complexity function

p
(

U

,
n
)

p(\mathcal U, n)

is of order

n
log
⁡
n

n\log n

. In the appendix, we construct a non-renormalizable map with a Cantor attractor for which

p
(

U

,
n
)

p(\mathcal {U}, n)

is bounded from above for any open cover

U

\mathcal {U}

.
Spoken Grammar: Where Are We and Where Are We Going?
Authors: Carter Ronald , McCarthy Michael
Published: February 2015

This article synthesises progress made in the description of spoken (especially conversational) grammar over the 20 years since the authors published a paper in this journal arguing for a re-thinking of grammatical description and pedagogy based on spoken corpus evidence. We begin with a glance back at the 16th century and the teaching of Latin grammar in England, with its emphasis on speaking the target language. Later grammars were dominated by written standards, a situation that persisted till the 20th century, when recording technology and spoken corpora enabled new insights into the grammar of everyday speaking. We highlight those insights which especially challenge grammars derived only or mainly from written sources. We evidence the view that conversational grammar is non-sentence-based, co-constructed and highly interactive, and that it poses questions concerning metalanguage. We briefly review debates concerning spoken grammar and ELT/ESL pedagogy. We then consider 21st-century Internet technologies and e-communication, and implications for the spoken/written grammar distinction, arguing that description and pedagogy may need to undergo further re-thinking in light of the multi-modality which characterises e-language.
Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus
Authors: Karp Peter D. , Berger Bonnie , Kovats Diane , Lengauer Thomas , Linial Michal , Sabeti Pardis , Hide Winston , Rost Burkhard
Published: February 2015

Speed is of the essence in combating Ebola; thus, computational approaches should form a significant component of Ebola research. As for the development of any modern drug, computational biology is uniquely positioned to contribute through comparative analysis of the genome sequences of Ebola strains and three-dimensional protein modeling. Other computational approaches to Ebola may include large-scale docking studies of Ebola proteins with human proteins and with small-molecule libraries, computational modeling of the spread of the virus, computational mining of the Ebola literature and creation of a curated Ebola database. Taken together, such computational efforts could significantly accelerate traditional scientific approaches. In recognition of the need for important and immediate solutions from the field of computational biology against Ebola, the International Society for Computational Biology (ISCB) announces a prize for an important computational advance in fighting the Ebola virus. ISCB will confer the ISCB Fight against Ebola Award, along with a prize of US$2000, at its July 2016 annual meeting (ISCB Intelligent Systems for Molecular Biology 2016, Orlando, FL).

Contact:  dkovats@iscb.org or rost@in.tum.de
Starcode: sequence clustering based on all-pairs search
Authors: Zorita Eduard , Cuscó Pol , Filion Guillaume J.
Published: February 2015

Motivation: The increasing throughput of sequencing technologies offers new applications and challenges for computational biology. In many of those applications, sequencing errors need to be corrected. This is particularly important when sequencing reads from an unknown reference such as random DNA barcodes. In this case, error correction can be done by performing a pairwise comparison of all the barcodes, which is a computationally complex problem.

Results: Here, we address this challenge and describe an exact algorithm to determine which pairs of sequences lie within a given Levenshtein distance. For error correction or redundancy reduction purposes, matched pairs are then merged into clusters of similar sequences. The efficiency of starcode is attributable to the poucet search, a novel implementation of the Needleman–Wunsch algorithm performed on the nodes of a trie. On the task of matching random barcodes, starcode outperforms sequence clustering algorithms in both speed and precision.

Availability and implementation: The C source code is available at http://github.com/gui11aume/starcode.

Contact:  guillaume.filion@gmail.com
Learning HMMs for nucleotide sequences from amino acid alignments
Authors: Fischer Carlos N. , Carareto Claudia M. A. , dos Santos Renato A. C. , Cerri Ricardo , Costa Eduardo , Schietgat Leander , Vens Celine
Published: February 2015

Profile hidden Markov models (profile HMMs) are known to efficiently predict whether an amino acid (AA) sequence belongs to a specific protein family. Profile HMMs can also be used to search for protein domains in genome sequences. In this case, HMMs are typically learned from AA sequences and then used to search on the six-frame translation of nucleotide (NT) sequences. However, this approach demands additional processing of the original data and search results. Here, we propose an alternative and more direct method which converts an AA alignment into an NT one, after which an NT-based HMM is trained to be applied directly on a genome.

Contact : carlos@rc.unesp.br

Supplementary information:  Supplementary data are available at Bioinformatics online.
Similarity-based prediction for Anatomical Therapeutic Chemical classification of drugs by integrating multiple data sources
Authors: Liu Zhongyang , Guo Feifei , Gu Jiangyong , Wang Yong , Li Yang , Wang Dan , Lu Liang , Li Dong , He Fuchu
Published: February 2015

Motivation: Anatomical Therapeutic Chemical (ATC) classification system, widely applied in almost all drug utilization studies, is currently the most widely recognized classification system for drugs. Currently, new drug entries are added into the system only on users’ requests, which leads to seriously incomplete drug coverage of the system, and bioinformatics prediction is helpful during this process.

Results: Here we propose a novel prediction model of drug-ATC code associations, using logistic regression to integrate multiple heterogeneous data sources including chemical structures, target proteins, gene expression, side-effects and chemical–chemical associations. The model obtains good performance for the prediction not only on ATC codes of unclassified drugs but also on new ATC codes of classified drugs assessed by cross-validation and independent test sets, and its efficacy exceeds previous methods. Further to facilitate the use, the model is developed into a user-friendly web service SPACE ( S imilarity-based P redictor of A TC C od E ), which for each submitted compound, will give candidate ATC codes (ranked according to the decreasing probability_score predicted by the model) together with corresponding supporting evidence. This work not only contributes to knowing drugs’ therapeutic, pharmacological and chemical properties, but also provides clues for drug repositioning and side-effect discovery. In addition, the construction of the prediction model also provides a general framework for similarity-based data integration which is suitable for other drug-related studies such as target, side-effect prediction etc.

Availability and implementation: The web service SPACE is available at http://www.bprc.ac.cn/space

Contact:  hefc@nic.bmi.ac.cn or lidong.bprc@foxmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
SPARQL-enabled identifier conversion with Identifiers.org
Authors: Wimalaratne Sarala M. , Bolleman Jerven , Juty Nick , Katayama Toshiaki , Dumontier Michel , Redaschi Nicole , Le Novère Nicolas , Hermjakob Henning , Laibe Camille
Published: February 2015

Motivation: On the semantic web, in life sciences in particular, data is often distributed via multiple resources. Each of these sources is likely to use their own International Resource Identifier for conceptually the same resource or database record. The lack of correspondence between identifiers introduces a barrier when executing federated SPARQL queries across life science data.

Results: We introduce a novel SPARQL-based service to enable on-the-fly integration of life science data. This service uses the identifier patterns defined in the Identifiers.org Registry to generate a plurality of identifier variants, which can then be used to match source identifiers with target identifiers. We demonstrate the utility of this identifier integration approach by answering queries across major producers of life science Linked Data.

Availability and implementation: The SPARQL-based identifier conversion service is available without restriction at http://identifiers.org/services/sparql .

Contact:  sarala@ebi.ac.uk
Where are we at regarding species translation? A review of the sbv IMPROVER challenge
Authors: Hoeng J. , Peitsch M.C. , Meyer P. , Jurisica I.
Published: February 2015

Contact:  Julia.Hoeng@pmi.com
PolyMarker: A fast polyploid primer design pipeline
Authors: Ramirez-Gonzalez Ricardo H. , Uauy Cristobal , Caccamo Mario
Published: February 2015

Summary: The design of genetic markers is of particular relevance in crop breeding programs. Despite many economically important crops being polyploid organisms, the current primer design tools are tailored for diploid species. Bread wheat, for instance, is a hexaploid comprising of three related genomes and the performance of genetic markers is diminished if the primers are not genome specific. PolyMarker is a pipeline that generates SNP markers by selecting candidate primers for a specified genome using local alignments and standard primer design tools to test the viability of the primers. A command line tool and a web interface are available to the community.

Availability and implementation: PolyMarker is available as a ruby BioGem: bio-polyploid-tools. Web interface: http://polymarker.tgac.ac.uk.

Contact:  Ricardo.Ramirez-Gonzalez@tgac.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Tobit
Authors: Kiel Micah D.
Published: February 2015

The book of Tobit tells the story of Tobit and his family, who are living as exiles from Israel after the Assyrian conquest. Through a series of events, Tobit goes blind and sends his son on a journey accompanied by the angel Raphael disguised as a human. On his journey, the son Tobias meets Sarah, who is afflicted by a demon. Raphael intervenes and dispatches the demon, allowing Tobias and Sarah to marry. They return to Tobit and his wife, Anna, Tobit’s sight returns and he dies old and happy because of God’s intervention in their travails. The book is not historical, but rather a folk tale with manifold entertaining elements, such as defecating birds, meddling fish, menacing demons, and disguised angels. Beneath the surface, however, the book interacts with deep theological questions at the core of the human condition, questions that also find expression—with various answers—throughout the Jewish scriptures: Where does suffering come from? What are the benefits of righteousness? What is the value of religious tradition? In answering such questions through its entertaining narrative, the book of Tobit weaves together an erudite panoply of religious, scriptural, and cultural traditions. Within scholarship, there are a number of debated issues with which treatments of the book have dealt, including: original language, provenance, date of composition, and ideological disposition. Until the discovery of the Dead Sea Scrolls, Tobit was primarily known from Greek and Latin manuscripts. Although some scholars had posited a Semitic Vorlage behind it, all major translations and interpretations of the book had to be made from Greek. Several Aramaic and Hebrew manuscripts of Tobit were found among the Dead Sea Scrolls, however, which provided a watershed in understanding the book. Analysis of the scrolls has provided widespread agreement that the book was originally written in Aramaic. These manuscripts, however, are fragmentary and translations are still made from the Greek version of Codex Sinaiticus. Association with the Qumran community has also led to some reassessment of the book’s theological outlook. The book of Tobit is one of the Deuterocanonical books, also known as the Apocrypha. As such, it is generally not included among Protestant Christians’ list of canonical texts, while it is for Roman Catholics and most Orthodox traditions. There is no evidence that the text was ever “canonical” in the Jewish tradition.
Ancient Medicine
Authors: Thompson Trevor
Published: February 2015

The experience of injury, illness, and disease unites human beings across time and place. Life in the ancient world was perilous. Disease, childbirth, food shortage, and war rendered it both short and brutish. Ancient medicine, like its modern counterpart, seeks to treat ailments and remedy pain. Homer’s Iliad begins with the god Apollo, an agent of both destruction and healing, spreading plague among the ranks of the Greek army (1.8–52). The same work presents Machaon, a physician from a long line of physicians, attending to wounds and employing pharmaceuticals without direct recourse to divine intervention (11.520–550). Injuries, illness, and disease admit different ascribed causes and prescribed therapeutic responses. Ancient medicinal thought varies considerably across cultures. Thus, for example, the famous humoral system of body fluids affirmed in the Hippocratic Corpus and subsequent medical thought does not easily map, despite some similarities, onto Ayurvedic medicine in ancient India. Physicians competed in a complex marketplace of medical ideas and practices. They plied their trade with insufficient, often erroneous, information about the body and the functions of its parts. It is difficult to fairly assess the efficacy of many treatments. Current knowledge of ancient medicine comes from a variety of different sources. These include a papyrus on gynecology from ancient Egypt; Neolithic skulls with trepanation holes; surgical instruments from the ruins of Pompeii (e.g., bone drills, catheters, spatula, lancet, scissors, vaginal specula, and cautery iron); terracotta votives of anatomical parts in Greek temples; a tombstone of an unnamed female physician in Gallo-Roman France; and a recently discovered moral-philosophical work, De indolentia, in which Galen records the loss of irreplaceable pharmaceutical recipes and one-off medical instruments in the fire that ravaged Rome in 192 ce. Lines between the practice of medicine and traditional cult or religion are blurry at best. Despite the ascendency of “rational” medicine in classical Greece, “irrational” medicine continued to exist. The former did not push out the latter. The ancients did not have a health-care system in the modern sense. Ancient healers comprise a diverse group of practitioners that include, among others, root-cutters, midwives, diviners, and surgeons. The threat of anachronism in recounting ancient medicine is ever-present. In fact, the use of “doctor” or “physician” to describe ancient therapists is seen by some to be anachronistic, as is the use of “medicine.” Precious little remains of a patient’s perspective. Despite the obstacles, the study of ancient medicine offers an invaluable glimpse into the thought, culture, and experience of ancient peoples.
Pedology
Authors: Brevik Eric C. , Weindorf David C. , Stiles Cynthia
Published: February 2015

In modern soil science pedology is widely viewed as the study of soils in their natural environment. Pedology has a fairly lengthy history within soil science, dating to the late 1800s and the work of Dokuchaev. The areas of soils study that fall under the pedology umbrella make pedology important for many modern applications of soils knowledge, including agriculture, agroforestry, environmental issues, and land-use planning. This makes a basic understanding of pedology important for anyone working in these areas. Future needs in pedology include improved knowledge of soil processes, information on soil surveys on soil change over time, a better understanding of soils and climate change interactions, and soil-water interactions. A particular need exists for pedologists to work with scientists in related fields to address pressing modern issues that cannot be covered by a single field alone. We thank Horea Cacovean and Damien Field for discussions concerning pedology textbooks used in Europe and Australia.
Geodiversity and Geoconservation
Authors: Gray Murray
Published: February 2015

Although nature is often equated with wildlife, it does in fact comprise both living and nonliving elements. The living elements are the plants and animals that make up the world’s biodiversity (biological diversity). Geodiversity (geological and geomorphological diversity) refers to the variety of nonliving nature, that is, the minerals, rocks, fossils, soils (though these also consist of organic matter and a soil ecology), landforms, and processes that make up the physical surface and subsurface of planet Earth. It does not generally include either the atmosphere (climate diversity) or the ocean waters, but it does include the physical diversity of the ocean floor and terrestrial water features (springs, rivers, ponds, lakes, etc.). The term geodiversity was first used in 1993, shortly after agreement of the Convention on Biological Diversity (CBD) at the Rio Earth Summit in 1992 made it difficult for geoscientists to avoid introducing the abiotic equivalent of the biological concept and term biodiversity.
Democratic Theory
Authors: Laurence Michael
Published: February 2015

Democratic theory is an established subfield of political theory that is primarily concerned with examining the definition and meaning of the concept of democracy, as well as the moral foundations, obligations, challenges, and overall desirability of democratic governance. Generally speaking, a commitment to democracy as an object of study and deliberation is what unites democratic theorists across a variety of academic disciplines and methodological orientations. When this commitment takes the form of a discussion of the moral foundations and desirability of democracy, normative theory results. When theorists concern themselves with the ways in which actual democracies function, their theories are empirical. Finally, when democratic theorists interrogate or formulate the meaning of the concept of democracy, their work is conceptual or semantic in orientation. Democratic theories typically operate at multiple levels of orientation. For example, definitions of democracy as well as normative arguments about when and why democracy is morally desirable are often rooted in empirical observations concerning the ways in which democracies have actually been known to function. In addition to a basic commitment to democracy as an object of study, most theorists agree that the concept democracy denotes some form or process of collective self-rule. The etymology of the word traces back to the Greek terms demos (the people, the many) and kratos (to rule). Yet beyond this basic meaning, a vast horizon of contestation opens up. Important questions arise: who constitutes the people and what obligations do individuals have in a democracy? What values are most important for a democracy and which ones make it desirable or undesirable as a form of government? How is democratic rule to be organized and exercised? What institutions should be used and how? Once instituted, does democracy require precise social, economic, or cultural conditions to survive in the long term? And why is it that democratic government is preferable to, say, aristocracy or oligarchy? These questions are not new. In fact, democratic theory traces its roots back to ancient Greece and the emergence of the first democratic governments in Western history. Ever since, philosophers, politicians, artists, and citizens have thought and written extensively about democracy. Yet democratic theory did not arise as an institutionalized academic or intellectual discipline until the 20th century. The works cited here privilege Anglo-American, western European, and, more generally, institutional variants of democratic theory, and, therefore, they do not exhaust the full range of thought on the subject.
3D Media
Authors: Baltruschat Doris
Published: February 2015

Media content can now be experienced on various “screens,” be it in traditional theater space, at home, or in transit via digital distribution platforms like the Internet and mobile and virtual reality devices. With recent innovations in 3D, media applications now have added another dimension to their digital-convergent universe. However, it may be surprising to learn that stereoscopic imaging and more recent 3D innovations (especially in 3D animation) precede the development of 2D cinema and television. Discovered in 1838, 3D arrived nearly fifty years before conventional cinema made its first mark at the turn of the 20th century. Stereoscopic still images, depicting nature scenes and historic sites, highlight the popularity of this early form of 3D entertainment. In the 1950s, the “golden age” of 3D entertainment arrived with films such as Bwana Devil (1952) and Kiss Me Kate (1953). However, audience fascination with the third dimension soon dimmed due to poor production values, bad scripts, and 3D technology being used mostly for a few surprise effects. 3D cinema experienced a brief revival in the 1980s with blockbuster hits like Jaws 3D (1983), only to fade into the background again for another three decades. This all changed with the arrival of the new generation of 3D films such as Avatar (2010). Indeed, 2010 marked a new era in 3D media with the standardization of 3D technologies and the dramatic increase of 3D movies in the cinema, which were then released on 3D Blu-ray to be enjoyed at home around the 3D television set. To date, 3D has advanced beyond traditional stereoscopic imaging to embrace innovations, especially with regard to 3D capture and display technologies. Additional differences between previous eras of stereoscopic entertainment and the current 3D renaissance is that the technology is now being rolled out across media platforms, from large cinema screens to television sets, game consoles, the Internet, and the mobile phone. Thus, this new era of digital 3D must be seen within the context of 3D entertainment across the field, from increasing 3D film production to event programing (e.g., 2012 Olympics) and the use of new 3D technologies to create virtual online worlds, as in “machinima.” 3D media also play an increasing role in education, the sciences, and the arts. Many books and articles exist on the history and technological evolution of 3D media. However, the implications for aesthetic and narrative development through the use of 3D are only gradually emerging, as are research studies on virtual 3D worlds and their impact on social relations, online communities, organizational development, and society.
Langston Hughes
Authors: Kutzinski Vera
Published: February 2015

Born James Langston Hughes in Joplin, Missouri, Langston Hughes (b. 1902–d. 1967) was likely the most influential writer who emerged from the Harlem Renaissance. He was the first one of this group to establish an enduring national and international reputation. Hughes established his national standing as the “Poet Laureate of the Negro Race” with The Weary Blues and the controversial essay “The Negro Artist and the Racial Mountain” in 1926. By the time he graduated from Lincoln University, Pennsylvania, in 1929, he had published a second volume of poems, Fine Clothes to the Jew (1927). Having lived in Mexico for more than a year as a teenager, by 1929 Hughes had also visited West Africa, France (where he spent several months), and Italy. Extended trips to Haiti, Cuba, the Soviet Union, and Spain followed, as did translations of his poems into Spanish, German, French, Russian, and many other languages. Though best known as a poet, Hughes was a prolific and versatile writer working in numerous literary genres as well as in journalism and popular history. Widely celebrated for his blues poetry and, more recently, for his experimental poems from the 1950s and early 1960s, Hispanic American audiences in particular praised Hughes for his verse influenced by international communism. However, this radical verse landed him in serious trouble at home. In the 1940s and 1950s, Hughes became the target of smear campaigns and FBI surveillance. Although Hughes disavowed his political past in his 1953 publicly broadcast testimony before Joseph McCarthy’s infamous Senate subcommittee, a measure of unease about his communist leanings has lingered in Hughes scholarship in the United States, where his radical poetry from the 1930s has traditionally had relatively few admirers—until now. Ironically, the very simplicity that made his writing accessible to and popular with so many different audiences across the world also fueled the belief among many scholars that Hughes’s writing lacked literary complexity. As a result, neither his novels nor his autobiographies have met with abundant critical analysis, much less acclaim. Quite in contrast to Hughes’s short fiction, especially the Simple stories from the 1940s and 1950s, these texts have attracted the critical attention they deserve only since the third quarter of the twentieth century, and especially in the early twenty-first century. Similarly, scholars have neglected Hughes’s plays, his translations of writers such as Federico García Lorca and Jacques Roumain, and his extensive journalism. Since the mid-1990s, however, the landscape of Hughes studies has changed significantly as scholars have increasingly challenged the view of Hughes as a straightforward and even shallow writer. It is changing even more in the twenty-first century.
Switch to Rilpivirine/Emtricitabine/Tenofovir Single-Tablet Regimen of Human Immunodeficiency Virus-1 RNA-Suppressed Patients, Agence Nationale de Recherches sur le SIDA et les Hépatites Virales CO3 Aquitaine Cohort, 2012–2014
Authors: Cazanave Charles , Reigadas Sandrine , Mazubert Cyril , Bellecave Pantxika , Hessamfar Mojgan , Le Marec Fabien , Lazaro Estibaliz , Peytavin Gilles , Bruyand Mathias , Fleury Hervé , Dabis François , Neau Didier
Published: February 2015

Background.  The purpose of this study was to assess the efficacy and tolerability of combined antiretroviral therapy (cART) in human immunodeficiency virus (HIV)-1 virologically suppressed patients who switched to rilpivirine (RPV)/tenofovir disoproxil fumarate (TDF)/emtricitabine (FTC) as a single-tablet regimen (STR).

Methods.  A retrospective multicenter cohort study was performed between September 2012 and February 2014 in Bordeaux University Hospital-affiliated clinics. Patients with a plasma HIV viral load (VL) lower than 50 copies/mL and switching to STR were evaluated at baseline, 3, 6, 9, and 12 months from switch time (M3, M6, M9, M12) for VL and other biological parameters. Change from baseline in CD4 cell counts was evaluated at M6 and M12. Virological failure (VF) was defined as 2 consecutive VL >50 copies/mL.

Results.  Three hundred four patients were included in the analysis. Single-tablet regimen switch was proposed to 116 patients with adverse events, mostly efavirenz (EFV)-based (n = 59), and to 224 patients for cART simplification. Thirty of 196 patients with available genotype resistance test results displayed virus with ≥1 drug resistance mutation on reverse-transcriptase gene. After 12 months of follow-up, 93.4% (95.5% confidence interval, 89.9–96.2) of patients remained virologically suppressed. There was no significant change in CD4 cell count. During the study period, 5 patients experienced VF, one of them harboring RPV resistance mutation. Clinical cART tolerability improved in 79 patients overall (29.9%) at M6, especially neurological symptoms related to EFV. Fasting serum lipid profiles improved, but a significant estimated glomerular function rate decrease (−11 mL/min/1.73 m2; P < 10−4) was observed.

Conclusions.  Overall, virologic suppression was maintained in patients after switching to RPV/TDF/ FTC. This STR strategy was associated with improved tolerability.
Heart failure diagnosis in acute conditions has high agreement with inpatient diagnosis
Authors: Seronde Marie-France , Laribi Said , Collins Sean P. , Deye Nicolas , Logeart Damien , Plaisance Patrick , Cohen-Solal Alain , Mebazaa Alexandre
Published: February 2015

Objectives

Acute heart failure (AHF) is frequently encountered in the emergency department (ED) or in the cardiac care unit (CCU)/ICU. Discrimination between cardiac and noncardiac cause of dyspnea by clinical means and standard testing is sometimes inadequate. The aim of our study was to assess AHF diagnosis agreement as determined by: (a) the attending physician, (b) the hospital discharge diagnosis, and (c) an adjudication committee.

Patients and methods

Between 2010 and 2011, consecutive patients arriving for dyspnea in our hospital were prospectively included. A convenience sample of patients was enrolled in this analysis. Patients were admitted through the ED (280 patients) or through CCU/ICU (112 patients) for undifferentiated dyspnea.

Results

Overall, few differences were observed between the initial diagnosis and the hospital discharge diagnosis or the adjudicated diagnosis. Among the 200 patients with an initial diagnosis of AHF, hospital discharge diagnosis confirmed AHF (alone or combined) in 191 (95.5%) patients and the adjudication committee confirmed AHF (alone or combined) in 196 (98%) patients.

Conclusion

Our study showed considerable agreement between different AHF diagnostic standards. An initial AHF diagnosis on the basis of clinical signs and biological parameters utilizing B-type natriuretic peptide testing has high agreement and accuracy with the hospital discharge and adjudicated diagnosis of AHF. The present study also shows that the accuracy of the initial AHF diagnosis allows rapid inclusion in AHF trials. These results, if confirmed in a broader cohort of patients, suggest that the initial ED diagnosis is highly accurate and reliable to guide further inpatient management.
Biliary Atresia Is Associated With Hypertension
Authors: Matloff Robyn G. , Diamond Rebekah , Weinberg Alan , Arnon Ronen , Saland Jeffrey M.
Published: February 2015

Objectives:

The improved survival of pediatric liver transplant recipients is accompanied by an increase in long‐term comorbidities. A recently highlighted concern, hypertension, is associated with chronic kidney disease (CKD) in this population and can result in other target‐organ damage during childhood. The prevalence of hypertension in pediatric liver transplantation is imprecisely known. In addition, individual etiologies of liver failure may convey different risks of hypertension. We sought to study the effect of liver transplantation on the prevalence of hypertension and CKD in patients with biliary atresia (BA).

Methods:

We conducted a retrospective chart review of 160 patients with BA followed at the Mount Sinai Medical Center, New York, from 1987 to 2012. Data were accumulated from the initial and subsequent visits at approximately 6 months, 1, 3, 5, 10, and 15 years of age. Hypertension was defined as systolic blood pressure ≥95th percentile for age, sex, height, and/or use of antihypertensive medication. Renal function was examined over time. Data were stratified by liver transplantation status at the time of visit.

Results:

A high prevalence of hypertension was observed from the initial visit through age 10, independent of transplant status (transplanted: 48% initial visit and 13% after 10 years vs nontransplanted: 55% initial visit and 17% after 10 years [P = ns for transplant status]). Mean estimated glomerular filtration rate (eGFR) was lower among liver transplant patients as compared with nontransplant patients and declined posttransplant. The incidence of CKD was higher among transplant patients.

Conclusions:

Hypertension is common among children with BA, independent of liver transplant status. Transplant patients had significantly reduced renal function, which continued to decline over time. Hypertension was not associated with reduced eGFR.
Difficulty Achieving Vitamin D Sufficiency With High‐Dose Oral Repletion Therapy in Infants With Cholestasis
Authors: Jensen Melissa , Abu‐El‐Haija Maisam , Bishop Warren , Rahhal Riad M.
Published: February 2015

Objectives:

Oral high‐dose repletion vitamin D therapy, also known as stoss therapy, can be effective in the treatment of nutritional vitamin D deficiency rickets in infants and young children without liver disease and in patients with cystic fibrosis. There is no literature about this approach in infants with new‐onset cholestasis.

Methods:

This was a retrospective chart review of infants with cholestasis from March 2010 to March 2012 at a pediatric tertiary care center. Four cases satisfied the inclusion criteria, and were described in detail.

Results:

All of the patients received oral high‐dose repletion therapy with ergocalciferol (vitamin D2) 300,000 IU daily for 2 to 3 days. Follow‐up vitamin D levels approximately 4 weeks later showed failure to achieve sufficiency levels (>20 ng/dL) in any patient.

Conclusions:

Unlike infants without liver disease, use of oral high‐dose repletion therapy may not be adequate as treatment of vitamin D deficiency in the setting of cholestasis.