bluuebunny/crossref_metadata_2025 huggingface dataset:
Using
media to improve the informed consent process for youth undergoing pediatric
endoscopy and their parents
Authors: Yeh Debra , Chun Stanford , Terrones Laura , Huang Jeannie
Published: January 2017

Background and study aims Youth undergoing pediatric endoscopic procedures
and their parents demonstrate suboptimal comprehension of the informed consent
(IC) process. We developed informational videos discussing key IC elements for
pediatric endoscopy and evaluated their effects on youth and parental
comprehension of the IC process.

Patients and methods A randomized controlled trial of the video
intervention was performed among youth undergoing endoscopy and their parents at
an academic children’s hospital. Randomization occurred at the time of
enrollment using permutated blocks. Following the IC process with the
proceduralist, subjects underwent structured interviews to assess IC
comprehension. An Informed Consent Overall Score (ICOS: range 0 – 4) for
comprehension was calculated.

Results Seventy-seven pairs of children and their parents participated.
Intervention recipients (N = 37 pairs) demonstrated higher ICOS scores as
compared to control counterparts (mean (standard deviation): 3.6 (0.7) v. 2.9
(0.9), intervention v. control parents, P < 0.0001 and 2.7 (1.1) v.
1.7 (1.1), intervention v. control youth, P < 0.0001).

Conclusions A media intervention addressing key elements of the IC process
for pediatric endoscopy was effective in improving comprehension of IC for youth
undergoing endoscopic procedures and their
parents.
Waterjet submucosal dissection of porcine esophagus with the HybridKnife and ERBEJET 2 system: a pilot study
Authors: Akutsu Daisuke , Suzuki Hideo , Narasaka Toshiaki , Terasaki Masahiko , Kaneko Tsuyoshi , Matsui Hirofumi , Mizokami Yuji , Hyodo Ichinosuke
Published: January 2017

Background and study aims Esophageal endoscopic submucosal dissection (ESD) is technically difficult because of narrow working spaces and ease of perforation due to the lack of serosa. HybridKnife is a recently developed ESD device that is combined with the high pressure waterjet ERBEJET 2 system to lift mucosa. We hypothesized that this waterjet could make submucosal dissection safer and studied this in porcine esophagus.

Materials and methods Water pressures of 30 – 70 bar were tested to determine the appropriate pressure for waterjet ESD with HybridKnife (WJ-ESD) in one pig. WJ-ESD safety and completion were compared with those of conventional ESD using DualKnife (C-ESD) as a reference. Each of three virtual esophageal lesions in two pigs were resected alternatively using both methods from the lower to upper esophagus. For WJ-ESD, the submucosa, apart from hard fibrous tissues, was dissected using water pressure alone.

Results Using 50 bar of water pressure resulted in the best balance between proper dissection and view-disturbing water backflow. The dissection speeds for the lower, middle, and upper esophagus were 0.2, 0.9, and 0.2 cm2/min in 50 bar WJ-ESD and 1.1, 0.5, and 1.0 cm2/min in C-ESD, respectively. Minor bleeding was frequent in WJ-ESD, but was easily stopped by electrocoagulation with the same needle. No perforation was observed in either procedure. Thermal damage to dissected tissues appeared mild, and the extent of muscle injury was lower for WJ-ESD (4, 6, and 8 %) compared with C-ESD (14, 16, and 7 %).

Conclusions WJ-ESD could be completed safely for porcine esophagus with less damage to the muscle layer compared with C-ESD.
Massenanfall von Verletzten auf hoher See
Authors: Weigeld M. , Smolarz N. , Beth P. , Guembel D. , Ekkernkamp A. , Schulz-Drost S.
Published: January 2017

Für die Erfassung von Schiffsunglücken (SU) mit einem Massenanfall von Verletzten (MANV) auf hoher See erfolgte eine systematische Recherche der öffentlich zugänglichen Quellen. Eine einheitliche und systematische Erfassung durch die Stellen der maritimen Gefahrenabwehr existiert bisher nicht.

Von 37 Schadenslagen in der Nord- und Ostsee ab 1990 konnten 22 auf die ausschließliche Wirtschaftszone Deutschlands begrenzt werden. Nach Elimination der küstennahen Ereignisse wurden 10 SU identifiziert. Hiervon konnten 7 in die Kategorie MANV eingeordnet werden. Der MANV wurde definiert als Großschadensereignis mit 5 oder mehr beteiligten Personen.

Die komplexen Schadenslagen stellen auf hoher See, neben den schon auf Land bestehenden Schwierigkeiten, eine besondere Herausforderung dar. Als Folgen der SU zeigen sich neben Verletzungen und Verbrennungen insbesondere die Rauchgasintoxikationen aufgrund der knappen Ressourcen an medizinischem Sauerstoff als relevant. Zudem besteht aufgrund der Witterung und dem Kontakt mit Wasser bei langen Rettungszeiten die Gefahr der Unterkühlung.

Mit dem Havariekommando sind bereits Strukturen zur Bewältigung etabliert worden, welche mit den vorhandenen Organisationen (DGzRS/Bundeswehr/Notschleppkonzept) eng zusammenarbeiten. Eine Einbindung der neu geschaffenen Strukturen für die medizinische Versorgung der Offshore-Windparks erscheint sinnvoll und vielversprechend.
Comparison of technologies for nano device prototyping with a special focus on ion beams: A review
Authors: Bruchhaus L. , Mazarov P. , Bischoff L. , Gierak J. , Wieck A. D. , Hövel H.
Published: January 2017

Nano device prototyping (NDP) is essential for realizing and assessing ideas as well as theories in the form of nano devices, before they can be made available in or as commercial products. In this review, application results patterned similarly to those in the semiconductor industry (for cell phone, computer processors, or memory) will be presented. For NDP, some requirements are different: thus, other technologies are employed. Currently, in NDP, for many applications direct write Gaussian vector scan electron beam lithography (EBL) is used to define the required features in organic resists on this scale. We will take a look at many application results carried out by EBL, self-organized 3D epitaxy, atomic probe microscopy (scanning tunneling microscope/atomic force microscope), and in more detail ion beam techniques. For ion beam techniques, there is a special focus on those based upon liquid metal (alloy) ion sources, as recent developments have significantly increased their applicability for NDP.
Investigation of p-type depletion doping for InGaN/GaN-based light-emitting diodes
Authors: Zhang Yiping , Zhang Zi-Hui , Tan Swee Tiam , Hernandez-Martinez Pedro Ludwig , Zhu Binbin , Lu Shunpeng , Kang Xue Jun , Sun Xiao Wei , Demir Hilmi Volkan
Published: January 2017

Due to the limitation of the hole injection, p-type doping is essential to improve the performance of InGaN/GaN multiple quantum well light-emitting diodes (LEDs). In this work, we propose and show a depletion-region Mg-doping method. Here we systematically analyze the effectiveness of different Mg-doping profiles ranging from the electron blocking layer to the active region. Numerical computations show that the Mg-doping decreases the valence band barrier for holes and thus enhances the hole transportation. The proposed depletion-region Mg-doping approach also increases the barrier height for electrons, which leads to a reduced electron overflow, while increasing the hole concentration in the p-GaN layer. Experimentally measured external quantum efficiency indicates that Mg-doping position is vitally important. The doping in or adjacent to the quantum well degrades the LED performance due to Mg diffusion, increasing the corresponding nonradiative recombination, which is well supported by the measured carrier lifetimes. The experimental results are well numerically reproduced by modifying the nonradiative recombination lifetimes, which further validate the effectiveness of our approach.
Transition moments between excited electronic states from the Hermitian formulation of the coupled cluster quadratic response function
Authors: Tucholska Aleksandra M. , Lesiuk Michał , Moszynski Robert
Published: January 2017

We introduce a new method for the computation of the transition moments between the excited electronic states based on the expectation value formalism of the coupled cluster theory [B. Jeziorski and R. Moszynski, Int. J. Quantum Chem. 48, 161 (1993)]. The working expressions of the new method solely employ the coupled cluster operator T and an auxiliary operator S that is expressed as a finite commutator expansion in terms of T and T†. In the approximation adopted in the present paper, the cluster expansion is limited to single, double, and linear triple excitations. The computed dipole transition probabilities for the singlet-singlet and triplet-triplet transitions in alkali earth atoms agree well with the available theoretical and experimental data. In contrast to the existing coupled cluster response theory, the matrix elements obtained by using our approach satisfy the Hermitian symmetry even if the excitations in the cluster operator are truncated, but the operator S is exact. The Hermitian symmetry is slightly broken if the commutator series for the operator S are truncated. As a part of the numerical evidence for the new method, we report calculations of the transition moments between the excited triplet states which have not yet been reported in the literature within the coupled cluster theory. Slater-type basis sets constructed according to the correlation-consistency principle are used in our calculations.
Effects of stereochemistry and copolymerization on the LCST of PNIPAm
Authors: de Oliveira Tiago E. , Mukherji Debashish , Kremer Kurt , Netz Paulo A.
Published: January 2017

Poly(N-isopropylacrylamide) (PNIPAm) is a smart polymer that presents a lower critical transition temperature (LCST) of 305 K. Interestingly, this transition point falls within the range of the human body temperature, making PNIPAm a highly suitable candidate for bio-medical applications. However, it is sometimes desirable to have a rather flexible tuning of the LCST of these polymers to further increase their range of applications. In this work, we use all-atom molecular dynamics simulations to study the LCST of PNIPAm-based (co-)polymers. We study different molecular architectures where the polymer sequences are tuned either by modifying its stereochemistry or by the co-polymerization of PNIPAm with acrylamide (Am) units. Our analysis connects global polymer conformations with the microscopic intermolecular interactions. These findings suggest that the collapse of a PNIPAm chain upon heating is dependent on the hydration structure around the monomers, which is strongly dependent on the tacticity and the presence of more hydrophilic acrylamide monomers. Our results are found to be in good agreement with the existing experimental data.
Effect of Joule heating and current crowding on electromigration in mobile technology
Authors: Tu K. N. , Liu Yingxia , Li Menglu
Published: January 2017

In the present era of big data and internet of things, the use of microelectronic products in all aspects of our life is manifested by the ubiquitous presence of mobile devices as i-phones and wearable i-products. These devices are facing the need for higher power and greater functionality applications such as in i-health, yet they are limited by physical size. At the moment, software (Apps) is much ahead of hardware in mobile technology. To advance hardware, the end of Moore's law in two-dimensional integrated circuits can be extended by three-dimensional integrated circuits (3D ICs). The concept of 3D ICs has been with us for more than ten years. The challenge in 3D IC technology is dense packing by using both vertical and horizontal interconnections. Mass production of 3D IC devices is behind schedule due to cost because of low yield and uncertain reliability. Joule heating is serious in a dense structure because of heat generation and dissipation. A change of reliability paradigm has advanced from failure at a specific circuit component to failure at a system level weak-link. Currently, the electronic industry is introducing 3D IC devices in mainframe computers, where cost is not an issue, for the purpose of collecting field data of failure, especially the effect of Joule heating and current crowding on electromigration. This review will concentrate on the positive feedback between Joule heating and electromigration, resulting in an accelerated system level weak-link failure. A new driving force of electromigration, the electric potential gradient force due to current crowding, will be reviewed critically. The induced failure tends to occur in the low current density region.
Proposal for a self-excited electrically driven surface plasmon polariton generator
Authors: Bordo V. G.
Published: January 2017

We propose a generator of surface plasmon polaritons (SPPs) which, unlike spasers or plasmon lasers, does not require stimulated emission in the system. Its principle of operation is based on a positive feedback which an ensemble of classical oscillating dipoles experiences from a reflective surface located in its near field. The generator design includes a nanocavity between two metal surfaces which contains metal nanoparticles in its interior. The whole structure is placed onto a prism surface that allows one to detect the generated SPPs in the Kretschmann configuration. The generation process is driven by a moderate DC voltage applied between the metal covers of the cavity. Both the generation criterion and the steady-state operation of the generator are investigated.
Electric field control of the small-polaron hopping conduction in spatial confined Pr0.7(Ca0.6Sr0.4)0.3MnO3/PMN-PT heterostructure
Authors: Kuang Hao , Wang Jing , Li Jia , Hu Feng-xia , Sun Ji-rong , Shen Bao-gen
Published: January 2017

The electric field dependent high-temperature small-polaron hopping conduction was investigated in patterned Pr0.7(Ca0.6Sr0.4)0.3MnO3 strips. The small-polaronic activation energy EA and the carrier localization were found to decrease with the reduction of the strip size. Meanwhile, a similar dependence on the strip size was also obtained for the calculated small-polaron coupling constants, which could be related to the strain relaxation in strips. These results indicate that the spatial confinement prefers to delocalize the carrier and reduce the electron-phonon interaction. Furthermore, opposite variation trends of EA under negative and positive electric field were found in the strips with small size, which could be attributed to the enhancement of polarization effect induced by the reduction of strip size.
Challenges in implementing individual placement and support in the Australian mental health service and policy context
Authors: Stirling Yolande , Higgins Kate , Petrakis Melissa
Published: January 2017

Objective
Although Australia’s service and policy context differs from that of the US, studies have highlighted potential for individual placement and support (IPS) to support competitive employment outcomes for people with severe and persistent mental illness. The aim of the present study was to explore why the model is not yet widely available.

Methods
A document analysis was conducted to discern reasons for challenges in implementation of IPS practice principles within the Australian service context.

Results
The document analysis illustrated that although policy acknowledges the importance of increasing employment rates for people with severe and persistent mental illness, consistent measures, change indicators, direction and time frames are lacking in policy and strategy documentation. Further, IPS principles are not consistently evident in guiding operational documentation that government-funded Disability Employment Services (DES) programs are mandated to adhere to.

Conclusions
For IPS to be readily implemented, it is necessary for government to offer support to agencies to partner and formal endorsement of the model as a preferred approach in tendering processes. Obligations and processes must be reviewed to ensure that model fidelity is achievable within the Australian Commonwealth policy and service context for programs to achieve competitive employment rates comparable to the most successful international programs.

What is known about the topic?
The IPS model has been established as the most efficacious approach to support people with severe and persistent mental ill health to gain and sustain employment internationally, yet little is known as to why this model has had very limited uptake in the Australian adult mental health service and policy context.

What does this paper add?
This paper provides an investigation into the achievability of IPS within DES philosophical and contractual arrangements.

What are the implications for practitioners?
Mental health practitioners are typically skilled in their understanding of individual or micro-level challenges faced by consumers in achieving vocational goals: working with symptoms, medication side effects, motivation and anxiety. The present study was designed to offer practitioners an increased understanding of service-level factors, because these present considerable challenges to achieving sustained employment. This paper is a call for greater advocacy towards better integration of employment and mental health service delivery in the Australian policy and practice context.
Poly(A)-binding proteins are required for translational regulation in vertebrate oocytes and early embryos
Authors: Ozturk Saffet , Uysal Fatma
Published: January 2017

Poly(A)-binding proteins (PABPs) function in the timely regulation of gene expression during oocyte maturation, fertilisation and early embryo development in vertebrates. To this end, PABPs bind to poly(A) tails or specific sequences of maternally stored mRNAs to protect them from degradation and to promote their translational activities. To date, two structurally different PABP groups have been identified: (1) cytoplasmic PABPs, including poly(A)-binding protein, cytoplasmic 1 (PABPC1), embryonic poly(A)-binding protein (EPAB), induced PABP and poly(A)-binding protein, cytoplasmic 3; and (2) nuclear PABPs, namely embryonic poly(A)-binding protein 2 and nuclear poly(A)-binding protein 1. Many studies have been undertaken to characterise the spatial and temporal expression patterns and subcellular localisations of PABPC1 and EPAB in vertebrate oocytes and early embryos. In the present review, we comprehensively evaluate and discuss the expression patterns and particular functions of the EPAB and PABPC1 genes, especially in mouse and human oocytes and early embryos.
Effects of Passive Integrated Transponder Tags on Survival, Growth, and Swimming Performance of Age‐0 Shovelnose Sturgeon
Authors: Schumann David A. , Deslauriers David , Wagner Matthew D. , Bertrand Katie N. , Graeb Brian D. S.
Published: January 2017

Innovative tools that benefit conservation biology are critical because freshwater fishes are being lost at unprecedented rates. Although mark–recapture is important to characterize population ecology and describe life history traits of declining species, techniques for tagging small‐bodied individuals are limited. Recent advances in passive integrated transponder (PIT) tag technology may transform our understanding of fish ecology by providing opportunities to tag small‐bodied fishes and early life stages of larger species. Despite the potential value of new PIT tags (8.4 × 1.4 mm), 30% smaller than those previously available, limited research has evaluated their suitability when implanted into small fishes. We evaluated the effectiveness of these tags when surgically implanted into two size‐classes (small: 40–70 mm FL; and large: 80–120 mm FL) of age‐0 Shovelnose SturgeonScaphirhynchus platorynchus. This species is closely related to the endangered Pallid SturgeonS. albusand is often used as a surrogate in research. We compared by size‐class, tag loss (retention and mortality), growth rates, and swimming performance (Ucrit) of Shovelnose Sturgeon implanted with PIT tags versus control and sham treatment groups. We found that application opportunities for advanced PIT tag technology for larger age‐0 sturgeon (>80 mm) are abundant due to little tag loss, uncompromised growth rates, and unchanged swimming performance. However, managers tagging smaller sturgeon earlier in the growing season should expect high mortality rates, impacts to growth, and worsened swimming performance. These findings provide critical information concerning the suitability of surgically implanted PIT tags in age‐0 sturgeon to study young sturgeon ecology that was previously unavailable.

Received June 23, 2016; accepted October 25, 2016 Published online January 20, 2017
Deletion and Copy Number Variation of Y‐Chromosomal Regions in Coho Salmon, Chum Salmon, and Pink Salmon Populations
Authors: Muttray A. F. , Sakhrani D. , Smith J. L. , Nakayama I. , Davidson W. S. , Park L. , Devlin R. H.
Published: January 2017

The linkage between the Y‐chromosomal DNA marker GH‐Y (growth hormone pseudogene) and the Y‐associated sex‐determining locus was examined in 31 populations of Coho Salmon Oncorhynchus kisutch, 29 populations of Chum Salmon O. keta, and 14 populations of Pink Salmon O. gorbuscha from North America (British Columbia [BC] and Yukon, Canada; Oregon and Washington, USA) and Japan to examine the stability of Y‐chromosome sequences in salmonids. This marker is used for genetic sexing of multiple salmon species both for population studies and for aquaculture strain development. We found a strong association between GH‐Y and sex in Coho Salmon (with rare exceptions seen in Washington and Oregon only), whereas the association of GH‐Y and sex was weak in Chum Salmon and Pink Salmon. Up to 100% of males lacking GH‐Y were found in some BC Chum Salmon populations, whereas there were no exceptional (GH‐Y‐negative) males in Japan, the Yukon, or Washington, indicating strong geographic clustering of GH‐Y marker deletion. For Pink Salmon, there was an average of 29% male exceptions in BC populations. For both Pink Salmon and Chum Salmon, many more GH‐Y‐negative males than GH‐Y‐positive females were observed. To investigate whether sex reversal, recombination, or differential mutation and selection mechanisms occur in Pink Salmon, we conducted reciprocal single‐pair crosses using regular males, regular females, and exceptional individuals (GH‐Y‐negative males and GH‐Y‐positive females). The results showed that the GH‐Y locus from GH‐Y‐positive males and females was stably inherited by the F1 progeny independently of the sex‐determining locus and that this chromosomal region was not necessary for male differentiation. The present data suggest that the genomic organization of the salmonid Y‐chromosome is highly dynamic and subject to multiple forms of sequence copy number variation at multiple loci. Whether this variation has fitness implications or is selectively neutral in populations remains to be examined.

Received July 13, 2016; accepted October 19, 2016 Published online January 20, 2017
Oikonymic Transformations in Romania in the Second Half of the Twentieth Century
Authors: Felecan Oliviu
Published: January 2017

The end of World War II caused numerous changes in the urban toponymy of Central and Eastern Europe. For instance, Brașov, one of the most important Romanian cities, bore the name Orașul Stalin (“Stalin city”) for 10 years. It was an homage paid to the Soviet leader, whose name could be identified in another 13 oikonyms in the Eastern bloc, behind the Iron Curtain: Stalingrad — Volgograd (USSR), Stalin — Varna (Bulgaria), Stalinstadt — Eisenhüttenstadt (German Democratic Republic), Stalinograd — Katowice (Poland), Stalino — Donețk (Ukraine), and Sztálinváros — Dunaújváros (Hungary), among others. Some of the city names abusively altered during communism were readopted after the Revolution of 1989, which brought about the demise of the totalitarian regime in Romania. However, this was not the case with several hundred villages and communes whose names had been changed in 1964 because central authorities believed they displayed negative or inappropriate connotations.
An inducible ER–Golgi tether facilitates ceramide transport to alleviate lipotoxicity
Authors: Liu Li-Ka , Choudhary Vineet , Toulmay Alexandre , Prinz William A.
Published: January 2017

Ceramides are key intermediates in sphingolipid biosynthesis and potent signaling molecules. However, excess ceramide is toxic, causing growth arrest and apoptosis. In this study, we identify a novel mechanism by which cells prevent the toxic accumulation of ceramides; they facilitate nonvesicular ceramide transfer from the endoplasmic reticulum (ER) to the Golgi complex, where ceramides are converted to complex sphingolipids. We find that the yeast protein Nvj2p promotes the nonvesicular transfer of ceramides from the ER to the Golgi complex. The protein is a tether that generates close contacts between these compartments and may directly transport ceramide. Nvj2p normally resides at contacts between the ER and other organelles, but during ER stress, it relocalizes to and increases ER–Golgi contacts. ER–Golgi contacts fail to form during ER stress in cells lacking Nvj2p. Our findings demonstrate that cells regulate ER–Golgi contacts in response to stress and reveal that nonvesicular ceramide transfer out of the ER prevents the buildup of toxic amounts of ceramides.
Two distinct membrane potential–dependent steps drive mitochondrial matrix protein translocation
Authors: Schendzielorz Alexander Benjamin , Schulz Christian , Lytovchenko Oleksandr , Clancy Anne , Guiard Bernard , Ieva Raffaele , van der Laan Martin , Rehling Peter
Published: January 2017

Two driving forces energize precursor translocation across the inner mitochondrial membrane. Although the membrane potential (Δψ) is considered to drive translocation of positively charged presequences through the TIM23 complex (presequence translocase), the activity of the Hsp70-powered import motor is crucial for the translocation of the mature protein portion into the matrix. In this study, we show that mitochondrial matrix proteins display surprisingly different dependencies on the Δψ. However, a precursor’s hypersensitivity to a reduction of the Δψ is not linked to the respective presequence, but rather to the mature portion of the polypeptide chain. The presequence translocase constituent Pam17 is specifically recruited by the receptor Tim50 to promote the transport of hypersensitive precursors into the matrix. Our analyses show that two distinct Δψ-driven translocation steps energize precursor passage across the inner mitochondrial membrane. The Δψ- and Pam17-dependent import step identified in this study is positioned between the two known energy-dependent steps: Δψ-driven presequence translocation and adenosine triphosphate–driven import motor activity.
Organoids: A historical perspective of thinking in three dimensions
Authors: Simian Marina , Bissell Mina J.
Published: January 2017

In the last ten years, there has been a dramatic surge in the number of publications where single or groups of cells are grown in substrata that have elements of basement membrane leading to the formation of tissue-like structures referred to as organoids. However, this field of research began many decades ago, when the pioneers of cell culture began to ask questions we still ask today: How does organogenesis occur? How do signals integrate to make such vastly different tissues and organs given that the sequence of the genome in our trillions of cells is identical? Here, we summarize how work over the past century generated the conceptual framework that has allowed us to make progress in the understanding of tissue-specific morphogenetic programs. The development of cell culture systems that provide accurate and physiologically relevant models are proving to be key in establishing appropriate platforms for the development of new therapeutic strategies.
ULK1 cycling: The ups and downs of the autophagy response
Authors: Zhao Yan G. , Zhang Hong
Published: January 2017

The Ser/Thr kinase ULK1/Atg1 controls autophagy initiation under nutrient starvation conditions. In this issue, Nazio et al. (2016. J. Cell Biol. https://doi.org/10.1083/jcb.201605089) demonstrate that oscillatory modulation of NEDD4L-mediated proteasomal degradation and mTOR-dependent de novo protein synthesis of ULK1 ensures the proper amplitude and duration of the autophagy response during prolonged starvation, thus maintaining cellular homeostasis.
Divisive suppression explains high-precision firing and contrast adaptation in retinal ganglion cells
Authors: Cui Yuwei , Wang Yanbin V. , Park Silvia J. H. , Demb Jonathan B. , Butts Daniel A.
Published: January 2017

Visual processing depends on specific computations implemented by complex neural circuits. Here, we present a circuit-inspired model of retinal ganglion cell computation, targeted to explain their temporal dynamics and adaptation to contrast. To localize the sources of such processing, we used recordings at the levels of synaptic input and spiking output in the in vitro mouse retina. We found that an ON-Alpha ganglion cell's excitatory synaptic inputs were described by a divisive interaction between excitation and delayed suppression, which explained nonlinear processing already present in ganglion cell inputs. Ganglion cell output was further shaped by spike generation mechanisms. The full model accurately predicted spike responses with unprecedented millisecond precision, and accurately described contrast adaption of the spike train. These results demonstrate how circuit and cell-intrinsic mechanisms interact for ganglion cell function and, more generally, illustrate the power of circuit-inspired modeling of sensory processing.
A data citation roadmap for scientific publishers
Authors: Cousijn Helena , Kenall Amye , Ganley Emma , Harrison Melissa , Kernohan David , Lemberger Thomas , Murphy Fiona , Polischuk Patrick , Taylor Simone , Martone Maryann , Clark Tim
Published: January 2017

This article presents a practical roadmap for scholarly publishers to implement data citation in accordance with the Joint Declaration of Data Citation Principles (JDDCP), a synopsis and harmonization of the recommendations of major science policy bodies. It was developed by the Publishers Early Adopters Expert Group as part of the Data Citation Implementation Pilot (DCIP) project, an initiative of FORCE11.org and the NIH BioCADDIE program. The structure of the roadmap presented here follows the “life of a paper” workflow and includes the categories Pre-submission, Submission, Production, and Publication. The roadmap is intended to be publisher-agnostic so that all publishers can use this as a starting point when implementing JDDCP-compliant data citation. Authors reading this roadmap will also better know what to expect from publishers and how to enable their own data citations to gain maximum impact, as well as complying with what will become increasingly common funder mandates on data transparency.
Real-time spike sorting platform for high-density extracellular probes with ground-truth validation and drift correction
Authors: Jun James J. , Mitelut Catalin , Lai Chongxi , Gratiy Sergey L. , Anastassiou Costas A. , Harris Timothy D.
Published: January 2017

Electrical recordings from a large array of electrodes give us access to neural population activity with single-cell, single-spike resolution. These recordings contain extracellular spikes which must be correctly detected and assigned to individual neurons. Despite numerous spike-sorting techniques developed in the past, a lack of high-quality ground-truth datasets hinders the validation of spike-sorting approaches. Furthermore, existing approaches requiring manual corrections are not scalable for hours of recordings exceeding 100 channels. To address these issues, we built a comprehensive spike-sorting pipeline that performs reliably under noise and probe drift by incorporating covariance-based features and unsupervised clustering based on fast density-peak finding. We validated performance of our workflow using multiple ground-truth datasets that recently became available. Our software scales linearly and processes up to 1000-channel recording in real-time using a single workstation. Accurate, real-time spike sorting from large recording arrays will enable more precise control of closed-loop feedback experiments and brain-computer interfaces.
Ensemble coding of crowd emotion: Differential hemispheric and visual stream contributions
Authors: Im Hee Yeon , Albohn Daniel N. , Steiner Troy G. , Cushing Cody A. , Adams Reginald B. , Kveraga Kestutis
Published: January 2017

The visual system takes advantage of redundancies in the scene by extracting summary statistics from a set of items. Similarly, in many social situations where scrutinizing each individual’s expression is inefficient, human observers make snap judgments of crowds of people by reading “crowd emotion” to avoid danger (e.g., mass panic or violent mobs) or to seek help. However, how the brain accomplishes this feat remains unaddressed. Here we report a set of behavioral and fMRI studies in which participants made avoidance or approach decisions by choosing between two facial crowds presented in the left and right visual fields (LVF/RVF). Participants were most accurate for crowds containing task-relevant cues: avoiding angry crowds and approaching happy crowds. This effect was amplified by sex-linked facial cues (angry male/happy female crowds) and highly lateralized, with better recognition of the task-congruent facial crowd when presented in LVF. fMRI results showed that the dorsal visual stream was preferentially activated in crowd emotion processing, with intraparietal sulcus and superior frontal gyrus predicting behavioral crowd emotion efficiency, whereas the ventral visual stream showed greater involvement in individual face emotion processing, with fusiform cortex activity predicting the accuracy of decisions about individual face emotion. Our results shed new light on the distinction between global vs. local processing of face stimuli, revealing differential involvement of the left and right hemispheres and the dorsal and ventral pathways in reading crowd vs. individual emotion.
The shape of the contact-density function matters when modelling parasite transmission in fluctuating populations
Authors: Borremans Benny , Reijniers Jonas , Hens Niel , Leirs Herwig
Published: January 2017

Models of disease transmission in a population with changing densities must assume a relation between infectious contacts and density. Typically, a choice is made between a constant (frequency-dependence) and a linear (density-dependence) contact-density function, but it is becoming increasingly clear that intermediate, nonlinear functions intermediate are more realistic. It is currently not clear however what the exact consequences would be of different contact-density functions in fluctuating populations. By combining field data on rodent host (Mastomys natalensis) demography, experimentally-derived contact-density data, and laboratory and field data Morogoro virus infection dynamics, we explored the effects of different contact-density function shapes on transmission dynamics and invasion/persistence. While invasion and persistence were clearly affected by the shape of the function, the effects on outbreak characteristics such as infection prevalence and seroprevalence were less obvious. This means that it may be difficult to distinguish between the different shapes based on how well models fit to real data. The shape of the transmission-density function should therefore be chosen with care, and is ideally based on existing information such as a previously quantified contact- or transmission-density relationship or the underlying biology of the host species in relation to the infectious agent.
Modeling Hormonal Control of Cambium Proliferation
Authors: Oles Vladyslav , Panchenko Alexander , Smertenko Andrei
Published: January 2017

Rise of atmospheric CO2is one of the main causes of global warming. Catastrophic climate change can be avoided by reducing emissions and increasing sequestration of CO2. Trees are known to sequester CO2during photosynthesis, and then store it as wood biomass. Thus, breeding of trees with higher wood yield would mitigate global warming as well as augment production of renewable construction materials, energy, and industrial feedstock. Wood is made of cellulose-rich xylem cells produced through proliferation of a specialized stem cell niche called cambium. Importance of cambium in xylem cells production makes it an ideal target for the tree breeding programs; however our knowledge about control of cambium proliferation remains limited. The morphology and regulation of cambium differs from stem cell niches that control axial growth. For this reason, translating the knowledge about axial growth to radial growth has limited use. Furthermore, genetic approaches cannot be easily applied because overlaying tissues conceal cambium from direct observation and complicate identification of mutants. To overcome the paucity of experimental tools in cambium biology, we constructed a Boolean network CARENET (CAmbium Regulation gene NETwork) for modelling cambium activity, which includes the key transcription factors WOX4 and HD-ZIP III as well as their potential regulators. Our simulations revealed that: (1) auxin, cytokinin, gibberellin, and brassinosteroids act cooperatively in promoting transcription ofWOX4andHD-ZIP III; (2) auxin and cytokinin pathways negatively regulate each other; (3) hormonal pathways act redundantly in sustaining cambium activity; (4) individual cells in the stem cell niches can have diverse molecular identities. CARENET can be extended to include components of other signalling pathways and be integrated with models of xylem and phloem differentiation. Such extended models would facilitate breeding trees with higher wood yield.
Long-term genomic coevolution of host-parasite interaction in the natural environment
Authors: Laanto Elina , Hoikkala Ville , Ravantti Janne , Sundberg Lotta-Riina
Published: January 2017

The antagonistic coevolution of parasite infectivity and host resistance alters the biological functionality of species, with effects spanning to communities and ecosystems. Still, studies describing long-term host-parasite coevolutionary dynamics in nature are largely missing. Furthermore, the role of host resistance mechanisms for parasite evolution is poorly understood, necessitating for the molecular and phenotypic characterization of both coevolving parasites and their hosts. We combined long-term field sampling (2007-2014),in vitrocross-infections and time-shift experiments with bacteriophage whole genome sequencing and bacterial (Flavobacterium columnare) CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) profiling to show the molecular details of the phage-bacterium arms race in the environment. Bacteria were generally resistant to phages from the past and susceptible to phages in the future. The bacterial resistance selected for increased phage infectivity and host range, correlating directly with the expansion of phage genome size by 2656 bp. In the bacterial host, two CRISPR loci were identified: a type II-C locus and an RNA-targeting type VI-B locus. While maintaining a core set of conserved spacers, phage-matching spacers appeared in the variable end of both CRISPR loci over time. The appearance of these CRISPR spacers in the bacterial host often corresponded with arms race -manner molecular changes in the protospacers of the coevolving phage population. However, the phenotypic data indicated that the relative role of constitutive defence may be more important in high phage pressure, highlighting the importance of our findings for understanding microbial community ecology and in the development of phage therapy applications.
Myosin II activity is required for structural plasticity at the axon initial segment
Authors: Evans Mark D , Tufo Candida , Dumitrescu Adna S , Grubb Matthew S
Published: January 2017

In neurons, axons possess a molecularly defined and highly organised proximal region – the axon initial segment (AIS) – that is a key regulator of both electrical excitability and cellular polarity. Despite existing as a large, dense structure with specialised cytoskeletal architecture, the AIS is surprisingly plastic, with sustained alterations in neuronal activity bringing about significant alterations to its position, length or molecular composition. However, although the upstream activity-dependent signalling pathways that lead to such plasticity have begun to be elucidated, the downstream mechanisms that produce structural changes at the AIS are completely unknown. Here, we use dissociated cultures of rat hippocampus to show that two forms of AIS plasticity in dentate granule cells – long-term relocation, and more rapid shortening – are completely blocked by treatment with blebbistatin, a potent and selective myosin II ATPase inhibitor. These data establish a link between myosin II and AIS function, and suggest that myosin II’s primary role at the structure may be to effect activity-dependent morphological alterations.
TheDrosophilaDosage Compensation Complex activates target genes by chromosome looping within the active compartment
Authors: Schauer Tamás , Ghavi-Helm Yad , Sexton Tom , Albig Christian , Regnard Catherine , Cavalli Giacomo , Furlong Eileen E M , Becker Peter B
Published: January 2017

X chromosome dosage compensation inDrosophilarequires chromosome-wide coordination of gene activation. The male-specific-lethal dosage compensation complex (DCC) identifies X chromosomal High Affinity Sites (HAS) from which it boosts transcription. A sub-class of HAS, PionX sites, represent first contacts on the X. Here, we explored the chromosomal interactions of representative PionX sites by high-resolution 4C and determined the global chromosome conformation by Hi-C in sex-sorted embryos. Male and female X chromosomes display similar nuclear architecture, concordant with clustered, constitutively active genes. PionX sites, like HAS, are evenly distributed in the active compartment and engage in short- and long-range interactions beyond compartment boundaries. Byde novoinduction of DCC in female cells, we monitored the extent of activation surrounding PionX sites. This revealed a remarkable range of DCC action not only in linear proximity, but also at megabase distance if close in space, suggesting that DCC profits from pre-existing chromosome folding to activate genes.
Incommensurate atomic density waves in the high-pressure IVb phase of barium
Authors: Arakcheeva Alla , Bykov Maxim , Bykova Elena , Dubrovinsky Leonid , Pattison Phil , Dmitriev Vladimir , Chapuis Gervais
Published: January 2017

The host–guest structures of elements at high pressure discovered a decade ago still leave many open questions due to the lack of precise models based on full exploitation of the diffraction data. This concerns in particular Ba IV, which is stable in the range 12–45 GPa. With the example of phase Ba IVb, which is characterized here for the first time, a systematic analysis is presented of possible host–guest structure models based on high-quality single-crystal diffraction data obtained with synchrotron radiation at six different pressures between 16.5 and 19.6 GPa. It is shown that a new incommensurately modulated (IM) structure model better fits the experimental data. Unlike the composite models which are commonly reported for the Ba IV phases, the IM model reveals a density wave and its pressure-dependent evolution. The crucial role played by the selected model in the interpretation of structure evolution under pressure is discussed. The findings give a new experimental basis for a better understanding of the nature of host–guest structures.
Crystal structure of trirubidium citrate monohydrate from laboratory X-ray powder diffraction data and DFT comparison
Authors: Rammohan Alagappa , Kaduk James A.
Published: January 2017

The crystal structure of the title compound, 3Rb+·C6H5O73−·H2O, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The hydroxy group participates in an intramolecular hydrogen bond to the deprotonated central carboxylate group with graph-set motifS(5). The water molecule acts as a hydrogen-bond donor to both terminal and central carboxylate O atoms. The three independent rubidium cations are seven-, six- and six-coordinate, with bond-valence sums of 0.84, 1.02, and 0.95, respectively. In the extended structure, their polyhedra share edges and corners to form a three-dimensional network. The hydrophobic methylene groups occupy channels along thebaxis.
fac-Acetonitriletricarbonyl(dimethylcarbamodithioato-κ2S,S′)rhenium(I): crystal structure and Hirshfeld surface analysis
Authors: Tan Sang Loon , Lee See Mun , Heard Peter J. , Halcovitch Nathan R. , Tiekink Edward R. T.
Published: January 2017

The title compound, [Re(C3H6NS2)(C2H3N)(CO)3], features an octahedrally coordinated ReIatom within a C3NS2donor set defined by three carbonyl ligands in afacialarrangement, an acetonitrile N atom and two S atoms derived from a symmetrically coordinating dithiocarbamate ligand. In the crystal, dithiocarbamate-methyl-H...O(carbonyl) interactions lead to supramolecular chains along [36-1]; both dithiocarbamate S atoms participate in intramolecular methyl-H...S interactions. Further but weaker acetonitrile-C—H...O(carbonyl) interactions assemble molecules in theabplane. The nature of the supramolecular assembly was also probed by a Hirshfeld surface analysis. Despite their weak nature, the C—H...O contacts are predominant on the Hirshfeld surface and, indeed, on those of related [Re(CO)3(C3H6NS2)L] structures.
Crystal structure of dicesium hydrogen citrate from laboratory single-crystal and powder X-ray diffraction data and DFT comparison
Authors: Rammohan Alagappa , Sarjeant Amy A. , Kaduk James A.
Published: January 2017

The crystal structure of dicesium hydrogen citrate, 2Cs+·C6H6O72−, has been solved using laboratory X-ray single-crystal diffraction data, refined using laboratory powder X-ray data, and optimized using density functional techniques. The Cs+cation is nine-coordinate, with a bond-valence sum of 0.92 valence units. The CsO9coordination polyhedra share edges and corners to form a three-dimensional framework. The citrate anion is located on a mirror plane. Its central hydroxy/carboxylate O—H...O hydrogen bond is short, and (unusually) intermolecular. The centrosymmetric end-end carboxylate hydrogen bond is exceptionally short (O...O = 2.416 Å) and strong. These hydrogen bonds contribute 16.5 and 21.7 kcal mol−1, respectively, to the crystal energy. The hydrophobic methylene groups occupy pockets in the framework.
Crystal structure ofcatena-poly[[copper(II)-μ2-salicylato-[diaquacopper(II)]-μ2-salicylato] dihydrate]
Authors: Horn Jitschaq A. van der , Lutz Martin
Published: January 2017

The title compound, {[Cu2(C7H4O3)2(H2O)2]·2H2O}n, contains two copper(II) cations in special positions (one on a twofold rotation axis and one on an inversion centre) and the the salicylate ligand in its dianionic form. By four- and six-coordinate metal coordination, chains are formed parallel to [001], which are extended by O—H...O hydrogen bonding into sheets extending parallel to (100). These sheets are weakly connected by O—H...O hydrogen bondingviathe non-coordinating lattice water molecules into a three-dimensional network.
2-(5-Bromothiophen-2-yl)-1-phenyl-1H-phenanthro[9,10-d]imidazole
Authors: Kavitha T. , Mayakrishnan Sivakalai , Perumal T. Paramasivam , Suvasini Chandramouleeswaran , Lakshmi Srinivasakannan
Published: January 2017

In the title molecule, C25H15BrN2S, the phenanthrene system is slightly skewed, with a dihedral angle of 8.94 (16)° between the outer benzene rings. The imidazole ring makes dihedral angles of 15.18 (16), 2.94 (15) and 88.46 (16)°, respectively, with the thiophene ring, the central benzene ring of the phenanthrene unit and the phenyl ring attached to the latter unit. In the molecule, there are two C—H...π interactions present involving the phenyl ring. In the crystal, molecules are linked by C—H...N and C—H...Br hydrogen bonds, forming zigzag chains along the a axis. The chains are linked by C—H...π interactions, forming a three-dimensional supramolecular structure.