bluuebunny/crossref_metadata_2025 huggingface dataset:
Dioxygen Binding in the Active Site of Histone Demethylase JMJD2A and the Role of the Protein Environment
Authors: Cortopassi Wilian A. , Simion Robert , Honsby Charles E. , França Tanos C. C. , Paton Robert S.
Published: November 2015

JMJD2A catalyses the demethylation of di‐ and trimethylated lysine residues in histone tails and is a target for the development of new anticancer medicines. Mechanistic details of demethylation are yet to be elucidated and are important for the understanding of epigenetic processes. We have evaluated the initial step of histone demethylation by JMJD2A and demonstrate the dramatic effect of the protein environment upon oxygen binding using quantum mechanics/molecular mechanics (QM/MM) calculations. The changes in electronic structure have been studied for possible spin states and different conformations of O2, using a combination of quantum and classical simulations. O2 binding to this histone demethylase is computed to occur preferentially as an end‐on superoxo radical bound to a high‐spin ferric centre, yielding an overall quintet ground state. The favourability of binding is strongly influenced by the surrounding protein: we have quantified this effect using an energy decomposition scheme into electrostatic and dispersion contributions. His182 and the methylated lysine assist while Glu184 and the oxoglutarate cofactor are deleterious for O2 binding. Charge separation in the superoxo‐intermediate benefits from the electrostatic stabilization provided by the surrounding residues, stabilizing the binding process significantly. This work demonstrates the importance of the extended protein environment in oxygen binding, and the role of energy decomposition in understanding the physical origin of binding/recognition.
Stabilization of the Low‐Spin State in a Mononuclear Iron(II) Complex and High‐Temperature Cooperative Spin Crossover Mediated by Hydrogen Bonding
Authors: Zheng Sipeng , Reintjens Niels R. M. , Siegler Maxime A. , Roubeau Olivier , Bouwman Elisabeth , Rudavskyi Andrii , Havenith Remco W. A. , Bonnet Sylvestre
Published: November 2015

The tetrapyridyl ligand bbpya (bbpya=N,N‐bis(2,2′‐bipyrid‐6‐yl)amine) and its mononuclear coordination compound [Fe(bbpya)(NCS)2] (1) were prepared. According to magnetic susceptibility, differential scanning calorimetry fitted to Sorai’s domain model, and powder X‐ray diffraction measurements, 1 is low‐spin at room temperature, and it exhibits spin crossover (SCO) at an exceptionally high transition temperature of T1/2=418 K. Although the SCO of compound 1 spans a temperature range of more than 150 K, it is characterized by a wide (21 K) and dissymmetric hysteresis cycle, which suggests cooperativity. The crystal structure of the LS phase of compound 1 shows strong NH⋅⋅⋅S intermolecular H‐bonding interactions that explain, at least in part, the cooperative SCO behavior observed for complex 1. DFT and CASPT2 calculations under vacuum demonstrate that the bbpya ligand generates a stronger ligand field around the iron(II) core than its analogue bapbpy (N,N′‐di(pyrid‐2‐yl)‐2,2′‐bipyridine‐6,6′‐diamine); this stabilizes the LS state and destabilizes the HS state in 1 compared with [Fe(bapbpy)(NCS)2] (2). Periodic DFT calculations suggest that crystal‐packing effects are significant for compound 2, in which they destabilize the HS state by about 1500 cm−1. The much lower transition temperature found for the SCO of 2 compared to 1 appears to be due to the combined effects of the different ligand field strengths and crystal packing.
Oxygen‐Assisted Synthesis of Mesoporous Palladium Nanoparticles as Highly Active Electrocatalysts
Authors: Li Cuiling , Jiang Bo , Imura Masataka , Umezawa Naoto , Malgras Victor , Yamauchi Yusuke
Published: November 2015

Mesoporous Pd nanoparticles (MPNs) enclosed by high‐index facets have been successfully prepared by taking advantage of successive oxygen adsorption and desorption caused by the oxidative etching effect. The as‐prepared MPNs exhibit excellent performance toward formic acid electro‐oxidation, which is due to the synergetic effect between the diffusion‐feasible tubular mesochannels and the high index facets.
Addressing the Glycine‐Rich Loop of Protein Kinases by a Multi‐Facetted Interaction Network: Inhibition of PKA and a PKB Mimic
Authors: Lauber Birgit S. , Hardegger Leo A. , Asraful Alam K. , Lund Bjarte A. , Dumele Oliver , Harder Michael , Kuhn Bernd , Engh Richard A. , Diederich François
Published: November 2015

Protein kinases continue to be hot targets in drug discovery research, as they are involved in many essential cellular processes and their deregulation can lead to a variety of diseases. A series of 32 enantiomerically pure inhibitors was synthesized and tested towards protein kinase A (PKA) and protein kinase B mimic PKAB3 (PKA triple mutant). The ligands bind to the hinge region, ribose pocket, and glycine‐rich loop at the ATP site. Biological assays showed high potency against PKA, with Ki values in the low nanomolar range. The investigation demonstrates the significance of targeting the often neglected glycine‐rich loop for gaining high binding potency. X‐ray co‐crystal structures revealed a multi‐facetted network of ligand–loop interactions for the tightest binders, involving orthogonal dipolar contacts, sulfur and other dispersive contacts, amide–π stacking, and H‐bonding to organofluorine, besides efficient water replacement. The network was analyzed in a computational approach.
Joachim Bohm – life and work
Authors: Heimann Robert B.
Published: November 2015

This contribution sketches important stages of the life and work of Professor Dr Joachim Bohm, together with an abbreviated bibliography that considers only those contributions that immediately relate to these stages. In total, the publication list of Joachim Bohm contains close to 200 entries, covering issues of crystal symmetry, physico‐chemical crystallography as well as growth and characterization of single crystals of advanced ceramic materials.
Effects of aluminum substitution on the structure and electric properties of langasite family crystals
Authors: Takeda Hiroaki , Yamaura Jun‐ichi , Nishida Takashi , Hoshina Takuya , Tsurumi Takaaki
Published: November 2015

The effects of aluminum substitution on the structure and electric properties of langasite (La3Ga5SiO14) family crystals are reported. The maximum Al content x of La3Ga5‐xAlxSiO14 (LGAS), La3Nb0.5Ga5.5‐xAlxO14 (LNGA), and La3Ta0.5Ga5.5‐xAlxO14 (LTGA) crystals grown by the conventional Czochralski technique are x = 0.9, 0.2, and 0.5, respectively. Single‐crystal X‐ray structural analysis reveals that Al atoms are distributed in all cation sites except for the decahedral one occupied by La, rather than favoring the smallest tetrahedral sites. The electrical properties of the Al‐substituted crystals were also compared with those of pure ones. Al substitution was found to affect the piezoelectric constant d14, but not d11. The LGAS and LTGA crystals exhibit higher electric resistivity ρ as a result of Al substitution. Among the Al‐substituted and pure crystals, the LTGA crystal featured the lowest temperature dependence of d11 and highest ρ, making it the most suitable of the group for high‐temperature piezoelectric applications.
Calibration of interphase fluorescence in situ hybridization cutoff by mathematical models
Authors: Du Qinghua , Li Qingshan , Sun Daochun , Chen Xiaoyan , Yu Bizhen , Ying Yi
Published: November 2015

Fluorescence in situ hybridization (FISH) continues to play an important role in clinical investigations. Laboratories may create their own cutoff, a percentage of positive nuclei to determine whether a specimen is positive or negative, to eliminate false positives that are created by signal overlap in most cases. In some cases, it is difficult to determine the cutoff value because of differences in both the area of nuclei and the number of signals. To address these problems, we established two mathematical models using probability theory. To verify these two models, normal disomy cells from healthy individuals were used to simulate cells with different numbers of signals by hybridization with different probes. We used an X/Y probe to obtain the average distance between two signals and the probability of signal overlap in different nuclei area. Frequencies of all signal patterns were scored and compared with theoretical frequencies, and models were assessed using a goodness of fit test. We used five BCR/ABL1‐positive samples, 20 BCR/ABL1‐negative samples and two samples with ambiguous results to verify the cutoff calibrated by these two models. The models were in agreement with experimental results. The dynamic cutoff can classify cases in routine analysis correctly, and it can also correct for influences from nuclei area and the number of signals in some ambiguous cases. The probability models can be used to assess the effect of signal overlap and calibrate the cutoff. © 2015 International Society for Advancement of Cytometry
Support your faculty when students request unreasonable accommodations
Authors: Gaddy Stephanie
Published: November 2015

In your role as a disability services provider you are primarily focused on the process of promoting equitable access for your students with disabilities. Generally, when you have students with disabilities who self‐advocate, follow the procedures to secure accommodations in their academic courses, and work collaboratively with their faculty members, this process is smooth. When the process becomes disrupted, that is usually a result of your students not self‐advocating or following the process.
Consider creative approaches to balancing family with career
Authors: McCarthy Claudine
Published: November 2015

ORLANDO, FLA. — Finding the right balance between family and work certainly has its challenges for any parent. But that juggle becomes even more challenging when you have a career with long hours and academic events that often overlap into nights and weekends. It's further complicated if you're a single parent or if your career takes you far from the support of extended family.
Consider needs of institution, students when planning your application strategy
Authors: Hope Joan
Published: November 2015

The application process can be an important part of your institution's recruitment strategy. So the decisions you make about the process should align with your institution's goals in terms of the types and numbers of students you wish to enroll.
Build a better team by engaging creative strengths
Authors: Sutton Halley
Published: November 2015

CHICAGO — As an enrollment manager, you constantly work on projects with teams. Without the proper understanding of the different creative styles your team members possess, you cannot tap the full potential of your team or manage the complicated dynamics that come from many different types of creative styles. In a session led by June Hanley during the annual convention for the Society for College and University Planning, participants were led through an exercise based on The Five Faces of Genius by Annette Moser‐Wellman and given instructions on how to create a well‐rounded team that takes advantage of different creative styles. Hanley outlined the following five types of creativity:
More rain, less soil: long‐term changes in rainfall intensity with climate change
Authors: Burt Tim , Boardman John , Foster Ian , Howden Nicholas
Published: November 2015

This commentary discusses the role of long‐term climate change in driving increases in soil erosion. Assuming that land use and management remain effectively constant, we discuss changes in the ability of rainfall to cause erosion (erosivity), using long daily rainfall data sets from southeast England. An upward trend in mean rainfall per rain day is detected at the century‐plus timescale. Implications for soil erosion and sediment delivery are discussed and evidence from other regions reviewed. We conclude that rates of soil erosion may well increase in a warmer, wetter world. Copyright © 2015 John Wiley & Sons, Ltd.
Some Remarks on Rainbow Connectivity
Authors: Kamčev Nina , Krivelevich Michael , Sudakov Benny
Published: November 2015

An edge (vertex) colored graph is rainbow‐connected if there is a rainbow path between any two vertices, i.e. a path all of whose edges (internal vertices) carry distinct colors. Rainbow edge (vertex) connectivity of a graph G is the smallest number of colors needed for a rainbow edge (vertex) coloring of G. In this article, we propose a very simple approach to studying rainbow connectivity in graphs. Using this idea, we give a unified proof of several known results, as well as some new ones.
Functional outcomes after different types of transoral supraglottic laryngectomy
Authors: Piazza Cesare , Barbieri Diego , Del Bon Francesca , Grazioli Paola , Perotti Pietro , Paderno Alberto , Frittoli Barbara , Mazza Giancarlo , Penco Sara , Gaggero Giovanna , Nicolai Piero , Peretti Giorgio
Published: November 2015

Objectives/Hypothesis

To seek a correlation between the four types of transoral supraglottic laryngectomies (TSLs) according to the European Laryngological Society (ELS) and postoperative morbidity.

Study Design

Retrospective case series at an academic institution.

Methods

Chart review was done for 96 patients affected by T1–T3 supraglottic cancers (28 pT1, 46 pT2, 22 pT3) treated by TSL (29 type I, 14 type II, 35 type III, 18 type IV) with CO2 laser. Five‐year overall survival (OS), disease‐specific survival (DSS), local control with laser alone (LCL), and organ preservation (OP) were calculated by Kaplan‐Meier curves. Thirty‐six patients were submitted to swallowing evaluation by M. D. Anderson Dysphagia Inventory (MDADI), videoendoscopy of swallow (VEES), and videofluoroscopy (VFS). Hospitalization, tracheotomy, nasogastric feeding tube (NGFT), and complications were compared between type I–II versus III–IV TSLs for the entire series. MDADI and VEES/VFS scores were compared in the subgroup of 36 patients.

Results

Five‐year OS, DSS, LCL, and OP rates were 69%, 85.9%, 89.2%, and 92.6%. Mean hospitalization was 9 days, tracheotomy was required in 7% of patients, an NGFT was required in 33%, and 11% experienced complications. Type III–IV TSLs were associated with increased hospitalization (P < .001), more NGFTs (P = .001), and 90% of complications (P = .021). Aspiration was seen in 0% and 9% of type I–II TSLs, and in 7% and 43% of type III–IV TSLs by VEES and VFS, respectively.

Conclusions

Type III–IV TSLs present higher morbidity and complications, thus confirming the utility of the ELS classification in preoperative counseling and therapeutic planning.

Level of Evidence

4 Laryngoscope, 126:1131–1135, 2016
Light on a beam splitter: More randomness with single photons
Authors: Oberreiter Lukas , Gerhardt Ilja
Published: November 2015

One of the most fundamental quantum random number generators is implemented with light impinging onto a beam splitter, and two single photon detectors at its output. Often, this generator is described as “a photon which takes one or other path towards a detector”. The input state of light in conjunction with the detector response is relevant for the amount, the pattern, and the correlation of the generated clicks. Only a fraction of all generator outcomes, the min‐entropy, can be used as a further resource for true randomness. This paper addresses the difference in the common description with incoming single photons and the often implemented scheme with a weak coherent light source, such as an attenuated laser. For this very fundamental and widely used configuration the amount of usable entropy is compared. If single photons from an anti‐bunched light source are supplied, the amount of entropy is higher than for the case of a supplied coherent state – although the latter can be arbitrarily bright unlike the single photon source.

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On the Environmental and Electrical Bias Stability of Radical Polymer Conductors in the Solid State
Authors: Baradwaj Aditya G. , Rostro Lizbeth , Boudouris Bryan W.
Published: November 2015

Radical polymers are emerging as a promising class of electronically active macromolecules for solid‐state organic electronic applications due to their synthetic flexibility and scalability; however, the electrical and chemical stability of radical polymer thin films has yet to be established. Here, it is demonstrated that the model radical polymer, poly(2,2,6,6‐tetramethylpiperidinyloxy methacrylate) (PTMA), shows excellent solid‐state electrochemical stability when exposed to both bias stressing and varying amounts of moisture in the environment. Specifically, PTMA thin films show consistent performance when continuously swept across a variety of voltage ranges. Furthermore, PTMA remains stable when exposed to a constantly applied bias for 20 h. These two key results demonstrate the stability of the open‐shell repeat unit and the reversibility of the chemical oxidation–reduction (redox) reaction that facilitates charge transport. Additionally, PTMA thin films that are exposed to a range of relative humidity values for 2 h retained consistent electronic performance before and after humidity exposure. This highlights that exposure to water vapor does not decrease the robustness associated with the nitroxide radical. These results establish the stoutness associated with radical polymers and highlight the potential for radical polymers to be implemented in a number of advanced organic electronic technologies.

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Reliability of eccentric position of the pedicle instead of central position in a thoracodorsal artery perforator flap
Authors: Kim Youn Hwan , Lee Han Earl , Lee Jang Hyun , Kim Jeong Tae , Kim Sang Wha
Published: November 2015

Introduction

To obtain longer vascular pedicle in perforator flaps, surgeons often use eccentrically rather than centrally located perforators. The aim of this study was to compare the safety and reliability of thoracodorsal artery perforator (TDAP) flaps harvested with centrally or eccentrically located perforators.

Methods

Between January 2008 and March 2012, 100 TDAP flaps were used to reconstruct the lower extremity defects. Flaps longer than 10 cm, with a single musculocutaneous perforator, and one artery‐one vein anastomoses were included. The cases were divided into two groups according to perforator location; Central perforators in 60 cases (group 1), and peripheral perforators in 40 cases (group 2). Total pedicle length was between the points where the perforator enters the flap to the end of the pedicle. Real pedicle length was from flap margin to the end of the pedicle. The flap dimension, total pedicle length, real pedicle length, and flap related complications were measured.

Results

The flaps were smaller in group 1 than in group 2 (159.6 ± 94.08 vs.189.95 ± 134.30 cm2, P = 0.455). Total pedicle length was almost the same (12.12 ± 1.57 vs.12.88 ± 2.10 cm, P = 0.420), but the mean real pedicle length was longer in group 2 (6.13 ± 1.33 vs.11.65 ± 2.08 cm, P < 0.05).

There were 4 cases of partial loss of flap in group 1 and 3 partial loss and one total flap loss in group 2 without significant difference (P = 0.547).

Conclusions

Using eccentrically located perforators is simple method of extending real pedicle length, but there have been concerns regarding flap perfusion and distal vascularity. Our findings suggest that, in TDAP flaps, both eccentric and central perforator are safe options. © 2014 Wiley Periodicals, Inc. Microsurgery 37:44–48, 2017.
Hydroxytyrosol, a product from olive oil, reduces colon cancer growth by enhancing epidermal growth factor receptor degradation
Authors: Terzuoli Erika , Giachetti Antonio , Ziche Marina , Donnini Sandra
Published: November 2015

Scope

We studied the effects and mechanism of 2‐(3,4‐dihydroxyphenil)ethanol (or hydroxytyrosol, HT), a polyphenol from extra virgin olive oil, investigating the regulation of epidermal growth factor receptor (EGFR) expression in colon tumour cells.

Methods and results

We demonstrate that HT significantly downregulates EGFR expression in human colorectal adenocarcinoma cells HT‐29, CaCo2, and WiDr, and in HT‐29 xenografts. HT accelerates EGFR degradation by reducing its half‐life. Specifically, HT induces EGFR ubiquitination that is mediated by phosphorylation at pY1045, the docking site for Cbl, thereby enabling receptor ubiquitination and degradation. Pretreatment with either the lysosomal inhibitor chloroquine, or the proteasomal inhibitor MG132 blocks HT‐induced EGFR downregulation. In colon cancer cells, EGFR downregulation by HT is associated with reduced cell proliferation. Tumour growth and EGFR expression levels are also decreased by HT treatment in HT‐29 xenograft.

Conclusion

We conclude that HT downregulates EGFR expression via lysosomal and proteasomal degradation, activated by HT‐induced EGFR phosphorylation at pY1045 and increased Cbl activity. Cbl activation induces, in turn, EGFR ubiquitination. Our results reveal a new mechanism for HT's antitumour effects that may be important for colon tumour prevention and treatment.
Modeling of anisotropic thermal conductivity of polymer composites containing aligned boron nitride platelets: Effect of processing methods
Authors: Chen Lin , Xu Hong‐Fei , Sun Ying‐Ying , Du Xiao‐Ze , He Shao‐Jian , Lin Jun , Nazarenko Sergei
Published: November 2015

Hexagonal boron nitride (h‐BN) can remarkably enhance the thermal conductivity (TC) of polymer composites, while maintaining high electrical insulation. In this article, the previously developed analytical model, which can simultaneously solve the anisotropic TC of polymer composites containing aligned h‐BN platelets, was improved by introducing a power function to define the polymer thickness ratio in the unit cell. The modified model was validated by an excellent agreement with the experimental results from three independent literatures, in which the samples were prepared by either casting (including tape casting and spin casting) or injection molding. The influence of key parameters on the composite TCs was analyzed. It was found that the power n closely relates to the possessing methods for the polymer composites, which are also well correlated with the behavior of anisotropic TC. POLYM. COMPOS., 38:2670–2678, 2017. © 2015 Society of Plastics Engineers
Wannier functions of cumulene: A tight‐binding approach
Authors: Ribeiro Allan V. , Nacbar Denis R. , Bruno‐Alfonso Alexys
Published: November 2015

Exponentially localized Wannier functions of cumulene are calculated from the Bloch functions obtained through a tight‐binding approach. Numerical results and discussions are given for the and bands. In the latter case, the single‐band Wannier functions are similar to the orbitals of a diatomic molecule, while the two‐band Wannier functions resemble hybrid atomic orbitals.

Contour plot of an sp‐like Wannier function of cumulene.
Alleviating the bias induced by the linear analysis update with an isopycnal ocean model
Authors: Wang Y. , Counillon F. , Bertino L.
Published: November 2015

This work is based on the Norwegian Climate Prediction Model (NorCPM), which applies the ensemble Kalman filter (EnKF) to a fully coupled Earth System Model (NorESM) with an isopycnic ocean model (MICOM) for climate predictions. An idealized assimilation framework is first developed to identify the origin of assimilation‐created bias in the current version of NorCPM. It is found that the bias in ocean heat and salt contents is introduced by the non‐negativity constraint of isopycnic layer thickness values. Secondly, a new and computationally efficient method (referred to as upscaling) is proposed and tested in the idealized framework. In the upscaling method, layers for which analysis yields negative values are grouped iteratively with neighbouring layers, resulting in a probability density function with a larger mean and smaller standard deviation that prevents the appearance of negative layer thickness values. Analysis increments of the grouped layer are then distributed proportionally, which also prevents empty layers from becoming filled and vice versa. The upscaling method acts as a moderation in the location where the non‐negativity constraint is not satisfied and, as such, is suboptimal. The upscaling method shows a reduction in heat and salt contents and sea‐surface height bias by a factor of 10. A small bias remains, due to the update of ensemble anomalies, but the upscaling method would be unbiased for the heat and salt contents with data assimilation methods that utilize a static forecast‐error covariance matrix (e.g. EnOI). Finally, the upscaling method is demonstrated in a realistic framework with NorCPM by assimilating sea‐surface temperature observations. Over a 25 year analysis period, the new method does not impair the predictive skill of the system but corrects the assimilation‐created bias in steric sea‐level rise and provides an estimation in better agreement with the Intergovernmental Panel on Climate Change.
A theoretical understanding of the energy difference between singlet and triplet states of oligoacene molecules
Authors: Kim Dongwook
Published: November 2015

The origin of singlet–triplet energy difference, ΔEST, in π‐conjugated molecules was elucidated by carrying out ab initio calculations of acene molecules at scaled opposite‐spin (SOS)‐CIS(D0) level of theory using aug‐cc‐pVDZ basis sets. Both singlet and triplet excitation energies decrease monotonously as π‐conjugation expands. However, ΔEST is found to evolve in rather complicated manner; it increases in going from benzene to anthracene and diminishes thereafter. To better understand this behavior, excitation energy decomposition at CIS level of theory was conducted, and the variations of Coulomb‐ and exchange‐type integrals between the excited and remnant electrons as a function of π‐conjugation length were discussed. The effects of dynamic electron correlation on both singlet and triplet excitation energies and ΔEST were also discussed. © 2015 Wiley Periodicals, Inc.
Hybrid Flexible Resistive Random Access Memory‐Gated Transistor for Novel Nonvolatile Data Storage
Authors: Han Su‐Ting , Zhou Ye , Chen Bo , Wang Chundong , Zhou Li , Yan Yan , Zhuang Jiaqing , Sun Qijun , Zhang Hua , Roy V. A. L.
Published: November 2015

Here, a single‐device demonstration of novel hybrid architecture is reported to achieve programmable transistor nodes which have analogies to flash memory by incorporating a resistive switching random access memory (RRAM) device as a resistive switch gate for field effect transistor (FET) on a flexible substrate. A high performance flexible RRAM with a three‐layered structure is fabricated by utilizing solution‐processed MoS2 nanosheets sandwiched between poly(methyl methacrylate) polymer layers. Gate coupling with the pentacene‐based transistor can be controlled by the RRAM memory state to produce a nonprogrammed state (inactive) and a programmed state (active) with a well‐defined memory window. Compared to the reference flash memory device based on the MoS2 floating gate, the hybrid device presents robust access speed and retention ability. Furthermore, the hybrid RRAM‐gated FET is used to build an integrated logic circuit and a wide logic window in inverter logic is achieved. The controllable, well‐defined memory window, long retention time, and fast access speed of this novel hybrid device may open up new possibilities of realizing fully functional nonvolatile memory for high‐performance flexible electronics.
Identification of Small Molecules Which Induce Skeletal Muscle Differentiation in Embryonic Stem Cells via Activation of the Wnt and Inhibition of Smad2/3 and Sonic Hedgehog Pathways
Authors: Lee Hyunwoo , Haller Corinne , Manneville Carole , Doll Thierry , Fruh Isabelle , Keller Caroline Gubser , Richards Shola M. , Ibig-Rehm Yvonne , Patoor Maude , Goette Marjo , Bouchez Laure C. , Mueller Matthias
Published: November 2015

The multilineage differentiation capacity of mouse and human embryonic stem (ES) cells offers a testing platform for small molecules that mediate mammalian lineage determination and cellular specialization. Here we report the identification of two small molecules which drives mouse 129 ES cell differentiation to skeletal muscle with high efficiency without any genetic modification. Mouse embryoid bodies (EBs) were used to screen a library of 1,000 small molecules to identify compounds capable of inducing high levels of Pax3 mRNA. Stimulation of EBs with SMIs (skeletal muscle inducer, SMI1 and SMI2) from the screen resulted in a high percentage of intensively twitching skeletal muscle fibers 3 weeks after induction. Gene expression profiling studies that were carried out for mode of actions analysis showed that SMIs activated genes regulated by the Wnt pathway and inhibited expression of Smad2/3 and Sonic Hedgehog (Shh) target genes. A combination of three small molecules known to modulate these three pathways acted similarly to the SMIs found here, driving ES cells from 129 as well as Balb/c and C57Bl/6 to skeletal muscle. Taken together, these data demonstrate that the SMI drives ES cells to skeletal muscle via concerted activation of the Wnt pathway, and inhibition of Smad2/3 signaling and Shh pathways. This provides important developmental biological information about skeletal muscle differentiation from embryonic stem cells and may lead to the development of new therapeutics for muscle disease.
Maternal dietary imbalance between omega-6 and omega-3 polyunsaturated fatty acids impairs neocortical development via epoxy metabolites
Authors: Sakayori Nobuyuki , Kikkawa Takako , Tokuda Hisanori , Kiryu Emiko , Yoshizaki Kaichi , Kawashima Hiroshi , Yamada Tetsuya , Arai Hiroyuki , Kang Jing X. , Katagiri Hideki , Shibata Hiroshi , Innis Sheila M. , Arita Makoto , Osumi Noriko
Published: November 2015

Omega-6 (n-6) and omega-3 (n-3) polyunsaturated fatty acids (PUFAs) are essential nutrients. Although several studies have suggested that a balanced dietary n-6:n-3 ratio is essential for brain development, the underlying cellular and molecular mechanism is poorly understood. Here, we found that feeding pregnant mice an n-6 excess/n-3 deficient diet, which reflects modern human diets, impairsed neocortical neurogenesis in the offspring. This impaired neurodevelopment occurs through a precocious fate transition of neural stem cells from the neurogenic to gliogenic lineage. A comprehensive mediator lipidomics screen revealed key mediators, epoxy metabolites, which were confirmed functionally using a neurosphere assay. Importantly, although the offspring were raised on a well-balanced n-6:n-3 diet, they exhibited increased anxiety-related behavior in adulthood. These findings provide compelling evidence that excess maternal consumption of n-6 PUFAs combined with insufficient intake of n-3 PUFAs causes abnormal brain development that can have long-lasting effects on the offspring's mental state.
Landmark‐based device calibration and region‐based modeling for RSS‐based localization
Authors: Manh Hung Nguyen , Huang Ching‐Chun , Hsiao‐Yi Lee
Published: November 2015

During the past decades, many fingerprint‐based indoor positioning systems have been proposed and have achieved great success. However, uncontrolled effects of device diversity, signal noise, and dynamic obstacles could recognizably degrade the performance of modern fingerprint‐based indoor localization systems. In this paper, to amend the variations in radio signal strengths (RSSs) caused by device diversity, we proposed an automatic device calibration process. Because of device diversity, the sensed RSS would deviate from the trained radio map and thus leads to poor positioning. An RSS transform function could be adopted to calibrate the RSS variation between different devices and overcome the device diversity problem. However, to train the transform function, a data collection process is required. Unlike conventional calibration methods requiring manual data collection, we proposed a landmark‐based automatic collection process. Based on the detection of Wi‐Fi landmarks, our system could automatically collect pair‐wise RSS samples between devices and train the RSS transform function without extra human power. In addition, to well represent the effects of signal noise and dynamic obstacles, a region‐based RSS modeling method was also proposed. The proposed modeling method allows our system to perform region‐based target localization and utilize more robust region information for localization. Experiments in various environments demonstrate that our system could give a better positioning performance by properly handling the RSS variation caused by signal noise, dynamic environment, and device diversity. Copyright © 2015 John Wiley & Sons, Ltd.
Crime, Policing and Punishment in England, 1750–1914
Authors: Taylor David
Published: November 2015

One of the fastest-growing and most exciting areas of historical research in recent years has been the study of crime and the criminal. The intrinsic fascination of the subject is enhanced by the fact that between the mid eighteenth century and early twentieth century, the English criminal justice system was fundamentally transformed as a new disciplinary state emerged. Drawing on recent research, this book provides a comprehensive and up-to-date synthesis of these important changes.
Communication of Psychiatric Risk in 22q11.2 Deletion Syndrome: A Pilot Project
Authors: Hart Sarah J. , Schoch Kelly , Shashi Vandana , Callanan Nancy
Published: November 2015

Individuals with 22q11.2 deletion syndrome (22q11.2DS) have an increased chance of developing a psychiatric disorder. While parents of children affected by 22q11.2DS typically receive counseling about risk for non‐psychiatric health concerns, genetic counselors may be reluctant to discuss psychiatric risk. Further education of genetic counselors may be necessary to encourage discussion of psychiatric risk with these families. The goal of this project was to develop recommendations for genetic counselors to provide psychiatric risk information to families affected by 22q11.2DS. The recommendations were developed by synthesizing resources in the literature about risk communication. These recommendations were refined following an online focus group meeting with five health care professionals who were recruited for participation from 22q11.2DS clinics across the U.S.A. The focus group data revealed three themes related to discussion of psychiatric risk: 1) Stepwise approach, 2) Discussing treatment options and reducing risks, and 3) Addressing stigma. These recommendations may be used as a foundation for a future clinical protocol to encourage discussion about the risk for psychiatric illness at an earlier point in the diagnostic process for 22q11.2DS and to provide improved information, support and resources to affected families.
Impact of Genetic Counseling and Testing on Altruistic Motivations to Test for BRCA1/2: a Longitudinal Study
Authors: Garg Rahul , Vogelgesang Joseph , Kelly Kimberly
Published: November 2015

Despite the importance of altruism in an individual's participation in genetic counseling and testing, little research has explored the change in altruistic motivations to test over time. This study analyzed altruistic motivations to test and change in altruistic motivations after genetic counseling and testing among individuals (N = 120) at elevated risk for BRCA1/2 mutations. The perceived benefits of genetic testing were assessed and utilized in a mixed‐methods, repeated measures design at three time points: pre‐counseling, counseling and post‐genetic testing, along with transcripts of genetic counseling sessions. Qualitative analysis using an immersion/crystallization method resulted in six common perceived benefits of testing: cancer prevention, awareness, family's survival, relief from anxiety, for science, and future planning. Perceived benefits were then coded into three categories according to Hamilton's kin selection theory: altruistic motivation, personal motivation, and motivation for mutual benefit. At pre‐counseling, those with a personal cancer history (p = 0.003) and those with one or more children (p = 0.013), were significantly more likely to cite altruistic motivations to test. Altruistic motivations significantly increased post‐counseling (p = 0.01) but declined post‐testing (p < 0.001). Labov's narrative analysis further elucidated the context of altruistic and personal motivations. The possibility of a positive test result might have led those with personal history of cancer to have altruistic motivations for testing. Genetic counseling may have increased altruistic motivations to help family and may be a prime opportunity to discuss other forms of altruism.
Structural Control of Landslides in Eastern Kumaun Himalaya: Case study from Sukhidhang-Ladhiya Section
Authors: Prakash Chandra , Agarwal K. K. , Sharma V. K.
Published: November 2015

Landslides are the most common hazards which modify the surface morphology of the orogenic belts. Structural conditions and nature of slope forming material play a vital role in the development of surface morphology. The paper highlights the influence of structure on slope morphology and consequent instability pattern in Sukhidang-Ladhiya section in Eastern Kumaun Himalaya. Rocks of lesser Himalayan sequences, Siwalik Group and veneer of Quaternary deposits occur in the area. The area is punctuated by many landslides of various dimensions affecting all the lithological units present; however, study is based on three major landslides occurring along the Main Boundary Thrust (MBT) and Himalayan Frontal Thrust (HFT) zone. Structural data shows that thrusts environment has manifested in crushing and shearing of rocks, which play an important role in landslide proneness along with the rainfall intensity. Evidences of active tectonics such as triangular facets (flatirons), tilting river terraces and active landslides zones have been noticed in the study area. Limited data on temporal details of landslide morphology (perimeter and area) from remote sensing and topographical sheets indicate that perimeters and area of active scars of landslides in the area are gradually expanding, probably associated with tectonic movements in proximal areas of thrusts.
Seismic Characterization of the Semutang Gas Field, Bengal Basin, Bangladesh
Authors: Afrin Tahera , Hossain Delwar , Imam Md. Hasan
Published: November 2015

The Semutang structure is an elongated NNW-SSE orientated anticline situated in the eastern Chittagong fold belt of the Bengal basin. The aim of the present study is to interpret the stratigraphy and structure of the Semutang area based on the analyses of a combination of geophysical well logs and 2-D seismic data set as well as the reservoir characterization using complex-trace attributes. The main seismic reflector (top of the upper gas sand) was picked, mapped and interpreted. Some direct hydrocarbon indicators (DHIs) deduced from complex-trace attributes analysis show the potentiality of the study area.
Integrating Core and Wireline Log Data to Evaluate Porosity of Jurassic Formations of Injra-1 and Nuryal-2 Wells, Western Potwar, Pakistan
Authors: Khalid Perveiz , Yasin Qamar , Sohail Gmd , Kashif Jam Muhammad
Published: November 2015

Petrophysical properties of rocks can be better understood by core and well log analysis. Exact porosity estimation in the Potwar sub-basin of Pakistan is one of the main issues because of complex tectonic settings. Core and wireline log data of two wells: Injra–1 and Nuryal–2 drilled in the study area are used for the porosity evaluation in the Jurassic reservoirs. The log interpretation and laboratory analysis show that the Datta Formation of the early Jurassic is mainly sandstone with minor shaly beds. A workflow is developed to correlate the calculated porosity from logs with the measured porosity from core plug samples. The results show that log porosity and core porosity of Datta sandstone are comparable. Porosity in the younger formations is higher than in the older formations, which is an indication of presence of secondary porosity and structurally deformed fractures in sandstone. The Datta sandstone encountered in Nuryal–2 is about 20–30 % less porous than in Injra–1 well.
Effects of Soaking of Shales on Rock-Slope Instability and Failure in Southeastern Nigeria
Authors: Okoro Una Chuku , Ogbonnaya Igwe , Raymond Anekwe Ejikeme
Published: November 2015

Landslide prevention and other civil engineering works on shales commonly fail after many cycles of soaking and alternate drying, typical of tropical climate. This work investigates the intrinsic changes in the geotechnical properties of shales collected at two different localities (Abakaliki and Nkporo) in southeastern Nigeria. Long soaking and subsequent drying were simulated using distilled water on the shales. Tests were first conducted on air dried crushed samples which served as the control. Then soaked crushed specimens in open cylinders with their bottom covered with mesh in separate water baths for varying periods of 24, 36 and 48 hours were evaluated at each interval after soaking. Specific gravity, plastic index, compaction characteristics, bearing capacity and unconfined compressive strength tests were conducted on the remoulded specimen. Results showed gradual reduction in specific gravity from 2.5 to 1.8 for Abakaliki shales and from 2.3 to 1.5 for Nkporo shales; unconfined compressive strength from 183 MPa to 120 MPa for Abakaliki shales, from 117 MPa to 85 MPa for Nkporo shales. Although, the net compaction showed reduction in value, maximum dry density (MDD) increased slightly. Plastic Index of the fines also increased from 13% to 18%, and 8% to 19% for Abakaliki and Nkporo shales respectively. Comparatively, the Abakaliki shales showed more resistance to soaking than the Nkporo shales. It is concluded that the engineering properties of shales decreases with long contact in water and subsequent drying.
New Report of Isocrinid Crinoid Chariocrinus from the Jurassic of Jaisalmer, Rajasthan, India
Authors: Kalita Kalpana Deka
Published: November 2015

This paper documents new record of the Isocrinid crinoid Chariocrinus Hess, 1972, from Jaisalmer, Rajasthan, India. It is the first record of the genus in the Indian subcontinent. Abundant disassociated columnal ossicles of Chariocrinus Hess, 1972, are reported from the Kuldhar Member of the Jaisalmer Formation in western Rajasthan, thus representing expansion of its distribution in the westernmost part of the Indian subcontinent.
Distribution of Sediments and Organic Matter Source: Berijam Lake, Tamil Nadu
Authors: Vijayaraj R. , Achyuthan Hema
Published: November 2015

Berijam lake, Tamil Nadu, situated at an elevation of 2165 m above mean sea level is a fresh water, irregular linear basin with two major linear arms located in the Palani hills. Lake floor sediments were collected covering the entire aerial extent of this lake basin to understand the sediment pattern distribution and plausible source of organic carbon. Textural pattern, CaCO3, Organic matter, TOC, TN content and the C/N ratio of the lake floor sediment samples were analysed and the data generated exhibit a distinct pattern of sediment distribution and deposition. Grain size data indicate that the clay is associated with both sand and silt and the lake is dominantly composed of sandy clay and silty clay. CaCO3 content is low (2.70 to 0.80%) as there is no major source for CaCO3. OM, TOC and TN show positive correlation with silt. C/N ratio varies from (12.2 to 9.6) indicating dominantly algal organic matter. NNW, NNE and SSE region of the lake seems to have supported thick water column as high organic carbon, silt and clay content occur in these directions. C/N ratio indicates that the major source of organic matter is from the lake algae, aquatic weeds and plants.
Web Resources for Metagenomics Studies
Authors: Dudhagara Pravin , Bhavsar Sunil , Bhagat Chintan , Ghelani Anjana , Bhatt Shreyas , Patel Rajesh
Published: November 2015

The development of next-generation sequencing (NGS) platforms spawned an enormous volume of data. This explosion in data has unearthed new scalability challenges for existing bioinformatics tools. The analysis of metagenomic sequences using bioinformatics pipelines is complicated by the substantial complexity of these data. In this article, we review several commonly-used online tools for metagenomics data analysis with respect to their quality and detail of analysis using simulated metagenomics data. There are at least a dozen such software tools presently available in the public domain. Among them, MGRAST, IMG/M, and METAVIR are the most well-known tools according to the number of citations by peer-reviewed scientific media up to mid-2015. Here, we describe 12 online tools with respect to their web link, annotation pipelines, clustering methods, online user support, and availability of data storage. We have also done the rating for each tool to screen more potential and preferential tools and evaluated five best tools using synthetic metagenome. The article comprehensively deals with the contemporary problems and the prospects of metagenomics from a bioinformatics viewpoint.
Effects of preoperative at-home preparation on children's behavioral outcomes in Japan
Authors: Wakimizu Rie
Published: November 2015

ABSTRACT

Introduction:

The objective of the study is to determine the effects of at-home psychological preparation mainly on adjustment in the aspect of children's behavior in a randomized controlled trial as an exploratory and pragmatic clinical trial.

Methods:

The eligible patients were randomly assigned to either of two groups that both watched a preparation video once as outpatients in a group of other patients prior to hospitalization (“standard care”); the control group later underwent surgery without any further preparation; the experimental group watched the same video repeatedly in reference to an auxiliary booklet at home with their caregivers prior to hospitalization.

Results:

No beneficial impact of at-home preparation program was determined on the children's behavioral outcomes. However, children in the experimental group showed no higher upset in OR and no more negative behavioral changes after discharge than the controls. Over 90% of the caregivers in the experimental group expressed satisfaction with at-home preparation.

Discussion:

These results suggested that at-home preparation program has no impact on the patients but resulted in high satisfaction from the caregivers in the experimental group.

Conclusion:

At-home preparation program using video and booklet had no beneficial impact on the behavioral outcomes of children undergoing minor surgery. However, it can be highly a desired program to prepare small children and their caregivers for surgical hospitalization.

Highlights: