bluuebunny/crossref_metadata_2025 huggingface dataset:
The roles of thermal insulation and heat storage in the energy performance of the wall materials: a simulation study
Authors: Long Linshuang , Ye Hong
Published: April 2016

A high-performance envelope is the prerequisite and foundation to a zero energy building. The thermal conductivity and volumetric heat capacity of a wall are two thermophysical properties that strongly influence the energy performance. Although many case studies have been performed, the results failed to give a big picture of the roles of these properties in the energy performance of an active building. In this work, a traversal study on the energy performance of a standard room with all potential wall materials was performed for the first time. It was revealed that both heat storage materials and insulation materials are suitable for external walls. However, the importances of those materials are distinct in different situations: the heat storage plays a primary role when the thermal conductivity of the material is relatively high, but the effect of the thermal insulation is dominant when the conductivity is relatively low. Regarding internal walls, they are less significant to the energy performance than the external ones, and they need exclusively the heat storage materials with a high thermal conductivity. These requirements for materials are consistent under various climate conditions. This study may provide a roadmap for the material scientists interested in developing high-performance wall materials.
Loss-of-function Mutation in PMVK Causes Autosomal Dominant Disseminated Superficial Porokeratosis
Authors: Wang Jiuxiang , Liu Ying , Liu Fei , Huang Changzheng , Han Shanshan , Lv Yuexia , Liu Chun-Jie , Zhang Su , Qin Yayun , Ling Lei , Gao Meng , Yu Shanshan , Li Chang , Huang Mi , Liao Shengjie , Hu Xuebin , Lu Zhaojing , Liu Xiliang , Jiang Tao , Tang Zhaohui , Zhang Huiping , Guo An-Yuan , Liu Mugen
Published: April 2016

Disseminated superficial porokeratosis (DSP) is a rare keratinization disorder of the epidermis. It is characterized by keratotic lesions with an atrophic center encircled by a prominent peripheral ridge. We investigated the genetic basis of DSP in two five-generation Chinese families with members diagnosed with DSP. By whole-exome sequencing, we sequencing identified a nonsense variation c.412C > T (p.Arg138*) in the phosphomevalonate kinase gene (PMVK), which encodes a cytoplasmic enzyme catalyzing the conversion of mevalonate 5-phosphate to mevalonate 5-diphosphate in the mevalonate pathway. By co-segregation and haplotype analyses as well as exclusion testing of 500 normal control subjects, we demonstrated that this genetic variant was involved in the development of DSP in both families. We obtained further evidence from studies using HaCaT cells as models that this variant disturbed subcellular localization, expression and solubility of PMVK. We also observed apparent apoptosis in and under the cornoid lamella of PMVK-deficient lesional tissues, with incomplete differentiation of keratinocytes. Our findings suggest that PMVK is a potential novel gene involved in the pathogenesis of DSP and PMVK deficiency or abnormal keratinocyte apoptosis could lead to porokeratosis.
Antidepressant-like Effects of LPM580153, A Novel Potent Triple Reuptake Inhibitor
Authors: Zhang Fangxi , Shao Jing , Tian Jingwei , Zhong Yan , Ye Liang , Meng Xiangjing , Liu Qiaofeng , Wang Hongbo
Published: April 2016

The purpose of this study was to characterize a novel compound, 4-[2-(dimethylamino)-1-(1-hydroxycyclohexyl) ethyl] phenyl 3-nitrophenyl ether, designated LPM580153. We used several well-validated animal models of depression to assess the antidepressant-like activity of LPM580153, followed by a neurotransmitter uptake assay and a corticosterone-induced cell injury model to explore its mechanism of action. In mice, LPM580153 reduced immobility time in the tail suspension test, and in rats subjected to chronic unpredictable mild stress it reversed reductions in body weight gain and ameliorated anhedonia. The neurotransmitter uptake assay results demonstrated that LPM580153 inhibited the uptake of serotonin, norepinephrine and dopamine. Furthermore, LPM580153 protected the SH-SY5Y cells against the cytotoxic activity of corticosterone, an action that might be related to the role of LPM580153 in increasing the protein levels of BDNF, p-ERK1/2, p-AKT, p-CREB and p-mTOR. Together, these findings indicate that LPM580153 is a novel triple reuptake inhibitor with robust antidepressant-like effects.
Production of FAME biodiesel in E. coli by direct methylation with an insect enzyme
Authors: Sherkhanov Saken , Korman Tyler P. , Clarke Steven G , Bowie James U.
Published: April 2016

Most biodiesel currently in use consists of fatty acid methyl esters (FAMEs) produced by transesterification of plant oils with methanol. To reduce competition with food supplies, it would be desirable to directly produce biodiesel in microorganisms. To date, the most effective pathway for the production of biodiesel in bacteria yields fatty acid ethyl esters (FAEEs) at up to ~1.5 g/L. A much simpler route to biodiesel produces FAMEs by direct S-adenosyl-L-methionine (SAM) dependent methylation of free fatty acids, but FAME production by this route has been limited to only ~16 mg/L. Here we employ an alternative, broad spectrum methyltransferase, Drosophila melanogaster Juvenile Hormone Acid O-Methyltransferase (DmJHAMT). By introducing DmJHAMT in E. coli engineered to produce medium chain fatty acids and overproduce SAM, we obtain medium chain FAMEs at titers of 0.56 g/L, a 35-fold increase over titers previously achieved. Although considerable improvements will be needed for viable bacterial production of FAMEs and FAEEs for biofuels, it may be easier to optimize and transport the FAME production pathway to other microorganisms because it involves fewer enzymes.
A new dipole index of the salinity anomalies of the tropical Indian Ocean
Authors: Li Junde , Liang Chujin , Tang Youmin , Dong Changming , Chen Dake , Liu Xiaohui , Jin Weifang
Published: April 2016

With the increased interest in studying the sea surface salinity anomaly (SSSA) of the tropical Indian Ocean during the Indian Ocean Dipole (IOD), an index describing the dipole variability of the SSSA has been pursued recently. In this study, we first use a regional ocean model with a high spatial resolution to produce a high-quality salinity simulation during the period from 1982 to 2014, from which the SSSA dipole structure is identified for boreal autumn. On this basis, by further analysing the observed data, we define a dipole index of the SSSA between the central equatorial Indian Ocean (CEIO: 70°E-90°E, 5°S-5°N) and the region off the Sumatra-Java coast (SJC: 100°E-110°E, 13°S-3°S). Compared with previous SSSA dipole indices, this index has advantages in detecting the dipole signals and in characterizing their relationship to the sea surface temperature anomaly (SSTA) dipole variability. Finally, the mechanism of the SSSA dipole is investigated by dynamical diagnosis. It is found that anomalous zonal advection dominates the SSSA in the CEIO region, whereas the SSSA in the SJC region are mainly influenced by the anomalous surface freshwater flux. This SSSA dipole provides a positive feedback to the formation of the IOD events.
Expression of Estrogen Receptor Beta Predicts Oncologic Outcome of pT3 Upper Urinary Tract Urothelial Carcinoma Better Than Aggressive Pathological Features
Authors: Luo Hao Lun , Sung Ming Tse , Tsai Eing Mei , Lin Chang Shen , Lee Nai Lun , Chung Yueh-Hua , Chiang Po Hui
Published: April 2016

Upper urinary tract urothelial carcinoma (UT-UC) is rare and treatment options or prognostic markers are limited. There is increasing evidence indicating that urothelial carcinoma may be an endocrine-related cancer. The aim of this study was to analyze the prognostic effect of estrogen receptor beta (ERβ) on the outcome of UT-UC. From 2005 to 2012, this study included 105 patients with pT3 UT-UC. Perioperative factors, pathological features and ERβ immunostaining were reviewed and prognostic effects were examined by multivariate analysis. This study divided patients into either the ERβ-high (n = 52) or ERβ-low (n = 53) group and analyzed their oncologic outcomes. All pathological features except infiltrating tumor architecture (significantly higher incidence in ERβ-low group, p = 0.004) are symmetric in both groups. Low ERβ expression was significantly correlated with local recurrence and distant metastasis in univariate analysis (p = 0.035 and 0.004, respectively) and multivariate analysis (p = 0.05 and 0.008, respectively). Cell line study also proved that knock down of ERβ cause less UTUC proliferation and migration. In addition, ERβ agonist also enhanced the cytotoxic and migration inhibition effect of cisplatin and ERβ antagonist cause the UTUC cell more resistant to cisplatin. This result may help identify patients in need of adjuvant therapy or develop potential targeted therapy.
Characterization of a temperature-responsive two component regulatory system from the Antarctic archaeon, Methanococcoides burtonii
Authors: Najnin T. , Siddiqui K. S. , Taha  , Elkaid N. , Kornfeld G. , Curmi P. M. G. , Cavicchioli R.
Published: April 2016

Cold environments dominate the Earth’s biosphere and the resident microorganisms play critical roles in fulfilling global biogeochemical cycles. However, only few studies have examined the molecular basis of thermosensing; an ability that microorganisms must possess in order to respond to environmental temperature and regulate cellular processes. Two component regulatory systems have been inferred to function in thermal regulation of gene expression, but biochemical studies assessing these systems inBacteriaare rare, and none have been performed inArchaeaor psychrophiles. Here we examined the LtrK/LtrR two component regulatory system from the Antarctic archaeon,Methanococcoides burtonii, assessing kinase and phosphatase activities of wild-type and mutant proteins. LtrK was thermally unstable and had optimal phosphorylation activity at 10 °C (the lowest optimum activity for any psychrophilic enzyme), high activity at 0 °C and was rapidly thermally inactivated at 30 °C. These biochemical properties match well with normal environmental temperatures ofM. burtonii(0–4 °C) and the temperature this psychrophile is capable of growing at in the laboratory (−2 to 28 °C). Our findings are consistent with a role for LtrK in performing phosphotransfer reactions with LtrR that could lead to temperature-dependent gene regulation.
Generation and detection of orbital angular momentum via metasurface
Authors: Jin Jinjin , Luo Jun , Zhang Xiaohu , Gao Hui , Li Xiong , Pu Mingbo , Gao Ping , Zhao Zeyu , Luo Xiangang
Published: April 2016

Beams carrying orbital angular momentum possess a significant potential for modern optical technologies ranging from classical and quantum communication to optical manipulation. In this paper, we theoretically design and experimentally demonstrate an ultracompact array of elliptical nanoholes, which could convert the circularly polarized light into the cross-polarized vortex beam. To measure the topological charges of orbital angular momentum in a simple manner, another elliptical nanoholes array is designed to generate reference beam as a reference light. This approach may provide a new way for the generation and detection of orbital angular momentum in a compact device.
Development of a memetic clustering algorithm for optimal spectral histology: application to FTIR images of normal human colon
Authors: Farah Ihsen , Nguyen Thi Nguyet Que , Groh Audrey , Guenot Dominique , Jeannesson Pierre , Gobinet Cyril
Published: April 2016

A memetic clustering algorithm combining a genetic algorithm withk-means clustering for an optimal spectral histology of a normal human colon.
A triphenylcyclopropenylium mass tag: synthesis and application to ultrasensitive LC/MS analysis of amines
Authors: Topolyan Artyom P. , Strizhevskaya Dina A. , Belyaeva Maria A. , Brylev Vladimir A. , Ustinov Alexey V. , Formanovsky Andrey A. , Korshun Vladimir A.
Published: April 2016

Thiol adducts of triphenylcyclopropenylium undergo efficient heterolytic dissociation in electrospray (ESI) or laser desorption ionization (LDI) mass spectrometry giving rise to a prominent signal of an aromatic C3Ph3+ cation.
Toward SERS-based point-of-care approaches for therapeutic drug monitoring: the case of methotrexate
Authors: Fornasaro Stefano , Marta Silvia Dalla , Rabusin Marco , Bonifacio Alois , Sergo Valter
Published: April 2016

To date, in spite of their toxicity, the plasmatic concentration of most chemotherapeutic drugs is difficult to monitor in oncological patients, because their quantitative determination is expensive and time consuming. This contribution reports a first attempt for the direct quantitative determination of a chemotherapeutic drug in human serum samples by means of Surface Enhanced Raman Spectroscopy (SERS). In this study, SERS substrates constituted by Au nanoparticles deposited on paper by a simple dipping method have been used for rapid (few minutes) analysis of diluted human serum spiked with different concentrations of methotrexate, MTX. The drug concentrations were chosen in a range designed to cover typical therapeutic plasmatic values (from nanomolar to millimolar) in oncological patients, and the pertinent calibration was obtained by Partial Least-Squares Regression (PLSR). Stability selection was employed to evaluate the capability of the PLSR model to accurately predict and extract spectral variations correlated to MTX concentration. Such a quantitative determination is crucial for frequent, and hence adherent, therapeutic drug monitoring, TDM, of chemiotherapic drugs, given their heavy side effects. Its low cost, rapid response and the possibility of obtaining spectra with simple and compact instruments, make SERS particularly apt for implementing effective TDM. The promising results obtained in the analytical validation indicate which steps are to be taken on the way toward a clinical validation with real samples from oncological patients, for MTX as well as for other chemotherapeutic drugs.
Flexible infrared detectors based on p–n junctions of multi-walled carbon nanotubes
Authors: Huang Zhenlong , Gao Min , Yan Zhuocheng , Pan Taisong , Liao Feiyi , Lin Yuan
Published: April 2016

Multi-walled CNT p–n junctions are used to construct flexible infrared detectors. The structure of the detector is demonstrated to have excellent mechanical stability.
Catalytic remediation of phenol contaminated wastewater using Cu–Zn hydroxide nitrate
Authors: Srikhaow Assadawoot , Smith S. Meejoo , Uraisin Kanchana , Suttiponparnit Komkrit , Kongmark Chanapa , Chuaicham Chitiphon
Published: April 2016

This work highlights an application of Cu–Zn hydroxide nitrate (denoted as 6Cu–Zn) as a highly effective and reusable catalyst for catalytic wet peroxide oxidation of phenol under mild conditions (35 °C).
A label-free Sirtuin 1 assay based on droplet-electrospray ionization mass spectrometry
Authors: Sun Shuwen , Buer Benjamin C. , Marsh E. Neil G. , Kennedy Robert T.
Published: April 2016

A reliable, label-free, ion suppression-free Sirtuin 1 assay has been developed. By interfacing multi-well plates to electrospray ionization mass spectrometry by oil-segmented droplets, the assay can be applied for high throughput Sirtuin 1 modulator screening.
An unprecedented single platform via cross-linking of zeolite and MOFs
Authors: Lim Dae-Woon , Lee Heeju , Kim Sungjune , Cho In Hwa , Yoon Minyoung , Choi Yong Nam
Published: April 2016

The unprecedented ternary nanocomposites have been synthesized as a single platform via cross-linking of two nanoporous materials, MOFs and Pt nanoparticle (NP) loaded zeolite.
A mechanistic insight into metal-cluster π-envelopment: a dual binding mode involving bent and planar ligand-conformers
Authors: Masai Kohei , Shirato Katsunori , Yamamoto Koji , Kurashige Yuki , Murahashi Tetsuro
Published: April 2016

We report a stepwise mechanism of the π-envelopment of a Pd4 chain cluster. Bent- and planar binding modes of π-conjugated unsaturated hydrocarbon ligands are involved in the π-envelopment process.
Ba4Ru3O10.2(OH)1.8: a new member of the layered hexagonal perovskite family crystallised from water
Authors: Hiley Craig I. , Lees Martin R. , Hammond David L. , Kashtiban Reza J. , Sloan Jeremy , Smith Ronald I. , Walton Richard I.
Published: April 2016

Two chemical reagents in water at 200 °C yield a complex barium ruthenate with a new 8H perovskite stacking sequence.
Cancer cell-targeted two-photon fluorescence probe for the real-time ratiometric imaging of DNA damage
Authors: Zhang Hua , Wang Kui , Xuan Xiaopeng , Lv Qingzhang , Nie Yamin , Guo Haiming
Published: April 2016

A sequential ICT fluorescence probe (ANF–Glu) was successfully utilized to spatially and temporally image DNA damage in cancer cells.
Novel nanorose-like Ce(iii)-doped and undoped Cu(ii)–biphenyl-4,4-dicarboxylic acid (Cu(ii)–BPDCA) MOSs as visible light photocatalysts: synthesis, characterization, photodegradation of toxic dyes and optimization
Authors: Mousavinia S. E. , Hajati S. , Ghaedi M. , Dashtian K.
Published: April 2016

A novel nanorose-like metal organic system (MOS) based on Cu(ii) and biphenyl-4,4-dicarboxylic acid (Cu–BPDCA) doped by Ce(iii) was hydrothermally synthesized and characterized via EDS, FE-SEM, XRD, DRS and FT-IR analysis.
29Si,47Ti,49Ti and195Pt solid state MAS NMR spectroscopic investigations of ternary silicides TPtSi, germanides TPtGe (T = Ti, Zr, Hf) and stannide TiPtSn
Authors: Benndorf Christopher , Eckert Hellmut , Pöttgen Rainer
Published: April 2016

Silicides TPtSi, germanides TPtGe (T = Ti, Zr, Hf) and stannide TiPtSn show well resolved29Si,47Ti,49Ti and195Pt solid state MAS NMR spectra.
Zebrafish dives into food research: effectiveness assessment of bioactive compounds
Authors: Caro M. , Iturria I. , Martinez-Santos M. , Pardo M. A. , Rainieri S. , Tueros I. , Navarro V.
Published: April 2016

Zebrafish ease of use and characteristics reveal it to be an interesting and underused model in food and nutrition research.
Supplemental levels of iron and calcium interfere with repletion of zinc status in zinc-deficient animals
Authors: Jayalakshmi S. , Platel Kalpana
Published: April 2016

Negative interactions between minerals interfering with each other's absorption are of concern when iron and calcium supplements are given to pregnant women and children.
Translesion synthesis past guanine(C8)–thymine(N3) intrastrand cross-links catalyzed by selected A- and Y-family polymerases
Authors: Lee Young-Ae , Lee Yuan-Cho , Geacintov Nicholas E. , Shafirovich Vladimir
Published: April 2016

Guanine(C8)–thymine(N3) intrastrand cross-links are bypassed with varying efficiencies by Y-family polymerases, but the A-family polymerase BF is strongly blocked.
Correlating Flavivirus virulence and levels of intrinsic disorder in shell proteins: protective roles vs. immune evasion
Authors: Goh Gerard Kian-Meng , Dunker A. Keith , Uversky Vladimir N.
Published: April 2016

Computational analyses revealed correlations between the intrinsic disorder propensity of shell proteins and case fatality rates (CFRs) among Flaviviruses and within at least two Flavivirus species, such as tick-borne encephalitis virus (TBEV) and dengue virus (DENV).
Spraying functional fibres by electrospinning
Authors: Zhang Chuan-Ling , Yu Shu-Hong
Published: April 2016

This brief focus article shows you how to prepare functional fibers with controllable morphology, alignment and composition via an electrospinning technique.
Phenylboronic acid-based amphiphilic glycopolymeric nanocarriers for in vivo insulin delivery
Authors: Guo Honglei , Li Hongmei , Gao Juntao , Zhao Guangxi , Ling Lilu , Wang Bin , Guo Qianqian , Gu Yong , Li Chaoxing
Published: April 2016

Diabetes mellitus, a disorder of glucose regulation, is a global burden affecting millions of people across the world.
Optically active helical vinylbiphenyl polymers with reversible thermally induced stereomutation
Authors: Wang Rong , Zheng Yijun , Li Xiaofu , Chen Junxian , Cui Jiaxi , Zhang Jie , Wan Xinhua
Published: April 2016

A series of novel chiral vinylbiphenyl monomers, (+)-2-[(S)-alkoxycarbonyl]-5-(4′-hexyloxyphenyl)styrene (S-(+)-I-Mm, m = 0, 1, 2, 3)/(−)-2-[(R)-sec-butyloxycarbonyl]-5-(4′-hexyloxyphenyl)styrene (R-(−)-I-M0), were designed and synthesized to search for new building blocks of optically active helical polymers.
Effect of cerous phosphates with different crystal structures on their acidity and catalytic activity for the dehydration of glucose into 5-(hydroxymethyl)furfural
Authors: Wang Lina , Yuan Fulong , Niu Xiaoyu , Kang Chuanhong , Li Pengying , Li Zhibin , Zhu Yujun
Published: April 2016

Cerous phosphate catalysts with different crystal structures show different catalytic performances for the dehydration of glucose into 5-(hydroxymethyl)furfural due to their surface Ce4+ amounts and acidities.
A sensitive electrochemical Hg2+ions sensor based on polypyrrole coated nanospherical platinum
Authors: Mahmoudian M. R. , Basirun W. J. , Alias Y.
Published: April 2016

We report the synthesis and characterization of polypyrrole coated on nanospherical platinum (Pt/PPy NSs) composites for the detection of mercury ions.
Metal–organic frameworks based on tri- and penta-nuclear manganese(ii) secondary building units self-assembled by a V-shaped silicon-containing dicarboxylate
Authors: Vlad Angelica , Zaltariov Mirela-Fernanda , Shova Sergiu , Novitchi Ghenadie , Train Cyrille , Cazacu Maria
Published: April 2016

SBUs consisting in penta- or trinuclear manganese(ii) are held together by cpdps2- or cpdps2- and Hcpdps- species derived from bis(p-carboxyphenyl)diphenylsilane in 2D (4,4) coordination polymers. Magnetic, thermal and moisture behaviors are studied.
Latent fingermarks light up: facile development of latent fingermarks using NIR-responsive upconversion fluorescent nanocrystals
Authors: Wang Meng
Published: April 2016

NaYF4:Yb,Er and NaYbF4:Er/Tm/Ho upconversion fluorescent nanocrystals were used in latent fingermark development with high contrast, high sensitivity, and high selectivity.
Isosteric substitution in cationic-amphiphilic polymers reveals an important role for hydrogen bonding in bacterial membrane interactions
Authors: Uppu D. S. S. M. , Konai M. M. , Baul U. , Singh P. , Siersma T. K. , Samaddar S. , Vemparala S. , Hamoen L. W. , Narayana C. , Haldar J.
Published: April 2016

The important role of hydrogen bonding in the interactions of cationic-amphiphilic polymers with bacterial membranes has been reported.
Effects of flux synthesis on SrNbO2N particles for photoelectrochemical water splitting
Authors: Kodera Masanori , Urabe Haruki , Katayama Masao , Hisatomi Takashi , Minegishi Tsutomu , Domen Kazunari
Published: April 2016

Flux synthesized SrNbO2N photoanode exhibited a photocurrent density of 1.5 mA cm−2 at 1.23 VRHE under AM 1.5G irradiation.
A pyrene-based electropolymerized film as a solid-state platform for multi-bit memory storage and fluorescence sensing of nitroaromatics in aqueous solutions
Authors: Chhatwal Megha , Kumar Anup , Gupta Rinkoo D. , Awasthi Satish K.
Published: April 2016

Elucidation of multi-state memory storage and sniffing of nitroaromatics by an osmium-based polypyrene film on ITO-coated glass electrodes.
Impact of Surgical Approach on Clinical Outcomes in the Treatment of Lumbar Pseudarthrosis
Authors: Owens R. Kirk , Djurasovic Mladen , Crawford Charles H. , Glassman Steven D. , Dimar John R. , Carreon Leah Y.
Published: April 2016

Study Design

Retrospective comparative cohort.

Objective

Pseudarthrosis following fusion for degenerative lumbar spine pathologies remains a substantial problem. Current data shows that patients who develop a pseudarthrosis have suboptimal outcomes. This study evaluates if treatment of pseudarthrosis can be affected by surgical approach.

Methods

Medical records of 63 female and 65 male patients (mean age 50.37) who were treated for nonunion following lumbar fusion were reviewed. Sixty patients underwent posterolateral fusion (PSF), 18 underwent PSF with transforaminal interbody fusion (TLIF), 32 underwent anterior and posterior spinal fusion (AP), and 24 underwent anterior lumbar interbody fusion (ALIF).

Results

Significant differences between the treatment groups were observed in length of stay ( p = 0.000), blood loss ( p = 0.000), and operative time ( p = 0.000). In the AP fusion group, minimal clinically important difference (MCID) was reached in 47% of patients for back pain, 28% for leg pain, and 28% for Oswestry Disability Index (ODI). PSF had the highest percentage of patients reaching MCID for Short Form-36 (SF-36) physical composite score at 25%. ALIF and TLIF subgroups reached MCID for ODI in 17% of patients. Linear regression analysis showed that type of surgical approach did not impact change in ODI scores.

Conclusion

Although not statistically significant, the AP fusion group reached MCID more frequently in all outcomes except SF-36 Physical Component Summary. All surgical approaches examined for treatment of lumbar pseudarthrosis resulted in only poor to modest improvement in ODI. This result further emphasizes the importance of achieving a solid fusion with the index surgery.
Analytical solutions of equation for the order parameter of dense superfluid neutron matter with anisotropic spin-triplet p-wave pairing at finite temperatures
Authors: Tarasov A. N.
Published: April 2016

The previously derived equations for the components of the order parameter (OP) of dense superfluid neutron matter (SNM) with anisotropic spin-triplet p-wave pairing and with taking into account the effects of magnetic field and finite temperatures are reduced to the single equation for the one-component OP in the limit of zero magnetic field. Here this equation is solved analytically for arbitrary parametrization of the effective Skyrme interaction in neutron matter and as the main results the energy gap (in the energy spectrum of neutrons in SNM) is obtained as nonlinear function of temperature T and density n in two limiting cases: for low temperatures near T = 0 and in the vicinity of phase transition temperature Tc0(n) for dense neutron matter from normal to superfluid state. These solutions for the energy gap are specified for generalized BSk21 and BSk24 parametrizations of the Skyrme forces (with additional terms dependent on density n) and figures are plotted on the interval 0.1n0 < n < 2.0n0, where n0 = 0.17 fm−3 is nuclear density.
Vibronic interactions proceeding from combined analytical and numerical considerations: Covalent functionalization of graphene by benzene, distortions, electronic transitions
Authors: Krasnenko V. , Boltrushko V. , Hizhnyakov V.
Published: April 2016

Chemically bound states of benzene molecules with graphene are studied both analytically and numerically. The states are formed by switching off intrabonds of π-electrons in C6 rings to interbonds. A number of different undistorted and distorted structures are established both with aligned and with transversal mutual orientation of benzene and graphene. The vibronic interactions causing distortions of bound states are found, by using a combination of analytical and numerical considerations. This allows one to determine all electronic transitions of π-electrons without explicit numerical calculations of excited states, to find the conical intersections of potentials, and to show that the mechanism of distortions is the pseudo-Jahn-Teller effect. It is found that the aligned distorted benzene molecule placed between two graphene sheets makes a chemical bond with both of them, which may be used for fastening of graphene sheets together.
Analysis of nucleation using mean first-passage time data from molecular dynamics simulation
Authors: Nicholson David A. , Rutledge Gregory C.
Published: April 2016

We introduce a method for the analysis of nucleation using mean first-passage time (MFPT) statistics obtained by molecular dynamics simulation. The method is based on the Becker-Döring model for the dynamics of a nucleation-mediated phase change and rigorously accounts for the system size dependence of first-passage statistics. It is thus suitable for the analysis of systems in which the separation between time scales for nucleation and growth is small, due to either a small free energy barrier or a large system size. The method is made computationally practical by an approximation of the first-passage time distribution based on its cumulant expansion. Using this approximation, the MFPT of the model can be fit to data from molecular dynamics simulation in order to estimate valuable kinetic parameters, including the free energy barrier, critical nucleus size, and monomer attachment pre-factor, as well as the steady-state rates of nucleation and growth. The method is demonstrated using a case study on nucleation of n-eicosane crystals from the melt. For this system, we found that the observed distribution of first-passage times do not follow an exponential distribution at short times, rendering it incompatible with the assumptions made by some other methods. Using our method, the observed distribution of first-passage times was accurately described, and reasonable estimates for the kinetic parameters and steady-state rates of nucleation and growth were obtained.
On the vertical stacking in semiconducting WSe2 bilayers
Authors: Sanchez A. M. , Peters J. J. P. , Wu S. , Huang C. , Cobden D. , Xu X. , Beanland R.
Published: April 2016

The vertical stacking in semiconducting WSe2 bilayers grown by physical vapour transport was studied using atomic resolution annular dark field imaging. Our results show that the most common geometry was consistent with AA′ , the most stable configuration. However in some areas AB alignment was also observed, as expected due to the small energy difference between AA′ and AB. Additionally, two different rotational stacking orientations were observed, with rotation angles of 12 and 21°. These different vertical WSe2 bilayers could provide a means of engineering electronic band structure for specific optoelectronic properties.
Prospects of eLISA for detecting Galactic binary black holes similar to GW150914
Authors: Seto Naoki
Published: April 2016

We discuss the prospects of eLISA for detecting gravitational waves (GWs) from Galactic binary black holes (BBHs) similar to GW150914. For a comoving merger rate that is consistent with current observation, eLISA is likely to identify at least one BBH with a sufficient signal-to-noise ratio. In addition, eLISA has a potential to measure the eccentricity of the BBH as small as e ∼ 0.02, corresponding to the residual value e ∼ 10−6 at 10 Hz. Therefore, eLISA could provide us with a crucial information to understand the formation processes of relatively massive BBHs like GW150914. We also derive a simple scaling relation for the expected number of detectable Galactic BBHs.
Morphological, Biometrical, Biochemical, and Molecular Characterization of the Coffee Root-Knot Nematode Meloidogyne megadora
Authors: Maleita Carla M. , de Almeida Ana M. S. F. , Vovlas Nicola , Abrantes Isabel
Published: April 2016

Meloidogyne megadora infects coffee trees, an economically important crop worldwide. The accurate identification of M. megadora is essential for the development of preventive measures to avoid the dispersion of this pathogen and establishment of efficient and sustainable integrated pest management programs. One M. megadora isolate was studied by biometrical, biochemical, and molecular characteristics (random amplified polymorphic DNA [RAPD] and PCR of internal transcribed spacer [ITS] region). Biometrical characteristics of M. megadora females, males, and second-stage juveniles were similar to the original description. Biochemical studies revealed a unique enzyme pattern for M. megadora esterases (Me3) that allowed for species differentiation. Three RAPD primers (OPG-4, OPG-5, and OPG-6) produced specific bands to all Meloidogyne spp. studied: M. megadora, M. arenaria, M. incognita, and M. javanica. Molecular analysis of the ITS region resulted in an amplification product of 700 bp. The phylogenetic relationship between M. megadora and several Meloidogyne spp. sequences was analyzed, revealing that M. megadora clearly differs from the most common root-knot nematode species. Based on the studies conducted, isozyme analysis remains a useful and efficient methodology for M. megadora identification when females are available. Further studies will be needed to convert the M. megadora differential DNA fragment obtained by RAPD and develop a species-specific sequence-characterized amplified region PCR assay for its diagnosis based on second-stage juveniles.
Molecular Mapping of the Stripe Rust Resistance Gene Yr69 on Wheat Chromosome 2AS
Authors: Hou Liyuan , Jia Juqing , Zhang Xiaojun , Li Xin , Yang Zujun , Ma Jian , Guo Huijuan , Zhan Haixian , Qiao Linyi , Chang Zhijian
Published: April 2016

Wheat is one of the major food crops in the world. Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an economically important disease that affects wheat worldwide. The discovery of novel resistance genes and the deployment of effectively resistant cultivars are important for the ongoing control of wheat stripe rust and the maintenance of the agricultural productivity of wheat. CH7086, a new stripe rust-resistant wheat introgression line, was selected by crossing susceptible cultivars with the resistant Thinopyrum ponticum-derived partial amphiploid Xiaoyan 7430. The resistance of CH7086 is effective against all current Chinese P. striiformis f. sp. tritici races. CH7086 was crossed with the stripe rust-susceptible cultivars to develop F1, F2, F3, and BC1 populations for genetic analysis. Segregation in the F2 and BC1 populations and F2:3 lines were tested for resistance against the P. striiformis f. sp. tritici race CYR32. This test showed that CH7086 carries a single dominant gene for stripe rust resistance, which was temporarily designated YrCH86. The closest of the eight simple sequence repeat (SSR) and expressed sequence tag-SSR markers flanking the locus were X2AS33, which is 1.9 cM distal, and Xmag3807, which is 3.1 cM proximal. The resistance gene and its polymorphic markers were placed in deletion bin 2AS-0.78-1.00 using the ‘Chinese Spring’ nullisomic-tetrasomic, ditelosomic, and deletion lines. The tests of both allelism and resistance specificity suggested that the resistance gene found in CH7086 was not Yr17, which was the only current formally named Yr gene on chromosome 2AS. Thus, YrCH86 appeared to be a new locus and was permanently designated Yr69.
Identification of Diaporthe longicolla on Dry Edible Pea, Dry Edible Bean, and Soybean in North Dakota
Authors: Mathew Febina M. , Castlebury Lisa A. , Alananbeh Kholoud , Jordahl James G. , Taylor Chris A. , Meyer Scott M. , Lamppa Robin S. , Pasche Julie A. , Markell Samuel G.
Published: April 2016

North Dakota soybean production has expanded geographically, and possible short rotations with dry edible bean and pea raise concerns of pathogens (such as Diaporthe longicolla, cause of Phomopsis seed decay and stem disease of soybean) developing overlapping host ranges. To the best of our knowledge, this is the first report of D. longicolla causing stem disease on dry edible beans and dry edible peas, and stem disease on soybean in North Dakota. Its impact on dry edible beans and dry edible peas is uncertain.

Accepted for publication 16 February 2015. Published 15 April 2015.
Etiology and Epidemiological Conditions Promoting Fusarium Root Rot in Sweetpotato
Authors: Scruggs A. C. , Quesada-Ocampo L. M.
Published: April 2016

Sweetpotato production in the United States is limited by several postharvest diseases, and one of the most common is Fusarium root rot. Although Fusarium solani is believed to be the primary causal agent of disease, numerous other Fusarium spp. have been reported to infect sweetpotato. However, the diversity of Fusarium spp. infecting sweetpotato in North Carolina is unknown. In addition, the lack of labeled and effective fungicides for control of Fusarium root rot in sweetpotato creates the need for integrated strategies to control disease. Nonetheless, epidemiological factors that promote Fusarium root rot in sweetpotato remain unexplored. A survey of Fusarium spp. infecting sweetpotato in North Carolina identified six species contributing to disease, with F. solani as the primary causal agent. The effects of storage temperature (13, 18, 23, 29, and 35°C), relative humidity (80, 90, and 100%), and initial inoculum level (3-, 5-, and 7-mm-diameter mycelia plug) were examined for progression of Fusarium root rot caused by F. solani and F. proliferatum on ‘Covington’ sweetpotato. Fusarium root rot was significantly reduced (P < 0.05) at lower temperatures (13°C), low relative humidity levels (80%), and low initial inoculum levels for both pathogens. Sporulation of F. proliferatum was also reduced under the same conditions. Qualitative mycotoxin analysis of roots infected with one of five Fusarium spp. revealed the production of fumonisin B1 by F. proliferatum when infecting sweetpotato. This study is a step toward characterizing the etiology and epidemiology of Fusarium root rot in sweetpotato, which allows for improved disease management recommendations to limit postharvest losses to this disease.
Role of Specificity Protein-1 and Activating Protein-2 Transcription Factors in the Regulation of the Gap Junction Protein Beta-2 Gene in the Epididymis of the Rat1
Authors: Adam Cécile , Cyr Daniel G.
Published: April 2016

In prepubertal rats, connexin 26 (GJB2) is expressed between adjacent columnar cells of the epididymis. At 28 days of age, when columnar cells differentiate into adult epithelial cell types, Gjb2 mRNA levels decrease to barely detectable levels. There is no information on the regulation of GJB2 in the epididymis. The present study characterized regulation of the Gjb2 gene promoter in the epididymis. A single transcription start site at position −3829 bp relative to the ATG was identified. Computational analysis revealed several TFAP2A, SP1, and KLF4 putative binding sites. A 1.5-kb fragment of the Gjb2 promoter was cloned into a vector containing a luciferase reporter gene. Transfection of the construct into immortalized rat caput epididymal (RCE-1) cells indicated that the promoter contained sufficient information to drive expression of the reporter gene. Deletion constructs showed that the basal activity of the promoter resides in the first −230 bp of the transcriptional start site. Two response elements necessary for GJB2 expression were identified: an overlapping TFAP2A/SP1 site (−136 to −126 bp) and an SP1 site (−50 bp). Chromatin immunoprecipitation (ChIP) and electrophoretic mobility shift assays confirmed that SP1 and TFAP2A were bound to the promoter. ChIP analysis of chromatin from young and pubertal rats indicated that TFAP2A and SP1 binding decreased with age. SP1 and TFAP2A knockdown indicated that SP1 is necessary for Gjb2 expression. DNA methylation did not appear to be involved in the regulation of Gjb2 expression. Results indicate that SP1 and TFAP2A regulate Gjb2 promoter activity during epididymal differentiation in rat.
Integrative pharmacogenomics to infer large-scale drug taxonomy
Authors: El-Hachem Nehme , Gendoo Deena M.A. , Ghoraie Laleh Soltan , Safikhani Zhaleh , Smirnov Petr , Chung Christina , Deng Kenan , Fang Ailsa , Birkwood Erin , Ho Chantal , Isserlin Ruth , Bader Gary D. , Goldenberg Anna , Haibe-Kains Benjamin
Published: April 2016

Identification of drug targets and mechanism of action (MoA) for new and uncharacterlzed drugs is important for optimization of drug efficacy. Current MoA prediction approaches largely rely on prior information including side effects, therapeutic indication and/or chemo-informatics. Such information is not transferable or applicable for newly identified, previously uncharacterlzed small molecules. Therefore, a shift in the paradigm of MoA predictions is necessary towards development of unbiased approaches that can elucidate drug relationships and efficiently classify new compounds with basic input data. We propose a new integrative computational pharmacogenomlc approach, referred to as Drug Network Fusion (DNF), to infer scalable drug taxonomies that relies only on basic drug characteristics towards elucidating drug-drug relationships. DNF is the first framework to integrate drug structural information, high-throughput drug perturbation and drug sensitivity profiles, enabling drug classification of new experimental compounds with minimal prior information. We demonstrate that the DNF taxonomy succeeds in identifying pertinent and novel drug-drug relationships, making it suitable for investigating experimental drugs with potential new targets or MoA. We highlight how the scalability of DNF facilitates identification of key drug relationships across different drug categories, and poses as a flexible tool for potential clinical applications in precision medicine. Our results support DNF as a valuable resource to the cancer research community by providing new hypotheses on the compound MoA and potential insights for drug repurposlng.
KinLinks: Software Toolkit for Kinship Analysis and Pedigree Generation from HTS Datasets
Authors: Shcherbina Anna , Ricke Darrell O. , Schwoebel Eric , Boettcher Tara , Zook Christina , Bobrow Johanna , Petrovick Martha , Wack Edward
Published: April 2016

The ability to predict familial relationships from source DNA in multiple samples has a number of forensic and medical applications. Kinship testing of suspect DNA profiles against relatives in a law enforcement database can provide valuable investigative leads, determination of familial relationships can inform immigration decisions, and remains identification can provide closure to families of missing individuals. The proliferation of High-Throughput Sequencing technologies allows for enhanced capabilities to accurately predict familial relationships to the third degree and beyond. KinLinks, developed by MIT Lincoln Laboratory, is a software tool that predicts pairwise relationships and reconstructs kinship pedigrees for multiple input samples using single-nucleotide polymorphism (SNP) profiles. The software has been trained and evaluated on a set of 175 subjects (30,450 pairwise relationships), consisting of three multi-generational families and 52 geographically diverse subjects. Though a panel of 5396 SNPs was selected for kinship prediction, KinLinks is highly modular, allowing for the substitution of expanded SNP panels and additional training models as sequencing capabilities continue to progress. KinLinks builds on the SNP-calling capabilities of Sherlocks Toolkit, and is fully integrated with the Sherlocks Toolkit pipeline.
An evolutionary medicine perspective on Neandertal extinction
Authors: Sullivan Alexis P. , de Manuel Marc , Marques-Bonet Tomas , Perry George H.
Published: April 2016

The Eurasian sympatry of Neandertals and anatomically modern humans – beginning at least 45,000 years ago and lasting for more than 5,000 years – has long sparked anthropological interest into the factors that potentially contributed to Neandertal extinction. Among many different hypotheses, the “differential pathogen resistance” extinction model posits that Neandertals were disproportionately affected by exposure to novel infectious diseases that were transmitted during the period of spatiotemporal sympatry with modern humans. Comparisons of new archaic hominin paleogenome sequences with modern human genomes have confirmed a history of genetic admixture – and thus direct contact – between humans and Neandertals. Analyses of these data have also shown that Neandertal nuclear genome genetic diversity was likely considerably lower than that of the Eurasian anatomically modern humans with whom they came into contact, perhaps leaving Neandertal innate immune systems relatively more susceptible to novel pathogens. In this study, we compared levels of genetic diversity in genes for which genetic variation is hypothesized to benefit pathogen defense among Neandertals and African, European, and Asian modern humans, using available exome sequencing data (six chromosomes per population). We observed that Neandertals had only 31-39% as many nonsynonymous (amino acid changing) polymorphisms across 73 innate immune system genes compared to modern human populations. We also found that Neandertal genetic diversity was relatively low in an unbiased set of balancing selection candidate genes for primates – genes with the highest 1% genetic diversity genome-wide in non-human apes. In contrast, Neandertals had similar to higher levels of genetic diversity than humans in 13 major histocompatibility complex (MHC) genes. Thus, while Neandertals may have been relatively more susceptible to some novel pathogens and differential pathogen resistance could be considered as one potential contributing factor in their extinction, this model does have limitations.
Language impairment resulting from a de novo deletion of 7q32.1-q33: a case report
Authors: Jiménez-Romero Ma Salud , Barcos-Martínez Montserrat , Espejo-Portero Isabel , Benítez-Burraco Antonio
Published: April 2016

Chromosome 7 is a hot spot for cognitive disorders involving language deficits. We report on a girl who presents with a cognitive and speech delay, motor problems, hearing loss, and behavioral disturbances, and a de novo deletion within 7q32.1-q33 (chromosome position: chr7:127109685-132492196, hg 18). Several genes involved in brain development and function are located within the deleted region. Many of them are related to developmental disorders encompassing language deficits (dyslexia, speech-sound disorder, and autism). The proband’s phenotype may result from a change in the expression level of some of these genes.
Nanoscale mechanical stimulation method for quantifyingC. elegansmechanosensory behavior and memory
Authors: Sugi Takuma , Okumura Etsuko , Kiso Kaori , Igarashi Ryuji
Published: April 2016

Here, we establish a novel economic system to quantifyC. elegansmechanosensory behavior and memory by a controllable nanoscale mechanical stimulation. Using piezoelectric sheet speaker, we can flexibly change the vibration properties at a nanoscale displacement level and quantify behavioral responses and memory under the control of each vibration property. This system will facilitate understanding of physiological aspects ofC. elegansmechanosensory behavior and memory.
Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia
Authors: Marrero Patricia , Abu-Amero Khaled K. , Larruga Jose M , Cabrera Vicente M
Published: April 2016

Objetives

We suggest that the phylogeny and phylogeography of mtDNA macrohaplogroup M in Eurasia and Australasia is better explained supposing an out of Africa of modern humans following a northern route across the Levant than the most prevalent southern coastal route across Arabia and India proposed by others.

Methods

A total 206 Saudi samples belonging to macrohaplogroup M have been analyzed. In addition, 4107 published complete or nearly complete Eurasian and Australasian mtDNA genomes ascribed to the same macrohaplogroup have been included in a global phylogeographic analysis.

Results

Macrohaplogroup M has only historical implantation in West Eurasia including the Arabian Peninsula. Founder ages of M lineages in India are significantly younger than those in East Asia, Southeast Asia and Near Oceania. These results point to a colonization of the Indian subcontinent by modern humans carrying M lineages from the east instead the west side.

Conclusions

The existence of a northern route previously advanced by the phylogeography of mtDNA macrohaplogroup N is confirmed here by that of macrohaplogroup M. Taking this genetic evidence and those reported by other disciplines we have constructed a new and more conciliatory model to explain the history of modern humans out of Africa.