bluuebunny/crossref_metadata_2025 huggingface dataset:
Long-term prospective longitudinal evaluation of emotional distress and quality of life in cervical cancer patients who remained disease-free 2-years from diagnosis
Authors: Mantegna Giovanna , Petrillo Marco , Fuoco Gilda , Venditti Laura , Terzano Serena , Anchora Luigi Pedone , Scambia Giovanni , Ferrandina Gabriella
Published: March 2013

Background

A long-term prospective assessment of QoL in cervical cancer patients is still lacking. Here, we provide the first 2-years prospective, longitudinal study evaluating emotional distress and QoL in early stage (ECC) and locally advanced (LACC) cervical cancer patients who remained disease-free 2-years from diagnosis.

Methods

The questionnaires: Hospital Anxiety and Depression Scale (HADS), Global Health Status items of EORTC QLQ-C30 (GHS), and EORTC QLQ-CX24 (CX24) have been administered by a dedicated team of psycho-oncologists, administered at baseline, and after 3, 6, 12 and 24 months from surgery The Generalized Linear Model for repeated measure was used to analyze modifications of QoL measures over time.

Results

In both groups, an early reduction of the percentage of patients with anxiety levels ≥11 was observed at the 3-month evaluation (ECC: 25.7% at baseline Vs 14.7% after 3 months, p value=0.001; LACC: 22.2% at baseline Vs 15.4% after 3 months, p value=0.001). Despite this favorable trend, after 2 years from diagnosis, 11.9% of ECC and 15.6% of LACC patients still showed an anxiety score ≥11. No significant changes over time were observed in term of Depression levels. Focusing on QoL issues, mean GHS and Sexual Activity scores showed an improvement over time in both groups compared to baseline (GHS: 5.7% difference for ECC, p value=0.001, and 11.0% in LACC, p value=0.001; SXA: 13.9% difference for ECC, p value=0.001; and 6.1% in LACC, p value=0.008). On the other hand, Body Image mean scores were significantly impaired by chemoradiation administration in LACC patients, without long-term recovery (7.5% difference, p value=0.001). Finally, in both groups, lymphedema (LY) and menopausal symptoms (MS) showed an early worsening which persisted 2-year after surgery (LY: 19.5% difference for ECC, p value=0.014, and 27.3% in LACC, p value=0.001; MS: 14.4% difference for ECC, p value=0.004, and 16.0% in LACC, p value=0.002).

Conclusions

Despite a significant improvement over time, elevated anxiety levels are still detectable at 24 months after surgery in approximately 10% of cervical cancer patients. Much more attention should be focused on surgical/medical approaches able to minimize the negative impact of lymphedema and menopausal symptoms on QoL.
A Chinese herbal formula, Yi-Qi-Fu-Sheng, inhibits migration/invasion of colorectal cancer by down-regulating MMP-2/9 via inhibiting the activation of ERK/MAPK signaling pathways
Authors: Deng Wanli , Sui Hua , Wang Qiaolin , He Nana , Duan Chunyan , Han Liang , Li Qi , Lu Ming , Lv Shuqin
Published: March 2013

Background

A Chinese herbal formula, Yi-Qi-Fu-Sheng (YQFS), has long been employed clinically to treat cancer patients. We aimed to determine its effectiveness as a treatment method for colorectal cancer. We investigated the therapeutic effects of YQFS on colorectal cancer, as well as the underlying mechanisms, which have not previously been explored.

Methods

First, YQFS was extracted and chemically characterized. We then tested the effects of YQFS on proliferation and migration by MTT and transwell migration assays in vitro. Mouse xenograft models of colorectal cancer were established by inoculation with HCT-116 cells, and mice received one of three oral doses (200, 400 and 800 mg/kg/day) to evaluate the effects of YQFS extract. Metalloproteinase-2/9 (MMP-2/9) expression in mice was evaluated by gelatin zymography assay. Apoptosis was evaluated by flow cytometry (FCM) analysis in vitro and by TUNEL assay in vivo. ERK and p-ERK expression were evaluated by western blot analysis at the protein level in vitro, and by quantitative RT-PCR at mRNA level in vivo.

Results

Our results show that YQFS significantly inhibits colorectal cancer cell proliferation and induces apoptosis and cell cycle arrest at the G1− and S-phase in HCT-116 cells. Furthermore, YQFS effectively retards tumor cell migration and invasion by inhibiting metalloproteinase-2/9 (MMP-2/9) expression, both in vitro and in vivo. Moreover, YQFS had an inhibitory effect on tumor growth in vivo, and induced apoptosis through the inhibition of the ERK1/2 pathway both in vitro and in vivo.

Conclusion

These findings demonstrate that YQFS extract has an anti-tumor effect in colorectal cancer, which could be attributed to ERK1/2-dependent inhibition of MMP-2/9 expression.
Predictive value of lymphocytopenia and the neutrophil-lymphocyte count ratio for severe imported malaria
Authors: van Wolfswinkel Marlies E , Vliegenthart-Jongbloed Klaske , de Mendonça Melo Mariana , Wever Peter C , McCall Matthew B , Koelewijn Rob , van Hellemond Jaap J , van Genderen Perry J
Published: March 2013

Background

Lymphocytopenia has frequently been described in patients with malaria, but studies on its association with disease severity have yielded conflicting results. The neutrophil/lymphocyte count ratio (NLCR) has been introduced as a parameter for systemic inflammation in critically ill patients and was found, together with lymphocytopenia, to be a better predictor of bacteraemia than routine parameters like C-reactive protein and total leukocyte count. In the present study, the predictive value of the NLCR and lymphocytopenia for severe disease was evaluated in patients with imported malaria.

Methods

All patients diagnosed with malaria at the Harbour Hospital between January 1st 1999 and January 1st 2012 with differential white cell counts determined within the first 24 hours after admission were included in this retrospective study. Severe malaria was defined according to the WHO criteria. The performance of the NLCR and lymphocytopenia as a marker of severe malarial disease was compared back-to-back with that of C-reactive protein as a reference biomarker.

Results

A total of 440 patients (severe falciparum malaria n = 61, non-severe falciparum malaria n = 259, non-falciparum malaria n=120) were included in the study. Lymphocytopenia was present in 52% of all patients and the median NLCR of all patients was 3.2. Total lymphocyte counts and NLCR did not differ significantly between groups. A significant correlation of total leukocyte count and NLCR, but not lymphocyte count, with parasitaemia was found. ROC analysis revealed a good negative predictive value but a poor positive predictive value of both lymphocytopenia and NLCR and performance was inferior to that of C-reactive protein. After complete parasite clearance a significant rise in total leukocyte count and lymphocyte count and a significant decrease in NLCR was observed.

Conclusion

The NLCR was found to correlate with parasitaemia, but both lymphocytopenia and the NLCR were inferior to C-reactive protein as markers for severe disease in patients with imported malaria. The NLCR and lymphocytopenia are not useful as predictive markers for severe disease in imported malaria in the acute care setting.
Performance of a constructed wetland in Grand Marais, Manitoba, Canada: Removal of nutrients, pharmaceuticals, and antibiotic resistance genes from municipal wastewater
Authors: Anderson Julie C , Carlson Jules C , Low Jennifer E , Challis Jonathan K , Wong Charles S , Knapp Charles W , Hanson Mark L
Published: March 2013

Background

The discharge of complex mixtures of nutrients, organic micropollutants, and antibiotic resistance genes from treated municipal wastewater into freshwater systems are global concerns for human health and aquatic organisms. Antibiotic resistance genes (ARGs) are genes that have the ability to impart resistance to antibiotics and reduce the efficacy of antibiotics in the systems in which they are found. In the rural community of Grand Marais, Manitoba, Canada, wastewater is treated passively in a sewage lagoon prior to passage through a treatment wetland and subsequent release into surface waters. Using this facility as a model system for the Canadian Prairies, the two aims of this study were to assess: (a) the presence of nutrients, micropollutants (i.e., pesticides, pharmaceuticals), and ARGs in lagoon outputs, and (b) their potential removal by the treatment wetland prior to release to surface waters in 2012.

Results

As expected, concentrations of nitrogen and phosphorus species were greatest in the lagoon and declined with movement through the wetland treatment system. Pharmaceutical and agricultural chemicals were detected at concentrations in the ng/L range. Concentrations of these compounds spiked downstream of the lagoon following discharge and attenuation was observed as the effluent migrated through the wetland system. Hazard quotients calculated for micropollutants of interest indicated minimal toxicological risk to aquatic biota, and results suggest that the wetland attenuated atrazine and carbamazepine significantly. There was no significant targeted removal of ARGs in the wetland and our data suggest that the bacterial population in this system may have genes imparting antibiotic resistance.

Conclusions

The results of this study indicate that while the treatment wetland may effectively attenuate excess nutrients and remove some micropollutants and bacteria, it does not specifically target ARGs for removal. Additional studies would be beneficial to determine whether upgrades to extend retention time or alter plant community structure within the wetland would optimize removal of micropollutants and ARGs to fully characterize the utility of these systems on the Canadian Prairies.
Characterisation of sleep in intensive care using 24-hour polysomnography: anobservational study
Authors: Elliott Rosalind , McKinley Sharon , Cistulli Peter , Fien Mary
Published: March 2013

Introduction

Many intensive care patients experience sleep disruption potentially related tonoise, light and treatment interventions. The purpose of this study was tocharacterise, in terms of quantity and quality, the sleep of intensive carepatients, taking into account the impact of environmental factors.

Methods

This observational study was conducted in the adult ICU of a tertiary referralhospital in Australia, enrolling 57 patients. Polysomnography (PSG) was performedover a 24-hour period to assess the quantity (total sleep time: hh:mm) and quality(percentage per stage, duration of sleep episode) of patients' sleep while in ICU.Rechtschaffen and Kales criteria were used to categorise sleep. Interrater checkswere performed. Sound pressure and illuminance levels and care events weresimultaneously recorded. Patients reported on their sleep quality in ICU using theRichards Campbell Sleep Questionnaire and the Sleep in Intensive CareQuestionnaire. Data were summarised using frequencies and proportions or measuresof central tendency and dispersion as appropriate and Cohen's Kappa statistic wasused for interrater reliability of the sleep data analysis.

Results

Patients' median total sleep time was 05:00 (IQR: 02:52 to 07:14). The majority ofsleep was stage 1 and 2 (medians: 19 and 73%) with scant slow wave and REM sleep.The median duration of sleep without waking was 00:03. Sound levels were high(mean Leq 53.95 dB(A) during the day and 50.20 dB(A) at night) and illuminancelevels were appropriate at night (median <2 lux) but low during the day(median: 74.20 lux). There was a median 1.7 care events/h. Patients' meanself-reported sleep quality was poor. Interrater reliability of sleep staging washighest for slow wave sleep and lowest for stage 1 sleep.

Conclusions

The quantity and quality of sleep in intensive care patients are poor and may berelated to noise, critical illness itself and treatment events that disturb sleep.The study highlights the challenge of quantifying sleep in the critical caresetting and the need for alternative methods of measuring sleep. The resultssuggest that a sound reduction program is required and other interventions toimprove clinical practices to promote sleep in intensive care patients.

Trial registration

Australian New Zealand clinical trial registry(http://www.anzctr.org.au/): ACTRN12610000688088.
Large-area Synthesis of Single-crystal PbTiO3 Nanobelts and Nanoflakes
Authors: Zhao Qingchun , Cao Tian
Published: March 2013

We first report large-area single-crystal PbTiO3 nanobelts and nanoflakes synthsized via sol–gel method. The experimental results show reaction temperature plays a decisive role in the formation PbTiO3 nanobelts and nanoflakes. X-ray diffraction (XRD), Raman spectroscopy, and transmission electron microscopy (TEM) investigations show the obtained PbTiO3 nanobelts and nanoflakes are pure tetragonal phase. TEM and scanning electron microscopy (SEM) observations show single-crystal PbTiO3 nanobelts with average breadth 80–200 nm and several micrometer length. The shape of the obtained nanoflakes with about 20–25 nm thickness is irregular and the nanoflakes are formed by PbTiO3 quantum dots. A possible mechanism for the formation has been proposed.
Settlement of the Sweet-spot Problem of MALDI Crystals Using Cyclodextrin-supported Matrix
Authors: Fujita Takashi , Fujino Tatsuya
Published: March 2013

One of the problems of matrix-assisted laser desorption/ionization (MALDI), the inhomogeneity of analyte–matrix mixed crystals, can be settled moderately by the clathration of organic matrices into a cyclodextrin cavity. The homogeneous distribution of matrix and analyte was confirmed by scanning electron microscopy (SEM) and position-dependent mass spectrometry.
Screen-printed Modified Diamond Electrode for Glucose Detection
Authors: Kondo Takeshi , Horitani Masaru , Sakamoto Hironori , Shitanda Isao , Hoshi Yoshinao , Itagaki Masayuki , Yuasa Makoto
Published: March 2013

An electrochemical glucose sensor based on a screen-printed diamond electrode was fabricated as a low-cost, disposable, and sensitive electrode. Amperometric detection of glucose was achieved by using a glucose-oxidase-immobilized cobalt phthalocyanine/boron-doped diamond powder (GOx-CoPc/BDDP)-printed electrode, with a linear calibration curve in the concentration range of 0.2–1.0 mM. The background current for the GOx-CoPc/BDDP-printed electrode stabilized faster than that for the GOx-CoPc/carbon-printed electrode, which confirms its practical usefulness for the detection of glucose at low concentrations.
In Vitro and In Vivo Evaluation of Hydroxyapatite Block and Granules Supported with Wheat Starch Set through the Process of Hydration under a Physiological Condition
Authors: Furusawa Toshitake , Oshino Ikue , Yoshida Kakeru , Oshiyama Naho , Kawai Takahiro , Sato Masaaki , Okudera Toshimitsu
Published: March 2013

Needle-like hydroxyapatites obtained through a hydration reaction process between anhydrous dicalcium phosphate (ADCP) and tetracalcium phosphate (TTCP) were reinforced with wheat starch to form composite blocks, and they showed mechanical properties corresponding to their compositions: mass fraction of calcium phosphate powders/starch solution and starch concentration. A kind of the composite granules was found to be osteoconductive in an in vivo examination with a rat model.
Synthesis and Oxidizing Ability of p-Chloranil Dimer
Authors: Hayashi Naoto , Nakagawa Hiroyuki , Sugiyama Yuko , Yoshino Junro , Higuchi Hiroyuki
Published: March 2013

A p-chloranil dimer (pCh2) has been synthesized. The first reduction potential of pCh2 shifted to a more positive value than that observed for the p-chloranil monomer (pCh1) and was more negative than that for 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ). As expected, pCh2 oxidized 9,10-dihydroanthracene and α-tetralol to give anthracene and α-tetralone, respectively, more efficiently than pCh1 did. The advantages of pCh2 were observed in oxidations of 2,4-di-tert-butylphenol and 2,6-di-tert-butyl-4-methylphenol. Although further oxidation took place in DDQ oxidations and no reaction occurred in pCh1 oxidations, initial oxidation products were solely obtained in pCh2 oxidation because of its moderate oxidizing ability.
Asymmetric Synthesis of 1,3-Oxazolidines via Intramolecular Aza-Michael Addition by Bifunctional Organocatalysts
Authors: Fukata Yukihiro , Asano Keisuke , Matsubara Seijiro
Published: March 2013

A novel synthetic route to optically active 1,3-oxazolidines via formal [3 + 2] cycloaddition in the presence of cinchona-alkaloid-thiourea-based bifunctional organocatalysts is reported. This protocol gives easy access to a wide range of chiral 1,3-oxazolidines. In addition, the results show that bifunctional organocatalysts can effect the intramolecular aza-Michael addition, leading to the asymmetric synthesis of nitrogen-containing heterocycles.
Triphenylene-based Host Materials for Low-voltage, Highly Efficient Red Phosphorescent Organic Light-emitting Diodes
Authors: Togashi Kazunori , Yasuda Takuma , Adachi Chihaya
Published: March 2013

Triphenylene-based host materials BDBF-TP and BDBT-TP were synthesized for use in red phosphorescent organic light-emitting diodes (PHOLEDs). The current–voltage characteristics of hole- and electron-only devices revealed that BDBT-TP exhibits better bipolar carrier transport properties than 4,4′-bis(carbazol-9-yl)-1,1′-biphenyl and BDBF-TP. Red PHOLEDs containing BDBF-TP or BDBT-TP as the host showed a lower driving voltage, higher external quantum efficiency, and lower efficiency roll-off at high current density.
Asymmetric Coupling Polymerizations of 2,3-Dihalido-N-substituted Maleimide Derivatives in the Presence of Chiral Bisoxazolines
Authors: Onimura Kenjiro , Nakamura Munetoshi , Amatsu Keisuke , Matsushima Mieko , Yamabuki Kazuhiro , Oishi Tsutomu
Published: March 2013

Yamamoto coupling polymerizations of 2,3-dihalido-N-substituted maleimides (DXRMI) were carried out using nickel catalysts. In addition, coupling reactions of 2,3-dihalido-N-cyclohexylmaleimide (DXCHMI) were performed with nickel complexes in the presence of directly coupled chiral bisoxazolines (R′box) to give optically active poly(N-substituted maleimide-2,3-diyl)s [poly(RMI)s] (specific rotation [α]435 = +6.0 to −34.6°). Polymers with number-average molecular weights (Mn) ranging from 270 to 36200 were obtained in 17% to quantitative yields. Poly(N-cyclohexylmaleimide-2,3-diyl) [poly(CHMI)] formed with [Ni(cod)2]–R′box exhibited the largest absolute value, [α]435 = −34.6°.
Efficient Electronic Communication in 4,9-Bis(ferrocenylethynyl)dimethyldihydropyrene
Authors: Kishida Masa-aki , Muratsugu Satoshi , Sakamoto Ryota , Kusamoto Tetsuro , Nishihara Hiroshi
Published: March 2013

We have prepared the dimethyldihydropyrene (DHP) derivative 2, which possesses two ferrocenyl groups at the 4- and 9-positions through ethynylene linkers. 2 shows intense electronic communication between the two ferrocenyl groups, which is promoted by the highly developed π orbital of the diethynyl DHP moiety.
Effects of Copper(II) Oxide Addition and Red Light Irradiation on Photocatalytic Activity of Indium Oxide under Irradiation of Visible Light
Authors: Sasaki Yasutomo , Tanaka Atsuhiro , Hashimoto Keiji , Kominami Hiroshi
Published: March 2013

Copper(II) oxide (CuO)-modified indium oxide (In2O3) prepared by physical mixing efficiently mineralized acetone under irradiation of light from a blue LED. The reaction rate increased with additional irradiation of light from a red LED, though no reactions occurred over CuO and In2O3 under irradiation of the red light, indicating that band-gap excitation of CuO contributed to photocatalytic reaction over CuO–In2O3. The effect of CuO modification was also observed in action spectra with and without irradiation of the red light.
Determination of Ni2+ in Waters with Sodium Poly(aspartic acid) as a Binding Phase in Diffusive Gradients in Thin Films
Authors: Chen Hong , Guo Lianwen , Cai Ranyong , Zhang Yangyang , Bo Le , Li Jianrong
Published: March 2013

The technique of diffusive gradients in thin films (DGT) for the measurement of Ni2+ in waters was developed using sodium poly(aspartic acid) (PASP) solution as the liquid binding phase in the liquid-type DGT devices (PASP DGT). The Ni2+ uptake of PASP DGT increased linearly with time (r2 = 0.9990) with a DGT-labile fraction (Ψ) of 98.04 ± 1.76% in synthetic solution. The Ψ values of Ni2+ were measured in spiked river water (37.82 ± 2.79%) and spiked domestic wastewater (28.46 ± 1.87%). The stability constant (log K) of PASP–Ni was 8.56, indicating that PASP can coordinate strongly to Ni2+. The binding capacity of PASP DGT decreased with increase of ionic strength, whereas it remained fairly constant in the pH range 4–9. The results show that PASP can be used as a binding phase in the liquid-type DGT device for the measurement of Ni2+ in waters.
DNA-templated Fabrication of Biphasic Calcium Phosphate Ceramics with a Bimodal Pore Structure for Tissue Engineering
Authors: Sugiyama Nami , Yanagi Yusuke , Yoshizawa-Fujita Masahiro , Aizawa Mamoru , Takeoka Yuko , Rikukawa Masahiro
Published: March 2013

Biphasic calcium phosphate (BCP) ceramics with well-controlled pores were fabricated by sintering mixtures of synthetic hydroxyapatite (HAp) and deoxyribonucleic acid (DNA). BCP ceramics with macro- and micropores revealed excellent cell proliferation as a result of suitable surface topography and phase composition.
Effect of Base Molecules on One-dimensional Assembly of Silica Nanospheres Mediated by a Block Copolymer
Authors: Zhou Shujun , Wang Junzheng , Sugawara-Narutaki Ayae , Shimojima Atsushi , Okubo Tatsuya
Published: March 2013

Silica nanospheres (SNSs) synthesized with different base catalysts assemble into one-dimensional (1D) chain-like nanostructures at proper pH levels in the presence of the block copolymer F127. The addition of basic amino acids or the removal of base catalysts by dialysis influences the pH of 1D assembly. The base molecules affect assembly by modifying the electrostatic repulsion among the SNSs; however, they are not indispensable for this 1D assembly phenomenon.
Substrate Dependence of the Proton Transport and Oriented Structure in Oligo[(1,2-propanediamine)-alt-(oxalic acid)] Thin Films
Authors: Nagao Yuki
Published: March 2013

Three oligo[(1,2-propanediamine)-alt-(oxalic acid)] thin films were prepared on SiO2, R-plane sapphire, and MgO(100) substrates, and their proton conductivities were investigated. Conductivity depended on the substrate and varied from 4 × 10−3 to 1 × 10−4 S cm−1 under the same conditions (80% relative humidity and 298 K). The thin films between the R-plane (1102) sapphire and MgO(100) substrates showed different molecular oriented structures. The thin film on the sapphire substrate, which shows higher proton conductivity, has a structure oriented parallel to the substrate. The molecular orientation in the thin film could be correlated with the proton-transport properties.
Adsorption of Ammonium by Soil in the Presence of Phosphate during Land-treatment Process of Nutrient-enriched Wastewater
Authors: Chen Xiaochen , Fukushi Kensuke
Published: March 2013

Ammonium adsorption tests were performed to investigate comprehensively the adsorption of ammonium by soil during the land-treatment process of nutrient-enriched wastewater. Accordingly, the conceptual pattern of ammonium adsorption isotherms, as affected by the associated phosphate concentration, and the ratio of ammonium to phosphate and nutrient cations represented by potassium, is clearly illustrated. The findings contribute to a better understanding of the treatment effect and are a useful guide for the design of wastewater land-treatment systems.
Macrodipole Moment of Polypeptides in β-Sheet and Its Prediction from Dipole Moments of Amino Acid Residues as Building Blocks: Alanine and Glycine in β-Strand
Authors: Mieda Shunsuke , Aida Misako
Published: March 2013

The macrodipole moment of a β-sheet depends on the number and length of β-strands, as well as whether it is parallel or antiparallel. Here, we propose the VSHBβ model, in which the dipole moments of amino acid residues are used as building blocks to predict the macrodipole moment of a β-sheet. Once a set of VSHBβ models is available, large-scale MO calculations will not be needed to obtain local dipole moments or macrodipole moments of large polypeptides in β-sheets.
Conjugate addition approach for natural product synthesis inspired by gibberellin and solanoeclepin A targets
Authors: Isobe Minoru
Published: March 2013

Trimethylzincate is known to react through conjugate addition to α,β-unsaturated ketones, but adds much faster to α,β-unsaturated esters at low temperatures. Since the intermediate zinc enolate behaves differently from that of dimethylcuprate, it offers scope for application in a partial synthesis of gibberellin A3. A second example involving vinylsulfones having an oxygen atom on the γ-carbon strongly directs incoming nucleophiles in conjugate addition mode. Heteroatom-directed conjugate addition (HADCA) provides very reactive carbanion intermediates leading to cyclobutane ring formation, necessary for synthesis of solanoeclepin A. An alternative reaction for the four-membered carbocyclic ring closure was explored to make a bond formation between the propargylic cation of Nicholas type and allyltrimethylsilane nucleophile of Hosomi–Sakurai type. This method allowed a formation of tricyclo[5.2.1.01,6]decene framework.
Substituent effects on the structure of hexacoordinate carbon bearing two thioxanthene ligands
Authors: Yamaguchi Torahiko , Yamamoto Yohsuke
Published: March 2013

In order to elucidate the electronic nature of our recently reported first hexacoordinated carbon (12-C-6), density functional theory (DFT) calculations of sulfide precursor, sulfone derivative, and S+-F derivative were carried out and compared with those of the reported S+-Me hexacoordinated carbon. Computations on the hexacoordinated carbon, indicating that four attractive C–O interactions with the central hexacoordinate carbon atom exist, also revealed that the interactions consist of two different types of three-center four-electron bonds, which can be regarded as electron donation by the lone pairs of the oxygen atoms to the empty low-lying π*-orbitals of the allene. The optimized structures of the sulfide, sulfone, S+-F, and the original S+-Me suggested that the introduction of electron-withdrawing groups at the sulfur atoms would make the C–O attractive interactions stronger by a larger contribution of the carbon dication resonance structure. Thus, allene compounds (sulfide, sulfone, sulfonium) with two different thioxanthene ligands (one with 1,8-dimethoxy groups as in the S+-Me compound and the other with 1,8-diphenoxy groups) were synthesized to confirm the predicted substituent effects on the C(central)–O interactions. Electron-withdrawing substituents at the sulfur atoms were found to give rise to strong C(central)–O attractive interactions; the average values of the four C–O distances were smaller as the electron-withdrawing ability of the sulfur atoms rose. Additionally, C(central)···OMe distances were shorter than the corresponding C(central)···OPh distances, reflecting the higher electron-donating ability of the oxygen atoms at these 1,8-positions of the thioxanthene skeleton.
Calcineurin Governs Thermotolerance and Virulence ofCryptococcus gattii
Authors: Chen Ying-Lien , Lehman Virginia N , Lewit Yonathan , Averette Anna F , Heitman Joseph
Published: March 2013

The pathogenic yeast Cryptococcus gattii, which is causing an outbreak in the Pacific Northwest region of North America, causes life-threatening pulmonary infections and meningoencephalitis in healthy individuals, unlike Cryptococcus neoformans, which commonly infects immunocompromised patients. In addition to a greater predilection for C. gattii to infect healthy hosts, the C. gattii genome sequence project revealed extensive chromosomal rearrangements compared with C. neoformans, showing genomic differences between the two Cryptococcus species. We investigated the roles of C. gattii calcineurin in three molecular types: VGIIa (R265), VGIIb (R272), and VGI (WM276). We found that calcineurin exhibits a differential requirement for growth on solid medium at 37°, as calcineurin mutants generated from R265 were more thermotolerant than mutants from R272 and WM276. We demonstrated that tolerance to calcineurin inhibitors (FK506, CsA) at 37° is linked with the VGIIa molecular type. The calcineurin mutants from the R272 background showed the most extensive growth and morphological defects (multivesicle and larger ring-like cells), as well as increased fluconazole susceptibility. Our cellular architecture examination showed that C. gattii and C. neoformans calcineurin mutants exhibit plasma membrane disruptions. Calcineurin in the C. gattii VGII molecular type plays a greater role in controlling cation homeostasis compared with that in C. gattii VGI and C. neoformans H99. Importantly, we demonstrate that C. gattii calcineurin is essential for virulence in a murine inhalation model, supporting C. gattii calcineurin as an attractive antifungal drug target.
Mature Microsatellites: Mechanisms Underlying Dinucleotide Microsatellite Mutational Biases in Human Cells
Authors: Baptiste Beverly A , Ananda Guruprasad , Strubczewski Noelle , Lutzkanin Andrew , Khoo Su Jen , Srikanth Abhinaya , Kim Nari , Makova Kateryna D , Krasilnikova Maria M , Eckert Kristin A
Published: March 2013

Dinucleotide microsatellites are dynamic DNA sequences that affect genome stability. Here, we focused on mature microsatellites, defined as pure repeats of lengths above the threshold and unlikely to mutate below it in a single mutational event. We investigated the prevalence and mutational behavior of these sequences by using human genome sequence data, human cells in culture, and purified DNA polymerases. Mature dinucleotides (≥10 units) are present within exonic sequences of >350 genes, resulting in vulnerability to cellular genetic integrity. Mature dinucleotide mutagenesis was examined experimentally using ex vivo and in vitro approaches. We observe an expansion bias for dinucleotide microsatellites up to 20 units in length in somatic human cells, in agreement with previous computational analyses of germ-line biases. Using purified DNA polymerases and human cell lines deficient for mismatch repair (MMR), we show that the expansion bias is caused by functional MMR and is not due to DNA polymerase error biases. Specifically, we observe that the MutSα and MutLα complexes protect against expansion mutations. Our data support a model wherein different MMR complexes shift the balance of mutations toward deletion or expansion. Finally, we show that replication fork progression is stalled within long dinucleotides, suggesting that mutational mechanisms within long repeats may be distinct from shorter lengths, depending on the biochemistry of fork resolution. Our work combines computational and experimental approaches to explain the complex mutational behavior of dinucleotide microsatellites in humans.
PolyCat: A Resource for Genome Categorization of Sequencing Reads From Allopolyploid Organisms
Authors: Page Justin T , Gingle Alan R , Udall Joshua A
Published: March 2013

Read mapping is a fundamental part of next-generation genomic research but is complicated by genome duplication in many plants. Categorizing DNA sequence reads into their respective genomes enables current methods to analyze polyploid genomes as if they were diploid. We present PolyCat—a pipeline for mapping and categorizing all types of next-generation sequence data produced from allopolyploid organisms. PolyCat uses GSNAP’s single-nucleotide polymorphism (SNP)-tolerant mapping to minimize the mapping efficiency bias caused by SNPs between genomes. PolyCat then uses SNPs between genomes to categorize reads according to their respective genomes. Bisulfite-treated reads have a significant reduction in nucleotide complexity because nucleotide conversion events are confounded with transition substitutions. PolyCat includes special provisions to properly handle bisulfite-treated data. We demonstrate the functionality of PolyCat on allotetraploid cotton, Gossypium hirsutum, and create a functional SNP index for efficiently mapping sequence reads to the D-genome sequence of G. raimondii. PolyCat is appropriate for all allopolyploids and all types of next-generation genome analysis, including differential expression (RNA sequencing), differential methylation (bisulfite sequencing), differential DNA-protein binding (chromatin immunoprecipitation sequencing), and population diversity.
Imputation of Unordered Markers and the Impact on Genomic Selection Accuracy
Authors: Rutkoski Jessica E , Poland Jesse , Jannink Jean-Luc , Sorrells Mark E
Published: March 2013

Genomic selection, a breeding method that promises to accelerate rates of genetic gain, requires dense, genome-wide marker data. Genotyping-by-sequencing can generate a large number of de novo markers. However, without a reference genome, these markers are unordered and typically have a large proportion of missing data. Because marker imputation algorithms were developed for species with a reference genome, algorithms suited for unordered markers have not been rigorously evaluated. Using four empirical datasets, we evaluate and characterize four such imputation methods, referred to as k-nearest neighbors, singular value decomposition, random forest regression, and expectation maximization imputation, in terms of their imputation accuracies and the factors affecting accuracy. The effect of imputation method on the genomic selection accuracy is assessed in comparison with mean imputation. The effect of excluding markers with a large proportion of missing data on the genomic selection accuracy is also examined. Our results show that imputation of unordered markers can be accurate, especially when linkage disequilibrium between markers is high and genotyped individuals are related. Of the methods evaluated, random forest regression imputation produced superior accuracy. In comparison with mean imputation, all four imputation methods we evaluated led to greater genomic selection accuracies when the level of missing data was high. Including rather than excluding markers with a large proportion of missing data nearly always led to greater GS accuracies. We conclude that high levels of missing data in dense marker sets is not a major obstacle for genomic selection, even when marker order is not known.
Fine-Mapping and Identification of a Candidate Gene Underlying thed2Dwarfing Phenotype in Pearl Millet,Cenchrus americanus(L.) Morrone
Authors: Parvathaneni Rajiv K , Jakkula Vinod , Padi Francis K , Faure Sebastien , Nagarajappa Nethra , Pontaroli Ana C , Wu Xiaomei , Bennetzen Jeffrey L , Devos Katrien M
Published: March 2013

Pearl millet is one of the most important subsistence crops grown in India and sub-Saharan Africa. In many cereal crops, reduced height is a key trait for enhancing yield, and dwarf mutants have been extensively used in breeding to reduce yield loss due to lodging under intense management. In pearl millet, the recessive d2 dwarfing gene has been deployed widely in commercial germplasm grown in India, the United States, and Australia. Despite its importance, very little research has gone into determining the identity of the d2 gene. We used comparative information, genetic mapping in two F2 populations representing a total of some 1500 progeny, and haplotype analysis of three tall and three dwarf inbred lines to delineate the d2 region by two genetic markers that, in sorghum, define a region of 410 kb with 40 annotated genes. One of the sorghum genes annotated within this region is ABCB1, which encodes a P-glycoprotein involved in auxin transport. This gene had previously been shown to underlie the economically important dw3 dwarf mutation in sorghum. The cosegregation of ABCB1 with the d2 phenotype, its differential expression in the tall inbred ICMP 451 and the dwarf inbred Tift 23DB, and the similar phenotype of stacked lower internodes in the sorghum dw3 and pearl millet d2 mutants suggest that ABCB1 is a likely candidate for d2.
Cats in the forest: predicting habitat adaptations from humerus morphometry in extant and fossil Felidae (Carnivora)
Authors: Meloro Carlo , Elton Sarah , Louys Julien , Bishop Laura C. , Ditchfield Peter
Published: March 2013

Mammalian carnivores are rarely incorporated in paleoenvironmental reconstructions, largely because of their rarity within the fossil record. However, multivariate statistical modeling can be successfully used to quantify specific anatomical features as environmental predictors. Here we explore morphological variability of the humerus in a closely related group of predators (Felidae) to investigate the relationship between morphometric descriptors and habitat categories. We analyze linear measurements of the humerus in three different morphometric combinations (log-transformed, size-free, and ratio), and explore four distinct ways of categorizing habitat adaptations. Open, Mixed, and Closed categories are defined according to criteria based on traditional descriptions of species, distributions, and biome occupancy. Extensive exploratory work is presented using linear discriminant analyses and several fossils are included to provide paleoecological reconstructions.

We found no significant differences in the predictive power of distinct morphometric descriptors or habitat criteria, although sample splitting into small and large cat guilds greatly improves the stability of the models. Significant insights emerge for three long-canine cats:Smilodon populator,Paramachairodus orientalis, andDinofelissp. from Olduvai Gorge (East Africa).S. populatorandP. orientalisare both predicted to have been closed-habitat adapted taxa. The false “sabertooth”Dinofelissp. from Olduvai Gorge is predicted to be adapted to mixed habitat. The application of felid humerus ecomorphology to the carnivoran record of Olduvai Gorge shows that the older stratigraphic levels (Bed I, 1.99–1.79 Ma) included a broader range of environments than Beds II or V, where there is an abundance of cats adapted to open environments.
Body size and growth patterns in the therocephalianMoschorhinus kitchingi(Therapsida: Eutheriodontia) before and after the end-Permian extinction in South Africa
Authors: Huttenlocker Adam K. , Botha-Brink Jennifer
Published: March 2013

The continuous fossil record of therocephalian therapsids (Eutheriodontia) across the Permo-Triassic boundary and their differential survivorship of the end-Permian extinction offer an exceptional deep-time perspective on vertebrate life-history evolution during episodes of large-scale ecological perturbation. To examine potential impacts of the extinction on body size evolution (e.g., “Lilliput” effects) and growth patterns, we investigated cranial sizes and limb bone histology in the therocephalianMoschorhinus kitchingiboth before and after the end-Permian extinction, facilitated by analysis of thin-sections of 23 limb bones from an ontogenetic sample of ten individuals across the Permo-Triassic boundary. In general, early subadultMoschorhinusdisplayed propodial cortices with extensive woven- and parallel-fibered bone (PFB) with dense radial and reticular vascularization and a moderately thickened bone wall with few growth marks. The outer cortex of propodials and epipodials showed a transition to PFB and lamellar bone with longitudinally oriented canals in individuals interpreted as late subadults or adults (>80% largest size). Most elements displayed several (3+) growth marks, though growth marks were more faithfully recorded in the epipodials of Permian individuals. Pearson product-moment correlation tests were performed to examine the relationship between size and robusticity on growth proxies (% cortical vascularity, mean primary osteon diameter), but variation in histomorphology could not be explained by size alone. Variation in body size may be affected by differences in juvenile growth rate and duration, which are highly variable in environmentally stressed extant reptile species. Geologic stage was a more consistent predictor of cortical vascularity. We suggest that Permian and TriassicMoschorhinusexhibited differential rates of early skeletal growth, corroborating the hypothesis that increased environmental variability in the earliest Triassic was associated with rapid growth to a minimum body size requirement and, consequently, shortened developmental times.
A modified Procrustes analysis for bilaterally symmetrical outlines, with an application to microevolution inBaculites
Authors: Bookstein Fred L. , Ward Peter D.
Published: March 2013

In quantitative paleobiology, one common format for image-derived information is the closed two-dimensional outline curve. Before the end of the last century a great variety of morphometric tools were on offer to deal with this data type, including diverse analyses of distance from a central point, “eigenshape analysis” of a carefully normalized tangent angle function, and Procrustes analysis of configurations of sliding semilandmarks. For the special case ofoutline forms that are nominally bilaterally symmetric, this paper offers a hybrid approach that fuses the Procrustes toolkit with a variant of a much older method, analysis of radial distance according to angles out of a center. The synthesis represents each outline as a regularly resampled data set of radially aligned shape coordinates analogous to bilateral Procrustes shape coordinates. When the center is iteratively located in one particular way, this representation has the same Procrustes distance statistics as a conventional radial representation, while the formalism of shape coordinates permits symmetrization, localizability, and thin-plate spline visualizations. We explain the method and sketch some of its advantages and limitations in the course of an example involving 99Baculites inornatusoutlines spanning 90 m of deposits from a high-precision measured section in the Campanian-age Rosario Formation cropping out at Punta San Jose, Baja California. This sequence shows substantial changes of pole curvature over time, changes that may involve a punctuation event regarding hydrostatics, hydrodynamics, or defense against predators. A concluding comment deals with implications of the developments here forBaculitesmicroevolution and for morphometrics.
Experimental harvesting of fish populations drives genetically based shifts in body size and maturation
Authors: van Wijk Serinde J , Taylor Martin I , Creer Simon , Dreyer Christine , Rodrigues Fernanda M , Ramnarine Indar W , van Oosterhout Cock , Carvalho Gary R
Published: March 2013

Size‐selective harvesting in commercial fisheries can induce rapid changes in biological traits. While experimental and wild harvested populations often exhibit clear shifts in body size and maturation associated with fishing pressure, the relative contributions of genetic and environmental factors to these shifts remain uncertain and have been much debated. To date, observations of so‐called fisheries‐induced evolution (FIE) have been based solely on phenotypic measures, such as size data. Genetic data are hitherto lacking. Here, we quantify genetic versus environmental change in response to size‐selective harvesting for small and large body size in guppies (Poecilia reticulata) across three generations of selection. We document for the first time significant changes at individual genetic loci, some of which have previously been associated with body size. In contrast, variation at neutral microsatellite markers was unaffected by selection, providing direct genetic evidence for rapid evolution induced by size‐selective harvesting. These findings demonstrate FIE in an experimental system, with major implications for the sustainability of harvested populations, as well as impacts on size‐structured communities and ecosystem processes. These findings highlight the need for scientists and managers to reconsider the capacity of harvested stocks to adapt to, and recover from, harvesting and predation.
Seasonal coupling of canopy structure and function in African tropical forests and its environmental controls
Authors: Guan Kaiyu , Wolf Adam , Medvigy David , Caylor Kelly K. , Pan Ming , Wood Eric F.
Published: March 2013

Tropical forests provide important ecosystem services in maintaining biodiversity, sequestering carbon and regulating climate regionally and globally. Climate triggers the seasonal transitions of vegetation structure and function in tropical forests. In turn, the seasonal cycles of structure and function in tropical forests feed back to the climate system through the control of land‐atmosphere exchange of carbon, water and energy fluxes. Large uncertainties exist in the carbon and water budgets of tropical forests, and environmental controls on phenology are among the least understood factors. Although field studies have identified patterns in the environmental controls on local‐scale species‐level phenology in the tropics, there is little consensus on large‐scale top‐down environmental controls on whole‐ecosystem seasonality. In this paper, we use both optical and microwave remote sensing to investigate the seasonality of vegetation canopy structure and function in three distinct tropical African forest types, and identify environmental triggers or controls of their variability. For most tropical forests that have a closed canopy and high leaf biomass, optical remote sensing (e.g., vegetation indices) captures canopy photosynthetic capacity (i.e., canopy function), while small‐wavelength microwave remote sensing characterizes the leaf biomass and leaf water content of the upper canopy (i.e., canopy structure). Our results reveal a strong coupling of canopy structure with canopy function in the tropical deciduous forests and woody savannas, and their seasonalities are both controlled by precipitation rather than solar radiation. By contrast, tropical evergreen forests in Africa exhibit a decoupling of canopy structure from canopy function revealed by different sensors: canopy photosynthetic capacity shown by the optical remote sensing is linked to the seasonal variation of precipitation, while microwave remote sensing captures semi‐annual leaf‐flushing that is synchronous with peak insolation intensity at the top of the atmosphere, which is bimodal. The differential coupling of canopy structure and function in tropical forests observed from remote sensing highlights differences inherent in distinct vegetation types within the tropics that may originate in the different life histories of their respective floras. This satellite‐based finding encourages more field‐based studies to clarify the interpretation of these large scale patterns.