bluuebunny/crossref_metadata_2025_split huggingface dataset:
Eco-physiological adaptation shapes the response of calcifying algae to nutrient limitation
Authors: Šupraha Luka , Gerecht Andrea C. , Probert Ian , Henderiks Jorijntje 
Published: November 2015

AbstractThe steady increase in global ocean temperature will most likely lead to nutrient limitation in the photic zone. This will impact the physiology of marine algae, including the globally important calcifying coccolithophores. Understanding their adaptive patterns is essential for modelling carbon production in a low-nutrient ocean. We investigated the physiology ofHelicosphaera carteri, a representative of the abundant but under-investigated flagellated functional group of coccolithophores. Two strains isolated from contrasting nutrient regimes (South Atlantic and Mediterranean Sea) were grown in phosphorus-replete and phosphorus-limited batch cultures. While growing exponentially in a phosphorus-replete medium, the Mediterranean strain exhibited on average 24% lower growth rate, 36% larger coccosphere volume and 21% lower particulate inorganic carbon (PIC) production than the Atlantic strain. Under phosphorus limitation, the same strain was capable of reaching a 2.6 times higher cell density than the Atlantic strain due to lower phosphorus requirements. These results suggest that local physiological adaptation can define the performance of this species under nutrient limitation.
Rapid whole genome sequencing of Miyazaki-Bali/2007 Pteropine orthoreovirus by modified rolling circular amplification with adaptor ligation – next generation sequencing
Authors: Singh Harpal , Yoshikawa Tomoki , Kobayashi Takeshi , Fukushi Shuetsu , Tani Hideki , Taniguchi Satoshi , Fukuma Aiko , Yang Ming , Sugamata Masami , Shimojima Masayuki , Saijo Masayuki 
Published: November 2015

AbstractThe emergence of orthoreoviruses as the causative agent of human respiratory illness over the past few years has led to a demand to determine their viral genome sequences. The whole genome sequencing of such RNA viruses using traditional methods, such as Sanger dideoxy sequencing following rapid amplification of cDNA ends presents a laborious challenge due to the numerous preparatory steps required before sequencing can commence. We developed a practical, time-efficient novel combination method capable of reducing the total time required from months to less than a week in the determination of whole genome sequence of Pteropine orthoreoviruses (PRV); through a combination of viral RNA purification and enrichment, adaptor ligation, reverse transcription, cDNA circularization and amplification and next generation sequencing. We propose to call the method “modified rolling circular amplification with adaptor ligation – next generation sequencing (mRCA-NGS)”. Here, we describe the technological focus and advantage of mRCA-NGS and its expansive application, exemplified through the phylogenetic understanding of the Miyazaki-Bali/2007 PRV.
Cofilin 1 activation prevents the defects in axon elongation and guidance induced by extracellular alpha-synuclein
Authors: Tilve Sharada , Difato Francesco , Chieregatti Evelina 
Published: November 2015

AbstractImpaired adult neurogenesis and axon traumatic injury participate in the severity of neurodegenerative diseases. Alpha-synuclein, a cytosolic protein involved in Parkinson’s disease, may be released from neurons, suggesting a role for excess secreted alpha-synuclein in the onset and spread of the pathology. Here we provide evidence that long term exposure of young neurons to extracellular alpha-synuclein hampers axon elongation and growth cone turning. We show that actin turnover and the rate of movement of actin waves along the axon are altered, due to alpha-synuclein-induced inactivation of cofilin. Upon laser disruption of microfilaments, healing of axons is favored by the increased phosphorylation of cofilin, however, at later time points; the defect in neurite extension prevails, being lost the regulation of cofilin activity. Importantly, overexpression of the active form of cofilin in neurons exposed to alpha-synuclein is able to restore the movement of actin waves, physiological axon elongation and growth cone turning. Our study reveals the molecular basis of alpha-synuclein-driven deficits in growth and migration of newborn neurons and in elongation and regeneration of adult neurons.
Spin Exchange Interaction in Substituted Copper Phthalocyanine Crystalline Thin Films
Authors: Rawat Naveen , Pan Zhenwen , Lamarche Cody J. , Wetherby Anthony , Waterman Rory , Tokumoto Takahisa , Cherian Judy G. , Headrick Randall L. , McGill Stephen A. , Furis Madalina I. 
Published: November 2015

AbstractThe origins of spin exchange in crystalline thin films of Copper Octabutoxy Phthalocyanine (Cu-OBPc) are investigated using Magnetic Circular Dichroism (MCD) spectroscopy. These studies are made possible by a solution deposition technique which produces highly ordered films with macroscopic grain sizes suitable for optical studies. For temperatures lower than 2 K, the contribution of a specific state in the valence band manifold originating from the hybridized lone pair in nitrogen orbitals of the Phthalocyanine ring, bears the Brillouin-like signature of an exchange interaction with the localized d-shell Cu spins. A comprehensive MCD spectral analysis coupled with a molecular field model of a σπ − d exchange analogous to sp-d interactions in Diluted Magnetic Semiconductors (DMS) renders an enhanced Zeeman splitting and a modified g-factor of −4 for the electrons that mediate the interaction. These studies define an experimental tool for identifying electronic states involved in spin-dependent exchange interactions in organic materials.
Electrochemical and Dry Sand Impact Erosion Studies on Carbon Steel
Authors: Naz M. Y. , Ismail N. I. , Sulaiman S. A. , Shukrullah S. 
Published: November 2015

AbstractThis study investigated the dry and aqueous erosion of mild steel using electrochemical and dry sand impact techniques. In dry sand impact experiments, mild steel was eroded with 45 μm and 150 μm sand particles. Scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX) and micro-hardness techniques were used to elaborate the surface morphology of the eroded samples. The results revealed significant change in morphology of the eroded samples. In-depth analysis showed that although the metal erosion due to larger particles was significantly higher, the fines also notably damaged the metal surface. The surface damages were appreciably reduced with decrease in impact angle of the accelerated particles. The maximum damages were observed at an impact angle of 90°. The hardness of the samples treated with 45 μm and 150 μm sand remained in the range of 88.34 to 102.31 VHN and 87.7 to 97.55 VHN, respectively. In electrochemical experiments, a triple electrode probe was added into the metal treatment process. The linear polarization resistance (LPR) measurements were performed in slurries having 5% (by weight) of sand particles. LPR of the samples treated with 45 μm and 150 μm sand slurries was calculated about 949 Ω.cm2and 809 Ω.cm2, respectively.
Superior removal of arsenic from water with zirconium metal-organic framework UiO-66
Authors: Wang Chenghong , Liu Xinlei , Chen J. Paul , Li Kang 
Published: November 2015

AbstractIn this study, water stable zirconium metal-organic framework (UiO-66) has been synthesized and for the first time applied as an adsorbent to remove aquatic arsenic contamination. The as-synthesized UiO-66 adsorbent functions excellently across a broad pH range of 1 to 10 and achieves a remarkable arsenate uptake capacity of 303 mg/g at the optimal pH, i.e., pH = 2. To the best of our knowledge, this is the highest arsenate As(V) adsorption capacity ever reported, much higher than that of currently available adsorbents (5–280 mg/g, generally less than 100 mg/g). The superior arsenic uptake performance of UiO-66 adsorbent could be attributed to the highly porous crystalline structure containing zirconium oxide clusters, which provides a large contact area and plenty of active sites in unit space. Two binding sites within the adsorbent framework are proposed for arsenic species, i.e., hydroxyl group and benzenedicarboxylate ligand. At equilibrium, seven equivalent arsenic species can be captured by one Zr6cluster through the formation of Zr-O-As coordination bonds.
Bt crops benefit natural enemies to control non-target pests
Authors: Tian Jun-Ce , Yao Ju , Long Li-Ping , Romeis Jörg , Shelton Anthony M. 
Published: November 2015

AbstractCrops producing insecticidal crystal (Cry) proteins from Bacillus thuringiensis (Bt) control important lepidopteran pests. However, pests such as aphids not susceptible to Cry proteins may require other integrated pest management (IPM) tactics, including biological control. We fed aphids on Bt and non-Bt plants and analyzed the Bt protein residue in aphids and compared the effects of Bt plants and a pyrethroid, lambda-cyhalothrin, on the performance of three natural enemies (predators: Coleomegilla maculata and Eupeodes americanus; parasitoid Aphidius colemani) of the green peach aphid, Myzus persicae. No Bt protein residues in aphids were detected and no significant differences were recorded in the performance of pyrethroid-resistant aphids that fed on Bt broccoli expressing Cry1Ab or Cry1C, or on non-Bt broccoli plants treated or not treated with the pyrethroid. This indicated the aphids were not affected by the Cry proteins or the pyrethroid, thus removing any effect of prey quality. Tri-trophic experiments demonstrated that no C. maculata and E. americanus survived consumption of pyrethroid-treated aphids and that ovipositional behavior of A. colemani was impaired when provided with pyrethroid-treated aphids. In contrast, natural enemies were not affected when fed aphids reared on Bt broccoli, thus demonstrating the safety of these Bt plants for IPM.
Species-specific duplications of NBS-encoding genes in Chinese chestnut (Castanea mollissima)
Authors: Zhong Yan , Li Yingjun , Huang Kaihui , Cheng Zong-Ming 
Published: November 2015

AbstractThe disease resistance (R) genes play an important role in protecting plants from infection by diverse pathogens in the environment. The nucleotide-binding site (NBS)-leucine-rich repeat (LRR) class of genes is one of the largest R gene families. Chinese chestnut (Castanea mollissima) is resistant to Chestnut Blight Disease, but relatively little is known about the resistance mechanism. We identified 519 NBS-encoding genes, including 374 NBS-LRR genes and 145 NBS-only genes. The majority of Ka/Ks were less than 1, suggesting the purifying selection operated during the evolutionary history of NBS-encoding genes. A minority (4/34) of Ka/Ks in non-TIR gene families were greater than 1, showing that some genes were under positive selection pressure. Furthermore, Ks peaked at a range of 0.4 to 0.5, indicating that ancient duplications arose during the evolution. The relationship between Ka/Ks and Ks indicated greater selective pressure on the newer and older genes with the critical value of Ks = 0.4–0.5. Notably, species-specific duplications were detected in NBS-encoding genes. In addition, the group of RPW8-NBS-encoding genes clustered together as an independent clade located at a relatively basal position in the phylogenetic tree. Many cis-acting elements related to plant defense responses were detected in promoters of NBS-encoding genes.
Deceleration of single-stranded DNA passing through a nanopore using a nanometre-sized bead structure
Authors: Goto Yusuke , Haga Takanobu , Yanagi Itaru , Yokoi Takahide , Takeda Ken-ichi 
Published: November 2015

AbstractDNA sequencing with a solid-state nanopore requires a reduction of the translocation speeds of single-stranded DNA (ssDNA) over 10 μs/base. In this study, we report that a nanometre-sized bead structure constructed around a nanopore can reduce the moving speed of ssDNA to 270 μs/base by adjusting the diameter of the bead and its surface chemical group. This decelerating effect originates from the strong interaction between ssDNA and the chemical group on the surface of the bead. This nanostructure was simply prepared by dip coating in which a substrate with a nanopore was immersed in a silica bead solution and then dried in an oven. As compared with conventional approaches, our novel method is less laborious, simpler to perform and more effective in reducing ssDNA translocation speed.
Single florescent nanodiamond in a three dimensional ABEL trap
Authors: Kayci Metin , Radenovic Aleksandra 
Published: November 2015

AbstractThree dimensional single particle trapping and manipulation is an outstanding challenge in various fields ranging from basic physics to life sciences. By monitoring the response of a trapped particle to a designed environment one can extract its characteristics. In addition, quantum dynamics of a spatially scanned well-known particle can provide environmental information. Precise tracking and positioning of such a particle in aqueous environment is crucial task for achieving nano-scale resolution. Here we experimentally demonstrate three dimensional ABEL trap operating at high frequency by employing a hybrid approach in particle tracking. The particle location in the transverse plane is detected via a scanning laser beam while the axial position is determined by defocused imaging. The scanning of the trapped particle is accomplished through a nano positioning stage integrated to the trap platform.
Comparative study on the capacity of a signalised roundabout
Authors: Sun Xiaotong , Ma Wanjing , Huang Wei 
Published: November 2015

Traffic signal control at roundabouts is proved to be effective in addressing heavy traffic. However, the applicability of a signalised roundabout, especially compared with a signalised intersection, in terms of capacity has not been investigated. For signalised roundabouts, unsignalised roundabout capacity models including gap‐acceptance theories and regression models are not applicable. This study first introduces a shockwave‐based model to capture the impacts of signals at circulatory lanes on queuing and clearance time of left‐turning vehicles. On this basis, a general signal timing model and a capacity model are developed. A sensitivity analysis is then elaborated to test how temporal and spatial parameters affect the capacity of a signalised roundabout. Capacity comparisons are made among signalised roundabouts, unsignalised roundabouts and signalised intersections. The results show that (i) under high traffic demand, a signalised roundabout outperforms an unsignalised roundabout; (ii) a signalised roundabout achieve higher capacity than a signalised intersection does under certain condition, (iii) but a signalised intersection outperforms a signalised roundabout when optimal cycle length is relatively short (65 seconds in this study), (iv) capacity of a signalised roundabout is very sensitive to the variation of signal parameters, hence care should be taken to design the parameters to ensure high capacity.
Electrochemical evidence that pyranopterin redox chemistry controls the catalysis of YedY, a mononuclear Mo enzyme
Authors: Adamson Hope , Simonov Alexandr N. , Kierzek Michelina , Rothery Richard A. , Weiner Joel H. , Bond Alan M. , Parkin Alison 
Published: November 2015

SignificanceThe mononuclear Mo enzymes are ubiquitous throughout life, and the notion that their activity arises from Mo(VI/V/IV) redox cycling is a central dogma of bioinorganic chemistry. We prove that YedY, a structurally simple mononuclear Mo enzyme, operates via a strikingly different mechanism: the catalytically active state is generated from addition of three electrons and three protons to the Mo(V) form of the enzyme, suggesting for the first time (to our knowledge) that organic-ligand–based electron transfer reactions at the pyranopterin play a role in catalysis. We showcase Fourier-transformed alternating-current voltammetry as a technique with powerful utility in metalloenzyme studies, allowing the simultaneous measurement of redox catalysis and the underlying electron transfer reactions.
An extracatalytic function of CD45 in B cells is mediated by CD22
Authors: Coughlin Sarah , Noviski Mark , Mueller James L. , Chuwonpad Ammarina , Raschke William C. , Weiss Arthur , Zikherman Julie 
Published: November 2015

SignificanceSignaling through antigen receptors is essential for lymphocyte development, survival, and function. The receptor-like tyrosine phosphatase CD45 plays a critical role in these processes by regulating antigen receptor signaling via its cytosolic phosphatase domain. Despite its abundance, the function of the large, alternatively spliced extracellular domain of CD45 has remained elusive. We used CD45 transgenes either incorporating a phosphatase-inactivating point mutation or lacking the cytoplasmic domain to uncouple the enzymatic and noncatalytic functions of CD45. Both transgenes partially rescue the phenotype of CD45-deficient B cells by modulating the B cell inhibitory surface coreceptor CD22. These data demonstrate an in vivo function for the extracellular domain of CD45 in restraining CD22 inhibitory function to maintain tonic B-cell antigen receptor signaling.
A Tale of Two Axolotls
Authors: Voss S. Randal , Woodcock M. Ryan , Zambrano Luis 
Published: November 2015

Abstract
The Mexican axolotl (Ambystoma mexicanum) is an icon of culture, a revered aquarium pet, and a highly valued animal model in biomedical research. Unfortunately, Mexican axolotls are critically endangered in their natural Xochimilco habitat in Mexico City. If axolotls go extinct, current efforts to conserve the Xochimilico ecosystem will be undermined, as will efforts to genetically manage the laboratory populations that are needed to sustain research efforts around the world. A concerted global effort is needed to protect and manage this irreplaceable species in natural and laboratory environments.
Superior Effectiveness of Zidovudine Compared With Tenofovir When Combined With Nevirapine-based Antiretroviral Therapy in a Large Nigerian Cohort
Authors: Scarsi Kimberly K. , Eisen Geoffrey , Darin Kristin M. , Meloni Seema T. , Rawizza Holly E. , Tchetgen Tchetgen Eric J. , Agbaji Oche O. , Onwujekwe Daniel I. , Gashau Wadzani , Nkado Reuben , Okonkwo Prosper , Murphy Robert L. , Kanki Phyllis J. 
Published: November 2015

Abstract
Background.  Despite sparse efficacy data, tenofovir–emtricitabine or tenofovir–lamivudine plus nevirapine is used in many resource-constrained settings.
Methods.  This retrospective cohort study included patients initiating nevirapine-based antiretroviral therapy (ART) with either tenofovir–emtricitabine or lamivudine (tenofovir group) or zidovudine–lamivudine (zidovudine group). Clinical, virologic, and immunologic evaluations were performed at baseline and every 6 months. Virologic failure was defined as 2 consecutive human immunodeficiency virus (HIV)-RNA values &gt;1000 copies/mL. Patients were included from ART initiation until time of failure, regimen switch, discontinuation, or last HIV-RNA measurement. Cox proportional hazards regression was used to model factors influencing time to failure. Bias due to dependent censoring was investigated via inverse probability weighted pooled logistic regression.
Results.  A total of 5547 patients were evaluated; 1484 (26.8%) were in the tenofovir group and 4063 (73.2%) were in the zidovudine group. In the adjusted model, tenofovir regimen (hazard ratio [HR], 1.47; 95% confidence interval [CI], 1.21–1.79) and higher baseline log10 HIV-RNA (HR, 1.15; 95% CI, 1.03–1.28) were associated with virologic failure. Higher baseline log10 CD4+ cell count (HR, 0.50; 95% CI, .40–.63) and increasing age (HR, 0.98; 95% CI, .97–.99) decreased the risk of virologic failure. Inverse probability weighting results were consistent with the primary analysis.
Conclusions.  Compared with zidovudine–lamivudine, the use of tenofovir–lamivudine or emtricitabine in combination with nevirapine was a strong predictor of virologic failure in our cohort, which was not explained by other risk factors or criteria for regimen selection.
Extranodal Rosai–Dorfman Disease of the Orbit: Clinical Features of 8 Cases
Authors: Tan Jeffrey J. , Narang Sherry , Purewal Baljeet , Langer Paul D. , Blaydon Sean , Schwarcz Robert M. , McCormick Steven A. , Kim Joon Y. , Walrath Joseph D. , Burt Benjamin O. , Shinder Roman 
Published: November 2015

Purpose:
To report on the presentation, radiography, histology, and treatment of 8 cases of extranodal Rosai–Dorfman disease involving the orbit.

Methods:
Multicenter retrospective case series.

Results:
Five males and 3 females had a median age of 10 years (range 2–78 years). Presenting signs and symptoms included proptosis, periorbital pain, palpable mass, blepharoptosis, decreased vision, diplopia, impaired extraocular motility, and afferent pupillary defect. Four patients had bilateral orbital disease, while 4 had unilateral disease. Six cases were extraconal, 1 was intraconal, and 1 was both intra- and extra-conal. Four cases had only extranodal disease without lymphadenopathy (3 of which had localized orbital disease). Diagnosis was confirmed by exam, orbital, and/or systemic radiography, and biopsy in all cases. Treatment strategies included excision or debulking, systemic corticosteroids, chemotherapy, radiotherapy, observation or a combination thereof. At last follow up, 4 patients were disease free, while 4 had residual improved disease.

Conclusions:
Rosai–Dorfman disease of the orbit is a rare clinical entity. Purely extranodal disease is rare, with isolated orbital disease being exceedingly rare. This study is unique in that 4 of 8 patients had strictly isolated extranodal disease of the orbit. A large majority of the cases had disease in the extraconal space, contrasting with previous reports. In addition, lacrimal gland disease, particularly bilateral involvement, was prominent in the current study. Although there is no consensus on treatment, surgical excision should be attempted if plausible in symptomatic patients especially if the orbit represents a localized site of disease.
Cerebral toxoplasmosis after rituximab therapy for splenic marginal zone lymphoma: a case report and review of the literature
Authors: Holland Mary Siobhan , Sharma Karan , Lee B. Craig 
Published: November 2015

Introduction:

Toxoplasma gondii is a parasite estimated to infect one-third of the global population, surviving in tissues in a latent form. Although cerebral toxoplasmosis is predominantly recognized as an opportunistic infection in hosts immunocompromised secondary to human immunodeficiency virus or bone marrow transplant, there is increasing recognition that this infection can occur in patients receiving immunomodulating agents such as mAb therapy targeted against T-cells, B-cells and TNF. The indications for these therapies are expanding, resulting in a larger at-risk population for this rare but serious and potentially avoidable complication.

Case Presentation:
This is one of the few case reports of cerebral toxoplasmosis following rituximab-based chemotherapy in a patient with a haematological malignancy. We describe a patient presenting with focal neurological deficits and radiographic evidence of multi-focal cerebral ring-enhancing lesions following completion of rituximab therapy for splenic marginal zone lymphoma. Brain biopsy confirmed a diagnosis of cerebral toxoplasmosis. Antibiotic treatment with trimethoprim/sulfamethoxazole resulted in near-complete radiological and clinical resolution of the neurological deficits, and a return to baseline functional status.

Conclusion:
Reactivation of toxoplasmosis resulting in intracerebral disease is a potential severe and preventable complication of rituximab therapy. Further studies are required to assess the need both for screening and prescribing primary chemoprophylaxis for toxoplasmosis when initiating rituximab therapy.