bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defining multiplicity of vector uptake in transfected Plasmodium parasites
Authors: Carrasquilla Manuela , Adjalley Sophie , Sanderson Theo , Marin-Menendez Alejandro , Coyle Rachael , Montandon Ruddy , Rayner Julian C. , Pance Alena , Lee Marcus C. S. 
Published: July 2020

AbstractThe recurrent emergence of drug resistance in Plasmodium falciparum increases the urgency to genetically validate drug resistance mechanisms and identify new targets. Reverse genetics have facilitated genome-scale knockout screens in Plasmodium berghei and Toxoplasma gondii, in which pooled transfections of multiple vectors were critical to increasing scale and throughput. These approaches have not yet been implemented in human malaria species such as P. falciparum and P. knowlesi, in part because the extent to which pooled transfections can be performed in these species remains to be evaluated. Here we use next-generation sequencing to quantitate uptake of a pool of 94 barcoded vectors. The distribution of vector acquisition allowed us to estimate the number of barcodes and DNA molecules taken up by the parasite population. Dilution cloning of P. falciparum transfectants showed that individual clones possess as many as seven episomal barcodes, revealing that an intake of multiple vectors is a frequent event despite the inefficient transfection efficiency. Transfection of three spectrally-distinct fluorescent reporters allowed us to evaluate different transfection methods and revealed that schizont-stage transfection limited the tendency for parasites to take up multiple vectors. In contrast to P. falciparum, we observed that the higher transfection efficiency of P. knowlesi resulted in near complete representation of the library. These findings have important implications for how reverse genetics can be scaled in culturable Plasmodium species.
Physical controls and ENSO event influence on weathering in the Panama Canal Watershed
Authors: Smith Devin F. , Goldsmith Steven T. , Harmon Brendan A. , Espinosa Jorge A. , Harmon Russell S. 
Published: July 2020

AbstractRecent empirical studies have documented the importance of tropical mountainous rivers on global silicate weathering and suspended sediment transport. Such field studies are typically based on limited temporal data, leaving uncertainty in the strength of observed relationships with controlling parameters over the long term. A deficiency of long-term data also prevents determination of the impact that multi-year or decadal climate patterns, such as the El Niño Southern Oscillation (ENSO), might have on weathering fluxes. Here we analyze an 18-year hydrochemical dataset for eight sub-basins of the Panama Canal Watershed of high-temporal frequency collected between 1998 and 2015 to address these knowledge gaps. We identified a strongly positive covariance of both cation (Ca2+, Mg2+, K+, Na+) and suspended sediment yields with precipitation and extent of forest cover, whereas we observed negative relationships with temperature and mosaic landcover. We also confirmed a statistical relationship between seasonality, ENSO, and river discharge, with significantly higher values occurring during La Niña events. These findings emphasize the importance that long-term datasets have on identifying short-term influences on chemical and physical weathering rates, especially, in ENSO-influenced regions.
Estimation of parasite age and synchrony status in Plasmodium falciparum infections
Authors: Ciuffreda Laura , Zoiku Felix Kwame , Quashie Neils B. , Ranford-Cartwright Lisa C. 
Published: July 2020

AbstractHuman malaria parasites have complex but poorly understood population dynamics inside their human host. In some but not all infections, parasites progress synchronously through the 48 h lifecycle following erythrocyte invasion, such that at any one time there is a limited spread of parasites at a particular time (hours) post-invasion. Patients presenting with older parasites, and with asynchronous infections, have been reported to have higher risks of fatal outcomes, associated with higher parasite biomass and multiplication rates respectively. However, practical tools to assess synchrony and estimate parasite age post-invasion in patient samples are lacking. We have developed a novel method based on three genes differentially expressed over the parasite intra-erythrocytic lifecycle, and applied it to samples from patients with uncomplicated malaria attending two health clinics in Ghana. We found that most patients presented with synchronous infections, and with parasites within 12 h of erythrocyte invasion. Finally we investigated if clinical features such as fever and parasite density could act as predictors of parasite age and synchrony. The new method is a simple and practicable approach to study parasite dynamics in naturally-infected patients, and is a significant improvement on the subjective microscopical methods for parasite staging in vivo, aiding patient management.
The role of RND-type efflux pumps in multidrug-resistant mutants of Klebsiella pneumoniae
Authors: Ni Rui Ting , Onishi Motoyasu , Mizusawa Minako , Kitagawa Ryoko , Kishino Takanori , Matsubara Futoshi , Tsuchiya Tomofusa , Kuroda Teruo , Ogawa Wakano 
Published: July 2020

AbstractThe emergence of multidrug-resistant Klebsiella pneumoniae is a worldwide problem. K. pneumoniae possesses numerous resistant genes in its genome. We isolated mutants resistant to various antimicrobials in vitro and investigated the importance of intrinsic genes in acquired resistance. The isolation frequency of the mutants was 10−7–10−9. Of the multidrug-resistant mutants, hyper-multidrug-resistant mutants (EB256-1, EB256-2, Nov1-8, Nov2-2, and OX128) were identified, and accelerated efflux activity of ethidium from the inside to the outside of the cells was observed in these mutants. Therefore, we hypothesized that the multidrug efflux pump, especially RND-type efflux pump, would be related to changes of the phenotype. We cloned all RND-type multidrug efflux pumps from the K. pneumoniae genome and characterized them. KexEF and KexC were powerful multidrug efflux pumps, in addition to AcrAB, KexD, OqxAB, and EefABC, which were reported previously. It was revealed that the expression of eefA was increased in EB256-1 and EB256-2: the expression of oqxA was increased in OX128; the expression of kexF was increased in Nov2-2. It was found that a region of 1,485 bp upstream of kexF, was deleted in the genome of Nov2-2. K. pneumoniae possesses more potent RND-multidrug efflux systems than E. coli. However, we revealed that most of them did not contribute to the drug resistance of our strain at basic levels of expression. On the other hand, it was also noted that the overexpression of these pumps could lead to multidrug resistance based on exposure to antimicrobial chemicals. We conclude that these pumps may have a role to maintain the intrinsic resistance of K. pneumoniae when they are overexpressed. The antimicrobial chemicals selected many resistant mutants at the same minimum inhibitory concentration (MIC) or a concentration slightly higher than the MIC. These results support the importance of using antibiotics at appropriate concentrations at clinical sites.
Solid-state synthesis, magnetic and structural properties of interfacial B2-FeRh(001) layers in Rh/Fe(001) films
Authors: Myagkov V. G. , Ivanenko A. A. , Bykova L. E. , Zhigalov V. S. , Volochaev M. N. , Velikanov D. A. , Matsynin A. A. , Bondarenko G. N. 
Published: July 2020

AbstractHere we first report results of the start of the solid-state reaction at the Rh/Fe(001) interface and the structural and magnetic phase transformations in 52Rh/48Fe(001), 45Rh/55Fe(001), 68Rh/32Fe(001) bilayers from room temperature to 800 °C. For all bilayers the non-magnetic nanocrystalline phase with a B2 structure (nfm-B2) is the first phase that is formed on the Rh/Fe(001) interface near 100 °C. Above 300 °C, without changing the nanocrystalline B2 structure, the phase grows into the low-magnetization modification αlʹ (MSl ~ 825 emu/cm3) of the ferromagnetic αʹ phase which has a reversible αlʹ ↔ αʺ transition. After annealing 52Rh/48Fe(001) bilayers above 600 °C the αlʹ phase increases in grain size and either develops into αhʹ with high magnetization (MSh ~ 1,220 emu/cm3) or remains in the αlʹ phase. In contrast to αlʹ, the αhʹ ↔ αʺ transition in the αhʹ films is completely suppressed. When the annealing temperature of the 45Rh/55Fe(001) samples is increased from 450 to 800 °C the low-magnetization nanocrystalline αlʹ films develop into high crystalline perfection epitaxial αhʹ(001) layers, which have a high magnetization of ~ 1,275 emu/cm3. αhʹ(001) films do not undergo a transition to an antiferromagnetic αʺ phase. In 68Rh/32Fe(001) samples above 500 °C non-magnetic epitaxial γ(001) layers grow on the Fe(001) interface as a result of the solid-state reaction between the epitaxial αlʹ(001) and polycrystalline Rh films. Our results demonstrate not only the complex nature of chemical interactions at the low-temperature synthesis of the nfm-B2 and αlʹ phases in Rh/Fe(001) bilayers, but also establish their continuous link with chemical mechanisms underlying reversible αlʹ ↔ αʺ transitions.
Preparation and characterization of myristic acid/expanded graphite composite phase change materials for thermal energy storage
Authors: Zhou Dongyi , Yuan Jiawei , Zhou Yuhong , Liu Yicai 
Published: July 2020

AbstractMyristic acid/expanded graphite (MA/EG) composite phase-change material (CPCM) was prepared by absorbing liquid MA (as the PCM) into EG (as the supporting material). Its chemical structure, microstructure, and thermal properties were characterized and studied. In the MA/EG CPCM, the largest mass content of MA was 93.5% by using the diffusion–exudation circle method for the first time. Fourier transform infrared spectroscopy (FTIR) analysis indicated that the MA and EG were a pure physical mixture of which the structure does not change, and they undergo no chemical reaction. Differential-scanning-calorimetry (DSC) analysis results showed that the melting and freezing temperatures of the MA/EG CPCM were 53.3 and $$52.4^{\,\circ }\hbox {C}$$52.4∘C, respectively, and the melting and freezing latent heats were 189.5 and 187.8 J/g, respectively. After several heat-cycle accelerations, the material still had good thermal-energy-storage effect. MA/EG CPCM thermoconductivity was greatly enhanced after adding EG, and the results of thermal-storage/-release experiments indicated that the thermal-storage and -release ratios of the MA/EG phase-change unit was greatly improved when compared with that of MA. These results indicated that the MA/EG CPCM was a suitable low-temperature thermal-energy-storage material.
Earthquake statistics changed by typhoon-driven erosion
Authors: Steer Philippe , Jeandet Louise , Cubas Nadaya , Marc Odin , Meunier Patrick , Simoes Martine , Cattin Rodolphe , Shyu J. Bruce H. , Mouyen Maxime , Liang Wen-Tzong , Theunissen Thomas , Chiang Shou-Hao , Hovius Niels 
Published: July 2020

AbstractTectonics and climate-driven surface processes govern the evolution of Earth’s surface topography. Topographic change in turn influences lithospheric deformation, but the elementary scale at which this feedback can be effective is unclear. Here we show that it operates in a single weather-driven erosion event. In 2009, typhoon Morakot delivered ~ 3 m of precipitation in southern Taiwan, causing exceptional landsliding and erosion. This event was followed by a step increase in the shallow (< 15 km depth) earthquake frequency lasting at least 2.5 years. Also, the scaling of earthquake magnitude and frequency underwent a sudden increase in the area where mass wasting was most intense. These observations suggest that the progressive removal of landslide debris by rivers from southern Taiwan has acted to increase the crustal stress rate to the extent that earthquake activity was demonstrably affected. Our study offers the first evidence of the impact of a single weather-driven erosion event on tectonics.
Evolution of lattice distortions in 4H-SiC wafers with varying doping
Authors: Mahadik Nadeemullah A. , Das Hrishikesh , Stoupin Stanislav , Stahlbush Robert E. , Bonanno Peter L. , Xu Xueping , Rengarajan Varatharajan , Ruland Gary E. 
Published: July 2020

AbstractLattice distortions (LD) in 4H-silicon carbide (SiC) wafers were quantified using synchrotron X-ray rocking curve mapping (RCM), and were resolved into their two components of lattice strain (Δd/d) and lattice plane curvature (LPC) for 150 mm diameter wafers. The evolution of these LDs were investigated for three sequential substrates from the same boule, one of which was the substrate reference, and the other two had a 10 µm thick, 1 × 1017 and 4 × 1014 cm-3 n-type doped epitaxial layer. The lattice strain, Δd/d, was highest for the lowest doped wafer due to higher mismatch with the substrate wafer. After epitaxial layer growth, the LPC variation across the wafer increases by a factor of 2, irrespective of doping. The LPC maps indicate presence of a twist in the lattice planes that increases after epitaxial growth. The LPC component has higher influence on wafer shape change, which can reduce device yields. The lattice strain component predominantly affects the glide of basal plane dislocations (BPDs), thereby reducing device reliability. From analysis of peak widths, it was determined that threading dislocations in the top 6 microns of the wafer increase after epitaxial layer growth.
Serum GFAP in multiple sclerosis: correlation with disease type and MRI markers of disease severity
Authors: Ayrignac Xavier , Le Bars Emmanuelle , Duflos Claire , Hirtz Christophe , Maleska Maceski Aleksandra , Carra-Dallière Clarisse , Charif Mahmoud , Pinna Frédéric , Prin Pauline , Menjot de Champfleur Nicolas , Deverdun Jérémy , Kober Tobias , Marechal Bénédicte , Fartaria Mario Joao , Corredor Jerez Ricardo , Labauge Pierre , Lehmann Sylvain 
Published: July 2020

AbstractNeurofilament light chain (NfL) has been demonstrated to correlate with multiple sclerosis disease severity as well as treatment response. Nevertheless, additional serum biomarkers are still needed to better differentiate disease activity from disease progression. The aim of our study was to assess serum glial fibrillary acid protein (s-GFAP) and neurofilament light chain (s-NfL) in a cohort of 129 multiple sclerosis (MS) patients. Eighteen primary progressive multiple sclerosis (PPMS) and 111 relapsing remitting MS (RRMS) were included. We showed that these 2 biomarkers were significantly correlated with each other (R = 0.72, p < 0.001). Moreover, both biomarkers were higher in PPMS than in RRMS even if multivariate analysis only confirmed this difference for s-GFAP (130.3 ± 72.8 pg/ml vs 83.4 ± 41.1 pg/ml, p = 0.008). Finally, s-GFAP was correlated with white matter lesion load and inversely correlated with WM and GM volume. Our results seem to confirm the added value of s-GFAP in the context of multiple sclerosis.
Cryobiopsy in the diagnosis of bronchiolitis: a retrospective analysis of twenty-three consecutive patients
Authors: Sirol Aflah Syazatul Syakirin , Piciucchi Sara , Tomassetti Sara , Ravaglia Claudia , Dubini Alessandra , Poletti Venerino 
Published: July 2020

AbstractBronchiolitis manifests as a variety of histological features that explain the complex clinical profiles and imaging aspects. In the period between January 2011 and June 2015, patients with a cryobiopsy diagnosis of bronchiolitis were retrospectively retrieved from the database of our institution. Clinical profiles, imaging features and histologic diagnoses were analysed to identify the role of cryobiopsy in the diagnostic process. Twenty-three patients with a multidisciplinary diagnosis of small airway disease were retrieved (14 females, 9 males; age range 31–74 years old; mean age 54.2 years old). The final MDT diagnoses were post-infectious bronchiolitis (n = 5), constrictive bronchiolitis (n = 3), DIPNECH (n = 1), idiopathic follicular bronchiolitis (n = 3), Sjogren’s disease (n = 1), GLILD (n = 1), smoking-related interstitial lung disease (n = 6), sarcoid with granulomatous bronchiolar disorder (n = 1), and subacute hypersensitivity pneumonitis (n = 2). Complications reported after the cryobiopsy procedure consisted of two cases of pneumothorax soon after the biopsy (8.7%), which were successfully managed with the insertion of a chest tube. Transbronchial cryobiopsy represents a robust and mini-invasive method in the characterization of small airway diseases, allowing a low percentage of complications and good diagnostic confidence.
Tetanus insensitive VAMP2 differentially restores synaptic and dense core vesicle fusion in tetanus neurotoxin treated neurons
Authors: Hoogstraaten Rein I. , van Keimpema Linda , Toonen Ruud F. , Verhage Matthijs 
Published: July 2020

AbstractThe SNARE proteins involved in the secretion of neuromodulators from dense core vesicles (DCVs) in mammalian neurons are still poorly characterized. Here we use tetanus neurotoxin (TeNT) light chain, which cleaves VAMP1, 2 and 3, to study DCV fusion in hippocampal neurons and compare the effects on DCV fusion to those on synaptic vesicle (SV) fusion. Both DCV and SV fusion were abolished upon TeNT expression. Expression of tetanus insensitive (TI)-VAMP2 restored SV fusion in the presence of TeNT, but not DCV fusion. Expression of TI-VAMP1 or TI-VAMP3 also failed to restore DCV fusion. Co-transport assays revealed that both TI-VAMP1 and TI-VAMP2 are targeted to DCVs and travel together with DCVs in neurons. Furthermore, expression of the TeNT-cleaved VAMP2 fragment or a protease defective TeNT in wild type neurons did not affect DCV fusion and therefore cannot explain the lack of rescue of DCV fusion by TI-VAMP2. Finally, to test if two different VAMPs might both be required in the DCV secretory pathway,Vamp1null mutants were tested. However, VAMP1 deficiency did not reduce DCV fusion. In conclusion, TeNT treatment combined with TI-VAMP2 expression differentially affects the two main regulated secretory pathways: while SV fusion is normal, DCV fusion is absent.
Application of auto-planning in radiotherapy for breast cancer after breast-conserving surgery
Authors: Chen Kunzhi , Wei Jinlong , Ge Chao , Xia Wenming , Shi Yinghua , Wang Huidong , Jiang Xin 
Published: July 2020

AbstractTo evaluate the quality of planning target volume (PTV) and organs at risk (OAR) generated by the manual Pinnacle planning (manP) and Auto-Planning (AP) modules and discuss the feasibility of AP in the application of radiotherapy for patients with breast cancer. Thirty patients who underwent breast-conserving therapy were randomly selected. The Philips Pinnacle 9.10 treatment planning system was used to design the manP and AP modules for PTV and OAR distribution on the same computed tomography. A physician compared the plans in terms of dosimetric parameters and monitor units (MUs) using blind qualitative scoring. Statistical differences were evaluated using paired two-sided Wilcoxon’s signed-rank test. On comparing the plans of AP and manP modules, the conformal index (P < 0.01) and D50 (P = 0.04) of PTV in the AP group was lower than those in the manP group, while D1 was higher (P = 0.03). In terms of dosimetry of OAR, ipsilateral lung V20 Gy (P < 0.01), V10 Gy (P < 0.01), V5 Gy (P < 0.05), and Dmean (P < 0.01) of the AP group were better than those of the manP group. Heart V40 Gy and Dmean of all patients with breast cancer in the AP group were lower than those in the manP group (P < 0.01). Moreover, 12 patients with left breast cancer had the same results (P < 0.01). The MU value of the intensity-modulated radiation therapy module designed using two different methods was higher in the AP group than in the manP group (P = 0.32), although there was no statistical significance. The AP module almost had an equal quality of PTV and dose distribution as the manP module, and its OAR was less irradiated.
PAM staining intensity of primary neuroendocrine neoplasms is a potential prognostic biomarker
Authors: Horton Timothy M. , Sundaram Vandana , Lee Christine Hye-Jin , Hornbacker Kathleen , Van Vleck Aidan , Benjamin Kaisha N. , Zemek Allison , Longacre Teri A. , Kunz Pamela L. , Annes Justin P. 
Published: July 2020

AbstractNeuroendocrine neoplasms (NENs) are rare epithelial tumors with heterogeneous and frequently unpredictable clinical behavior. Available biomarkers are insufficient to guide individual patient prognosis or therapy selection. Peptidylglycine α-amidating monooxygenase (PAM) is an enzyme expressed by neuroendocrine cells that participates in hormone maturation. The objective of this study was to assess the distribution, clinical associations and survival implications of PAM immunoreactivity in primary NENs. Of 109 primary NENs, 7% were PAM-negative, 25% were PAM-low and 68% were PAM-high. Staining intensity was high in small bowel (p = 0.04) and low in stomach (p = 0.004) NENs. PAM staining was lower in higher grade tumors (p < 0.001) and patients who died (p < 0.001) but did not vary by tumor size or stage at surgery. In patients who died, time to death was shorter in patients with reduced PAM immunoreactivity: median times to death were 11.3 (PAM-negative), 29.4 (PAM-low) and 61.7 (PAM-high) months. Lower PAM staining was associated with increased risk of death after adjusting for disease stage [PAM negative, HR = 13.8 (CI: 4.2–45.5)]. PAM immunoreactivity in primary NENs is readily assessable and a potentially useful stage-independent predictor of survival.
A new inclusive MLVA assay to investigate genetic variability of Xylella fastidiosa with a specific focus on the Apulian outbreak in Italy
Authors: Mazzaglia Angelo , Rahi Yaseen Jundi , Taratufolo Maria Claudia , Tatì Marta , Turco Silvia , Ciarroni Serena , Tagliavento Vincenzo , Valentini Franco , D’Onghia Anna Maria , Balestra Giorgio Mariano 
Published: July 2020

AbstractThe Olive Quick Decline Syndrome byXylella fastidiosasubspeciespaucais among the most severe phytopathological emergencies nowadays. In few years, the outbreak devastated olive groves in Apulia (Italy), potentially endangering the entire Mediterranean basin. This research aimed to develop a multiple locus VNTR analysis assay, a molecular tool to differentiate between populations of the pathogen. It has already been successfully applied to differentX. fastidiosasubspecies from various plant hosts. The previously published TR loci, together with a set of new design, have been tested in silico on the genome of the Apulian De Donno strain. The resulting selection of 37 TR loci was amplified on the genomic DNAs of the Apulian strains and from representatives ofX. fastidiosasubspecies, and directly on DNA extracted from infected plants. The assay clearly discerned among subspecies or even sequence types (ST), but also pointed out variants within the same ST so as to provide more detailed information on the dynamics and pathogen diffusion pathways. Its effective application even on total DNAs extracted from infected tissues of different host plants makes it particularly useful for large-scale screening of infection and for the strengthening of containment measures.