bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of resistance loci against new pathotypes of Plasmodiophora brassicae in Brassica napus based on genome-wide association mapping
Authors: Dakouri Abdulsalam , Lamara Mebarek , Karim Md. Masud , Wang Jinghe , Chen Qilin , Gossen Bruce D. , Strelkov Stephen E. , Hwang Sheau-Fang , Peng Gary , Yu Fengqun 
Published: March 2021

AbstractGenetic resistance is a successful strategy for management of clubroot (Plasmodiophora brassicae) of brassica crops, but resistance can break down quickly. Identification of novel sources of resistance is especially important when new pathotypes arise. In the current study, the reaction of 177 accessions of Brassica napus to four new, virulent pathotypes of P. brassicae was assessed. Each accession was genotyped using genotyping by sequencing to identify and map novel sources of clubroot resistance using mixed linear model (MLM) analysis. The majority of accessions were highly susceptible (70–100 DSI), but a few accessions exhibited strong resistance (0–20 DSI) to pathotypes 5X (21 accessions), 3A (8), 2B (7), and 3D (15), based on the Canadian Clubroot Differential system. In total, 301,753 SNPs were mapped to 19 chromosomes. Population structure analysis indicated that the 177 accessions belong to seven major populations. SNPs were associated with resistance to each pathotype using MLM. In total, 13 important SNP loci were identified, with 9 SNPs mapped to the A-genome and 4 to the C-genome. The SNPs were associated with resistance to pathotypes 5X (2 SNPs), 3A (4), 2B (5) and 3D (6). A Blast search of 1.6 Mb upstream and downstream from each SNP identified 13 disease-resistance genes or domains. The distance between a SNP locus and the nearest resistance gene ranged from 0.04 to 0.74 Mb. The resistant lines and SNP markers identified in this study can be used to breed for resistance to the most prevalent new pathotypes of P. brassicae in Canada.
Origin and diffusion of human Y chromosome haplogroup J1-M267
Authors: Sahakyan Hovhannes , Margaryan Ashot , Saag Lauri , Karmin Monika , Flores Rodrigo , Haber Marc , Kushniarevich Alena , Khachatryan Zaruhi , Bahmanimehr Ardeshir , Parik Jüri , Karafet Tatiana , Yunusbayev Bayazit , Reisberg Tuuli , Solnik Anu , Metspalu Ene , Hovhannisyan Anahit , Khusnutdinova Elza K. , Behar Doron M. , Metspalu Mait , Yepiskoposyan Levon , Rootsi Siiri , Villems Richard 
Published: March 2021

AbstractHuman Y chromosome haplogroup J1-M267 is a common male lineage in West Asia. One high-frequency region—encompassing the Arabian Peninsula, southern Mesopotamia, and the southern Levant—resides ~ 2000 km away from the other one found in the Caucasus. The region between them, although has a lower frequency, nevertheless demonstrates high genetic diversity. Studies associate this haplogroup with the spread of farming from the Fertile Crescent to Europe, the spread of mobile pastoralism in the desert regions of the Arabian Peninsula, the history of the Jews, and the spread of Islam. Here, we study past human male demography in West Asia with 172 high-coverage whole Y chromosome sequences and 889 genotyped samples of haplogroup J1-M267. We show that this haplogroup evolved ~ 20,000 years ago somewhere in northwestern Iran, the Caucasus, the Armenian Highland, and northern Mesopotamia. The major branch—J1a1a1-P58—evolved during the early Holocene ~ 9500 years ago somewhere in the Arabian Peninsula, the Levant, and southern Mesopotamia. Haplogroup J1-M267 expanded during the Chalcolithic, the Bronze Age, and the Iron Age. Most probably, the spread of Afro-Asiatic languages, the spread of mobile pastoralism in the arid zones, or both of these events together explain the distribution of haplogroup J1-M267 we see today in the southern regions of West Asia.
Evaluation of the gut microbiome in association with biological signatures of inflammation in murine polytrauma and shock
Authors: Appiah Sandra A. , Foxx Christine L. , Langgartner Dominik , Palmer Annette , Zambrano Cristian A. , Braumüller Sonja , Schaefer Evan J. , Wachter Ulrich , Elam Brooke L. , Radermacher Peter , Stamper Christopher E. , Heinze Jared D. , Salazar Stephanie N. , Luthens Amalia K. , Arnold Andrea L. , Reber Stefan O. , Huber-Lang Markus , Lowry Christopher A. , Halbgebauer Rebecca 
Published: March 2021

AbstractSevere injuries are frequently accompanied by hemorrhagic shock and harbor an increased risk for complications. Local or systemic inflammation after trauma/hemorrhage may lead to a leaky intestinal epithelial barrier and subsequent translocation of gut microbiota, potentially worsening outcomes. To evaluate the extent with which trauma affects the gut microbiota composition, we performed a post hoc analysis of a murine model of polytrauma and hemorrhage. Four hours after injury, organs and plasma samples were collected, and the diversity and composition of the cecal microbiome were evaluated using 16S rRNA gene sequencing. Although cecal microbial alpha diversity and microbial community composition were not found to be different between experimental groups, norepinephrine support in shock animals resulted in increased alpha diversity, as indicated by higher numbers of distinct microbial features. We observed that the concentrations of proinflammatory mediators in plasma and intestinal tissue were associated with measures of microbial alpha and beta diversity and the presence of specific microbial drivers of inflammation, suggesting that the composition of the gut microbiome at the time of trauma, or shortly after trauma exposure, may play an important role in determining physiological outcomes. In conclusion, we found associations between measures of gut microbial alpha and beta diversity and the severity of systemic and local gut inflammation. Furthermore, our data suggest that four hours following injury is too early for development of global changes in the alpha diversity or community composition of the intestinal microbiome. Future investigations with increased temporal-spatial resolution are needed in order to fully elucidate the effects of trauma and shock on the gut microbiome, biological signatures of inflammation, and proximal and distal outcomes.
Recovering wasted nutrients from shrimp farming through the combined culture of polychaetes and halophytes
Authors: Jerónimo Daniel , Lillebø Ana Isabel , Cremades Javier , Cartaxana Paulo , Calado Ricardo 
Published: March 2021

AbstractThe bioremediation and biomass production of organic extractive organisms (polychaetes Arenicola marina, Hediste diversicolor and halophyte Salicornia ramosissima) was assessed in an integrated multi-trophic aquaculture (IMTA) framework. Culture trials were performed outdoors using the nutient rich effluent from a shrimp farm employing recirculated aquaculture systems. Similar bioremediation efficiencies were obtained in cultures using a single polyculture tank (1 T) or two trophic levels separated tanks (2 T; ≈ 0.3 and 0.6 m2 operational area, respectively), with a reduction of 74–87% for particulate organic matter (POM), 56–64% for dissolved inorganic nitrogen (DIN) and 60–65% for dissolved inorganic phosphorus (DIP). Hediste diversicolor adapted well to culture conditions, reaching densities up to 5.000 ind. m−2 (≈ 78–98 g m−2). Arenicola marina failed to cope with water temperature that exceeded the species thermal limits, displaying a survival < 10% (20 °C often pointed as the maximum thermal threshold for this species). Productivity of S. ramosissima with 1 T was about twice that obtained with 2 T (≈ 150–170 and ≈ 60–90 g FW m−2 edible aboveground biomass, respectively). The yellowish coloration of cultured plants was likely due to the chemical oxidation and rapid sand filtration pre-treatment applied to the brackish groundwater used in the aquaculture facility, that removed iron (and probably other essential elements). Overall, 1 T design combining H. diversicolor and S. ramosissima displayed the best bioremediation performance and biomass production, while also allowing reducing in half the operational area required to implement this IMTA framework.
Imaging the transmembrane and transendothelial sodium gradients in gliomas
Authors: Khan Muhammad H. , Walsh John J. , Mihailović Jelena M. , Mishra Sandeep K. , Coman Daniel , Hyder Fahmeed 
Published: March 2021

AbstractUnder normal conditions, high sodium (Na+) in extracellular (Na+e) and blood (Na+b) compartments and low Na+ in intracellular milieu (Na+i) produce strong transmembrane (ΔNa+mem) and weak transendothelial (ΔNa+end) gradients respectively, and these manifest the cell membrane potential (Vm) as well as blood–brain barrier (BBB) integrity. We developed a sodium (23Na) magnetic resonance spectroscopic imaging (MRSI) method using an intravenously-administered paramagnetic polyanionic agent to measure ΔNa+mem and ΔNa+end. In vitro 23Na-MRSI established that the 23Na signal is intensely shifted by the agent compared to other biological factors (e.g., pH and temperature). In vivo 23Na-MRSI showed Na+i remained unshifted and Na+b was more shifted than Na+e, and these together revealed weakened ΔNa+mem and enhanced ΔNa+end in rat gliomas (vs. normal tissue). Compared to normal tissue, RG2 and U87 tumors maintained weakened ΔNa+mem (i.e., depolarized Vm) implying an aggressive state for proliferation, whereas RG2 tumors displayed elevated ∆Na+end suggesting altered BBB integrity. We anticipate that 23Na-MRSI will allow biomedical explorations of perturbed Na+ homeostasis in vivo.
Impact of device scaling on the electrical properties of MoS2 field-effect transistors
Authors: Arutchelvan Goutham , Smets Quentin , Verreck Devin , Ahmed Zubair , Gaur Abhinav , Sutar Surajit , Jussot Julien , Groven Benjamin , Heyns Marc , Lin Dennis , Asselberghs Inge , Radu Iuliana 
Published: March 2021

AbstractTwo-dimensional semiconducting materials are considered as ideal candidates for ultimate device scaling. However, a systematic study on the performance and variability impact of scaling the different device dimensions is still lacking. Here we investigate the scaling behavior across 1300 devices fabricated on large-area grown MoS2 material with channel length down to 30 nm, contact length down to 13 nm and capacitive effective oxide thickness (CET) down to 1.9 nm. These devices show best-in-class performance with transconductance of 185 μS/μm and a minimum subthreshold swing (SS) of 86 mV/dec. We find that scaling the top-contact length has no impact on the contact resistance and electrostatics of three monolayers MoS2 transistors, because edge injection is dominant. Further, we identify that SS degradation occurs at short channel length and can be mitigated by reducing the CET and lowering the Schottky barrier height. Finally, using a power performance area (PPA) analysis, we present a roadmap of material improvements to make 2D devices competitive with silicon gate-all-around devices.
Antibacterial activity testing methods for hydrophobic patterned surfaces
Authors: Perez-Gavilan Ana , de Castro Joana Vieira , Arana Ainara , Merino Santos , Retolaza Aritz , Alves Sofia A. , Francone Achille , Kehagias Nikolaos , Sotomayor-Torres Clivia M. , Cocina Donato , Mortera Renato , Crapanzano Salvatore , Pelegrín Carlos Javier , Garrigos María Carmen , Jiménez Alfonso , Galindo Begoña , Araque Mari Carmen , Dykeman Donna , Neves Nuno M. , Marimón Jose Maria 
Published: March 2021

AbstractOne strategy to decrease the incidence of hospital-acquired infections is to avoid the survival of pathogens in the environment by the development of surfaces with antimicrobial activity. To study the antibacterial behaviour of active surfaces, different approaches have been developed of which ISO 22916 is the standard. To assess the performance of different testing methodologies to analyse the antibacterial activity of hydrophobic surface patterned plastics as part of a Horizon 2020 European research project. Four different testing methods were used to study the antibacterial activity of a patterned film, including the ISO 22916 standard, the immersion method, the touch-transfer inoculation method, and the swab inoculation method, this latter developed specifically for this project. The non-realistic test conditions of the ISO 22916 standard showed this method to be non-appropriate in the study of hydrophobic patterned surfaces. The immersion method also showed no differences between patterned films and smooth controls due to the lack of attachment of testing bacteria on both surfaces. The antibacterial activity of films could be demonstrated by the touch-transfer and the swab inoculation methods, that more precisely mimicked the way of high-touch surfaces contamination, and showed to be the best methodologies to test the antibacterial activity of patterned hydrophobic surfaces. A new ISO standard would be desirable as the reference method to study the antibacterial behaviour of patterned surfaces.
Risk and mortality of aspiration pneumonia in Parkinson’s disease: a nationwide database study
Authors: Won Jun Hee , Byun Seong Jun , Oh Byung-Mo , Park Sang Jun , Seo Han Gil 
Published: March 2021

AbstractThis retrospective cohort study investigated the risk and mortality rate due to aspiration pneumonia in patients with Parkinson’s disease (PD) using a nationwide database. We identified 10,159 newly diagnosed PD patients between 2004 and 2006, and four age- and sex-matched controls for each PD patient from the National Health Insurance Service database in Korea. We analyzed the relative risk of aspiration pneumonia and mortality after the first occurrence of aspiration pneumonia until 2017. Throughout the study period, PD patients showed a higher incidence of aspiration pneumonia than their matched controls (3.01 vs. 0.59 events per 1,000 person-years), and they were at an increased risk of aspiration pneumonia (hazard ratio = 4.21; 95% confidence interval, 3.87–4.58). After the first occurrence of aspiration pneumonia, the mortality rate of PD patients was 23.9% after one month, 65.2% after 1 year, and 91.8% after 5 years, while that of controls was 30.9%, 67.4%, and 88.9%, respectively. Patients with PD are at an increased risk of aspiration pneumonia, and approximately two-thirds of the patients die within a year after experiencing aspiration pneumonia. Further studies are warranted to prevent aspiration pneumonia and implement proper treatments to prevent death after aspiration pneumonia in patients with PD.
Efficacy of combination treatment using YHO-1701, an orally active STAT3 inhibitor, with molecular-targeted agents on cancer cell lines
Authors: Taniguchi Keisuke , Konishi Hiroaki , Yoshinaga Akiko , Tsugane Momomi , Takahashi Hiroyuki , Nishisaka Fukiko , Shishido Yoshiyuki , Asai Akira 
Published: March 2021

AbstractSignal transducer and activator of transcription 3 (STAT3) plays a critical role in regulating cell growth, survival, and metastasis. STAT3 signaling is constitutively activated in various types of hematologic or solid malignancies. YHO-1701 has been developed as an orally available STAT3 inhibitor. Herein, YHO-1701 in combination with molecular-targeted agents was evaluated. Additive or synergistic effects were observed in a broad spectrum of “combination treatment + cell line” pairs. Of particular interest was the synergistic effect observed when YHO-1701 was combined with imatinib or dasatinib [breakpoint cluster region-abelson (BCR-ABL) inhibitors], osimertinib [epidermal growth factor receptor (EGFR) inhibitor], crizotinib, alectinib, or ceritinib [anaplastic lymphoma kinase (ALK) inhibitors]. The results further showed a close relationship between these synergistic effects and the cellular levels of the key molecules involved in the target pathways for YHO-1701 and each combination drug. The combination of YHO-1701 with alectinib resulted in significantly greater antitumor activity without exhibiting body weight loss in an NCI-H2228 [echinoderm microtubule-associated protein-like 4 (EML4)-ALK fusion] xenograft mouse model. Our results strongly suggest that the logical strategy in combination with the novel STAT3 inhibitor YHO-1701 and other mechanistically different targeted agents, could be a promising approach in future clinical settings.
Implication of O2 dynamics for both N2O and CH4 emissions from soil during biological soil disinfestation
Authors: Wang Chen , Ma Xuehong , Wang Gang , Li Guitong , Zhu Kun 
Published: March 2021

AbstractSoil O2 dynamics have significant influences on greenhouse gas emissions during soil management practice. In this study, we deployed O2-specific planar optodes to visualize spatiotemporal distribution of O2 in soils treated with biological soil disinfestation (BSD). This study aimed to reveal the role of anoxia development on emissions of N2O and CH4 from soil amended with crop residues during BSD period. The incorporation of crop residues includes wheat straw only, wheat straw with biochar and early straw incorporation. The anoxia in soil developed very fast within 3 days, while the O2 in headspace decreased much slower and it became anaerobic after 5 days, which was significantly affected by straw and biochar additions. The N2O emissions were positively correlated with soil hypoxic fraction. The CH4 emissions were not significant until the anoxia dominated in both soil and headspace. The co-application of biochar with straw delayed the anoxia development and extended the hypoxic area in soil, resulting in lower emissions of N2O and CH4. Those results highlight that the soil O2 dynamic was the key variable triggering the N2O and CH4 productions. Therefore, detailed information of soil O2 availability could be highly beneficial for optimizing the strategies of organic amendments incorporation in the BSD technique.
PPV distribution of sidewalls induced by underground cavern blasting excavation
Authors: Luo Yi , Wei Xiaoqing , Huang Junhong , Zhang Guang , Bian Xing , Li Xinping 
Published: March 2021

AbstractThe peak particle velocity (PPV) is an important indicator for predicting blasting excavation disturbances. However, the PPV distribution in the deep underground space is significantly different from that on the outdoor ground. Therefore, it is difficult to predict the underground PPV by Sadovsky’s vibration formula. The PPV sidewall distribution characteristics were studied during site blasting in an underground cavern in the Taohuazui mine in China, and a similar numerical model was used to verify the site test data. We derived a PPV prediction formula for the underground cavern sidewall surrounding rock using a mechanical analysis model of a simply supported plate and beam in combination with dimensional analysis. The model considered derived boundary constraints, comparison with site measured data, the value predicted by Sadovsky’s vibration formula, and numerical simulation results. The results showed that the PPV distribution on the middle 1/3 section of the underground cavern sidewall showed a “platform” or “bulge” different from the curve from Sadovsky’s vibration formula. The PPV amplification coefficient in this section was distributed in a drum shape. The PPV prediction formula for the middle section of the sidewall derived in this paper was highly consistent with the data measured on-site and the numerical simulation results. The mechanical analysis model with a simply supported plate and beam included an underground cavern sidewall length–height ratio of 5 and effectively supplemented the PPV prediction formula for the middle section of the traditional underground cavern sidewall.
Mid infrared polarization engineering via sub-wavelength biaxial hyperbolic van der Waals crystals
Authors: Dixit Saurabh , Sahoo Nihar Ranjan , Mall Abhishek , Kumar Anshuman 
Published: March 2021

AbstractMid-infrared (IR) spectral region is of immense importance for astronomy, medical diagnosis, security and imaging due to the existence of the vibrational modes of many important molecules in this spectral range. Therefore, there is a particular interest in miniaturization and integration of IR optical components. To this end, 2D van der Waals (vdW) crystals have shown great potential owing to their ease of integration with other optoelectronic platforms and room temperature operation. Recently, 2D vdW crystals of $$\alpha$$
α
-$$\hbox {MoO}_{3}$$

MoO
3

and $$\alpha$$
α
-$$\hbox {V}_2 \hbox {O}_5$$

V
2

O
5

have been shown to possess the unique phenomenon of natural in-plane biaxial hyperbolicity in the mid-infrared frequency regime at room temperature. Here, we report a unique application of this in-plane hyperbolicity for designing highly efficient, lithography free and extremely subwavelength mid-IR photonic devices for polarization engineering. In particular, we show the possibility of a significant reduction in the device footprint while maintaining an enormous extinction ratio from $$\alpha$$
α
-$$\hbox {MoO}_{3}$$

MoO
3

and $$\alpha$$
α
-$$\hbox {V}_2$$

V
2

$$\hbox {O}_5$$

O
5

based mid-IR polarizers. Furthermore, we investigate the application of sub-wavelength thin films of these vdW crystals towards engineering the polarization state of incident mid-IR light via precise control of polarization rotation, ellipticity and relative phase. We explain our results using natural in-plane hyperbolic anisotropy of $$\alpha$$
α
-$$\hbox {MoO}_{3}$$

MoO
3

and $$\alpha$$
α
-$$\hbox {V}_2$$

V
2

$$\hbox {O}_5$$

O
5

via both analytical and full-wave electromagnetic simulations. This work provides a lithography free alternative for miniaturized mid-infrared photonic devices using the hyperbolic anisotropy of $$\alpha$$
α
-$$\hbox {MoO}_{3}$$

MoO
3

and $$\alpha$$
α
-$$\hbox {V}_2$$

V
2

$$\hbox {O}_5$$

O
5

.
Improved biodiesel production from waste cooking oil with mixed methanol–ethanol using enhanced eggshell-derived CaO nano-catalyst
Authors: Erchamo Yeshimebet Simeon , Mamo Tadios Tesfaye , Workneh Getachew Adam , Mekonnen Yedilfana Setarge 
Published: March 2021

AbstractIn this report, the utilization of mixed methanol–ethanol system for the production of biodiesel from waste cooking oil (WCO) using enhanced eggshell-derived calcium oxide (CaO) nano-catalyst was investigated. CaO nano-catalyst was produced by calcination of eggshell powder at 900 °C and followed by hydration-dehydration treatment to improve its catalytic activity. The particle size, morphology, and elemental composition of a catalyst were characterized by using XRD, SEM, and EDX techniques, respectively. After hydration-dehydration the shape of a catalyst was changed from a rod-like to honeycomb-like porous microstructure. Likewise, average particle size was reduced from 21.30 to 13.53 nm, as a result, its surface area increases. The main factors affecting the biodiesel yield were investigated, accordingly, an optimal biodiesel yield of 94% was obtained at 1:12 oil to methanol molar ratio, 2.5 wt% catalyst loading, 60 °C, and 120-min reaction time. A biodiesel yield of 88% was obtained using 6:6 equimolar ratio of methanol to ethanol, the yield even increased to 91% by increasing the catalyst loading to 3.5 wt%. Moreover, by slightly increasing the share of methanol in the mixture, at 8:4 ratio, the maximum biodiesel yield could reach 92%. Therefore, we suggest the utilization of methanol–ethanol mixture as a reactant and eggshell-derived CaO as a catalyst for enhanced conversion of WCO into biodiesel. It is a very promising approach for the development of low-cost and environmentally friendly technology. Properties of the biodiesel were also found in good agreement with the American (ASTM D6571) fuel standards.