bluuebunny/crossref_metadata_2025 huggingface dataset:
A Proof‐of‐Concept Study of Using a Less Permeable Slice Along the Shoreline to Increase Fresh Groundwater Storage of Oceanic Islands: Analytical and Experimental Validation
Authors: Lu Chunhui , Cao Hongfan , Ma Jing , Shi Wenlong , Rathore Saubhagya Singh , Wu Jichun , Luo Jian
Published: June 2019

We propose a new concept that has the potential to mitigate seawater intrusion and increase the fresh groundwater storage of oceanic islands by creating a less permeable slice along the shoreline. We present a proof‐of‐concept study to examine its effectiveness through analytical and experimental studies. Analytical expressions for calculating the freshwater‐seawater interface location, water table elevation, fresh groundwater volume, and groundwater travel time are presented for both barrier and circular islands, which are found dependent on three different scenarios of interface locations. The analytical solution of the interface location in a barrier island is verified through sand‐tank experiments. Sensitivity analyses based on a simplified conceptual model of St. George Island in Florida, USA, indicate that the fresh groundwater volume monotonically increases with the decrease in the hydraulic conductivity of the coastal less permeable hydrogeologic unit. On the other hand, the increase of the coastal less permeable unit extent leads to an increased fresh groundwater volume. However, when the interface tip is on the aquifer bed of the coastal less permeable unit, a further increase of the less permeable unit extent only slightly increases the fresh groundwater volume, since the interface does not change any more and only the water table is elevated. We demonstrate here that the concept proposed has the potential in increasing the fresh groundwater storage of oceanic islands. Analytical expressions presented can improve our understanding of seawater intrusion in a dual‐unit oceanic island.
Characteristics of Rising Tone Whistler Mode Waves Inside the Earth's Plasmasphere, Plasmaspheric Plumes, and Plasmatrough
Authors: Teng S. , Li W. , Tao X. , Shen X.‐C. , Ma Q.
Published: June 2019

Whistler mode waves, particularly rising tone emissions, are important for nonlinear interactions with energetic electrons in the Earth's magnetosphere. In this letter, we evaluate the characteristics of rising tone whistler mode waves in three distinct regions: (1) inside the plasmasphere, (2) plasmapheric plumes, and (3) plasmatrough (outside the plasmapause). Our statistical results indicate that the occurrence rate of rising tone emissions tends to increase with increasing geomagnetic activity and is highest in plasmaspheric plumes among these three regions. Inside the plasmasphere, rising tone emissions typically occur in the outer portion of the plasmasphere, particularly near the dawnside. Moreover, the rising tone emissions inside the plasmasphere and plumes tend to be more field aligned than those in the plasmatrough. Our new findings of global wave properties of rising tone emissions are critical for understanding the generation of rising tone emissions and their effects on radiation belt electron dynamics.
Observational Evidence for Throat Aurora Being Associated With Magnetopause Reconnection
Authors: Han De‐Sheng , Xu Tong , Jin Yaqi , Oksavik K. , Chen Xiang‐Cai , Liu Jian‐Jun , Zhang Qinghe , Baddeley Lisa , Herlingshaw Katie
Published: June 2019

Throat auroras have been suggested to be related to indentations on the subsolar magnetopause. However, the indentation generation process and the resulting ionospheric responses have remained unknown. An EISCAT Svalbard Radar experiment was designed to run with all‐sky cameras, which enabled us for the first time to observe the temporal and spatial evolution of flow reversals, Joule heating, and ion upflows associated with throat aurora. The high‐resolution data enabled us to discriminate that the flow bursts and Joule heating were concurrent and co‐located, but were always observed on the west side of the associated throat auroras, reflecting that the upward/downward field‐aligned currents associated with throat aurora are always to the east/west, respectively. These results are consistent with the geometry of Southwood (1987) flux transfer event model and provide strong evidence for throat aurora being associated with magnetopause reconnection events. The results also support a conceptual model of the throat aurora.
Microglia-derived TNF-α mediates endothelial necroptosis aggravating blood brain–barrier disruption after ischemic stroke
Authors: Chen An-Qi , Fang Zhi , Chen Xiao-Lu , Yang Shuai , Zhou Yi-Fan , Mao Ling , Xia Yuan-Peng , Jin Hui-Juan , Li Ya-Nan , You Ming-Feng , Wang Xu-Xia , Lei Hao , He Quan-Wei , Hu Bo
Published: June 2019

Endothelium (EC) is a key component of blood–brain barrier (BBB), and has an important position in the neurovascular unit. Its dysfunction and death after cerebral ischemic/reperfusion (I/R) injury not only promote evolution of neuroinflammation and brain edema, but also increase the risk of intracerebral hemorrhage of thrombolytic therapies. However, the mechanism and specific interventions of EC death after I/R injury are poorly understood. Here we showed that necroptosis was a mechanism underlying EC death, which promoted BBB breakdown after I/R injury. Treatment of rats with receptor interacting protein kinase 1 (RIPK1)-inhibitor, necrostatin-1 reduced endothelial necroptosis and BBB leakage. We furthermore showed that perivascular M1-like microglia-induced endothelial necroptosis leading to BBB disruption requires tumor necrosis factor-α (TNF-α) secreted by M1 type microglia and its receptor, TNF receptor 1 (TNFR1), on endothelium as the primary mediators of these effects. More importantly, anti-TNFα (infliximab, a potent clinically used drug) treatment significantly ameliorate endothelial necroptosis, BBB destruction and improve stroke outcomes. Our data identify a previously unexplored role for endothelial necroptosis in BBB disruption and suggest infliximab might serve as a potential drug for stroke therapy.
Room temperature hidden state in a manganite observed by time-resolved X-ray diffraction
Authors: Zhang Haijuan , Zhang Yuanyuan , Li Runze , Yu Junxiao , Dong Wenxia , Chen Conglong , Wang Kuidong , Tang Xiaodong , Chen Jie
Published: June 2019

Realizing active quantum control of materials near room temperature is one of the ultimate aims for their practical applications. Recent technological breakthroughs demonstrated that optical stimulation may lead to thermally inaccessible hidden states with unique properties. However, most of the reported hidden states were induced around or below liquid nitrogen temperature. Here, we optically manipulated a manganite near its Curie temperature of 300 K, where typically complex phase competitions locate as well as opportunities for new functionality. A room temperature hidden state was formed with threshold behavior evidenced by a femtosecond paramagnetic to ferromagnetic order switching and a structural change distinct from thermal induced lattice expansion in tens of picoseconds accompanying with phonon softening. We propose that such a hidden state originates from the charge transfer between antiferromagnetic chains after strongly correlated spin-charge quantum excitation, which subsequently initiates an orbital polarization rearrangement described as $${\mathrm{Mn}}_{3x^2 - {r}^2/3y^2 - {r}^2}^{3 + }{\mathrm{Mn}}^{4 + } \to {\mathrm{Mn}}^{4 + }{\mathrm{Mn}}_{3z^2 - {r}^2}^{3 + }$$

Mn

3

x

2

-

r

2

∕
3

y

2

-

r

2

3
+

Mn

4
+

→

Mn

4
+

Mn

3

z

2

-

r

2

3
+

and associated non-thermal lattice change. This study started from room temperature yet near a phase transition point, which suggests a new route to create or manipulate novel phases for practical purpose.
Publisher Correction: IFN-γ-independent immune markers of Mycobacterium tuberculosis exposure
Authors: Lu Lenette L. , Smith Malisa T. , Yu Krystle K. Q. , Luedemann Corinne , Suscovich Todd J. , Grace Patricia S. , Cain Adam , Yu Wen Han , McKitrick Tanya R. , Lauffenburger Douglas , Cummings Richard D. , Mayanja-Kizza Harriet , Hawn Thomas R. , Boom W. Henry , Stein Catherine M. , Fortune Sarah M. , Seshadri Chetan , Alter Galit
Published: June 2019

In the version of this article originally published, there was an error in the abstract. The word disease should not have been included in the sentence “These individuals were highly exposed to Mtb but tested negative disease by IFN-γ release assay and tuberculin skin test, ‘resisting’ development of classic LTBI”. The sentence should have been “These individuals were highly exposed to Mtb but tested negative by IFN-γ release assay and tuberculin skin test, ‘resisting’ development of classic LTBI.” The error has been corrected in the HTML and PDF versions of this article.
Orobol, an Enzyme-Convertible Product of Genistein, exerts Anti-Obesity Effects by Targeting Casein Kinase 1 Epsilon
Authors: Yang Hee , Lee Sang‐Hyuk , Ji Hae , Kim Jong-Eun , Yoo Ra , Kim Jong Hun , Suk Sujin , Huh Chul Sung , Park Jung Han Yoon , Heo Yong-Seok , Shin Han-Seoung , Kim Byung-Gee , Lee Ki Won
Published: June 2019

Soy isoflavones, particularly genistein, have been shown to exhibit anti-obesity effects. When compared with the isoflavones genistin, daidzin, coumestrol, genistein, daidzein, 6-o-dihydroxyisoflavone, equol, 3′-o-dihydroxyisoflavone, and 8-o-dihydroxyisoflavone, a remarkably higher inhibitory effect on lipid accumulation was observed for orobol treatment during adipogenesis in 3T3-L1 cells. To identify the cellular target of orobol, its pharmacological effect on 395 human kinases was analyzed. Of the 395 kinases, orobol showed the lowest half maximal inhibitory concentration (IC50) for Casein Kinase 1 epsilon (CK1ε), and bound to this target in an ATP-competitive manner. A computer modeling study revealed that orobol may potentially dock with the ATP-binding site of CK1ε via several hydrogen bonds and van der Waals interactions. The phosphorylation of eukaryotic translation initiation factor 4E-binding protein 1, a substrate of CK1ε, was inhibited by orobol in isobutylmethylxanthine, dexamethasone and insulin (MDI)-induced 3T3-L1 cells. It was also found that orobol attenuates high fat diet-induced weight gain and lipid accumulation without affecting food intake in C57BL/6J mice. These findings underline orobol’s potential for development as a novel agent for the prevention and treatment of obesity.
Frequency-dependent exacerbation of Alzheimer’s disease neuropathophysiology
Authors: Kastanenka Ksenia V. , Calvo-Rodriguez Maria , Hou Steven S. , Zhou Heng , Takeda Shuko , Arbel-Ornath Michal , Lariviere Amanda , Lee Yee Fun , Kim Alex , Hawkes Jonathan M. , Logan Robert , Feng Danielle , Chen Xiqun , Gomperts Stephen N. , Bacskai Brian J.
Published: June 2019

Neuronal activity patterns are disrupted in neurodegenerative disorders, including Alzheimer’s disease (AD). One example is disruption of corticothalamic slow oscillations responsible for sleep-dependent memory consolidation. Slow waves are periodic oscillations in neuronal activity occurring at frequencies of <1 Hz. The power, but not the frequency of slow oscillations is altered in a mouse model of AD. Optogenetic rescue of slow oscillations by increasing activity in cortical pyramidal neurons at the frequency of slow waves restores slow wave power, halts deposition of amyloid plaques and prevents neuronal calcium dysregulation. Here we determined whether driving this circuit at an increased rate would exacerbate the amyloid-dependent calcium dyshomeostasis in transgenic mice. Doubling the frequency of slow waves for one month with optogenetics resulted in increased amyloid beta - dependent disruptions in neuronal calcium homeostasis and loss of synaptic spines. Therefore, while restoration of physiological circuit dynamics is sufficient to abrogate the progression of Alzheimer’s disease pathology and should be considered an avenue for clinical treatment of AD patients with sleep disorders, pathophysiological stimulation of neuronal circuits leads to activity - dependent acceleration of amyloid production, aggregation and downstream neuronal dysfunction.
Nematode-free agricultural system of a fungus-growing termite
Authors: Kanzaki Natsumi , Liang Wei-Ren , Chiu Chun-I , Yang Ching-Ting , Hsueh Yen-Ping , Li Hou-Feng
Published: June 2019

Fungus-growing termites forage dead plant materials from the field to cultivate symbiotic Termitomyces fungi in the nest. Termite foraging behavior and the entry of symbiotic arthropod inquilines may transfer nematodes into a nest and adversely affect fungus production. To test whether nematodes were transferred to fungus gardens by termites and inquilines, we examined the occurrence of nematodes in fungus gardens, five termite castes, and nine species of inquilines of a fungus-growing termite, Odontotermes formosanus. Our results revealed that nematodes were commonly carried by foraging termites and beetle inquilines. Numerous nematodes were found under the beetle elytra. No nematodes were found on termite larvae, eggs, and wingless inquilines. In addition, nematodes rarely occurred in the fungus garden. By observing the response of nematodes to three species of Termitomyces spp. and the fungus gardens, we confirmed that the fungus and fungus gardens are not actually toxic to nematodes. We suggest that nematodes were suppressed through grooming behavior and gut antimicrobial activity in termites, rather than through the antimicrobial activity of the fungus.
Biofilm formation by multidrug resistant Enterobacteriaceae strains isolated from solid organ transplant recipients
Authors: Ramos-Vivas José , Chapartegui-González Itziar , Fernández-Martínez Marta , González-Rico Claudia , Fortún Jesús , Escudero Rosa , Marco Francesc , Linares Laura , Montejo Miguel , Aranzamendi Maitane , Muñoz Patricia , Valerio Maricela , Aguado Jose María , Resino Elena , Ahufinger Irene Gracia , Vega Aurora Paz , Martínez-Martínez Luis , Fariñas María Carmen ,   The ENTHERE Study Group, the Group for Study of Infection in Transplantation of the Spanish Society of Infectious Diseases and Clinical Microbiology (GESITRA-SEIMC) and the Spanish Network for Research in Infectious Diseases (REIPI), Ruiz San Millán Juan Carlos , Rodrigo Emilio , Casafont Morencos Fernando , Fabrega Emilio , Cuadrado Antonio , Fariñas-Alvarez Concepción , Gozalo Mónica , Arnaíz de las Revillas Francisco , Martín Dávila Pilar , Martínez Adolfo , Ruíz Garbajosa Patricia , Moreno Asunción , Bodro Marta , Solano María Fernanda , Blanco María José , Nieto Javier , Machado Marina , Olmedo María , Rodríguez Fernández Sara , Rincón Sanz Cristina , Vicente Range Teresa , Agnelli Bento Caroline , Galar Recalde Alicia , Eworo Alia , Fernández-Lomana Fernando Anaya , Rodríguez-Ferrero María Luisa , Sánchez Cámara Luis Alberto , Chaves Fernando , de la Torre Cisneros Julián
Published: June 2019

Solid organ transplant (SOT) recipients are especially at risk of developing infections by multidrug resistant bacteria (MDR). In this study, the biofilm-forming capability of 209 MDR strains (Escherichia coli n = 106, Klebsiella pneumoniae n = 78, and Enterobacter spp. n = 25) isolated from rectal swabs in the first 48 hours before or after kidney (93 patients), liver (60 patients) or kidney/pancreas transplants (5 patients) were evaluated by using a microplate assay. Thirty-nine strains were isolated before transplant and 170 strains were isolated post-transplant. Overall, 16% of E. coli strains, 73% of K. pneumoniae strains and 4% Enterobacter strains showed moderate or strong biofilm production. Nine strains isolated from infection sites after transplantation were responsible of infections in the first month. Of these, 4 K. pneumoniae, 1 E. coli and 1 Enterobacter spp. strains isolated pre-transplant or post-transplant as colonizers caused infections in the post-transplant period. Our results suggest that in vitro biofilm formation could be an important factor for adhesion to intestine and colonization in MDR K. pneumoniae strains in SOT recipients, but this factor appears to be less important for MDR E. coli and Enterobacter spp.
Metabolomics reveals novel insight on dormancy of aquatic invertebrate encysted embryos
Authors: Rozema Evelien , Kierszniowska Sylwia , Almog-Gabai Oshri , Wilson Erica G. , Choi Young Hae , Verpoorte Robert , Hamo Reini , Chalifa-Caspi Vered , Assaraf Yehuda G. , Lubzens Esther
Published: June 2019

Numerous aquatic invertebrates survive harsh environments by displaying dormancy as encysted embryos. This study aimed at determining whether metabolomics could provide molecular insight to explain the “dormancy syndrome” by highlighting functional pathways and metabolites, hence offering a novel comprehensive molecular view of dormancy. We compared the metabolome of morphologically distinct dormant encysted embryos (resting eggs) and non-dormant embryos (amictic eggs) of a rotifer (Brachionus plicatilis). Metabolome profiling revealed ~5,000 features, 1,079 of which were annotated. Most of the features were represented at significantly higher levels in non-dormant than dormant embryos. A large number of features was assigned to putative functional pathways indicating novel differences between dormant and non-dormant states. These include features associated with glycolysis, the TCA and urea cycles, amino acid, purine and pyrimidine metabolism. Interestingly, ATP, nucleobases, cyclic nucleotides, thymidine and uracil, were not detected in dormant resting eggs, suggesting an impairment of response to environmental and internal cues, cessation of DNA synthesis, transcription and plausibly translation in the dormant embryos. The levels of trehalose or its analogues, with a role in survival under desiccation conditions, were higher in resting eggs. In conclusion, the current study highlights metabolomics as a major analytical tool to functionally compare dormancy across species.
Plasma channel formation in NIR laser-irradiated carrier gas from an aerosol nanoparticle injector
Authors: Klimešová Eva , Kulyk Olena , Gu Yanjun , Dittrich Laura , Korn Georg , Hajdu Janos , Krikunova Maria , Andreasson Jakob
Published: June 2019

Aerosol nanoparticle injectors are fundamentally important for experiments where container-free sample handling is needed to study isolated nanoparticles. The injector consists of a nebuliser, a differential pumping unit, and an aerodynamic lens to create and deliver a focused particle beam to the interaction point inside a vacuum chamber. The tightest focus of the particle beam is close to the injector tip. The density of the focusing carrier gas is high at this point. We show here how this gas interacts with a near infrared laser pulse (800 nm wavelength, 120 fs pulse duration) at intensities approaching 1016 Wcm−2. We observe acceleration of gas ions to kinetic energies of 100s eV and study their energies as a function of the carrier gas density. Our results indicate that field ionisation by the intense near-infrared laser pulse opens up a plasma channel behind the laser pulse. The observations can be understood in terms of a Coulomb explosion of the created underdense plasma channel. The results can be used to estimate gas background in experiments with the injector and they open up opportunities for a new class of studies on electron and ion dynamics in nanoparticles surrounded by a low-density gas.
Facile One-Pot Synthesis of Bimetallic Co/Mn-MOFs@Rice Husks, and its Carbonization for Supercapacitor Electrodes
Authors: Kim Hyunuk , Sohail Muhammad , Wang Chenbo , Rosillo-Lopez Martin , Baek Kangkyun , Koo Jaehyoung , Seo Myung Won , Kim Seyoung , Foord John S. , Han Seong Ok
Published: June 2019

Novel hybrid nanomaterials comprising metal-organic framework compounds carbonised in the presence of biomass material derived from rice husk have been investigated as a new class of sustainable supercapacitor materials for electrochemical energy storage. Specifically, two synthetic routes were employed to grow Co/Mn metal-organic framework compounds in the channels of rice husks, which had been activated previously by heat treatment in air at 400 °C to produce a highly porous network. Pyrolysis of these hybrid materials under nitrogen at 700 °C for 6 h produced metal-containing phases within the nanocarbon, comprising intimate mixtures of Co, MnO and CoMn2O4. The materials thus produced are characterized in detail using a range of physical methods including XRD, electron microscopy and X-ray photoelectron spectroscopy. The synthetic pathway to the metal-organic framework compound is shown to influence significantly the physical properties of the resulting material. Electrochemical evaluation of the materials fabricated revealed that higher specific capacitances were obtained when smaller crystallite sized bimetallic Co/Mn-MOFs were grown inside the rice husks channels compared to larger crystallite sizes. This was in-part due to increased metal oxide loading into the rice husk owing to the smaller crystallite size as well as the increased pseudocapacitance exhibited by the smaller crystallite sizes and increased porosity.
A Guide for Ex Vivo Handling and Storage of Stool Samples Intended for Fecal Microbiota Transplantation
Authors: Burz Sebastian D. , Abraham Anne-Laure , Fonseca Fernanda , David Olivier , Chapron Audrey , Béguet-Crespel Fabienne , Cénard Stéphanie , Le Roux Karine , Patrascu Orlane , Levenez Florence , Schwintner Carole , Blottière Hervé M. , Béra-Maillet Christel , Lepage Patricia , Doré Joël , Juste Catherine
Published: June 2019

Owing to the growing recognition of the gut microbiota as a main partner of human health, we are expecting that the number of indications for fecal microbiota transplantation (FMT) will increase. Thus, there is an urgent need for standardization of the entire process of fecal transplant production. This study provides a complete standardized procedure to prepare and store live and ready-to-use transplants that meet the standard requirements of good practices to applied use in pharmaceutical industry. We show that, if time before transformation to transplants would exceed 24 hours, fresh samples should not be exposed to temperatures above 20 °C, and refrigeration at 4 °C can be a safe solution. Oxygen-free atmosphere was not necessary and simply removing air above collected samples was sufficient to preserve viability. Transplants prepared in maltodextrin-trehalose solutions, stored in a -80 °C standard freezer and then rapidly thawed at 37 °C, retained the best revivification potential as  proven by 16S rRNA profiles, metabolomic fingerprints, and flow cytometry assays over a 3-month observation period. Maltodextrin-trehalose containing cryoprotectants were also efficient in preserving viability of lyophilized transplants, either in their crude or purified form, an option that can be attractive for fecal transplant biobanking and oral formulation.
High-Resolution Copy Number Patterns From Clinically Relevant FFPE Material
Authors: Filia Anastasia , Droop Alastair , Harland Mark , Thygesen Helene , Randerson-Moor Juliette , Snowden Helen , Taylor Claire , Diaz Joey Mark S. , Pozniak Joanna , Nsengimana Jérémie , Laye Jon , Newton-Bishop Julia A. , Bishop D. Timothy
Published: June 2019

Systematic tumour profiling is essential for biomarker research and clinically for assessing response to therapy. Solving the challenge of delivering informative copy number (CN) profiles from formalin-fixed paraffin embedded (FFPE) material, the only likely readily available biospecimen for most cancers, involves successful processing of small quantities of degraded DNA. To investigate the potential for analysis of such lesions, whole-genome CNVseq was applied to 300 FFPE primary tumour samples, obtained from a large-scale epidemiological study of melanoma. The quality and the discriminatory power of CNVseq was assessed. Libraries were successfully generated for 93% of blocks, with input DNA quantity being the only predictor of success (success rate dropped to 65% if <20 ng available); 3% of libraries were dropped because of low sequence alignment rates. Technical replicates showed high reproducibility. Comparison with targeted CN assessment showed consistency with the Next Generation Sequencing (NGS) analysis. We were able to detect and distinguish CN changes with a resolution of ≤10 kb. To demonstrate performance, we report the spectrum of genomic CN alterations (CNAs) detected at 9p21, the major site of CN change in melanoma. This successful analysis of CN in FFPE material using NGS provides proof of principle for intensive examination of population-based samples.
Simultaneous observation of higher-order non-classicalities based on experimental photocount moments and probabilities
Authors: Peřina Jan , Haderka Ondřej , Michálek Václav
Published: June 2019

Using a sub-Poissonian optical field generated from a weak twin beam by photon-number resolving post-selection we have simultaneously observed higher-order non-classicalities in photocount moments (sub-Poissonian statistics) and probabilities (witnessed by the Klyshko inequalities). Up to the seventh-order non-classicalities in photocount moments simultaneously with up to the eleventh-order non-classicalities in photocount probabilities have been experimentally observed. Non-classicality counting parameters of different orders as experimental counterparts of the theoretical Lee non-classicality depth have been suggested to quantify and also mutually compare the robustness of these non-classicalities against the noise.
Microevolution of antimicrobial resistance and biofilm formation of Salmonella Typhimurium during persistence on pig farms
Authors: Tassinari Eleonora , Duffy Geraldine , Bawn Matt , Burgess Catherine M. , McCabe Evonne M. , Lawlor Peadar G. , Gardiner Gillian , Kingsley Robert A.
Published: June 2019

Salmonella Typhimurium and its monophasic variant S. 4,[5],12:i:- are the dominant serotypes associated with pigs in many countries. We investigated their population structure on nine farms using whole genome sequencing, and their genotypic and phenotypic variation. The population structure revealed the presence of phylogenetically distinct clades consisting of closely related clones of S. Typhimurium or S. 4,[5],12:i:- on each pig farm, that persisted between production cycles. All the S. 4,[5],12:i:- strains carried the Salmonella genomic island-4 (SGI-4), which confers resistance to heavy metals, and half of the strains contained the mTmV prophage, harbouring the sopE virulence gene. Most clonal groups were highly drug resistant due to the presence of multiple antimicrobial resistance (AMR) genes, and two clades exhibited evidence of recent on-farm plasmid-mediated acquisition of additional AMR genes, including an IncHI2 plasmid. Biofilm formation was highly variable but had a strong phylogenetic signature. Strains capable of forming biofilm with the greatest biomass were from the S. 4,[5],12:i:- and S. Typhimurium DT104 clades, the two dominant pandemic clones found over the last 25 years. On-farm microevolution resulted in enhanced biofilm formation in subsequent production cycle.
Multi-Method Molecular Characterisation of Human Dust-Mite-associated Allergic Asthma
Authors: Whittle E. , Leonard M. O. , Gant T. W. , Tonge D. P
Published: June 2019

Asthma is a chronic inflammatory disorder of the airways. Disease presentation varies greatly in terms of cause, development, severity, and response to medication, and thus the condition has been subdivided into a number of asthma phenotypes. There is still an unmet need for the identification of phenotype-specific markers and accompanying molecular tools that facilitate the classification of asthma phenotype. To this end, we utilised a range of molecular tools to characterise a well-defined group of female adults with poorly controlled atopic asthma associated with house dust mite (HDM) allergy, relative to non-asthmatic control subjects. Circulating messenger RNA (mRNA) and microRNA (miRNA) were sequenced and quantified, and a differential expression analysis of the two RNA populations performed to determine how gene expression and regulation varied in the disease state. Further, a number of circulating proteins (IL-4, 5, 10, 13, 17 A, Eotaxin, GM-CSF, IFNy, MCP-1, TARC, TNFα, Total IgE, and Endotoxin) were quantified to determine whether the protein profiles differed significantly dependent on disease state. Finally, we utilised a previously published assessment of the circulating “blood microbiome” performed using 16S rRNA amplification and sequencing. Asthmatic subjects displayed a range of significant alterations to circulating gene expression and regulation, relative to healthy control subjects, that may influence systemic immune activity. Notably, several circulating mRNAs were detected in just the asthma group or just in the control group, and many more were observed to be expressed at significantly different levels in the asthma group compared to the control group. Proteomic analysis revealed increased levels of inflammatory proteins within the serum, and decreased levels of the bacterial endotoxin protein in the asthmatic state. Comparison of blood microbiome composition revealed a significant increase in the Firmicutes phylum with asthma that was associated with a concomitant reduction in the Proteobacteria phylum. This study provides a valuable insight into the systemic changes evident in the HDM-associated asthma, identifies a range of molecules that are present in the circulation in a condition-specific manner (with clear biomarker potential), and highlights a range of hypotheses for further study.
Impact of body mass index on robotic transaxillary thyroidectomy
Authors: Yap Zeng , Kim Won Woong , Kang Sang-Wook , Lee Cho Rok , Lee Jandee , Jeong Jong Ju , Nam Kee-Hyun , Chung Woong Youn
Published: June 2019

Obesity is associated with increased operating times and higher complication rates in many types of surgery. Its impact on robotic thyroidectomy however, is not well documented. The aim of this study was to investigate the relationship between body mass index (BMI) and robotic transaxillary thyroidectomy (RTAT). A retrospective review of prospectively collected data of all patients who underwent RTAT at Yonsei University Health System from October 2007 to December 2014 was performed. Patients were divided into three groups based on BMI (Group 1: BMI < 25, Group 2: BMI 25–29.99, Group 3: BMI ≥ 30), and compared. A total of 3697 patients were analyzed. No differences between the three groups were observed in clinicopathological factors, extent of surgery or length of stay. After multivariate analysis, only seroma and transient voice hoarseness were related to increasing BMI. Total operative time was significantly longer for Group 3 patients with less-than-bilateral total thyroidectomy (BTT), but was not significantly different for patients with BTT. Although obese patients undergoing RTAT have a slightly higher risk of seroma, transient voice hoarseness, and longer operative times, BMI did not influence the other important surgical outcomes of thyroidectomy. Therefore, obesity should not be a contraindication for performing RTAT.
A universal fluorescence-based toolkit for real-time quantification of DNA and RNA nuclease activity
Authors: Sheppard Emily C. , Rogers Sally , Harmer Nicholas J. , Chahwan Richard
Published: June 2019

DNA and RNA nucleases play a critical role in a growing number of cellular processes ranging from DNA repair to immune surveillance. Nevertheless, many nucleases have unknown or poorly characterized activities. Elucidating nuclease substrate specificities and co-factors can support a more definitive understanding of cellular mechanisms in physiology and disease. Using fluorescence-based methods, we present a quick, safe, cost-effective, and real-time versatile nuclease assay, which uniquely studies nuclease enzyme kinetics. In conjunction with a substrate library we can now analyse nuclease catalytic rates, directionality, and substrate preferences. The assay is sensitive enough to detect kinetics of repair enzymes when confronted with DNA mismatches or DNA methylation sites. We have also extended our analysis to study the kinetics of human single-strand DNA nuclease TREX2, DNA polymerases, RNA, and RNA:DNA nucleases. These nucleases are involved in DNA repair, immune regulation, and have been associated with various diseases, including cancer and immune disorders.
Temporal changes in the spatial distribution of carabid beetles around arable field-woodlot boundaries
Authors: Knapp Michal , Seidl Miroslav , Knappová Jana , Macek Martin , Saska Pavel
Published: June 2019

Carabids are considered beneficial arthropods in agroecosystems, where they prey on crop pests or consume weed seeds. Therefore, knowledge of the spatial distribution of carabids in agricultural landscapes is crucial to efficiently manage the ecosystem services that they provide. In the present study, we investigated the spatial distribution of carabids around arable field-woodlot boundaries in different seasons: (1) early spring, (2) late spring, (3) summer and (4) late autumn. The spatial distribution of carabid abundance (activity-density) and species richness varied seasonally, and the total abundance was highest within arable fields, except in early spring when it peaked at the boundaries. The observed pattern was mainly driven by the spatial distribution of the open-habitat species, which aggregated near the field boundaries during winter and early spring. The open-habitat species penetrated into woodlots during the summer season but occurred almost exclusively outside woodlots in the other sampling periods. The abundance of the forest species was highest within woodlots with the exception of the early spring season, when their abundance peaked at the boundaries. Carabid species richness was highest within arable fields in close proximity to woodlot boundaries with the exception of the summer season, when the total species richness was similar across habitats.
Complex molecular mechanisms underlying MYMIV-resistance in Vigna mungo revealed by comparative transcriptome profiling
Authors: Kundu Anirban , Singh Pankaj Kumar , Dey Avishek , Ganguli Sayak , Pal Amita
Published: June 2019

Mungbean Yellow Mosaic India Virus (MYMIV)-infection creates major hindrance in V. mungo cultivation and poses significant threat to other grain legume production. Symptoms associated include severe patho-physiological alterations characterized by chlorotic foliar lesion accompanied by reduced growth. However, dissection of the host’s defense machinery remains a tough challenge due to limited of host’s genomic resources. A comparative RNA-Seq transcriptomes of resistant (VM84) and susceptible (T9) plants was carried out to identify genes potentially involved in V. mungo resistance against MYMIV. Distinct gene expression landscapes were observed in VM84 and T9 with 2158 and 1679 differentially expressed genes (DEGs), respectively. Transcriptomic responses in VM84 reflect a prompt and intense immune reaction demonstrating an efficient pathogen surveillance leading to activation of basal and induced immune responses. Functional analysis of the altered DEGs identified multiple regulatory pathways to be activated or repressed over time. Up-regulation of DEGs including NB-LRR, WRKY33, ankyrin, argonaute and NAC transcription factor revealed an insight on their potential roles in MYMIV-resistance; and qPCR validation shows a propensity of their accumulation in VM84. Analyses of the current RNA-Seq dataset contribute immensely to decipher molecular responses that underlie MYMIV-resistance and will aid in the improvement strategy of V. mungo and other legumes through comparative functional genomics.
Regional Rainfall Warning System for Landslides with Creep Deformation in Three Gorges using a Statistical Black Box Model
Authors: Guo Zizheng , Yin Kunlong , Gui Lei , Liu Qingli , Huang Faming , Wang Tengfei
Published: June 2019

Establishing an efficient regional landslide rainfall warning system plays an important role in landslide prevention. To forecast the performance of landslides with creep deformation at a regional scale, a black box model based on statistical analysis was proposed and was applied to Yunyang County in the Three Gorges Reservoir area (TGRA), China. The data samples were selected according to the characteristics of the landslide displacement monitoring data. Then, the rainfall criteria applied to different time periods were determined by correlation analysis between rainfall events and landslides and by numerical simulation on landslide movement under certain rainfall conditions. The cumulative rainfall thresholds that were determined relied on the displacement ratio model, which considered landslide scale characteristics and the statistical relationship between daily rainfall data and monthly displacement data. These thresholds were then applied to a warning system to determine a five-level warning partition of landslides with creep deformation in Yunyang County. Finally, landslide cases and displacement monitoring data were used to validate the accuracy of the model. The validation procedure showed that the warning results of the model fit well with actual conditions and that this model could provide the basis for early warning of landslides with creep deformation.
QR code micro-certified gemstones: femtosecond writing and Raman characterization in Diamond, Ruby and Sapphire
Authors: Batista Andre Jaques , Vianna Pilar Gregory , Ribeiro Henrique Bucker , Matos Christiano Jose Santiago de , Gomes Anderson Stevens Leonidas
Published: June 2019

This paper reports on a micro-certification procedure using femtosecond laser irradiation to microscopically mark a single-crystalline gemological and natural diamond, synthetic ruby and synthetic sapphire, inscribing a QR Code on them. The QR-code was composed of a set of 25 × 25 micropoints, and the irradiation energy was optimized at 1kHz repetition rate. The code was made at a 20 µm relative depth into the gemstone surfaces by controlling the incident laser energy, that was set to 3 μJ for all the samples. Characterization by optical and electron microscopy, as well as micro-Raman hyperspectral imaging showed that the microdots have a diameter of about 14 µm perpendicular to the irradiation direction, being laterally spaced by 14 µm-18 µm applied for each sample. This work corroborates the feasibility of using ultrafast laser inscription technology to fabricate microdots with great quality on gemstone surfaces, which offers a great potential for the jewelry industry to safely micro-encrypt gemological certifications. The compositional and morphological characterization of the modified surface was carried by micro-Raman spectroscopy and scanning electron microscopy.
Machine-assisted cultivation and analysis of biofilms
Authors: Hansen Silla H. , Kabbeck Tobias , Radtke Carsten P. , Krause Susanne , Krolitzki Eva , Peschke Theo , Gasmi Jannis , Rabe Kersten S. , Wagner Michael , Horn Harald , Hubbuch Jürgen , Gescher Johannes , Niemeyer Christof M.
Published: June 2019

Biofilms are the natural form of life of the majority of microorganisms. These multispecies consortia are intensively studied not only for their effects on health and environment but also because they have an enormous potential as tools for biotechnological processes. Further exploration and exploitation of these complex systems will benefit from technical solutions that enable integrated, machine-assisted cultivation and analysis. We here introduce a microfluidic platform, where readily available microfluidic chips are connected by automated liquid handling with analysis instrumentation, such as fluorescence detection, microscopy, chromatography and optical coherence tomography. The system is operable under oxic and anoxic conditions, allowing for different gases and nutrients as feeding sources and it offers high spatiotemporal resolution in the analysis of metabolites and biofilm composition. We demonstrate the platform’s performance by monitoring the productivity of biofilms as well as the spatial organization of two bacterial species in a co-culture, which is driven by chemical gradients along the microfluidic channel.
Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota)
Authors: Widhelm Todd J. , Grewe Felix , Huang Jen-Pan , Mercado-Díaz Joel A. , Goffinet Bernard , Lücking Robert , Moncada Bibiana , Mason-Gamer Roberta , Lumbsch H. Thorsten
Published: June 2019

In the age of next-generation sequencing, the number of loci available for phylogenetic analyses has increased by orders of magnitude. But despite this dramatic increase in the amount of data, some phylogenomic studies have revealed rampant gene-tree discordance that can be caused by many historical processes, such as rapid diversification, gene duplication, or reticulate evolution. We used a target enrichment approach to sample 400 single-copy nuclear genes and estimate the phylogenetic relationships of 13 genera in the lichen-forming family Lobariaceae to address the effect of data type (nucleotides and amino acids) and phylogenetic reconstruction method (concatenation and species tree approaches). Furthermore, we examined datasets for evidence of historical processes, such as rapid diversification and reticulate evolution. We found incongruence associated with sequence data types (nucleotide vs. amino acid sequences) and with different methods of phylogenetic reconstruction (species tree vs. concatenation). The resulting phylogenetic trees provided evidence for rapid and reticulate evolution based on extremely short branches in the backbone of the phylogenies. The observed rapid and reticulate diversifications may explain conflicts among gene trees and the challenges to resolving evolutionary relationships. Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.
Antibiotic-induced decreases in the levels of microbial-derived short-chain fatty acids correlate with increased gastrointestinal colonization of Candida albicans
Authors: Guinan Jack , Wang Shaohua , Hazbun Tony R. , Yadav Hariom , Thangamani Shankar
Published: June 2019

Candida albicans is the fourth most common cause of systemic nosocomial infections, posing a significant risk in immunocompromised individuals. As the majority of systemic C. albicans infections stem from endogenous gastrointestinal (GI) colonization, understanding the mechanisms associated with GI colonization is essential in the development of novel methods to prevent C. albicans-related mortality. In this study, we investigated the role of microbial-derived short-chain fatty acids (SCFAs) including acetate, butyrate, and propionate on growth, morphogenesis, and GI colonization of C. albicans. Our results indicate that cefoperazone-treated mice susceptible to C. albicans infection had significantly decreased levels of SCFAs in the cecal contents that correlate with a higher fungal load in the feces. Further, using in vivo concentration of SCFAs, we demonstrated that SCFAs inhibit the growth, germ tube, hyphae and biofilm development of C. albicans in vitro. Collectively, results from this study suggest that antibiotic-induced decreases in the levels of SCFAs in the cecum enhances the growth and GI colonization of C. albicans.
Diphtheria Toxin A-Resistant Cell Lines Enable Robust Production and Evaluation of DTA-Encoding Lentiviruses
Authors: Lange Margaret J. , Lyddon Terri D. , Johnson Marc C.
Published: June 2019

Suicide genes have been widely investigated for their utility as therapeutic agents and as tools for in vitro negative selection strategies. Several methods for delivery of suicide genes have been explored. Two important considerations for delivery are the quantity of delivered cargo and the ability to target the cargo to specific cells. Delivery using a lentiviral vector is particularly attractive due to the ability to encode the gene within the viral genome, as well as the ability to limit off-target effects by using cell type-specific glycoproteins. Here, we present the design and validation of a diphtheria toxin A (DTA)-encoding lentiviral vector expressing DTA under the control of a constituitive promoter to allow for expression of DTA in a variety of cell types, with specificity provided via selection of glycoproteins for pseudotyping of the lentiviral particles. DTA exerts its toxic activity through inhibition of eukaryotic translation elongation factor 2 (eEF2) via adenosine diphosphate (ADP)-ribosylation of a modified histidine residue, diphthamide, at His715, which blocks protein translation and leads to cell death. Thus, we also detail development of DTA-resistant cell lines, engineered through CRISPR/Cas9-mediated knockout of the diphthamide 1 (DPH1) gene, which enable both robust virus production by transfection and evaluation of DTA-expressing virus infectivity.
Artificial skin through super-sensing method and electrical impedance data from conductive fabric with aid of deep learning
Authors: Duan Xi , Taurand Sebastien , Soleimani Manuchehr
Published: June 2019

Sense of touch is a major part of man’s communication with their environment. Artificial skins can help robots to have the same sense of touch, especially for their social interactions. This paper presents a pressure mapping sensing using piezo-resistive fabric to represent aspects of the sense of touch. In past few years’ electrical impedance tomography (EIT) is considered to be able offer a good alternative for artificial skin in particular for its ease of adaptation for large area skin compared to individual matrix based sensors. The EIT has also very good temporal performance in data collection allowing for monitoring of fast responses to touch stimulation, enabling a truly real time touch sensing. Electromechanical responses of a conductive fabric can be exploited using EIT to create a low cost and large area touch sensing. Such electromechanical properties are often very complex, so to improve the imaging resolution and touch visibility an artificial intelligent (AI) was used in addition to the state of the art spatio-temporal imaging algorithm. This work demonstrates a step towards an integrated seamless skin with large area sensing in dynamical settings, closer to natural human skin’s behaviour. For the first time a dynamical touch sensing are studies by means of a spatio-temporal based electrical impedance tomography (EIT) imaging on a conductive fabric. The experimental results demonstrated the successful results by a combined AI with dynamical EIT imaging results in single and multiple points of touch.