bluuebunny/crossref_metadata_2025 huggingface dataset:
The heterogeneous nucleation of threading dislocations on partial dislocations in III-nitride epilayers
Authors: Smalc-Koziorοwska J. , Moneta J. , Chatzopoulou P. , Vasileiadis I. G. , Bazioti C. , Prytz Ø. , Belabbas I. , Komninou Ph. , Dimitrakopulos G. P.
Published: October 2020

III-nitride compound semiconductors are breakthrough materials regarding device applications. However, their heterostructures suffer from very high threading dislocation (TD) densities that impair several aspects of their performance. The physical mechanisms leading to TD nucleation in these materials are still not fully elucidated. An overlooked but apparently important mechanism is their heterogeneous nucleation on domains of basal stacking faults (BSFs). Based on experimental observations by transmission electron microscopy, we present a concise model of this phenomenon occurring in III-nitride alloy heterostructures. Such domains comprise overlapping intrinsic I1 BSFs with parallel translation vectors. Overlapping of two BSFs annihilates most of the local elastic strain of their delimiting partial dislocations. What remains combines to yield partial dislocations that are always of screw character. As a result, TD nucleation becomes geometrically necessary, as well as energetically favorable, due to the coexistence of crystallographically equivalent prismatic facets surrounding the BSF domain. The presented model explains all observed BSF domain morphologies, and constitutes a physical mechanism that provides insight regarding dislocation nucleation in wurtzite-structured alloy epilayers.
Broadband optical ultrafast reflectivity of Si, Ge and GaAs
Authors: Di Cicco A. , Polzoni G. , Gunnella R. , Trapananti A. , Minicucci M. , Rezvani S. J. , Catone D. , Di Mario L. , Pelli Cresi J. S. , Turchini S. , Martelli F.
Published: October 2020

Ultrafast optical reflectivity measurements of silicon, germanium, and gallium arsenide have been carried out using an advanced set-up providing intense subpicosecond pulses (35 fs FWHM, $$\lambda $$
λ
= 400 nm) as a pump and broadband 340–780 nm ultrafast pulses as a white supercontinuum probe. Measurements have been performed for selected pump fluence conditions below the damage thresholds, that were carefully characterized. The obtained fluence damage thresholds are 30, 20.8, 9.6 mJ/$$\hbox {cm}^2$$

cm
2

for Si, Ge and GaAs respectively. Ultrafast reflectivity patterns show clear differences in the Si, Ge, and GaAs trends both for the wavelength and time dependences. Important changes were observed near the wavelength regions corresponding to the $$E_1$$

E
1

, $$E_1+\Delta $$

E
1

+
Δ

singularities in the joint density of states, so related to the peculiar band structure of the three systems. For Ge, ultrafast reflectivity spectra were also collected at low temperature (down to 80 K) showing a shift of the characteristic doublet peak around 2.23 eV and a reduction of the recovery times.
Multivalent tumor suppressor adenomatous polyposis coli promotes Axin biomolecular condensate formation and efficient β-catenin degradation
Authors: Li Tie-Mei , Ren Jing , Husmann Dylan , Coan John P. , Gozani Or , Chua Katrin F.
Published: October 2020

The tumor suppressor adenomatous polyposis coli (APC) is frequently mutated in colorectal cancers. APC and Axin are core components of a destruction complex that scaffolds GSK3β and CK1 to earmark β-catenin for proteosomal degradation. Disruption of APC results in pathologic stabilization of β-catenin and oncogenesis. However, the molecular mechanism by which APC promotes β-catenin degradation is unclear. Here, we find that the intrinsically disordered region (IDR) of APC, which contains multiple β-catenin and Axin interacting sites, undergoes liquid–liquid phase separation (LLPS) in vitro. Expression of the APC IDR in colorectal cells promotes Axin puncta formation and β-catenin degradation. Our results support the model that multivalent interactions between APC and Axin drives the β-catenin destruction complex to form biomolecular condensates in cells, which concentrate key components to achieve high efficient degradation of β-catenin.
Effects of feeding frequency on juvenile Chinese sturgeon Acipenser sinensis
Authors: Hu Yacheng , Xiao Kan , Yang Jing , Liu Xueqing , Wang Binzhong , Zeng Qingkai , Du Hejun
Published: October 2020

In this study, the effects of different feeding frequencies on the growth and the expression of genes in the GH/IGF axis were assessed in juvenile Chinese sturgeon. The newly hatched Chinese sturgeons were bred for 38 days at three different feeding frequencies groups (feeding frequency of two times a day, TWD; three times a day, THD; and four times a day, FOD), and the expression levels of the GH/IGF axis responses to feeding frequency were determined by quantitative real-time PCR. In addition, the full-length of the Coding Sequences of IGF I and IGF II genes (489-bp and 660-bp, respectively), were cloned and analyzed from Chinese sturgeon the first time. Multiple sequence alignments of IGFs revealed that Chinese sturgeon are high sequence identity to IGFs from other species. The phylogenetic relationships based on the IGF I and IGF II amino acid sequences were consistent with the traditional classification. After 38 days of growth, the three different feeding frequencies groups of Chinese sturgeon had no significant difference of body length, body weight, specific growth rate, the survival rate, the rate of weight gain and the condition factor. However, the relative expression of Chinese sturgeon GH in the pituitary decreased with increasing feeding frequency. The relative expression of Chinese sturgeon GHR in liver and skeletal muscle was deceased with increasing feeding frequency, while the relative expression of GHR in stomach and intestines at THD group was significantly higher than that of at TWD group and FOD group (p < 0.05). The relative expression of Chinese sturgeon IGF I in liver increased significantly with increasing feeding frequency (p < 0.05). The relative expression of IGF I in stomach and skeletal muscle was similar at the three groups. The relative expression of IGF I in intestines was significantly higher at FOD group than at TWD group and THD group (p < 0.05). The relative expression of Chinese sturgeon IGF II in liver at TWD group was significantly higher than that at THD group and FOD group (p < 0.05). However, the relative expression of IGF II in stomach, intestines and skeletal muscle at THD group was higher than that at TWD group and FOD group. Based on these previous studies that liver IGF I is regarded as a biomarker of growth performance, this result suggested that the juvenile Chinese sturgeon is better for growth when feeding four times daily compared to twice and thrice daily.
Optimized DNA extraction and purification method for characterization of bacterial and fungal communities in lung tissue samples
Authors: Pérez-Brocal Vicente , Magne Fabien , Ruiz-Ruiz Susana , Ponce Carolina A. , Bustamante Rebeca , Martin Viviana San , Gutierrez Mireya , Gatti Gianna , Vargas Sergio L. , Moya Andrés
Published: October 2020

Human lungs harbor a scarce microbial community, requiring to develop methods to enhance the recovery of nucleic acids from bacteria and fungi, leading to a more efficient analysis of the lung tissue microbiota. Here we describe five extraction protocols including pre-treatment, bead-beating and/or Phenol:Chloroform:Isoamyl alcohol steps, applied to lung tissue samples from autopsied individuals. The resulting total DNA yield and quality, bacterial and fungal DNA amount and the microbial community structure were analyzed by qPCR and Illumina sequencing of bacterial 16S rRNA and fungal ITS genes. Bioinformatic modeling revealed that a large part of microbiome from lung tissue is composed of microbial contaminants, although our controls clustered separately from biological samples. After removal of contaminant sequences, the effects of extraction protocols on the microbiota were assessed. The major differences among samples could be attributed to inter-individual variations rather than DNA extraction protocols. However, inclusion of the bead-beater and Phenol:Chloroform:Isoamyl alcohol steps resulted in changes in the relative abundance of some bacterial/fungal taxa. Furthermore, inclusion of a pre-treatment step increased microbial DNA concentration but not diversity and it may contribute to eliminate DNA fragments from dead microorganisms in lung tissue samples, making the microbial profile closer to the actual one.
The three-stage rock failure dynamics of the Drus (Mont Blanc massif, France) since the June 2005 large event
Authors: Guerin Antoine , Ravanel Ludovic , Matasci Battista , Jaboyedoff Michel , Deline Philip
Published: October 2020

Since the end of the Little Ice Age, the west face of the Drus (Mont Blanc massif, France) has been affected by a retrogressive erosion dynamic marked by large rockfall events. From the 1950s onwards, the rock failure frequency gradually increased until the large rockfall event (292,680 m3) of June 2005, which made the Bonatti Pillar disappear. Aiming to characterize the rock failure activity following this major event, which may be related to permafrost warming, the granitic rock face was scanned each autumn between October 2005 and September 2016 using medium- and long-range terrestrial laser scanners. All the point clouds were successively compared to establish a rockfall source inventory and determine a volume-frequency relationship. Eleven years of monitoring revealed a phase of rock failure activity decay until September 2008, a destabilization phase between September 2008 and November 2011, and a new phase of rock failure activity decay from November 2011 to September 2016. The destabilization phase was marked by three major rockfall events covering a total volume of 61,494 m3, resulting in the progressive collapse of a new pillar located in the northern part of the June 2005 rockfall scar. In the same way as for the Bonatti Pillar, rock failure instability propagated upward with increasing volumes. In addition to these major events, 304 rockfall sources ranging from 0.002 to 476 m3 were detected between 2005 and 2016. The temporal evolution of rock failure activity reveals that after a major event, the number of rockfall sources and the eroded volume both follow a rapid decrease. The rock failure activity is characterized by an exponential decay during the period following the major event and by a power-law decay for the eroded volume. The power law describing the distribution of the source volumes detected between 2005 and 2016 indicates an exponent of 0.48 and an average rock failure activity larger of more than six events larger than 1 m3 per year. Over the 1905–2016 period, a total of 426,611 m3 of rock collapsed from the Drus west face, indicating a very high rock wall retreat rate of 14.4 mm year−1 over a surface of 266,700 m2. Averaged over a time window of 1000 years, the long-term retreat rate derived from the frequency density integration of rock failure volumes is 2.9 mm year−1. Despite difficulty in accessing and monitoring the site, our study demonstrates that long-term surveys of high-elevation rock faces are possible and provide valuable information that helps improve our understanding of landscape evolution in mountainous settings subject to permafrost warming.
The role of IL-6-174 G/C polymorphism and intraocular IL-6 levels in the pathogenesis of ocular diseases: a systematic review and meta-analysis
Authors: Ulhaq Zulvikar Syambani , Soraya Gita Vita , Budu  , Wulandari Lely Retno
Published: October 2020

Interleukin-6 (IL-6) is one of the key regulators behind the inflammatory and pathological process associated with ophthalmic diseases. The role of IL-6-174 G/C polymorphism as well as intraocular IL-6 levels among various eye disease patients differ across studies and has not been systematically reviewed. Thus, this study aims to provide a summary to understand the relationship between IL-6 and ophthalmic disease. In total, 8,252 and 11,014 subjects for IL-6-174 G/C and intraocular levels of IL-6, respectively, were retrieved from PubMed, Scopus and Web of Science. No association was found between IL-6-174 G/C polymorphisms with ocular diseases. Subgroup analyses revealed a suggestive association between the GC genotype of IL-6-174 G/C with proliferative diabetic retinopathy (PDR). Further, the level of intraocular IL-6 among ocular disease patients in general was found to be higher than the control group [standardized mean difference (SMD) = 1.41, 95% confidence interval (CI) 1.24–1.58, P < 0.00001]. Closer examination through subgroup analyses yielded similar results in several ocular diseases. This study thus indicates that the IL-6-174 G/C polymorphism does not predispose patients to ocular disease, although the GC genotype is likely to be a genetic biomarker for PDR. Moreover, intraocular IL-6 concentrations are related to the specific manifestations of the ophthalmic diseases. Further studies with larger sample sizes are warranted to confirm this conclusion.
Implantation of Impella CP left ventricular assist device under the guidance of three-dimensional intracardiac echocardiography
Authors: Yastrebov Konstantin , Brunel Laurencie , Paterson Hugh S. , Williams Zoe A. , Wise Innes K. , Burrows Christopher S. , Bannon Paul G.
Published: October 2020

Impella CP is a percutaneously inserted left ventricular assist device indicated for temporary mechanical cardiac support during high risk percutaneous coronary interventions and for cardiogenic shock. The potential application of Impella has become particularly relevant during the current COVID-19 pandemic, for patients with acute severe heart failure complicating viral illness. Standard implantation of the Impella CP is performed under fluoroscopic guidance. Positioning of the Impella CP can be confirmed with transthoracic or transoesophageal echocardiography. We describe an alternative approach to guide intracardiac implantation of the Impella CP using two-dimensional and three-dimensional intracardiac echocardiography. This new technique can be useful in selected groups of patients when fluoroscopy, transthoracic and transoesophageal echocardiography is deemed inapplicable or limited for epidemiological or clinical reasons. Intracardiac three-dimensional echocardiography is a feasible alternative to the traditional techniques for implantation of an Impella CP device but careful consideration must be given to the potential limitations and complications of this technique.
Influence of tunnel ionization to third-harmonic generation of infrared femtosecond laser pulses in air
Authors: Tamulienė Viktorija , Juškevičiūtė Greta , Buožius Danas , Vaičaitis Virgilijus , Babushkin Ihar , Morgner Uwe
Published: October 2020

Here we present an experimental as well as theoretical study of third-harmonic generation in tightly focused femtosecond filaments in air at the wavelength of $$1.5 \,\upmu \hbox {m}$$

1.5

μ
m

. At low intensities, longitudinal phase matching is dominating in the formation of 3rd harmonics, whereas at higher intensities locked X-waves are formed. We provide the arguments that the X-wave formation is governed mainly by the tunnel-like ionization dynamics rather than by the multiphoton one. Despite of this fact, the impact of the ionization-induced nonlinearity is lower than the one from bound–bound transitions at all intensities.
On the effects of memory and topology on the controllability of complex dynamical networks
Authors: Kyriakis Panagiotis , Pequito Sérgio , Bogdan Paul
Published: October 2020

Recent advances in network science, control theory, and fractional calculus provide us with mathematical tools necessary for modeling and controlling complex dynamical networks (CDNs) that exhibit long-term memory. Selecting the minimum number of driven nodes such that the network is steered to a prescribed state is a key problem to guarantee that complex networks have a desirable behavior. Therefore, in this paper, we study the effects of long-term memory and of the topological properties on the minimum number of driven nodes and the required control energy. To this end, we introduce Gramian-based methods for optimal driven node selection for complex dynamical networks with long-term memory and by leveraging the structure of the cost function, we design a greedy algorithm to obtain near-optimal approximations in a computationally efficiently manner. We investigate how the memory and topological properties influence the control effort by considering Erdős–Rényi, Barabási–Albert and Watts–Strogatz networks whose temporal dynamics follow a fractional order state equation. We provide evidence that scale-free and small-world networks are easier to control in terms of both the number of required actuators and the average control energy. Additionally, we show how our method could be applied to control complex networks originating from the human brain and we discover that certain brain cortex regions have a stronger impact on the controllability of network than others.
Explosive-driven double-blast exposure: molecular, histopathological, and behavioral consequences
Authors: Murphy Erin K. , Iacono Diego , Pan Hongna , Grimes Jamie B. , Parks Steven , Raiciulescu Sorana , Leonessa Fabio , Perl Daniel P.
Published: October 2020

Traumatic brain injury generated by blast may induce long-term neurological and psychiatric sequelae. We aimed to identify molecular, histopathological, and behavioral changes in rats 2 weeks after explosive-driven double-blast exposure. Rats received two 30-psi (~ 207-kPa) blasts 24 h apart or were handled identically without blast. All rats were behaviorally assessed over 2 weeks. At Day 15, rats were euthanized, and brains removed. Brains were dissected into frontal cortex, hippocampus, cerebellum, and brainstem. Western blotting was performed to measure levels of total-Tau, phosphorylated-Tau (pTau), amyloid precursor protein (APP), GFAP, Iba1, αII-spectrin, and spectrin breakdown products (SBDP). Kinases and phosphatases, correlated with tau phosphorylation were also measured. Immunohistochemistry for pTau, APP, GFAP, and Iba1 was performed. pTau protein level was greater in the hippocampus, cerebellum, and brainstem and APP protein level was greater in cerebellum of blast vs control rats (p < 0.05). GFAP, Iba1, αII-spectrin, and SBDP remained unchanged. No immunohistochemical or neurobehavioral changes were observed. The dissociation between increased pTau and APP in different regions in the absence of neurobehavioral changes 2 weeks after double blast exposure is a relevant finding, consistent with human data showing that battlefield blasts might be associated with molecular changes before signs of neurological and psychiatric disorders manifest.
Mechano-chemistry of human femoral diaphysis revealed by correlative Brillouin–Raman microspectroscopy
Authors: Cardinali M. A. , Govoni M. , Dallari D. , Caponi S. , Fioretto D. , Morresi A.
Published: October 2020

Brillouin–Raman microspectroscopy is presented as an innovative label-free all-optical investigation approachable to characterize the chemical composition and the mechanical properties of human tissues at micrometric resolution. Brillouin maps unveil mechanical heterogeneities in a human femoral diaphysis, showing a ubiquitous co-existence of hard and soft components, even in the most compact sections. The novel correlative analysis of Brillouin and Raman maps shows that the relative intensity of Brillouin peaks is a good proxy for the fraction of mineralized fibers and that the stiffness (longitudinal elastic modulus) of the hard component is linearly dependent on the hydroxyapatite concentration. For the soft component, a gradient of composition is found, ranging from an abundance of proteins in the more compact, external, bone to abundance of lipids, carotenoids, and heme groups approaching the trabecular, inner, part of the diaphysis. This work unveils the strong potential of correlative mechano-chemical characterization of human tissues at a micrometric resolution for both fundamental and translational research.
Quantitative bone single photon emission computed tomography analysis of the effects of duration of bisphosphonate administration on the parietal bone
Authors: Hata Hironobu , Kitao Tomoka , Sato Jun , Asaka Takuya , Imamachi Kenji , Miyakoshi Masaaki , Hirata Kenji , Magota Keiichi , Munakata Yamato , Shiga Tohru , Yamazaki Yutaka , Kitagawa Yoshimasa
Published: October 2020

Effects of long-term bisphosphonate (BP) administration on the metabolism of healthy bone and the concomitant changes in imaging are unclear. Hence, we aimed to retrospectively investigate the effects of long-term BP administration on the intact parietal bone using the standardised uptake value (SUV) derived from single photon emission computed tomography (SPECT). We enrolled 29 patients who had odontogenic infection, osteoporosis, bone metastasis cancer, or rheumatoid arthritis, and classified them into BP-naïve: A (14 patients) and BP-treated: B, < 4 years (7 patients) and C, ≥ 4 years (8 patients) groups. We measured the maximum bilateral SUV (SUVmax) of the parietal bone using quantitative bone SPECT software. There were significant differences in the duration of BP administration and SUVmax of the parietal bone among the diseases (P < 0.0001 and P = 0.0086, respectively). There was a positive correlation between the duration of BP administration and SUVmax of the parietal bone (rs = 0.65, P = 0.0002). The SUVmax was significantly different between A and B (P = 0.02) and between A and C (P = 0.0024) groups. This is the first report on the correlation between long-term BP administration and the SUVmax of the parietal bone using the quantitative bone SPECT analysis.
The daily resolved temperature dependence and structure of planktonic foraminifera blooms
Authors: Chernihovsky N. , Almogi-Labin A. , Kienast S. S. , Torfstein A.
Published: October 2020

Planktonic foraminifera (PF) life cycles are highly sensitive to marine conditions, which are evolving rapidly due to anthropogenic climate change. Even though PF shells in the sedimentary record serve as prominent proxies of past ocean conditions, very little is still known about their life cycles, particularly in oligotrophic environments. Here, we present a full annual record of PF fluxes (> 63 µm) from the oligotrophic Gulf of Aqaba, northern Red Sea, sampled at daily timescales during 2015–2016 using an automated time-series sediment trap. These results are coupled with daily surface chlorophyll-a concentrations, sea surface temperatures (SSTs), particulate organic carbon and bulk fluxes, together with monthly resolved vertical profiles of chlorophyll-a, temperatures and nutrient concentrations. The annual cycle of PF fluxes is controlled by SST changes that drive water column mixing and changes in food availability. PF species flux patterns and succession dynamics vary throughout the year, displaying large variability on previously undocumented daily-weekly timescales, and are not synchronized with lunar periodicity. On daily timescales, spring blooms show a complex structure and interplay between SSTs, chlorophyll-a surface concentrations and PF fluxes. These events deliver about a third of the total annual PF flux over a period of several weeks.
Easy-hard phase transition in parameter estimation for optical waveguides
Authors: Claussen Gunnar , Hartmann Alexander K.
Published: October 2020

The determination of the parameters of cylindrical optical waveguides, e.g. the diameters $$\vec {d}=(d_1,\ldots ,d_r)$$

d
→

=

(

d
1

,
…
,

d
r

)

of r layers of (semi-) transparent optical fibres, can be executed by inverse evaluation of the scattering intensities that emerge under monochromatic illumination. The inverse problem can be solved by optimising the mismatch $$R(\vec {d})$$

R
(

d
→

)

between the measured and simulated scattering patterns. The global optimum corresponds to the correct parameter values. The mismatch $$R(\vec {d})$$

R
(

d
→

)

can be seen as an energy landscape as a function of the diameters. In this work, we study the structure of the energy landscape for different values of the complex refractive indices $$\vec {n}$$

n
→

, for $$r=1$$

r
=
1

and $$r=2$$

r
=
2

layers. We find that for both values of r, depending on the values of $$\vec {n}$$

n
→

, two very different types of energy landscapes exist, respectively. One type is dominated by one global minimum and the other type exhibits a multitude of local minima. From an algorithmic viewpoint, this corresponds to easy and hard phases, respectively. Our results indicate that the two phases are separated by sharp phase-transition lines and that the shape of these lines can be described by one “critical” exponent b, which depends slightly on r. Interestingly, the same exponent also describes the dependence of the number of local minima on the diameters. Thus, our findings are comparable to previous theoretical studies on easy-hard transitions in basic combinatorial optimisation or decision problems like Travelling Salesperson and Satisfiability. To our knowledge our results are the first indicating the existence of easy-hard transitions for a real-world optimisation problem of technological relevance.
Exciton-to-trion conversion as a control mechanism for valley polarization in room-temperature monolayer WS2
Authors: Carmiggelt Joris J. , Borst Michael , van der Sar Toeno
Published: October 2020

Transition metal dichalcogenide (TMD) monolayers are two-dimensional semiconductors with two valleys in their band structure that can be selectively addressed using circularly polarized light. Their photoluminescence spectrum is characterized by neutral and charged excitons (trions) that form a chemical equilibrium governed by the net charge density. Here, we use chemical doping to drive the conversion of excitons into trions in $$\text {WS}_{2}$$

WS
2

monolayers at room temperature, and study the resulting valley polarization via photoluminescence measurements under valley-selective optical excitation. We show that the doping causes the emission to become dominated by trions with a strong valley polarization associated with rapid non-radiative recombination. Simultaneously, the doping results in strongly quenched but highly valley-polarized exciton emission due to the enhanced conversion into trions. A rate equation model explains the observed valley polarization in terms of the doping-controlled exciton-trion equilibrium. Our results shed light on the important role of exciton-trion conversion on valley polarization in monolayer TMDs.
Spontaneous transition rates near the focus of a parabolic mirror with identification of the vectorial modes involved
Authors: Gutiérrez-Jáuregui R. , Jáuregui R.
Published: October 2020

Each natural mode of the electromagnetic field within a parabolic mirror exhibits spatial localization and polarization properties that can be exploited for the quantum control of its interaction with atomic systems. The region of localization is not restricted to the focus of the mirror leading to a selective response of atomic systems trapped on its vicinity. We report calculations of the spontaneous emission rates for an atom trapped inside the mirror accounting for all atomic polarizations and diverse trapping regions. It is shown that electric dipole transitions can be enhanced near the focus of a deep parabolic mirror with a clear identification of the few vectorial modes involved. Out of the focus the enhancement vanishes gradually, but the number of relevant modes remains small. Ultimately this represents a quantum electrodynamic system where internal and external degrees of freedom cooperate to maximize a selective exchange and detection of single excitations.
Bioprocessing optimization for efficient simultaneous removal of methylene blue and nickel by Gracilaria seaweed biomass
Authors: El-Naggar Noura El-Ahmady , Rabei Nashwa H.
Published: October 2020

The pollution of water by heavy metal ions and dyes, particularly from industrial effluents, has become a global environmental issue. Therefore, the treatment of wastewater generated from different industrial wastes is essential to restore environmental quality. The efficiency ofGracilariaseaweed biomass as a sustainable biosorbent for simultaneous bioremoval of Ni2+and methylene blue from aqueous solution was studied. Optimization of the biosorption process parameters was performed using face-centered central composite design (FCCCD). The highest bioremoval percentages of Ni2+and methylene blue were 97.53% and 94.86%; respectively, obtained under optimum experimental conditions: 6 g/LGracilariabiomass, initial pH 8, 20 mg/L of methylene blue, 150 mg/L of Ni2+and 180 min of contact time. Fourier Transform Infrared Spectroscopy (FTIR) spectra demonstrated the presence of methyl, alkynes, amide, phenolic, carbonyl, nitrile and phosphate groups which are important binding sites involved in Ni2+and methylene blue biosorption process. SEM analysis reveals the appearance of shiny large particles and layers on the biosorbent surface after biosorption that are absent before the biosorption process. In conclusion, it is demonstrated that theGracilariaseaweed biomass is a promising, biodegradable, ecofriendly, cost-effective and efficient biosorbent for simultaneous bioremoval of Ni2+and methylene blue from wastewater effluents.
The structure of the antimicrobial human cathelicidin LL-37 shows oligomerization and channel formation in the presence of membrane mimics
Authors: Sancho-Vaello Enea , Gil-Carton David , François Patrice , Bonetti Eve-Julie , Kreir Mohamed , Pothula Karunakar Reddy , Kleinekathöfer Ulrich , Zeth Kornelius
Published: October 2020

The human cathelicidin LL-37 serves a critical role in the innate immune system defending bacterial infections. LL-37 can interact with molecules of the cell wall and perforate cytoplasmic membranes resulting in bacterial cell death. To test the interactions of LL-37 and bacterial cell wall components we crystallized LL-37 in the presence of detergents and obtained the structure of a narrow tetrameric channel with a strongly charged core. The formation of a tetramer was further studied by cross-linking in the presence of detergents and lipids. Using planar lipid membranes a small but defined conductivity of this channel could be demonstrated. Molecular dynamic simulations underline the stability of this channel in membranes and demonstrate pathways for the passage of water molecules. Time lapse studies of E. coli cells treated with LL-37 show membrane discontinuities in the outer membrane followed by cell wall damage and cell death. Collectively, our results open a venue to the understanding of a novel AMP killing mechanism and allows the rational design of LL-37 derivatives with enhanced bactericidal activity.
Nonsense-associated altered splicing of MAP3K1 in two siblings with 46,XY disorders of sex development
Authors: Igarashi Maki , Masunaga Yohei , Hasegawa Yuichi , Kinjo Kenichi , Miyado Mami , Saitsu Hirotomo , Kato-Fukui Yuko , Horikawa Reiko , Okubo Yomiko , Ogata Tsutomu , Fukami Maki
Published: October 2020

Although splicing errors due to single nucleotide variants represent a common cause of monogenic disorders, only a few variants have been shown to create new splice sites in exons. Here, we report an MAP3K1 splice variant identified in two siblings with 46,XY disorder of sex development. The patients carried a maternally derived c.2254C>T variant. The variant was initially recognized as a nonsense substitution leading to nonsense-mediated mRNA decay (p.Gln752Ter); however, RT-PCR for lymphoblastoid cell lines showed that this variant created a new splice donor site and caused 39 amino acid deletion (p.Gln752_Arg790del). All transcripts from the variant allele appeared to undergo altered splicing. The two patients exhibited undermasculinized genitalia with and without hypergonadotropism. Testosterone enanthate injections and dihydrotestosterone ointment applications yielded only slight increase in their penile length. Dihydrotestosterone-induced APOD transactivation was less significant in patients’ genital skin fibroblasts compared with that in control samples. This study provides an example of nonsense-associated altered splicing, in which a highly potent exonic splice site was created. Furthermore, our data, in conjunction with the previous data indicating the association between MAP3K1 and androgen receptor signaling, imply that the combination of testicular dysgenesis and androgen insensitivity may be a unique phenotype of MAP3K1 abnormalities.
Retroviral analysis reveals the ancient origin of Kihnu native sheep in Estonia: implications for breed conservation
Authors: Rannamäe Eve , Saarma Urmas , Ärmpalu-Idvand Anneli , Teasdale Matthew D. , Speller Camilla
Published: October 2020

Native animal breeds constitute an invaluable pool of genetic resources in a changing environment. Discovering native breeds and safeguarding their genetic diversity through specific conservation programs is therefore of high importance. Endogenous retroviruses have proved to be a reliable genetic marker for studying the demographic history of sheep (Ovis aries). Previous research has revealed two migratory episodes of domesticated sheep from the Middle East to Europe. The first episode included predominantly ‘primitive populations’, while the second and most recent is hypothesised to have included sheep with markedly improved wool production. To examine whether the recently discovered Kihnu native sheep in Estonia have historically been part of the first migratory episode and to what extent they have preserved primitive genetic characters, we analysed retroviral insertions in 80 modern Kihnu sheep and 83 ancient sheep from the Bronze Age to Modern Period (850 BCE–1950 CE). We identified that the Kihnu sheep have preserved ‘primitive’, ‘Nordic’, and other ‘ancient’ retrotypes that were present both in archaeological and modern samples, confirming their shared ancestry and suggesting that contemporary Kihnu native sheep originate from the first migratory episode. However, over the course of history, there has been a gradual decrease in the frequency of primitive retrotypes. Furthermore, Kihnu sheep possessed several ‘novel’ retrotypes that were absent in archaeological individuals, but were shared with improvement breeds, suggesting recent crossing within the last two centuries. To preserve these ancient lineages, our results are being applied in the conservation program of the Kihnu Native Sheep Society.
Photodynamic inactivation of Botrytis cinerea by an anionic porphyrin: an alternative pest management of grapevine
Authors: Ambrosini Veronica , Issawi Mohammad , Sol Vincent , Riou Catherine
Published: October 2020

Botrytis cinerea is a necrotic plant fungus that causes gray mold disease in over 200 crops, including grapevine. Due to its genetic plasticity, this fungus presents strong resistance to many fungicides. Thus, new strategies against B. cinerea are urgently needed. In this context, antimicrobial photodynamic treatment (APDT) was considered. APDT involves the use of a photosensitizer that generates reactive oxygen species upon illumination with white light. Tetra-4-sulfonatophenyl porphyrin tetra-ammonium (TPPS) was tested on B. cinerea using light. 1.5 µM TPPS completely inhibited mycelial growth. TPPS (12.5 µM) was tested on three grapevine clones from Chardonnay, Merlot and Sauvignon, grown in vitro for 2 months. Treated root apparatus of the three backgrounds increased thiol production as a molecular protection against photoactivated TPPS, leading to a normal phenotype as compared with control plantlets. Finally, 2-month-old grapevine leaves were infected with 4-day-old mycelium of B. cinerea pre-incubated or not with TPPS. The pre-treated mycelium was unable to infect the detached leaves of any of the three grapevine varieties after 72 h growth when subjected to a 16 h photoperiod, contrary to untreated mycelium. These results suggest a strong potential of photo-treatment against B. cinerea mycelium for future agricultural practices in vineyard or other cultures.
Individual head models for estimating the TMS-induced electric field in rat brain
Authors: Koponen Lari M. , Stenroos Matti , Nieminen Jaakko O. , Jokivarsi Kimmo , Gröhn Olli , Ilmoniemi Risto J.
Published: October 2020

In transcranial magnetic stimulation (TMS), the initial cortical activation due to stimulation is determined by the state of the brain and the magnitude, waveform, and direction of the induced electric field (E-field) in the cortex. The E-field distribution depends on the conductivity geometry of the head. The effects of deviations from a spherically symmetric conductivity profile have been studied in detail in humans. In small mammals, such as rats, these effects are more pronounced due to their less spherical head, proportionally much thicker neck region, and overall much smaller size compared to the TMS coils. In this study, we describe a simple method for building individual realistically shaped head models for rats from high-resolution X-ray tomography images. We computed the TMS-induced E-field with the boundary element method and assessed the effect of head-model simplifications on the estimated E-field. The deviations from spherical symmetry have large, non-trivial effects on the E-field distribution: for some coil orientations, the strongest stimulation is in the brainstem even when the coil is over the motor cortex. With modelling prior to an experiment, such problematic coil orientations can be avoided for more accurate targeting.
Seasonal synchronization of foodborne outbreaks in the United States, 1996–2017
Authors: Simpson Ryan B. , Zhou Bingjie , Naumova Elena N.
Published: October 2020

Modern food systems represent complex dynamic networks vulnerable to foodborne infectious outbreaks difficult to track and control. Seasonal co-occurrences (alignment of seasonal peaks) and synchronization (similarity of seasonal patterns) of infections are noted, yet rarely explored due to their complexity and methodological limitations. We proposed a systematic approach to evaluate the co-occurrence of seasonal peaks using a combination of L-moments, seasonality characteristics such as the timing (phase) and intensity (amplitude) of peaks, and three metrics of serial, phase-phase, and phase-amplitude synchronization. We used public records on counts of nine foodborne infections abstracted from CDC’s FoodNet Fast online platform for the US and ten representative states from 1996 to 2017 (264 months). Based on annualized and trend-adjusted Negative Binomial Harmonic Regression (NBHR) models augmented with the δ-method, we determined that seasonal peaks ofCampylobacter,Salmonella, and Shiga toxin-producingEscherichia Coli(STEC) were tightly clustered in late-July at the national and state levels. Phase-phase synchronization was observed betweenCryptosporidiumandShigella,Listeria, andSalmonella(ρ = 0.51, 0.51, 0.46; p < 0.04). Later peak timing of STEC was associated with greater amplitude nationally (ρ = 0.50, p = 0.02) indicating phase-amplitude synchronization. Understanding of disease seasonal synchronization is essential for developing reliable outbreak forecasts and informing stakeholders on mitigation and preventive measures.
Blood pool activity on F-18 FDG PET/CT as a possible imaging biomarker of metabolic syndrome
Authors: Bang Ji-In , Moon Chang Mo , Kim Hye Ok , Kang Seo Young , Yoon Hai-Jeon , Kim Bom Sahn
Published: October 2020

Association of blood pool (BP) and adipose tissue activity from F-18 fluorodeoxyglucose positron-emission tomography/computed tomography (FDG PET/CT) with the parameters of metabolic syndrome (MetS) and different MetS/obesity types were investigated. 245 subjects underwent FDG PET/CT scan for health check-ups were investigated retrospectively. Associations of BP (BP SUV: SUVmax, SUVmean), visceral (VAT SUV), and subcutaneous adipose tissue (SAT SUV) activity with parameters of MetS, body mass index (BMI), and lipid profiles were analyzed. MetS/obesity types were subdivided into metabolically healthy obese (MHO) and metabolically unhealthy obese (MUO). BP SUV was higher in subjects with MetS (t-test, P < 0.005), and was associated with MetS from multivariable binary logistic regression (OR 5.232 P = 0.010). BP SUV was statistically higher in MUO than in MHO (P < 0.05) along with blood pressure, triglycerides, and HDL-cholesterol. Multivariable binary logistic regression analysis showed MUO had higher blood pressure and BP SUV, while lower HDL-cholesterol relative to MHO after adjusting for triglycerides.
Towards shifted position-diffuse reflectance imaging of anatomically correctly scaled human microvasculature
Authors: Späth Moritz , Hohmann Martin , Roider Clemens , Lengenfelder Benjamin , Stelzle Florian , Wirtz Stefan , Klämpfl Florian
Published: October 2020

Due to significant advantages, the trend in the field of medical technology is moving towards minimally or even non-invasive examination methods. In this respect, optical methods offer inherent benefits, as does diffuse reflectance imaging (DRI). The present study attempts to prove the suitability of DRI—when implemented alongside a suitable setup and data evaluation algorithm—to derive information from anatomically correctly scaled human capillaries (diameter: $$10\,\upmu \hbox {m}$$

10

μ
m

, length: $$45\,\upmu \hbox {m}$$

45

μ
m

) by conducting extensive Monte–Carlo simulations and by verifying the findings through laboratory experiments. As a result, the method of shifted position-diffuse reflectance imaging (SP-DRI) is established by which average signal modulations of up to 5% could be generated with an illumination wavelength of $$\lambda =424\,\hbox {nm}$$

λ
=
424

nm

and a core diameter of the illumination fiber of $$50\,\upmu \hbox {m}$$

50

μ
m

. No reference image is needed for this technique. The present study reveals that the diffuse reflectance data in combination with the SP-DRI normalization are suitable to localize human capillaries within turbid media.
Cir-ITCH inhibits gastric cancer migration, invasion and proliferation by regulating the Wnt/β-catenin pathway
Authors: Peng Yang , Wang Hong Hong
Published: October 2020

Circular RNAs (circRNAs) are differentially expressed in various tumours, but the expression and regulatory mechanisms of circular RNA ITCH (cir-ITCH) in gastric cancer remain unclear. For this reason, in the present study, we assessed the expression of cir-ITCH and the associated regulatory mechanism of cir-ITCH in gastric cancer. Through RTq-PCR assays, we observed that cir-ITCH expression was attenuated in gastric cancer cell lines and tissues, with cir-ITCH expression in gastric cancer tissues with lymph node metastasis being considerably lower than that observed in gastric cancer tissues without lymph node metastasis. In addition, we demonstrated that cir-ITCH or linear ITCH may be a useful marker for gastric cancer prognosis by Kaplan–Meier survival analysis. We also showed that cir-ITCH overexpression could increase linear ITCH expression through miR-17 via RNA immunoprecipitation (RIP) and luciferase reporter assays. Moreover, in vivo and in vitro experimental results showed that cir-ITCH can act as a tumour suppressor to prevent gastric cancer tumourgenesis by sponging miR-17. The Wnt/β-catenin pathway plays a crucial role during the carcinogenesis of cancers, and we observed that cir-ITCH could negatively regulate Wnt/β-catenin signalling, which could be restored by miR-17. In summary, cir-ITCH was shown to prevent gastric cancer tumourgenesis through the Wnt/β-catenin signalling pathway by sequestering miR-17.
KRAS K104 modification affects the KRASG12D-GEF interaction and mediates cell growth and motility
Authors: Chen Chih-Chieh , Hsu Chia-Yi , Lin Hsiao-Yun , Zeng Hong-Qi , Cheng Kuang-Hung , Wu Chia-Wei , Tsai Eing-Mei , Hsieh Tsung-Hua
Published: October 2020

Mutant RAS genes play an important role in regulating tumors through lysine residue 104 to impair GEF-induced nucleotide exchange, but the regulatory role of KRAS K104 modification on the KRASG12D mutant remains unclear. Therefore, we simulated the acetylation site on the KRASG12D three-dimensional protein structure, including KRASG12D, KRASG12D/K104A and KRASG12D/K104Q, and determined their trajectories and binding free energy with GEF. KRASG12D/K104Q induced structural changes in the α2- and α3-helices, promoted KRAS instability and hampered GEF binding (ΔΔG = 6.14 kJ/mol). We found decreased binding to the Raf1 RBD by KRASG12D/K104Q and reduced cell growth, invasion and migration. Based on whole-genome cDNA microarray analysis, KRASG12D/K104Q decreased expression of NPIPA2, DUSP1 and IL6 in lung and ovarian cancer cells. This study reports computational and experimental analyses of Lys104 of KRASG12D and GEF, and the findings provide a target for exploration for future treatment.
Genome targeting by hybrid Flp-TAL recombinases
Authors: Voziyanova Eugenia , Li Feng , Shah Riddhi , Voziyanov Yuri
Published: October 2020

Genome engineering is a rapidly evolving field that benefits from the availability of different tools that can be used to perform genome manipulation tasks. We describe here the development of the Flp-TAL recombinases that can target genomic FRT-like sequences in their native chromosomal locations. Flp-TAL recombinases are hybrid enzymes that are composed of two functional modules: a variant of site-specific tyrosine recombinase Flp, which can have either narrow or broad target specificity, and the DNA-binding domain of the transcription activator-like effector, TAL. In Flp-TAL, the TAL module is responsible for delivering and stabilizing the Flp module onto the desired genomic FRT-like sequence where the Flp module mediates recombination. We demonstrate the functionality of the Flp-TAL recombinases by performing integration and deletion experiments in human HEK-293 cells. In the integration experiments we targeted a vector to three genomic FRT-like sequences located in the β-globin locus. In the deletion experiments we excised ~ 15 kilobases of DNA that contained a fragment of the integrated vector sequence and the neighboring genome sequence. On average, the efficiency of the integration and deletion reactions was about 0.1% and 20%, respectively.
Identification of epigenetic variation associated with synchronous pod maturity in mungbean (Vigna radiata L.)
Authors: Ha Jungmin , Kwon Hakyung , Cho Kang-Heum , Yoon Min Young , Kim Moon Young , Lee Suk-Ha
Published: October 2020

Cytosine methylation in genomic DNA affects gene expression, potentially causing phenotypic variation. Mungbean, an agronomically and nutritionally important legume species, is characterized by nonsynchronous pod maturity, resulting in multiple harvest which costs extra time and labor. To elucidate the epigenetic influences on synchronous pod maturity (SPM) in mungbean, we determined the genome-wide DNA methylation profiles of eight mungbean recombinant inbred lines (RILs) and their parental genotypes, and compared DNA methylation profiles between high SPM and low SPM RILs, thus revealing differentially methylated regions (DMRs). A total of 3, 18, and 28 pure DMRs, defined as regions showing no significant correlation between nucleotide sequence variation and methylation level, were identified in CpG, CHG, and CHH contexts, respectively. These DMRs were proximal to 20 genes. Among the 544 single nucleotide polymorphisms identified near the 20 genes, only one caused critical change in gene expression by early termination. Analysis of these genome-wide DNA methylation profiles suggests that epigenetic changes can influence the expression of proximal genes, regardless of nucleotide sequence variation, and that SPM is mediated through gibberellin-mediated hormone signaling pathways. These results provide insights into how epialleles contribute to phenotypic variation and improve SPM in mungbean cultivars.