bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acoustoelectric current in graphene nanoribbon due to Landau damping
Authors: Dompreh K. A. , Adu K. W. , Sakyi-Arthur D. , Mensah N. G. , Mensah S. Y. , Twum A. , Amekpewu M. 
Published: September 2021

AbstractWe perform self-consistent analysis of the Boltzmann transport equation for momentum and energy in the hypersound regime i.e., $$ql \gg 1$$

q
l
≫
1

($$q$$
q
is the acoustic wavenumber and l is the mean free path). We investigate the Landau damping of acoustic phonons ($$LDOAP$$

LDOAP

) in graphene nanoribbons, which leads to acoustoelectric current generation. Under a non-quantized field with drift velocity, we observed an acoustic phonon energy quantization that depends on the energy gap, the width, and the sub-index of the material. An effect similar to Cerenkov emission was observed, where the electron absorbed the confined acoustic phonon energy, causing the generation of acoustoelectric current in the graphene nanoribbon. A qualitative analysis of the dependence of the absorption coefficient and the acoustoelectric current on the phonon frequency is in agreement with experimental reports. We observed a shift in the peaks when the energy gap and the drift velocity were varied. Most importantly, a transparency window appears when the absorption coefficient is zero, making graphene nanoribbons a potential candidate for use as an acoustic wave filter with applications in tunable gate-controlled quantum information devices and phonon spectrometers.
First evidence of yawn contagion in a wild monkey species
Authors: Gallo Alessandro , Zanoli Anna , Caselli Marta , Palagi Elisabetta , Norscia Ivan 
Published: September 2021

AbstractYawn contagion occurs when individuals yawn in response to the yawn of others (triggers). This is the first account of yawn contagion in wild geladas (Theropithecus gelada), a monkey species that shows yawn contagion in captivity and is organized in core units (one-male/bachelor groups) forming multilevel associations. In a population of geladas from the Kundi plateau (Ethiopia) we found that the yawning response was highest when geladas could perceive a triggering yawn, which confirms that yawn contagion is present in the wild. Yawn duration, mouth-opening degree and presence/absence of vocalisation (possibly modulating yawn detectability) did not affect the likelihood of contagion. Males and females, known to be both implicated in movement initiation within groups, were similarly powerful as yawn triggers. Instead, group membership and responder sex had a significant role in shaping the phenomenon. Yawn contagion was highest between individuals belonging to different core units and males were most likely to respond to others’ yawns. Because males have a non-negligible role in inter-group coordination, our results suggest that yawn contagion may have a communicative function that goes beyond the basic unit level.
HES and Mox genes are expressed during early mesoderm formation in a mollusk with putative ancestral features
Authors: Sachslehner Attila , Zieger Elisabeth , Calcino Andrew , Wanninger Andreas 
Published: September 2021

AbstractThe mesoderm is considered the youngest of the three germ layers. Although its morphogenesis has been studied in some metazoans, the molecular components underlying this process remain obscure for numerous phyla including the highly diverse Mollusca. Here, expression of Hairy and enhancer of split (HES), Mox, and myosin heavy chain (MHC) was investigated in Acanthochitona fascicularis, a representative of Polyplacophora with putative ancestral molluscan features. While AfaMHC is expressed throughout myogenesis, AfaMox1 is only expressed during early stages of mesodermal band formation and in the ventrolateral muscle, an autapomorphy of the polyplacophoran trochophore. Comparing our findings to previously published data across Metazoa reveals Mox expression in the mesoderm in numerous bilaterians including gastropods, polychaetes, and brachiopods. It is also involved in myogenesis in molluscs, annelids, tunicates, and craniates, suggesting a dual role of Mox in mesoderm and muscle formation in the last common bilaterian ancestor. AfaHESC2 is expressed in the ectoderm of the polyplacophoran gastrula and later in the mesodermal bands and in putative neural tissue, whereas AfaHESC7 is expressed in the trochoblasts of the gastrula and during foregut formation. This confirms the high developmental variability of HES gene expression and demonstrates that Mox and HES genes are pleiotropic.
Label-free microfluidic enrichment of cancer cells from non-cancer cells in ascites
Authors: Stone Nicholas E. , Raj Abhishek , Young Katherine M. , DeLuca Adam P. , Chrit Fatima Ezahra , Tucker Budd A. , Alexeev Alexander , McDonald John , Benigno Benedict B. , Sulchek Todd 
Published: September 2021

AbstractThe isolation of a patient's metastatic cancer cells is the first, enabling step toward treatment of that patient using modern personalized medicine techniques. Whereas traditional standard-of-care approaches select treatments for cancer patients based on the histological classification of cancerous tissue at the time of diagnosis, personalized medicine techniques leverage molecular and functional analysis of a patient's own cancer cells to select treatments with the highest likelihood of being effective. Unfortunately, the pure populations of cancer cells required for these analyses can be difficult to acquire, given that metastatic cancer cells typically reside in fluid containing many different cell populations. Detection and analyses of cancer cells therefore require separation from these contaminating cells. Conventional cell sorting approaches such as Fluorescence Activated Cell Sorting or Magnetic Activated Cell Sorting rely on the presence of distinct surface markers on cells of interest which may not be known nor exist for cancer applications. In this work, we present a microfluidic platform capable of label-free enrichment of tumor cells from the ascites fluid of ovarian cancer patients. This approach sorts cells based on differences in biomechanical properties, and therefore does not require any labeling or other pre-sort interference with the cells. The method is also useful in the cases when specific surface markers do not exist for cells of interest. In model ovarian cancer cell lines, the method was used to separate invasive subtypes from less invasive subtypes with an enrichment of ~ sixfold. In ascites specimens from ovarian cancer patients, we found the enrichment protocol resulted in an improved purity of P53 mutant cells indicative of the presence of ovarian cancer cells. We believe that this technology could enable the application of personalized medicine based on analysis of liquid biopsy patient specimens, such as ascites from ovarian cancer patients, for quick evaluation of metastatic disease progression and determination of patient-specific treatment.
Dynamic prokaryotic communities in the dark western Mediterranean Sea
Authors: Mena Catalina , Balbín Rosa , Reglero Patricia , Martín Melissa , Santiago Rocío , Sintes Eva 
Published: September 2021

AbstractDark ocean microbial dynamics are fundamental to understand ecosystem metabolism and ocean biogeochemical processes. Yet, the ecological response of deep ocean communities to environmental perturbations remains largely unknown. Temporal and spatial dynamics of the meso- and bathypelagic prokaryotic communities were assessed throughout a 2-year seasonal sampling across the western Mediterranean Sea. A common pattern of prokaryotic communities’ depth stratification was observed across the different regions and throughout the seasons. However, sporadic and drastic alterations of the community composition and diversity occurred either at specific water masses or throughout the aphotic zone and at a basin scale. Environmental changes resulted in a major increase in the abundance of rare or low abundant phylotypes and a profound change of the community composition. Our study evidences the temporal dynamism of dark ocean prokaryotic communities, exhibiting long periods of stability but also drastic changes, with implications in community metabolism and carbon fluxes. Taken together, the results highlight the importance of monitoring the temporal patterns of dark ocean prokaryotic communities.
Effects of radiation damage and inelastic scattering on single-particle imaging of hydrated proteins with an X-ray Free-Electron Laser
Authors: E Juncheng , Stransky Michal , Jurek Zoltan , Fortmann-Grote Carsten , Juha Libor , Santra Robin , Ziaja Beata , Mancuso Adrian P. 
Published: September 2021

AbstractWe present a computational case study of X-ray single-particle imaging of hydrated proteins on an example of 2-Nitrogenase–Iron protein covered with water layers of various thickness, using a start-to-end simulation platform and experimental parameters of the SPB/SFX instrument at the European X-ray Free-Electron Laser facility. The simulations identify an optimal thickness of the water layer at which the effective resolution for imaging the hydrated sample becomes significantly higher than for the non-hydrated sample. This effect is lost when the water layer becomes too thick. Even though the detailed results presented pertain to the specific sample studied, the trends which we identify should also hold in a general case. We expect these findings will guide future single-particle imaging experiments using hydrated proteins.
Glycosylation reduces the glycan-independent immunomodulatory effect of recombinant Orysata lectin in Drosophila S2 cells
Authors: Chen Pengyu , De Schutter Kristof , Serna Sonia , Chen Simin , Yang Qun , Reichardt Niels-Christian , Van Damme Els J. M. , Smagghe Guy 
Published: September 2021

AbstractSeveral plant lectins, or carbohydrate-binding proteins, interact with glycan moieties on the surface of immune cells, thereby influencing the immune response of these cells. Orysata, a mannose-binding lectin from rice, has been reported to exert immunomodulatory activities on insect cells. While the natural lectin is non-glycosylated, recombinant Orysata produced in the yeast Pichia pastoris (YOry) is modified with a hyper-mannosylated N-glycan. Since it is unclear whether this glycosylation can affect the YOry activity, non-glycosylated rOrysata was produced in Escherichia coli (BOry). In a comparative analysis, both recombinant Orysata proteins were tested for their carbohydrate specificity on a glycan array, followed by the investigation of the carbohydrate-dependent agglutination of red blood cells (RBCs) and the carbohydrate-independent immune responses in Drosophila melanogaster S2 cells. Although YOry and BOry showed a similar carbohydrate-binding profiles, lower concentration of BOry were sufficient for the agglutination of RBCs and BOry induced stronger immune responses in S2 cells. The data are discussed in relation to different hypotheses explaining the weaker responses of glycosylated YOry. In conclusion, these observations contribute to the understanding how post-translational modification can affect protein function, and provide guidance in the selection of the proper expression system for the recombinant production of lectins.
A robust model of Stimulus-Specific Adaptation validated on neuromorphic hardware
Authors: Vanattou-Saïfoudine Natacha , Han Chao , Krause Renate , Vasilaki Eleni , von der Behrens Wolfger , Indiveri Giacomo 
Published: September 2021

AbstractStimulus-Specific Adaptation (SSA) to repetitive stimulation is a phenomenon that has been observed across many different species and in several brain sensory areas. It has been proposed as a computational mechanism, responsible for separating behaviorally relevant information from the continuous stream of sensory information. Although SSA can be induced and measured reliably in a wide variety of conditions, the network details and intracellular mechanisms giving rise to SSA still remain unclear. Recent computational studies proposed that SSA could be associated with a fast and synchronous neuronal firing phenomenon called Population Spikes (PS). Here, we test this hypothesis using a mean-field rate model and corroborate it using a neuromorphic hardware. As the neuromorphic circuits used in this study operate in real-time with biologically realistic time constants, they can reproduce the same dynamics observed in biological systems, together with the exploration of different connectivity schemes, with complete control of the system parameter settings. Besides, the hardware permits the iteration of multiple experiments over many trials, for extended amounts of time and without losing the networks and individual neural processes being studied. Following this “neuromorphic engineering” approach, we therefore study the PS hypothesis in a biophysically inspired recurrent networks of spiking neurons and evaluate the role of different linear and non-linear dynamic computational primitives such as spike-frequency adaptation or short-term depression (STD). We compare both the theoretical mean-field model of SSA and PS to previously obtained experimental results in the area of novelty detection and observe its behavior on its neuromorphic physical equivalent model. We show how the approach proposed can be extended to other computational neuroscience modelling efforts for understanding high-level phenomena in mechanistic models.
Simultaneous in vivo imaging with PET and SPECT tracers using a Compton-PET hybrid camera
Authors: Uenomachi Mizuki , Takahashi Miwako , Shimazoe Kenji , Takahashi Hiroyuki , Kamada Kei , Orita Tadashi , Ogane Kenichiro , Tsuji Atsushi B. 
Published: September 2021

AbstractPositron-emission tomography (PET) and single-photon-emission computed tomography (SPECT) are well-established nuclear-medicine imaging methods used in modern medical diagnoses. Combining PET with 18F-fluorodeoxyglucose (FDG) and SPECT with an 111In-labelled ligand provides clinicians with information about the aggressiveness and specific types of tumors. However, it is difficult to integrate a SPECT system with a PET system because SPECT requires a collimator. Herein, we describe a novel method that provides simultaneous imaging with PET and SPECT nuclides by combining PET imaging and Compton imaging. The latter is an imaging method that utilizes Compton scattering to visualize gamma rays over a wide range of energies without requiring a collimator. Using Compton imaging with SPECT nuclides, instead of the conventional SPECT imaging method, enables PET imaging and Compton imaging to be performed with one system. In this research, we have demonstrated simultaneous in vivo imaging of a tumor-bearing mouse injected with 18F-FDG and an 111In-antibody by using a prototype Compton-PET hybrid camera. We have succeeded in visualizing accumulations of 18F-FDG and 111In-antibody by performing PET imaging and Compton imaging simultaneously. As simultaneous imaging utilizes the same coordinate axes, it is expected to improve the accuracy of diagnoses.
Competitive ELISA for a serologic test to detect dengue serotype-specific anti-NS1 IgGs using high-affinity UB-DNA aptamers
Authors: Matsunaga Ken-ichiro , Kimoto Michiko , Lim Vanessa Weixun , Thein Tun-Linn , Vasoo Shawn , Leo Yee-Sin , Sun William , Hirao Ichiro 
Published: September 2021

AbstractSerologic tests to detect specific IgGs to antigens related to viral infections are urgently needed for diagnostics and therapeutics. We present a diagnostic method for serotype-specific IgG identification of dengue infection by a competitive enzyme-linked immunosorbent assay (ELISA), using high-affinity unnatural-base-containing DNA (UB-DNA) aptamers that recognize the four categorized serotypes. Using UB-DNA aptamers specific to each serotype of dengue NS1 proteins (DEN-NS1), we developed our aptamer–antibody sandwich ELISA for dengue diagnostics. Furthermore, IgGs highly specific to DEN-NS1 inhibited the serotype-specific NS1 detection, inspiring us to develop the competitive ELISA format for dengue serotype-specific IgG detection. Blood samples from Singaporean patients with primary or secondary dengue infections confirmed the highly specific IgG detection of this format, and the IgG production initially reflected the serotype of the past infection, rather than the recent infection. Using this dengue competitive ELISA format, cross-reactivity tests of 21 plasma samples from Singaporean Zika virus-infected patients revealed two distinct patterns: 8 lacked cross-reactivity, and 13 were positive with unique dengue serotype specificities, indicating previous dengue infection. This antigen-detection ELISA and antibody-detection competitive ELISA combination using the UB-DNA aptamers identifies both past and current viral infections and will facilitate specific medical care and vaccine development for infectious diseases.
Photodynamic therapy outcome modelling for patients with spinal metastases: a simulation-based study
Authors: Yassine Abdul-Amir , Lo William C. Y. , Saeidi Tina , Ferguson Dallis , Whyne Cari M. , Akens Margarete K. , Betz Vaughn , Lilge Lothar 
Published: September 2021

AbstractSpinal metastases often occur in the advanced stages of breast, lung or prostate cancer, resulting in a significant impact on the patient’s quality of life. Current treatment modalities for spinal metastases include both systemic and localized treatments that aim to decrease pain, improve mobility and structural stability, and control tumour growth. With the development of non-toxic photosensitizer drugs, photodynamic therapy (PDT) has shown promise as a minimally invasive non-thermal alternative in oncology, including for spinal metastases. To apply PDT to spinal metastases, predictive algorithms that optimize tumour treatment and minimize the risk of spinal cord damage are needed to assess the feasibility of the treatment and encourage a broad acceptance of PDT in clinical trials. This work presents a framework for PDT modelling and planning, and simulates the feasibility of using a BPD-MA mediated PDT to treat bone metastases at two different wavelengths (690 nm and 565 nm). An open-source software for PDT planning, PDT-SPACE, is used to evaluate different configurations of light diffusers (cut-end and cylindrical) fibres with optimized power allocation in order to minimize the damage to spinal cord or maximize tumour destruction. The work is simulated on three CT images of metastatically involved vertebrae acquired from three patients with spinal metastases secondary to colorectal or lung cancer. Simulation results show that PDT at a 565 nm wavelength has the ability to treat 90% of the metastatic lesion with less than 17% damage to the spinal cord. However, the energy required, and hence treatment time, to achieve this outcome with the 565 nm is infeasible. The energy required and treatment time for the longer wavelength of 690 nm is feasible ($${\sim }\,40$$

∼

40

min), but treatment aimed at 90% of the metastatic lesion would severely damage the proximal spinal cord. PDT-SPACE provides a simulation platform that can be used to optimize PDT delivery in the metastatic spine. While this work serves as a prospective methodology to analyze the feasibility of PDT for tumour ablation in the spine, preclinical studies in an animal model are ongoing to elucidate the spinal cord damage extent as a function of PDT dose, and the resulting short and long term functional impairments. These will be required before there can be any consideration of clinical trials.
Dynapenia is highly prevalent in older patients with advanced idiopathic pulmonary fibrosis
Authors: Bocchino Marialuisa , Alicante Paola , Capitelli Ludovica , Stanziola Anna Agnese , Gallotti Lorena , Di Gregorio Ada , Rea Gaetano , Sanduzzi Zamparelli Alessandro , Scalfi Luca 
Published: September 2021

AbstractBody composition and muscle strength are emerging aspects in idiopathic pulmonary fibrosis (IPF) clinical assessment. We aimed to study the relationships of handgrip strength (HGS) with anthropometric variables, body composition, and disease staging, and to evaluate the prevalence of dynapenia in 102 clinically stable IPF patients (70 M; mean age: 69.4 years). Fat-free mass (FFM), skeletal muscle (SM) were estimated with bioimpedance analysis. HGS was measured with a digital handle dynamometer for both dominant and non-dominant body sides. Dynapenia was identified according to six recognized criteria sets. Mean body mass index (BMI) was 28.2 ± 4.7 kg/m2, with a prevalence of overweight (BMI > 25 and < 30 kg/m2) and obesity (BMI ≥ 30 kg/m2) of 35% and 37%, respectively. FFM and SM were greater in males, whereas percentage body fat was higher in women. HGS was higher and declined with age slightly more rapidly in men, showing a stronger correlation with FFM and SM. Dynapenia prevalence ranged from 20.6 to 56.9%, depending on the criteria used, and was more frequent in older patients and advanced disease. Dynapenia is highly prevalent in IPF. HGS is a promising proxy marker of muscle function to be used in clinical evaluation and follow-up programs.
Multibiomarker responses to polycyclic aromatic hydrocarbons and microplastics in thumbprint emperor Lethrinus harak from a South Pacific locally managed marine area
Authors: Varea Rufino , Paris Andrew , Ferreira Marta , Piovano Susanna 
Published: September 2021

AbstractTo determine the baseline threat of microplastics and polycyclic aromatic hydrocarbons (PAHs) in an important seafood fish from Vueti Navakavu locally managed marine area, a multibiomarker risk assessment was conducted on the thumbprint emperor fish Lethrinus harak. Condition factor, a measure of relative general health condition of fish, was significantly lower in samples from the wet season compared to the dry season but no significant differences were observed for hepatosomatic index, a measure of relative stored energy/nutrition, between seasonal groups. PAHs levels of four metabolites in emperor fish from Fiji waters are reported here for the first time; seasonal groups showed no significant differences, but all samples presented levels of biliary PAHs. Each specimen also contained at least one microplastic in its gastrointestinal system; fibres were the predominant form-type and ingestion levels showed that more than 80% of fragment sizes were below 1.0 mm. Biochemical responses were observed for ethoxyresorufin-O-deethylase and glutathioneS-transferase biotransformation activity, oxidative stress (glutathione peroxidase and glutathione reductase activity; lipid peroxidation) and genotoxicity (micronuclei assay). Though there were no statistically significant differences found, there were biological significances that were important to note; relatively low levels of pollutant exposure and low levels of biochemical responses showed enzymes response in thumbprint emperor were as expected to their roles in the body. In this multibiomarker approach, the observation of pollutants presence and histopathological injuries are considered biologically relevant from a toxicological perspective and serve as a baseline for future pollution studies in seafood fishes in Fiji, with site differences and the inclusion of fish species comparison. We recommend adopting a suite of biomarkers in future regional biomonitoring studies to develop holistic baseline information for other marine settings in Fiji and other Pacific Island countries.