bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nurture might be nature: cautionary tales and proposed solutions
Authors: Hart Sara A. , Little Callie , van Bergen Elsje 
Published: January 2021

AbstractAcross a wide range of studies, researchers often conclude that the home environment and children’s outcomes are causally linked. In contrast, behavioral genetic studies show that parents influence their children by providing them with both environment and genes, meaning the environment that parents provide should not be considered in the absence of genetic influences, because that can lead to erroneous conclusions on causation. This article seeks to provide behavioral scientists with a synopsis of numerous methods to estimate the direct effect of the environment, controlling for the potential of genetic confounding. Ideally, using genetically sensitive designs can fully disentangle this genetic confound, but these require specialized samples. In the near future, researchers will likely have access to measured DNA variants (summarized in a polygenic scores), which could serve as a partial genetic control, but that is currently not an option that is ideal or widely available. We also propose a work around for when genetically sensitive data are not readily available: the Familial Control Method. In this method, one measures the same trait in the parents as the child, and the parents’ trait is then used as a covariate (e.g., a genetic proxy). When these options are all not possible, we plead with our colleagues to clearly mention genetic confound as a limitation, and to be cautious with any environmental causal statements which could lead to unnecessary parent blaming.
Suppression of mucosal Th17 memory responses by acellular pertussis vaccines enhances nasal Bordetella pertussis carriage
Authors: Dubois Violaine , Chatagnon Jonathan , Thiriard Anaïs , Bauderlique-Le Roy Hélène , Debrie Anne-Sophie , Coutte Loïc , Locht Camille 
Published: January 2021

AbstractPertussis has made a spectacular rebound in countries that have switched from whole-cell (wPV) to acellular pertussis vaccines (aPV). Here, we show that, unlike wPV, aPV, while protective against lung colonization byBordetella pertussis(Bp), did not protect BALB/c mice from nasal colonization, but instead substantially prolonged nasal carriage. aPV prevented the natural induction of nasal interleukin-17 (IL-17)-producing and interferon-γ (IFN-γ)-producing CD103+CD44+CD69+CD4+-resident memory T (TRM) cells. IL-17-deficient, but not IFN-γ-deficient, mice failed to clear nasal Bp, indicating a key role of IL-17+TRMcells in the control of nasal infection. These cells appeared essential for neutrophil recruitment, crucial for clearance of Bp tightly bound to the nasal epithelium. Transfer of IL-17+TRMcells from Bp-infected mice to IL-17-deficient mice resulted in neutrophil recruitment and protection against nasal colonization. Thus, aPV may have augmented the Bp reservoir by inhibiting natural TRMcell induction and neutrophil recruitment, thereby contributing to the pertussis resurgence.
Deregulation of extracellular matrix modeling with molecular prognostic markers revealed by transcriptome sequencing and validations in Oral Tongue squamous cell carcinoma
Authors: Thangaraj Soundara Viveka , Shyamsundar Vidyarani , Krishnamurthy Arvind , Ramshankar Vijayalakshmi 
Published: January 2021

AbstractOral Tongue Squamous Cell Carcinoma (OTSCC), a distinct sub-group of head and neck cancers, is characteristically aggressive in nature with a higher incidence of recurrence and metastasis. Recent advances in therapeutics have not improved patient survival. The phenomenon of occult node metastasis, even among the purportedly good prognosis group of early-stage and node-negative tongue tumors, leads to a high incidence of locoregional failure in OTSCC which needs to be addressed. In the current study, transcriptome analysis of OTSCC patients identified the key genes and deregulated pathways. A panel of 26 marker genes was shortlisted and validated using real-time PCR in a prospective cohort of 100 patients. The gene expression was correlated with clinicopathological features including occult node metastasis, survival, and therapeutic outcome. The up-regulation of a panel of 6 genes namely, matrix metalloproteinase 9 (MMP9), Laminin subunit Gamma 2 (LAMC2), Desmoglein 2 (DSG2), Plasminogen Activator Urokinase (PLAU), Forkhead Box M1 (FOXM1), and Myosin 1B (MYO1B) was associated with failure of treatment in the early stage (T1, T2). Up-regulation of Tenacin C (TNC) and Podoplanin (PDPN) was significantly correlated with occult node positivity. Immunohistochemical analysis of LAMC2, MMP9, and E-Cadherin (ECAD) confirmed these markers to be indicators of poor prognosis. We propose this panel of valuable prognostic markers can be clinically useful to identify poor prognosis and occult node metastasis in OTSCC patients.
Spatiotemporal analysis of soluble aggregates and autophagy markers in the R6/2 mouse model
Authors: Kumar M. J. Vijay , Shah Devanshi , Giridharan Mridhula , Yadav Niraj , Manjithaya Ravi , Clement James P. 
Published: January 2021

AbstractMaintenance of cellular proteostasis is vital for post-mitotic cells like neurons to sustain normal physiological function and homeostasis, defects in which are established hallmarks of several age-related conditions like AD, PD, HD, and ALS. The Spatio-temporal accumulation of aggregated proteins in the form of inclusion bodies/plaques is one of the major characteristics of many neurodegenerative diseases, including Huntington’s disease (HD). Toxic accumulation of HUNTINGTIN (HTT) aggregates in neurons bring about the aberrant phenotypes of HD, including severe motor dysfunction, dementia, and cognitive impairment at the organismal level, in an age-dependent manner. In several cellular and animal models, aggrephagy induction has been shown to clear aggregate-prone proteins like HTT and ameliorate disease pathology by conferring neuroprotection. In this study, we used the mouse model of HD, R6/2, to understand the pathogenicity of mHTT aggregates, primarily focusing on autophagy dysfunction. We report that basal autophagy is not altered in R6/2 mice, whilst being functional at a steady-state level in neurons. Moreover, we tested the efficacy of a known autophagy modulator, Nilotinib (Tasigna™), presently in clinical trials for PD, and HD, in curbing mHTT aggregate growth and their potential clearance, which was ineffective in both inducing autophagy and rescuing the pathological phenotypes in R6/2 mice.
An interactive holographic projection system that uses a hand-drawn interface with a consumer CPU
Authors: Nishitsuji Takashi , Kakue Takashi , Blinder David , Shimobaba Tomoyoshi , Ito Tomoyoshi 
Published: January 2021

AbstractHolography is a promising technology for photo-realistic three-dimensional (3D) displays because of its ability to replay the light reflected from an object using a spatial light modulator (SLM). However, the enormous computational requirements for calculating computer-generated holograms (CGHs)—which are displayed on an SLM as a diffraction pattern—are a significant problem for practical uses (e.g., for interactive 3D displays for remote navigation systems). Here, we demonstrate an interactive 3D display system using electro-holography that can operate with a consumer’s CPU. The proposed system integrates an efficient and fast CGH computation algorithm for line-drawn 3D objects with inter-frame differencing, so that the trajectory of a line-drawn object that is handwritten on a drawing tablet can be played back interactively using only the CPU. In this system, we used an SLM with 1,920 $$\times $$
×
1,080 pixels and a pixel pitch of 8 μm × 8 μm, a drawing tablet as an interface, and an Intel Core i9–9900K 3.60 GHz CPU. Numerical and optical experiments using a dataset of handwritten inputs show that the proposed system is capable of reproducing handwritten 3D images in real time with sufficient interactivity and image quality.
Gene diversity explains variation in biological features of insect killing fungus, Beauveria bassiana
Authors: Gasmi Laila , Baek Sehyeon , Kim Jong Cheol , Kim Sihyeon , Lee Mi Rong , Park So Eun , Shin Tae Young , Lee Se Jin , Parker Bruce L. , Kim Jae Su 
Published: January 2021

AbstractBeauveria bassianais a species complex whose isolates show considerable natural genetic variability. However, little is known about how this genetic diversity affects the fungus performance. Herein, we characterized the diversity of genes involved in various mechanisms of the infective cycle of 42 isolates that have different growth rates, thermotolerance and virulence. The analysed genes showed general genetic diversity measured as non-synonymous changes (NSC) and copy number variation (CNV), with most of them being subjected to positive episodic diversifying selection. Correlation analyses between NSC or CNV and the isolate virulence, thermotolerance and growth rate revealed that various genes shaped the biological features of the fungus. Lectin-like, mucin signalling, Biotrophy associated and chitinase genes NSCs correlated with the three biological features ofB. bassiana. In addition, other genes (i.e.DNA photolyaseandcyclophilin B) that had relatively conserved sequences, had variable CNs across the isolates which were correlated with the variability of either virulence or thermotolerance ofB. bassianaisolates. The data obtained is important for a better understanding of population structure, ecological and potential impact when isolates are used as mycoinsecticides and can justify industrialization of new isolates.
A 3D-CNN model with CT-based parametric response mapping for classifying COPD subjects
Authors: Ho Thao Thi , Kim Taewoo , Kim Woo Jin , Lee Chang Hyun , Chae Kum Ju , Bak So Hyeon , Kwon Sung Ok , Jin Gong Yong , Park Eun-Kee , Choi Sanghun 
Published: January 2021

AbstractChronic obstructive pulmonary disease (COPD) is a respiratory disorder involving abnormalities of lung parenchymal morphology with different severities. COPD is assessed by pulmonary-function tests and computed tomography-based approaches. We introduce a new classification method for COPD grouping based on deep learning and a parametric-response mapping (PRM) method. We extracted parenchymal functional variables of functional small airway disease percentage (fSAD%) and emphysema percentage (Emph%) with an image registration technique, being provided as input parameters of 3D convolutional neural network (CNN). The integrated 3D-CNN and PRM (3D-cPRM) achieved a classification accuracy of 89.3% and a sensitivity of 88.3% in five-fold cross-validation. The prediction accuracy of the proposed 3D-cPRM exceeded those of the 2D model and traditional 3D CNNs with the same neural network, and was comparable to that of 2D pretrained PRM models. We then applied a gradient-weighted class activation mapping (Grad-CAM) that highlights the key features in the CNN learning process. Most of the class-discriminative regions appeared in the upper and middle lobes of the lung, consistent with the regions of elevated fSAD% and Emph% in COPD subjects. The 3D-cPRM successfully represented the parenchymal abnormalities in COPD and matched the CT-based diagnosis of COPD.
Prognostic gene expression signatures of breast cancer are lacking a sensible biological meaning
Authors: Manjang Kalifa , Tripathi Shailesh , Yli-Harja Olli , Dehmer Matthias , Glazko Galina , Emmert-Streib Frank 
Published: January 2021

AbstractThe identification of prognostic biomarkers for predicting cancer progression is an important problem for two reasons. First, such biomarkers find practical application in a clinical context for the treatment of patients. Second, interrogation of the biomarkers themselves is assumed to lead to novel insights of disease mechanisms and the underlying molecular processes that cause the pathological behavior. For breast cancer, many signatures based on gene expression values have been reported to be associated with overall survival. Consequently, such signatures have been used for suggesting biological explanations of breast cancer and drug mechanisms. In this paper, we demonstrate for a large number of breast cancer signatures that such an implication is not justified. Our approach eliminates systematically all traces of biological meaning of signature genes and shows that among the remaining genes, surrogate gene sets can be formed with indistinguishable prognostic prediction capabilities and opposite biological meaning. Hence, our results demonstrate that none of the studied signatures has a sensible biological interpretation or meaning with respect to disease etiology. Overall, this shows that prognostic signatures are black-box models with sensible predictions of breast cancer outcome but no value for revealing causal connections. Furthermore, we show that the number of such surrogate gene sets is not small but very large.
A heat-melt adhesive-assisted transferable electrode films
Authors: Maruyama Yuki , Nagamine Kuniaki , Iwasa Shigeyuki , Miyabo Atsushi , Tokito Shizuo 
Published: January 2021

AbstractThis report is the first on heat-assisted transferable battery components, enabling manufacturing batteries on non-planer surfaces such as a curved surface and an edge. The transferrable battery components were composed of two layers: a cathode or an anode and a conductive heal-melt adhesive layer on a silicone-based flexible supporting paper. These mechanically-durable, flexible components enabled conformable adhesion even on curved surfaces and substrate edges. As a model battery, the manganese dioxide-zinc system was constructed on a curved surface using transfer techniques and showed a practical capacity of 1.8 mAh cm−2 per unit electrode area. These transferable electrodes allow arbitrary design of batteries according to the power consumption of IoT devices to be fabricated on unreported geometries where has been considered as a dead space.
Direct entry of cell-penetrating peptide can be controlled by maneuvering the membrane curvature
Authors: Sakamoto Kazutami , Morishita Taku , Aburai Kenichi , Ito Daisuke , Imura Tomohiro , Sakai Kenichi , Abe Masahiko , Nakase Ikuhiko , Futaki Shiroh , Sakai Hideki 
Published: January 2021

AbstractA biomembrane's role is to be a barrier for interior cytosol from an exterior environment to execute the cell's normal biological functions. However, a water-soluble peptide called cell-penetrating peptide (CPP) has been known for its ability to directly penetrate through the biomembranes into cells (cytolysis) without perturbating cell viability and expected to be a promising drug delivery vector. Examples of CPP include peptides with multiple arginine units with strong cationic properties, which is the key to cytolysis. Here we show the conclusive evidence to support the mechanism of CPP’s cytolysis and way to control it. The mechanism we proposed is attributed to biomembrane’s physicochemical nature as lamellar liquid crystal (Lα). Cytolysis occurs as the temporal and local dynamic phase transitions from Lα to an undulated lamellar with pores called Mesh1. We have shown this phase transfer of Lα composed of dioleoyl-phosphatidylcholine (DOPC) with water by adding oligo-arginine (Rx) as CPP at the equilibrium. Using giant unilamellar vesicle composed of DOPC as a single cell model, we could control the level of cytolysis of CPP (FITC-R8) by changing the curvature of the membrane through osmotic pressure modulation. The cytolysis of CPP utilizes biomembrane's inherent topological and functional flexibility corresponding to the stimuli.
Valproic acid-exposed astrocytes impair inhibitory synapse formation and function
Authors: Takeda Kotomi , Watanabe Takuya , Oyabu Kohei , Tsukamoto Shuntaro , Oba Yuki , Nakano Takafumi , Kubota Kaori , Katsurabayashi Shutaro , Iwasaki Katsunori 
Published: January 2021

AbstractValproic acid (VPA) is widely prescribed to treat epilepsy. Maternal VPA use is, however, clinically restricted because of the severe risk that VPA may cause neurodevelopmental disorders in offspring, such as autism spectrum disorder. Understanding the negative action of VPA may help to prevent VPA-induced neurodevelopmental disorders. Astrocytes play a vital role in neurodevelopment and synapse function; however, the impact of VPA on astrocyte involvement in neurodevelopment and synapse function has not been examined. In this study, we examined whether exposure of cultured astrocytes to VPA alters neuronal morphology and synapse function of co-cultured neurons. We show that synaptic transmission by inhibitory neurons was small because VPA-exposed astrocytes reduced the number of inhibitory synapses. However, synaptic transmission by excitatory neurons and the number of excitatory synapses were normal with VPA-exposed astrocytes. VPA-exposed astrocytes did not affect the morphology of inhibitory neurons. These data indicate that VPA-exposed astrocytes impair synaptogenesis specifically of inhibitory neurons. Our results indicate that maternal use of VPA would affect not only neurons but also astrocytes and would result in perturbed astrocyte-mediated neurodevelopment.
Laser pulse-electron beam synergy effect on electron self-injection and higher energy gain in laser wakefield accelerators
Authors: Barzegar Sahar , Niknam Ali Reza 
Published: January 2021

AbstractA new scheme for injection and acceleration of electrons in wakefield accelerators is suggested based on the co-action of a laser pulse and an electron beam. This synergy leads to stronger wakefield generation and higher energy gain in the bubble regime. The strong deformation of the whole bubble leads to electron self-injection at lower laser powers and lower plasma densities. To predict the practical ranges of electron beam and laser pulse parameters an interpretive model is proposed. The effects of altering the initial electron beam position on self-trapping of plasma electrons are studied. It is observed that an ultra-short (25 fs), high charge (340 pC), 1 GeV electron bunch is produced by injection of a 280 pC electron beam in the decelerating phase of the 75 TW laser driven wakefield.
Acoustic frequency combs using gas bubble cluster oscillations in liquids: a proof of concept
Authors: Nguyen Bui Quoc Huy , Maksymov Ivan S. , Suslov Sergey A. 
Published: January 2021

AbstractWe propose a new approach to the generation of acoustic frequency combs (AFC)—signals with spectra containing equidistant coherent peaks. AFCs are essential for a number of sensing and measurement applications, where the established technology of optical frequency combs suffers from fundamental physical limitations. Our proof-of-principle experiments demonstrate that nonlinear oscillations of a gas bubble cluster in water insonated by a low-pressure single-frequency ultrasound wave produce signals with spectra consisting of equally spaced peaks originating from the interaction of the driving ultrasound wave with the response of the bubble cluster at its natural frequency. The so-generated AFC posses essential characteristics of optical frequency combs and thus, similar to their optical counterparts, can be used to measure various physical, chemical and biological quantities.
Predominant role of Haemophilus influenzae in the association of conjunctivitis, acute otitis media and acute bacterial paranasal sinusitis in children
Authors: Hu Ya-Li , Lee Ping-Ing , Hsueh Po-Ren , Lu Chun-Yi , Chang Luan-Yin , Huang Li-Min , Chang Tu-Hsuan , Chen Jong-Min 
Published: January 2021

AbstractHaemophilus influenzae is a predominant pathogen for conjunctivitis, acute otitis media and acute bacterial paranasal sinusitis in children. We undertook this study to investigate the possible association among these diseases. Children younger than 18-year-old with a diagnosis of bacterial conjunctivitis plus acute otitis media and/or acute bacterial paranasal sinusitis during 2009–2018 were included. Sampling for bacterial cultures was obtained from the lower palpebral conjunctiva and/or ear discharge with cotton-tipped swabs. A total of 67 children were recruited and the age was 29.5 (± 22.4) months in average. Fifty-seven children had conjunctivitis–otitis media syndrome and eight of them had a concurrent diagnosis of acute paranasal sinusitis. Ten children had conjunctivitis and acute paranasal sinusitis simultaneously. Clusters in household were observed in 50.7% children. Most common isolates were Haemophilus influenzae (70%), Moraxella catarrhalis (18%), and Staphylococcus aureus (8%). Antibiotic resistance rate of H. influenzae was 80% for ampicillin, 18% for amoxicillin–clavulanate, and 11% for the second or third-generation cephalosporins. Apart from well-known conjunctivitis–otitis media syndrome, acute paranasal sinusitis may also be linked to conjunctivitis with a similar pathogenic process. Simultaneous presence of these infections may guide the choice of empiric antibiotics toward H. influenzae.
Neonatal mice resist Plasmodium yoelii infection until exposed to para-aminobenzoic acid containing diet after weaning
Authors: Parra Marcela , Yang Jiyeon , Weitner Megan , Akkoyunlu Mustafa 
Published: January 2021

AbstractWe developed a newborn (NB) mouse Plasmodium yoelii NL infection model to study malaria in early age. Surprisingly, the onset of parasitemia in P. yoelii challenged NB mice was delayed compared to adults and coincided with the weaning date when weanlings switched from maternal milk to normal chow diet. Also, compared to adult mice, parasitemia resolved much later (48 days vs 20 days post challenge) and the peak parasitemia was twice as high in weanlings. Concurrently, weanlings’ germinal center reaction was delayed and diminished compared to adult mice. Maternal milk is deficient in para-aminobenzoic acid (PABA), which is required for de novo folate synthesis by Plasmodium. Suggesting a possible role for the protection afforded by PABA-deficient maternal milk, mice fed with a PABA-deficient diet after the weaning continued to control parasitemia. Despite the reduced parasitemia, these mice developed robust T follicular helper (Tfh) responses and were protected from a second P. yoelii challenge. The NB malaria model provides mechanistic insight into the human infant malaria manifestations where a diet solely based on breast-feeding reduces the incidence of severe malaria in infants. NB mice experiments also support further studies to investigate dietary PABA restriction in the management of severe malaria in infants.
Applying the economic concept of profitability to leaves
Authors: Villar Rafael , Olmo Manuel , Atienza Pedro , Garzón Antonio J. , Wright Ian J. , Poorter Hendrik , Hierro Luis A. 
Published: January 2021

AbstractEconomic principles can be extended to biological organisms as they optimize the use of resources, but their use in biology has been limited. We applied concepts from traditional economics to the main production unit of plants, the leaf. We quantified the profitability (profit/cost of investment) of leaves from seven biomes worldwide and compared those to the profitability of companies. Here we demonstrate for the first time key similarities and differences between leaf and human economics. First, there was a weak, but positive relationship between profitability and size, both for leaves and companies. Second, environment has a strong effect on profitability, with high values in leaves from biomes with short growth periods and, for companies associated with innovation. Third, shorter longevity of productive units was related to higher profitability. In summary, by comparing economic behaviours of plants and humans there is potential to develop new perspectives on plant ecological strategies and plant evolution.