bluuebunny/crossref_metadata_2025 huggingface dataset:
An empirical meta-analysis of the life sciences linked open data on the web
Authors: Kamdar Maulik R. , Musen Mark A.
Published: January 2021

While the biomedical community has published several “open data” sources in the last decade, most researchers still endure severe logistical and technical challenges to discover, query, and integrate heterogeneous data and knowledge from multiple sources. To tackle these challenges, the community has experimented with Semantic Web and linked data technologies to create the Life Sciences Linked Open Data (LSLOD) cloud. In this paper, we extract schemas from more than 80 biomedical linked open data sources into an LSLOD schema graph and conduct an empirical meta-analysis to evaluate the extent of semantic heterogeneity across the LSLOD cloud. We observe that several LSLOD sources exist as stand-alone data sources that are not inter-linked with other sources, use unpublished schemas with minimal reuse or mappings, and have elements that are not useful for data integration from a biomedical perspective. We envision that the LSLOD schema graph and the findings from this research will aid researchers who wish to query and integrate data and knowledge from multiple biomedical sources simultaneously on the Web.
Integrative multiomics analysis of Premolis semirufa caterpillar venom in the search for molecules leading to a joint disease
Authors: Pidde Giselle , Nishiyama Milton Y. , de Oliveira Ursula Castro , Villas-Boas Isadora M. , Paes-Leme Adriana F. , Junqueira-de-Azevedo Inácio L. , Marques-Porto Rafael , Squaiella-Baptistão Carla C. , Tambourgi Denise V.
Published: January 2021

The joint disease called pararamosis is an occupational disease caused by accidental contact with bristles of the caterpillar Premolis semirufa. The chronic inflammatory process narrows the joint space and causes alterations in bone structure and cartilage degeneration, leading to joint stiffness. Aiming to determine the bristle components that could be responsible for this peculiar envenomation, in this work we have examined the toxin composition of the caterpillar bristles extract and compared it with the differentially expressed genes (DEGs) in synovial biopsies of patients affected with rheumatoid arthritis (RA) and osteoarthritis (OA). Among the proteins identified, 129 presented an average of 63% homology with human proteins and shared important conserved domains. Among the human homologous proteins, we identified seven DEGs upregulated in synovial biopsies from RA or OA patients using meta-analysis. This approach allowed us to suggest possible toxins from the pararama bristles that could be responsible for starting the joint disease observed in pararamosis. Moreover, the study of pararamosis, in turn, may lead to the discovery of specific pharmacological targets related to the early stages of articular diseases.
Alleviatory effects of Silicon on the morphology, physiology, and antioxidative mechanisms of wheat (Triticum aestivum L.) roots under cadmium stress in acidic nutrient solutions
Authors: ur Rahman Shafeeq , Xuebin Qi , Zhao Zhijuan , Du Zhenjie , Imtiaz Muhammad , Mehmood Faisal , Hongfei Lu , Hussain Babar , Ashraf Muhammad Nadeem
Published: January 2021

Silicon (Si), as a quasi-essential element, has a vital role in alleviating the damaging effects of various environmental stresses on plants. Cadmium (Cd) stress is severe abiotic stress, especially in acidic ecological conditions, and Si can demolish the toxicity induced by Cd as well as acidic pH on plants. Based on these hypotheses, we demonstrated 2-repeated experiments to unfold the effects of Si as silica gel on the root morphology and physiology of wheat seedling under Cd as well as acidic stresses. For this purpose, we used nine treatments with three levels of Si nanoparticles (0, 1, and 3 mmol L−1) derived from sodium silicate (Na2SiO3) against three concentrations of Cd (0, 50, and 200 µmol L−1) in the form of cadmium chloride (CdCl2) with three replications were arranged in a complete randomized design. The pH of the nutrient solution was adjusted at 5. The averages of three random replications showed that the mutual impacts of Si and Cd in acidic pH on wheat roots depend on the concentrations of Si and Cd. The collective or particular influence of low or high levels of Si (1 or 3 mM) and acidic pH (5) improved the development of wheat roots, and the collective influence was more significant than that of a single parallel treatment. The combined effects of low or high concentrations of Cd (50 or 200 µM) and acidic pH significantly reduced root growth and biomass while increased antioxidants, and reactive oxygen species (ROS) contents. The incorporation of Si (1 or 3 mmol L−1) in Cd-contaminated acidic nutrient solution promoted the wheat root growth, decreased ROS contents, and further increased the antioxidants in the wheat roots compared with Cd single treatments in acidic pH. The demolishing effects were better with a high level of Si (3 mM) than the low level of Si (1 Mm). In conclusion, we could suggest Si as an effective beneficial nutrient that could participate actively in several morphological and physiological activities of roots in wheat plants grown under Cd and acidic pH stresses.
In vitro synthesis of 32 translation-factor proteins from a single template reveals impaired ribosomal processivity
Authors: Doerr Anne , Foschepoth David , Forster Anthony C. , Danelon Christophe
Published: January 2021

The Protein synthesis Using Recombinant Elements (PURE) system enables transcription and translation of a DNA template from purified components. Therefore, the PURE system-catalyzed generation of RNAs and proteins constituting the PURE system itself represents a major challenge toward a self-replicating minimal cell. In this work, we show that all translation factors (except elongation factor Tu) and 20 aminoacyl-tRNA synthetases can be expressed in the PURE system from a single plasmid encoding 32 proteins in 30 cistrons. Cell-free synthesis of all 32 proteins is confirmed by quantitative mass spectrometry-based proteomic analysis using isotopically labeled amino acids. We find that a significant fraction of the gene products consists of proteins missing their C-terminal ends. The per-codon processivity loss that we measure lies between 1.3 × 10–3 and 13.2 × 10–3, depending on the expression conditions, the version of the PURE system, and the coding sequence. These values are 5 to 50 times higher than those measured in vivo in E. coli. With such an impaired processivity, a considerable fraction of the biosynthesis capacity of the PURE system is wasted, posing an unforeseen challenge toward the development of a self-regenerating PURE system.
Systemic AAV6-synapsin-GFP administration results in lower liver biodistribution, compared to AAV1&2 and AAV9, with neuronal expression following ultrasound-mediated brain delivery
Authors: Weber-Adrian Danielle , Kofoed Rikke Hahn , Silburt Joseph , Noroozian Zeinab , Shah Kairavi , Burgess Alison , Rideout Shawna , Kügler Sebastian , Hynynen Kullervo , Aubert Isabelle
Published: January 2021

Non-surgical gene delivery to the brain can be achieved following intravenous injection of viral vectors coupled with transcranial MRI-guided focused ultrasound (MRIgFUS) to temporarily and locally permeabilize the blood–brain barrier. Vector and promoter selection can provide neuronal expression in the brain, while limiting biodistribution and expression in peripheral organs. To date, the biodistribution of adeno-associated viruses (AAVs) within peripheral organs had not been quantified following intravenous injection and MRIgFUS delivery to the brain. We evaluated the quantity of viral DNA from the serotypes AAV9, AAV6, and a mosaic AAV1&2, expressing green fluorescent protein (GFP) under the neuron-specific synapsin promoter (syn). AAVs were administered intravenously during MRIgFUS targeting to the striatum and hippocampus in mice. The syn promoter led to undetectable levels of GFP expression in peripheral organs. In the liver, the biodistribution of AAV9 and AAV1&2 was 12.9- and 4.4-fold higher, respectively, compared to AAV6. The percentage of GFP-positive neurons in the FUS-targeted areas of the brain was comparable for AAV6-syn-GFP and AAV1&2-syn-GFP. In summary, MRIgFUS-mediated gene delivery with AAV6-syn-GFP had lower off-target biodistribution in the liver compared to AAV9 and AAV1&2, while providing neuronal GFP expression in the striatum and hippocampus.
Dynamic temporal modulation of somatosensory processing during reaching
Authors: Voudouris Dimitris , Fiehler Katja
Published: January 2021

Sensorimotor control of human action integrates feedforward policies that predict future body states with online sensory feedback. These predictions lead to a suppression of the associated feedback signals. Here, we examine whether somatosensory processing throughout a goal-directed movement is constantly suppressed or dynamically tuned so that online feedback processing is enhanced at critical moments of the movement. Participants reached towards their other hand in the absence of visual input and detected a probing tactile stimulus on their moving or static hand. Somatosensory processing on the moving hand was dynamically tuned over the time course of reaching, being hampered in early and late stages of the movement, but, interestingly, recovering around the time of maximal speed. This novel finding of temporal somatosensory tuning was further corroborated in a second experiment, in which larger movement amplitudes shifted the absolute time of maximal speed later in the movement. We further show that the release from suppression on the moving limb was temporally coupled with enhanced somatosensory processing on the target hand. We discuss these results in the context of optimal feedforward control and suggest that somatosensory processing is dynamically tuned during the time course of reaching by enhancing sensory processing at critical moments of the movement.
Differential expression and correlation analysis of miRNA–mRNA profiles in swine testicular cells infected with porcine epidemic diarrhea virus
Authors: Zhang Xiaoqian , Li Chang , Zhang Bingzhou , Li Zhonghua , Zeng Wei , Luo Rui , Cao Jiyue , Cheng Guofu , Fan Shengxian , He Qigai
Published: January 2021

The variant virulent porcine epidemic diarrhea virus (PEDV) strain (YN15) can cause severe porcine epidemic diarrhea (PED); however, the attenuated vaccine-like PEDV strain (YN144) can induce immunity in piglets. To investigate the differences in pathogenesis and epigenetic mechanisms between the two strains, differential expression and correlation analyses of the microRNA (miRNA) and mRNA in swine testicular (ST) cells infected with YN15, YN144, and mock were performed on three comparison groups (YN15 vs Control, YN144 vs Control, and YN15 vs YN144). The mRNA and miRNA expression profiles were obtained using next-generation sequencing (NGS), and the differentially expressed (DE) (p-value < 0.05) mRNA and miRNA were obtained using DESeq R package. mRNAs targeted by DE miRNAs were predicted using the miRanda algortithm. 8039, 8631 and 3310 DE mRNAs, and 36, 36, and 22 DE miRNAs were identified in the three comparison groups, respectively. 14,140, 15,367 and 3771 DE miRNA–mRNA (targeted by DE miRNAs) interaction pairs with negatively correlated expression patterns were identified, and interaction networks were constructed using Cytoscape. Six DE miRNAs and six DE mRNAs were randomly selected to verify the sequencing data by real-time relative quantitative reverse transcription polymerase chain reaction (qRT-PCR). Based on bioinformatics analysis, we discovered the differences were mostly involved in host immune responses and viral pathogenicity, including NF-κB signaling pathway and bacterial invasion of epithelial cells, etc. This is the first comprehensive comparison of DE miRNA–mRNA pairs in YN15 and YN144 infection in vitro, which could provide novel strategies for the prevention and control of PED.
An in-vivo study of BOLD laminar responses as a function of echo time and static magnetic field strength
Authors: Markuerkiaga Irati , Marques José P. , Bains Lauren J. , Norris David G.
Published: January 2021

Layer specific functional MRI requires high spatial resolution data. To compensate the associated poor signal to noise ratio it is common to integrate the signal from voxels at a given cortical depth. If the region is sufficiently large then physiological noise will be the dominant noise source. In this work, activation profiles in response to the same visual stimulus are compared at 1.5 T, 3 T and 7 T using a multi-echo, gradient echo (GE) FLASH sequence, with a 0.75 mm isotropic voxel size and the cortical integration approach. The results show that after integrating over a cortical volume of 40, 60 and 100 mm3 (at 7 T, 3 T, and 1.5 T, respectively), the signal is in the physiological noise dominated regime. The activation profiles obtained are similar for equivalent echo times. BOLD-like noise is found to be the dominant source of physiological noise. Consequently, the functional contrast to noise ratio is not strongly echo-time or field-strength dependent. We conclude that laminar GE-BOLD fMRI at lower field strengths is feasible but that larger patches of cortex will need to be examined, and that the acquisition efficiency is reduced.
Isolation of Borrelia miyamotoi and other Borreliae using a modified BSK medium
Authors: Replogle Adam J. , Sexton Christopher , Young John , Kingry Luke C. , Schriefer Martin E. , Dolan Marc , Johnson Tammi L. , Connally Neeta P. , Padgett Kerry A. , Petersen Jeannine M.
Published: January 2021

Borrelia spirochetes are the causative agents of Lyme borreliosis (LB) and relapsing fever (RF). Despite the steady rise in infections and the identification of new species causing human illness over the last decade, isolation of borreliae in culture has become increasingly rare. A modified Barbour-Stoenner-Kelly (BSK) media formulation, BSK-R, was developed for isolation of the emerging RF pathogen, Borrelia miyamotoi. BSK-R is a diluted BSK-II derivative supplemented with Lebovitz’s L-15, mouse and fetal calf serum. Decreasing the concentration of CMRL 1066 and other components was essential for growth of North American B. miyamotoi. Sixteen B. miyamotoi isolates, originating from Ixodes scapularis ticks, rodent and human blood collected in the eastern and upper midwestern United States, were isolated and propagated to densities > 108 spirochetes/mL. Growth of five other RF and ten different LB borreliae readily occurred in BSK-R. Additionally, primary culture recovery of 20 isolates of Borrelia hermsii, Borrelia turicatae, Borrelia burgdorferi and Borrelia mayonii was achieved in BSK-R using whole blood from infected patients. These data indicate this broadly encompassing borreliae media can aid in in vitro culture recovery of RF and LB spirochetes, including the direct isolation of new and emerging human pathogens.
Mating and starvation modulate feeding and host-seeking responses in female bed bugs, Cimex lectularius
Authors: Saveer Ahmed M. , DeVries Zachary C. , Santangelo Richard G. , Schal Coby
Published: January 2021

Reproductive fitness and survival are enhanced by adaptive behaviors that are modulated by internal physiological states and external social contexts. The common bed bug,Cimex lectularius, is an obligate hematophagous ectoparasite that requires host blood for growth, development, and reproduction. We investigated how mating, starvation and social interactions affect host-seeking, blood feeding, oviposition, and survival of female bed bugs. The percentage of females that fed and the amount of blood they ingested were greater in mated females (90–100%) than in unmated females (48–60%). Mating state also modulated the female’s orientation towards human skin odor in an olfactometer; more mated (69%) than unmated (23%) females responded to human odors. The response rate of unmated females (60%) to skin odor increased with longer starvation period, while the opposite pattern was observed in mated females (20%). Although fecundity after a single blood meal was unaffected by long or short residence and interaction with males, females subjected to frequent copulation attempts had lower survivorship and lifespan than females housed with males for only 24 h. Taken together, these results indicate that by adaptively and coordinately expressing behaviors based on the internal physiological state, females maximize their survival and reproductive fitness.
Mobile device use among emergency department healthcare professionals: prevalence, utilization and attitudes
Authors: Hitti Eveline , Hadid Dima , Melki Jad , Kaddoura Rima , Alameddine Mohamad
Published: January 2021

Mobile devices are increasingly permeating healthcare and are being regularly used by healthcare providers. We examined the prevalence and frequency of mobile device use, and perceptions around clinical and personal usage, among healthcare providers (attending physicians, residents, and nurses) in the Emergency Department (ED) of a large academic medical center in Lebanon. Half of the target population (N = 236) completed the cross-sectional electronic questionnaire. Mobile device usage for personal matters was uniform across all providers, with the highest usage reported by medical students (81.3%) and lowest by attendings (75.0%). Medical formulary/drug referencing applications were the most common application used by providers followed by disease diagnosis/management applications, 84.4% and 69.5% respectively. Most respondents agreed that mobile devices enabled better-coordinated care among providers and were beneficial to patient care. Most respondents also agreed that mobile device use assisted in quickly resolving personal issues and reduced their feeling of stress, yet the majority did not feel that personal usage improved performance at work. Study findings revealed that although healthcare providers value mobile devices’ positive impact on coordination of care, the reverse spillover effect of personal issues into the workplace enabled by mobile devices might have some negative impact on performance of staff at work.
Corneal confocal microscopy identifies small fibre damage and progression of diabetic neuropathy
Authors: Dhage Shaishav , Ferdousi Maryam , Adam Safwaan , Ho Jan Hoong , Kalteniece Alise , Azmi Shazli , Alam Uazman , Ponirakis Georgios , Petropoulos Ioannis , Atkinson Andrew J. , Marshall Andrew , Jeziorska Maria , Soran Handrean , Malik Rayaz A.
Published: January 2021

Accurately quantifying the progression of diabetic peripheral neuropathy is key to identify individuals who will progress to foot ulceration and to power clinical intervention trials. We have undertaken detailed neuropathy phenotyping to assess the longitudinal utility of different measures of neuropathy in patients with diabetes. Nineteen patients with diabetes (age 52.5 ± 14.7 years, duration of diabetes 26.0 ± 13.8 years) and 19 healthy controls underwent assessment of symptoms and signs of neuropathy, quantitative sensory testing, autonomic nerve function, neurophysiology, intra-epidermal nerve fibre density (IENFD) and corneal confocal microscopy (CCM) to quantify corneal nerve fibre density (CNFD), branch density (CNBD) and fibre length (CNFL). Mean follow-up was 6.5 years. Glycated haemoglobin (p = 0.04), low-density lipoprotein-cholesterol (LDL-C) (p = 0.0009) and urinary albumin creatinine ratio (p < 0.0001) improved. Neuropathy symptom profile (p = 0.03), neuropathy disability score (p = 0.04), vibration perception threshold (p = 0.02), cold perception threshold (p = 0.006), CNFD (p = 0.03), CNBD (p < 0.0001), CNFL (p < 0.0001), IENFD (p = 0.04), sural (p = 0.02) and peroneal motor nerve conduction velocity (p = 0.03) deteriorated significantly. Change (∆) in CNFL correlated with ∆CPT (p = 0.006) and ∆Expiration/Inspiration ratio (p = 0.002) and ∆IENFD correlated with ∆CNFD (p = 0.005), ∆CNBD (p = 0.02) and ∆CNFL (p = 0.01). This study shows worsening of diabetic neuropathy across a range of neuropathy measures, especially CCM, despite an improvement in HbA1c and LDL-C. It further supports the utility of CCM as a rapid, non-invasive surrogate measure of diabetic neuropathy.
Comparative neuroanatomy of the lumbosacral spinal cord of the rat, cat, pig, monkey, and human
Authors: Toossi Amirali , Bergin Bradley , Marefatallah Maedeh , Parhizi Behdad , Tyreman Neil , Everaert Dirk G. , Rezaei Sabereh , Seres Peter , Gatenby J. Christopher , Perlmutter Steve I. , Mushahwar Vivian K.
Published: January 2021

The overall goal of this work was to create a high-resolution MRI atlas of the lumbosacral enlargement of the spinal cord of the rat (Sprague–Dawley), cat, domestic pig, rhesus monkey, and human. These species were chosen because they are commonly used in basic and translational research in spinal cord injuries and diseases. Six spinal cord specimens from each of the studied species (total of 30 specimens) were fixed, extracted, and imaged. Sizes of the spinal cord segments, cross-sectional dimensions, and locations of the spinal cord gray and white matter were quantified and compared across species. The lumbar enlargement spans spinal cord levels L3-S1 in rats, L4-S1 in cats, L3-S1 in pigs, L2/L3-L7/S1 in monkeys, and T12/L1-S1/S2 in humans. The enlargements in pigs and humans are largest and most similar in size (length and cross-sectional area); followed by monkeys and cats; and followed by rats. The obtained atlas establishes a neuroanatomical reference for the intact lumbosacral spinal cord in these species. It can also be used to guide the planning of surgical procedures of the spinal cord and technology design and development of spinal cord neuroprostheses, as well as precise delivery of cells/drugs into target regions within the spinal cord parenchyma.
Screening and development of monoclonal antibodies for identification of ferret T follicular helper cells
Authors: Jiang Wenbo , Wong Julius , Tan Hyon-Xhi , Kelly Hannah G. , Whitney Paul G. , Barr Ian , Layton Daniel S. , Kent Stephen J. , Wheatley Adam K. , Juno Jennifer A.
Published: January 2021

The ferret is a key animal model for investigating the pathogenicity and transmissibility of important human viruses, and for the pre‐clinical assessment of vaccines. However, relatively little is known about the ferret immune system, due in part to a paucity of ferret‐reactive reagents. In particular, T follicular helper (Tfh) cells are critical in the generation of effective humoral responses in humans, mice and other animal models but to date it has not been possible to identify Tfh in ferrets. Here, we describe the screening and development of ferret-reactive BCL6, CXCR5 and PD-1 monoclonal antibodies. We found two commercial anti-BCL6 antibodies (clone K112-91 and clone IG191E/A8) had cross-reactivity with lymph node cells from influenza-infected ferrets. We next developed two murine monoclonal antibodies against ferret CXCR5 (clone feX5-C05) and PD-1 (clone fePD-CL1) using a single B cell PCR-based method. We were able to clearly identify Tfh cells in lymph nodes from influenza infected ferrets using these antibodies. The development of ferret Tfh marker antibodies and the identification of ferret Tfh cells will assist the evaluation of vaccine-induced Tfh responses in the ferret model and the design of novel vaccines against the infection of influenza and other viruses, including SARS-CoV2.
A radiomics-based model for predicting prognosis of locally advanced gastric cancer in the preoperative setting
Authors: Shin Jaeseung , Lim Joon Seok , Huh Yong-Min , Kim Jie-Hyun , Hyung Woo Jin , Chung Jae-Joon , Han Kyunghwa , Kim Sungwon
Published: January 2021

This study aims to evaluate the performance of a radiomic signature-based model for predicting recurrence-free survival (RFS) of locally advanced gastric cancer (LAGC) using preoperative contrast-enhanced CT. This retrospective study included a training cohort (349 patients) and an external validation cohort (61 patients) who underwent curative resection for LAGC in 2010 without neoadjuvant therapies. Available preoperative clinical factors, including conventional CT staging and endoscopic data, and 438 radiomic features from the preoperative CT were obtained. To predict RFS, a radiomic model was developed using penalized Cox regression with the least absolute shrinkage and selection operator with ten-fold cross-validation. Internal and external validations were performed using a bootstrapping method. With the final 410 patients (58.2 ± 13.0 years-old; 268 female), the radiomic model consisted of seven selected features. In both of the internal and the external validation, the integrated area under the receiver operating characteristic curve values of both the radiomic model (0.714, P < 0.001 [internal validation]; 0.652, P = 0.010 [external validation]) and the merged model (0.719, P < 0.001; 0.651, P = 0.014) were significantly higher than those of the clinical model (0.616; 0.594). The radiomics-based model on preoperative CT images may improve RFS prediction and high-risk stratification in the preoperative setting of LAGC.
Deep learning based prediction of extraction difficulty for mandibular third molars
Authors: Yoo Jeong-Hun , Yeom Han-Gyeol , Shin WooSang , Yun Jong Pil , Lee Jong Hyun , Jeong Seung Hyun , Lim Hun Jun , Lee Jun , Kim Bong Chul
Published: January 2021

This paper proposes a convolutional neural network (CNN)-based deep learning model for predicting the difficulty of extracting a mandibular third molar using a panoramic radiographic image. The applied dataset includes a total of 1053 mandibular third molars from 600 preoperative panoramic radiographic images. The extraction difficulty was evaluated based on the consensus of three human observers using the Pederson difficulty score (PDS). The classification model used a ResNet-34 pretrained on the ImageNet dataset. The correlation between the PDS values determined by the proposed model and those measured by the experts was calculated. The prediction accuracies for C1 (depth), C2 (ramal relationship), and C3 (angulation) were 78.91%, 82.03%, and 90.23%, respectively. The results confirm that the proposed CNN-based deep learning model could be used to predict the difficulty of extracting a mandibular third molar using a panoramic radiographic image.
Acoustotactic response of mosquitoes in untethered flight to incidental sound
Authors: Dou Zhongwang , Madan Aditi , Carlson Jenny S. , Chung Joseph , Spoleti Tyler , Dimopoulos George , Cammarato Anthony , Mittal Rajat
Published: January 2021

Mosquitoes are vectors for some of the most devastating diseases on the planet. Given the centrality of acoustic sensing in the precopulatory behavior of these vectors, the use of an exogenous acoustic stimulus offers the potential of interfering with the courtship behavior of these insects. Previous research on the acoustotactic response of mosquitoes has been conducted on tethered preparations using low-intensity sound stimuli. To quantify differences in acoustotactic responses between mosquitos of distinct sex and species, we examined the effects of incidental sound stimuli on the flight behavior of free-flying male vs. female Aedes aegypti and Anopheles gambiae mosquitoes. The key variables were sound frequency (100–1000 Hz) and intensity (67–103 dB, measured at 12.5 cm from the source), and the acoustotactic response was measured in terms of the relative increase in flight speed in response to the stimulus. The data show, for the first time, significant sex- and species-specific differences in acoustotactic responses. A. aegypti exhibited a greater response to sound stimulus compared to An. gambiae, and the response also extended over a larger range of frequencies. Furthermore, the males of both species displayed a greater acoustotactic response than females, with An. gambiae females exhibiting minimal response to sound.
Understanding the seasonality of performance resilience to climate volatility in Mediterranean dairy sheep
Authors: Tsartsianidou Valentina , Kapsona Vanessa Varvara , Sánchez-Molano Enrique , Basdagianni Zoitsa , Carabaño Maria Jesús , Chatziplis Dimitrios , Arsenos Georgios , Triantafyllidis Alexandros , Banos Georgios
Published: January 2021

As future climate challenges become increasingly evident, enhancing performance resilience of farm animals may contribute to mitigation against adverse weather and seasonal variation, and underpin livestock farming sustainability. In the present study, we develop novel seasonal resilience phenotypes reflecting milk production changes to fluctuating weather. We evaluate the impact of calendar season (autumn, winter and spring) on animal performance resilience by analysing 420,534 milk records of 36,908 milking ewes of the Chios breed together with relevant meteorological data from eastern Mediterranean. We reveal substantial seasonal effects on resilience and significant heritable trait variation (h2 = 0.03–0.17). Resilience to cold weather (10 °C) of animals that start producing milk in spring was under different genetic control compared to autumn and winter as exemplified by negative genetic correlations (− 0.09 to − 0.27). Animal resilience to hot weather (25 °C) was partially under the same genetic control with genetic correlations between seasons ranging from 0.43 to 0.86. We report both favourable and antagonistic associations between animal resilience and lifetime milk production, depending on calendar season and the desirable direction of genetic selection. Concluding, we emphasise on seasonal adaptation of animals to climate and the need to incorporate the novel seasonal traits in future selective breeding programmes.
Catechin and curcumin interact with S protein of SARS-CoV2 and ACE2 of human cell membrane: insights from computational studies
Authors: Jena Atala B. , Kanungo Namrata , Nayak Vinayak , Chainy G. B. N. , Dandapat Jagneshwar
Published: January 2021

The recent outbreak of the coronavirus (SARS-CoV2) is an unprecedented threat to human health and society across the globe. In this context, development of suitable interventions is the need of the hour. The viral spike protein (S Protein) and the cognate host cell receptor ACE2 can be considered as effective and appropriate targets for interventions. It is evident from the present computational study, that catechin and curcumin, not only exhibit strong binding affinity to viral S Protein and host receptor ACE2 but also to their complex (receptor-binding domain (RBD) of the spike protein of SARS-CoV2 and ACE2; RBD/ACE2-complex). The binding affinity values of catechin and curcumin for the S protein, ACE2 and RBD/ACE2-complex are − 10.5 and − 7.9 kcal/mol; − 8.9 and − 7.8 kcal/mol; and − 9.1 and − 7.6 kcal/mol, respectively. Curcumin directly binds to the receptor binding domain (RBD) of viral S Protein. Molecular simulation study over a period of 100 ns further substantiates that such interaction within RBD site of S Protein occurs during 40–100 ns out of 100 ns simulation trajectory. Contrary to this, catechin binds with amino acid residues present near the RBD site of S Protein and causes fluctuation in the amino acid residues of the RBD and its near proximity. Both catechin and curcumin bind the interface of ‘RBD/ACE2-complex’ and intervene in causing fluctuation of the alpha helices and beta-strands of the protein complex. Protein–protein interaction studies in presence of curcumin or catechin also corroborate the above findings suggesting the efficacy of these two polyphenols in hindering the formation of S Protein-ACE2 complex. In conclusion, this computational study for the first time predicts the possibility of above two polyphenols for therapeutic strategy against SARS-CoV2.
Hyperglycemia-induced VEGF and ROS production in retinal cells is inhibited by the mTOR inhibitor, rapamycin
Authors: Kida Teruyo , Oku Hidehiro , Osuka Sho , Horie Taeko , Ikeda Tsunehiko
Published: January 2021

Determine the impact of the mTOR inhibitor, rapamycin, on the hyperglycemia-induced expression of vascular endothelial growth factor (VEGF) and the production of reactive oxygen species (ROS) in retinal cells. Rats made hyperglycemic for 8 weeks by streptozotocin, as well as control rats, received i.p. rapamycin (1 mg/kg) for 3 days prior to immunostaining of their retinas with anti-VEGF and anti-glial fibrillary acidic protein (GFAP) and measuring retinal protein levels of VEGF and GFAP by Western blotting. In other experiments, flow cytometry analysis of ethidium fluorescence determined intracellular ROS levels in the absence or presence of rapamycin (1 μM) under normoglycemic (5.5 mM) and hyperglycemic (25 mM) conditions in a rat retinal Müller cell line (TR-MUL5) and primary human retinal microvascular endothelial cells (HRMECs). In the diabetic retina, VEGF was elevated and colocalized with the glial marker, GFAP, whose level was also elevated. Treatment with rapamycin inhibited the diabetes-induced VEGF and GFAP increases. We also found that raising extracellular glucose from 5.5 mM to 25 mM resulted in significant rapamycin-sensitive increases in the ROS levels of TR-MUL5 cells and HRMECs. In rat retina, rapamycin attenuates the diabetes-induced VEGF overexpression, and in cultured Müller cells and HRMECs, inhibits the hyperglycemia-induced boost ROS.
Mobile and immobile boundaries in ferroelectric films
Authors: Yudin P. , Shapovalov K. , Sluka T. , Peräntie J. , Jantunen H. , Dejneka A. , Tyunina M.
Published: January 2021

The intrinsic mobile interfaces in ferroelectrics—the domain walls can drive and enhance diverse ferroelectric properties, essential for modern applications. Control over the motion of domain walls is of high practical importance. Here we analyse theoretically and show experimentally epitaxial ferroelectric films, where mobile domain walls coexist and interact with immobile growth-induced interfaces—columnar boundaries. Whereas these boundaries do not disturb the long-range crystal order, they affect the behaviour of domain walls in a peculiar selective manner. The columnar boundaries substantially modify the behaviour of non-ferroelastic domains walls, but have negligible impact on the ferroelastic ones. The results suggest that introduction of immobile boundaries into ferroelectric films is a viable method to modify domain structures and dynamic responses at nano-scale that may serve to functionalization of a broader range of ferroelectric films where columnar boundaries naturally appear as a result of the 3D growth.
Self-organized wavy infection curve of COVID-19
Authors: Odagaki Takashi
Published: January 2021

Exploiting the SIQR model for COVID-19, I show that the wavy infection curve in Japan is the result of fluctuation of policy on isolation measure imposed by the government and obeyed by citizens. Assuming the infection coefficient be a two-valued function of the number of daily confirmed new cases, I show that when the removal rate of infected individuals is between these two values, the wavy infection curve is self-organized. On the basis of the infection curve, I classify the outbreak of COVID-19 into five types and show that these differences can be related to the relative magnitude of the transmission coefficient and the quarantine rate of infected individuals.
Experimental study on thermal effect and gas release laws of coal-polyurethane cooperative spontaneous combustion
Authors: Wang Haiyan , Tian Yao , Li Jinglei , Chen Xiao
Published: January 2021

This paper presents a research on the kinetics and gas release laws of the cooperative spontaneous combustion of coal-polyurethane binary system by means of thermogravimetric analysis and spontaneous combustion simulation experiments. The coal-polyurethane binary system is more prone than individual samples to combustion. The polyurethane mass fraction has a great influence on the cooperative spontaneous combustion process. As the polyurethane mass fraction rises, the activation energies of oxygen absorption stage and pyrolysis stage decrease. The combustion residues of coal-polyurethane binary system scorches into lumps and the surfaces of the particles become rougher. During spontaneous combustion, the initial release temperatures of the four gases CO2, CO, C2H6and C2H4drop as the polyurethane mass fraction increases. The gas release amount of them increases with increasing polyurethane mass fraction. And the amount of CH4decreases as the polyurethane mass fraction increases. The CO/CO2ratio with temperature for different polyurethane mass fraction have the same trends. The results of this study have implications concerning polyurethane materials application and fire protection in coal mine.
Holistic processing of Chinese characters in college students with dyslexia
Authors: Tso Ricky Van-yip , Chan Ronald Tsz-chung , Chan Yin-fei , Lin Dan
Published: January 2021

Expert face recognition has long been marked by holistic processing. Hence, due to the many visual properties shared between face perception and Chinese characters, it has been suggested that Chinese character recognition may induce stronger holistic processing in expert readers than in novices. However, there have been different viewpoints presented about Chinese character recognition, one of which suggests that expertise in this skill involved reduced holistic processing which may be modulated by writing experiences/performances. In this study we examined holistic processing in Chinese character recognition in adults with and without dyslexia, using the complete composite paradigm. Our results showed that the adults with dyslexia recognized Chinese characters with a stronger holistic processing effect than the typical controls. It seems that those with dyslexia relied overly on the visual spatial information of characters and showed deficits in attending selectively to their components when processing Chinese characters, which hindered the development of expert reading and writing skills. This effect was in contrast to previous perceptual expertise studies in which reduced holistic processing marked deficits in face/visual object recognition. This study is also the first to show that Chinese adults with dyslexia had persistent below average performances in Chinese literacy.
Supercontinuum generation in dispersion engineered AlGaAs-on-insulator waveguides
Authors: May Stuart , Clerici Matteo , Sorel Marc
Published: January 2021

The effect of engineering the dispersion of AlGaAs-on-insulator (AlGaAs-OI) waveguides on supercontinuum generation is investigated at telecom wavelengths. The pronounced effect the waveguide width has on the nonlinear dynamics governing the supercontinua is systematically analyzed and the coherence of the spectra verified with numerical simulations. Using dispersion engineered AlGaAs-OI waveguides, broadband supercontinua were readily obtained for pulse energies of $$\sim \text {3 pJ}$$

∼
3 pJ

and a device length of only 3 mm. The results presented here, further understanding of the design and fabrication of this novel platform and describe the soliton and dispersive wave dynamics responsible for supercontinuum generation. This study showcases the potential of AlGaAs-OI for exploring fundamental physics and realizing highly efficient, compact, nonlinear devices.
A theoretical design of evanescent wave biosensors based on gate-controlled graphene surface plasmon resonance
Authors: Hwang Ruey-Bing
Published: January 2021

A surface plasmon resonance (SPR) sensor based on gate-controlled periodic graphene ribbons array is reported. Different from the conventional methods by monitoring reflectivity variations with respect to incident angle or wavelength, this approach measures the change in SPR curve against the variation of graphene chemical potential (via dynamically tuning the gate voltage) at both fixed incident angle and wavelength without the need of rotating mirror, tunable filter or spectrometer for angular or wavelength interrogation. Theoretical calculations show that the sensitivities are 36,401.1 mV/RIU, 40,676.5 mV/RIU, 40,918.2 mV/RIU, and 41,160 mV/RIU for analyte refractive index (RI) equal to 1.33, 1.34, 1.35 and 1.36; their figure of merit (1/RIU) are 21.84, 24, 23.74 and 23.69, respectively. Significantly, the enhancement in the non-uniform local field due to the subwavelength graphene ribbon resonator can facilitate the detection in redistribution of protein monolayers modeled as dielectric bricks.
Rhizobia use a pathogenic-like effector to hijack leguminous nodulation signalling
Authors: Ratu Safirah Tasa Nerves , Teulet Albin , Miwa Hiroki , Masuda Sachiko , Nguyen Hien P. , Yasuda Michiko , Sato Shusei , Kaneko Takakazu , Hayashi Makoto , Giraud Eric , Okazaki Shin
Published: January 2021

Legume plants form a root-nodule symbiosis with rhizobia. This symbiosis establishment generally relies on rhizobium-produced Nod factors (NFs) and their perception by leguminous receptors (NFRs) that trigger nodulation. However, certain rhizobia hijack leguminous nodulation signalling via their type III secretion system, which functions in pathogenic bacteria to deliver effector proteins into host cells. Here, we report that rhizobia use pathogenic-like effectors to hijack legume nodulation signalling. The rhizobial effector Bel2-5 resembles the XopD effector of the plant pathogen Xanthomonas campestris and could induce nitrogen-fixing nodules on soybean nfr mutant. The soybean root transcriptome revealed that Bel2-5 induces expression of cytokinin-related genes, which are important for nodule organogenesis and represses ethylene- and defense-related genes that are deleterious to nodulation. Remarkably, Bel2-5 introduction into a strain unable to nodulate soybean mutant affected in NF perception conferred nodulation ability. Our findings show that rhizobia employ and have customized pathogenic effectors to promote leguminous nodulation signalling.
SARS-CoV-2 neutralizing antibodies in patients with varying severity of acute COVID-19 illness
Authors: Jeewandara Chandima , Jayathilaka Deshni , Gomes Laksiri , Wijewickrama Ananda , Narangoda Eranga , Idampitiya Damayanthi , Guruge Dinuka , Wijayamuni Ruwan , Manilgama Suranga , Ogg Graham S. , Tan Chee Wah , Wang Lin-Fa , Malavige Gathsaurie Neelika
Published: January 2021

In order to support vaccine development, and to aid convalescent plasma therapy, it would be important to understand the kinetics, timing and persistence of SARS-CoV-2 neutralizing antibodies (NAbs), and their association with clinical disease severity. Therefore, we used a surrogate viral neutralization test to evaluate their levels in patients with varying severity of illness, in those with prolonged shedding and those with mild/asymptomatic illness at various time points. Patients with severe or moderate COVID-19 illness had earlier appearance of NAbs at higher levels compared to those with mild or asymptomatic illness. Furthermore, those who had prolonged shedding of the virus, had NAbs appearing faster and at higher levels than those who cleared the virus earlier. During the first week of illness the NAb levels of those with mild illness was significantly less (p = 0.01), compared to those with moderate and severe illness. At the end of 4 weeks (28 days), although 89% had NAbs, 38/76 (50%) in those with > 90 days had a negative result for the presence of NAbs. The Ab levels significantly declined during convalescence (> 90 days since onset of illness), compared to 4 to 8 weeks since onset of illness. Our data show that high levels of NAbs during early illness associated with clinical disease severity and that these antibodies declined in 50% of individuals after 3 months since onset of illness.
High-throughput microbioreactor provides a capable tool for early stage bioprocess development
Authors: Fink Mathias , Cserjan-Puschmann Monika , Reinisch Daniela , Striedner Gerald
Published: January 2021

Tremendous advancements in cell and protein engineering methodologies and bioinformatics have led to a vast increase in bacterial production clones and recombinant protein variants to be screened and evaluated. Consequently, an urgent need exists for efficient high-throughput (HTP) screening approaches to improve the efficiency in early process development as a basis to speed-up all subsequent steps in the course of process design and engineering. In this study, we selected the BioLector micro-bioreactor (µ-bioreactor) system as an HTP cultivation platform to screen E. coli expression clones producing representative protein candidates for biopharmaceutical applications. We evaluated the extent to which generated clones and condition screening results were transferable and comparable to results from fully controlled bioreactor systems operated in fed-batch mode at moderate or high cell densities. Direct comparison of 22 different production clones showed great transferability. We observed the same growth and expression characteristics, and identical clone rankings except one host-Fab-leader combination. This outcome demonstrates the explanatory power of HTP µ-bioreactor data and the suitability of this platform as a screening tool in upstream development of microbial systems. Fast, reliable, and transferable screening data significantly reduce experiments in fully controlled bioreactor systems and accelerate process development at lower cost.
Metachronous advanced neoplasia after submucosal invasive colorectal cancer resection
Authors: Minamide Tatsunori , Ikematsu Hiroaki , Murano Tatsuro , Kadota Tomohiro , Shinmura Kensuke , Yoda Yusuke , Hori Keisuke , Ito Masaaki , Yano Tomonori
Published: January 2021

Little is known about the incidence of metachronous advanced neoplasia (AN) following resection of submucosal invasive colorectal cancer (SM-CRC). Here, we aimed to assess the occurrence of metachronous AN following SM-CRC resection. We retrospectively reviewed consecutive patients who underwent SM-CRC resection at an academic medical center between 2005 and 2013. Among 343 patients, 250 (72.9%) underwent surgical resection or endoscopic resection followed by surgical resection and 93 (27.1%) underwent only endoscopic resection. During a median follow-up period of 61.5 months, the overall incidence of metachronous AN was 7.6%, and the cumulative incidence at 5 years was 6.1%. The cumulative incidence was significantly higher in the endoscopic resection group than in surgical resection group, in patients with colonic disease than in those with rectal disease, and in patients with synchronous AN than in those without. Multivariate analysis revealed that synchronous AN was the only significant risk factor for metachronous AN (HR 4.35; 95% CI 1.88–10.1). These findings imply that depending on synchronous AN, a surveillance protocol following SM-CRC resection can be changed for better detection of metachronous AN.
Clinicopathological characteristics and outcomes of anti-neutrophil cytoplasmic autoantibody-related renal vasculitis with hyperuricemia: a retrospective case-control study
Authors: Wang Ruiqiang , An Dongyue , Wu Yunqi , Ma Pupu , Guo Yuanyuan , Tang Lin
Published: January 2021

The objective of the study was to evaluate the clinicopathological characteristics and investigate the clinical determinants of patient and renal survival in the first 12 months after diagnosis in anti-neutrophil cytoplasmic antibody (ANCA)-associated renal vasculitis (AAV) patients with hyperuricemia. This was a retrospective case-control study in patients with AAV-related renal injury in the First Affiliated Hospital of Zhengzhou University from January 2014 to April 2019. Patients who met the study criteria were divided into two groups: patients without hyperuricemia (n = 92) and patients with hyperuricemia (n = 55). Participants were followed-up for 12 months, and progressing to end-stage renal disease (ESRD) and death was treated as the endpoint event. We found that the level of serum creatinine was an independent risk factor for hyperuricemia, and the level of serum uric acid was an independent risk factors for renal survival and patient survival in ANCA-associated renal vasculitis patients. The crescents formation and the proportion of fibrous crescent likely contributed to severe clinical characteristics and renal pathological changes in ANCA-associated renal vasculitis patients with hyperuricemia. Hyperuricemia has an important influence on the progression of ANCA-associated renal vasculitis. A good control of serum uric acid may improve the prognosis.