bluuebunny/crossref_metadata_2025 huggingface dataset:
Super-resolution label-free volumetric vibrational imaging
Authors: Qian Chenxi , Miao Kun , Lin Li-En , Chen Xinhong , Du Jiajun , Wei Lu
Published: June 2021

Innovations in high-resolution optical imaging have allowed visualization of nanoscale biological structures and connections. However, super-resolution fluorescence techniques, including both optics-oriented and sample-expansion based, are limited in quantification and throughput especially in tissues from photobleaching or quenching of the fluorophores, and low-efficiency or non-uniform delivery of the probes. Here, we report a general sample-expansion vibrational imaging strategy, termed VISTA, for scalable label-free high-resolution interrogations of protein-rich biological structures with resolution down to 78 nm. VISTA achieves decent three-dimensional image quality through optimal retention of endogenous proteins, isotropic sample expansion, and deprivation of scattering lipids. Free from probe-labeling associated issues, VISTA offers unbiased and high-throughput tissue investigations. With correlative VISTA and immunofluorescence, we further validated the imaging specificity of VISTA and trained an image-segmentation model for label-free multi-component and volumetric prediction of nucleus, blood vessels, neuronal cells and dendrites in complex mouse brain tissues. VISTA could hence open new avenues for versatile biomedical studies.
Study of disorder in pulsed laser deposited double perovskite oxides by first-principle structure prediction
Authors: Fertitta Edoardo , Das Sujit , Banerjee Debalina , Ebrahimi Farbod , Barraud Clément , Du Kai , Tian He , Pickard Chris J. , Weber Cedric , Ramesh Ramamoorthy , Littlewood Peter , Dubbink David
Published: June 2021

Double perovskite oxides, with generalized formula A2BB$$^{\prime}$$

′

O6, attract wide interest due to their multiferroic and charge transfer properties. They offer a wide range of potential applications such as spintronics and electrically tunable devices. However, great practical limitations are encountered, since a spontaneous order of the B-site cations is notoriously hard to achieve. In this joint experimental-theoretical work, we focused on the characterization of double perovskites La2TiFeO6 and La2VCuO6 films grown by pulsed laser deposition and interpretation of the observed B-site disorder and partial charge transfer between the B-site ions. A random structure sampling method was used to show that several phases compete due to their corresponding configurational entropy. In order to capture a representative picture of the most relevant competing microstates in realistic experimental conditions, this search included the potential formation of non-stoichiometric phases as well, which could also be directly related to the observed partial charge transfer. We optimized the information encapsulated in the potential energy landscape, captured via structure sampling, by evaluating both enthalpic and entropic terms. These terms were employed as a metric for the competition of different phases. This approach, applied herein specifically to La2TiFeO6, highlights the presence of highly entropic phases above the ground state which can explain the disorder observed frequently in the broader class of double perovskite oxides.
Integrated diagnosis based on transcriptome analysis in suspected pediatric sarcomas
Authors: Ichikawa Daisuke , Yamashita Kyoko , Okuno Yusuke , Muramatsu Hideki , Murakami Norihiro , Suzuki Kyogo , Kojima Daiei , Kataoka Shinsuke , Hamada Motoharu , Taniguchi Rieko , Nishikawa Eri , Kawashima Nozomu , Narita Atsushi , Nishio Nobuhiro , Hama Asahito , Kasai Kenji , Mizuno Seiji , Shimoyama Yoshie , Nakaguro Masato , Okita Hajime , Kojima Seiji , Nakazawa Atsuko , Takahashi Yoshiyuki
Published: June 2021

Pediatric solid tumors are a heterogeneous group of neoplasms with over 100 subtypes. Clinical and histopathological diagnosis remains challenging due to the overlapping morphological and immunohistochemical findings and the presence of atypical cases. To evaluate the potential utility of including RNA-sequencing (RNA-seq) in the diagnostic process, we performed RNA-seq in 47 patients with suspected pediatric sarcomas. Histopathologists specialized in pediatric cancer re-evaluated pathological specimens to reach a consensus diagnosis; 42 patients were diagnosed with known subtypes of solid tumors whereas 5 patients were diagnosed with undifferentiated sarcoma. RNA-seq analysis confirmed and refined consensus diagnoses and further identified diagnostic genetic variants in four of the five patients with undifferentiated sarcoma. Genetic lesions were detected in 23 patients, including the novel SMARCA4-THOP1 fusion gene and 22 conventional or recently reported genetic events. Unsupervised clustering analysis of the RNA-seq data identified a distinct cluster defined by the overexpression of rhabdomyosarcoma-associated genes including MYOG and CHRNG. These findings suggest that RNA-seq-based genetic analysis may aid in the diagnosis of suspected pediatric sarcomas, which would be useful for the development of stratified treatment strategies.
Belief propagation with quantum messages for quantum-enhanced classical communications
Authors: Rengaswamy Narayanan , Seshadreesan Kaushik P. , Guha Saikat , Pfister Henry D.
Published: June 2021

For space-based laser communications, when the mean photon number per received optical pulse is much smaller than one, there is a large gap between communications capacity achievable with a receiver that performs individual pulse-by-pulse detection, and the quantum-optimal “joint-detection receiver” that acts collectively on long codeword-blocks of modulated pulses; an effect often termed “superadditive capacity”. In this paper, we consider the simplest scenario where a large superadditive capacity is known: a pure-loss channel with a coherent-state binary phase-shift keyed (BPSK) modulation. The two BPSK states can be mapped conceptually to two non-orthogonal states of a qubit, described by an inner product that is a function of the mean photon number per pulse. Using this map, we derive an explicit construction of the quantum circuit of a joint-detection receiver based on a recent idea of “belief-propagation with quantum messages” (BPQM). We quantify its performance improvement over the Dolinar receiver that performs optimal pulse-by-pulse detection, which represents the best “classical” approach. We analyze the scheme rigorously and show that it achieves the quantum limit of minimum average error probability in discriminating 8 (BPSK) codewords of a length-5 binary linear code with a tree factor graph. Our result suggests that a BPQM receiver might attain the Holevo capacity of this BPSK-modulated pure-loss channel. Moreover, our receiver circuit provides an alternative proposal for a quantum supremacy experiment, targeted at a specific application that can potentially be implemented on a small, special-purpose, photonic quantum computer capable of performing cat-basis universal qubit logic.
Probabilistic one-time programs using quantum entanglement
Authors: Roehsner Marie-Christine , Kettlewell Joshua A. , Fitzsimons Joseph , Walther Philip
Published: June 2021

Quantum technology allows for unparalleled levels of data and software protection. Probabilistic one-time programs harness these capabilities for quantum-assisted classical computations by encoding classical software in small quantum states resulting in computer programs that can be used only once. Such self-destructing one-time programs facilitate a variety of applications reaching from software distribution to one-time delegation of signature authority. Whereas previous experiments demonstrated the feasibility of such schemes, the practical applications were limited. Here we present an improved protocol for one-time programs that resolves major drawbacks of previous schemes, by employing entangled qubit pairs. This results in four orders of magnitude higher count rates and the ability to execute a program long after the quantum information exchange has taken place. We implement a one-time delegation of signature authority over an underground fiber link between university buildings in downtown Vienna, emphasizing the compatibility of our scheme with prepare-and-measure quantum internet networks.
Associations between school enjoyment at age 6 and later educational achievement: evidence from a UK cohort study
Authors: Morris Tim T. , Dorling Danny , Davies Neil M. , Davey Smith George
Published: June 2021

Education is influenced by a broad range of factors but there has been limited research into the role that early school enjoyment plays in pupil’s educational achievement. Here we used data from a UK cohort to answer three research questions. What is the association between early school enjoyment and later academic achievement? To what extent do family background factors underlie this association? Do sex differences in school enjoyment underlie sex differences in achievement? School enjoyment was self-reported in two questionnaires completed at age 6. We used multiple imputation to account for missing covariates in this study, giving an imputed sample size of 12,135. Children’s school enjoyment at age 6 associated with sex and cognitive ability but not family socioeconomic background. For example, girls were twice as likely to report enjoying school than boys (OR: 1.97; 95% CI: 1.56, 2.48). School enjoyment strongly associated with later achievement in age 16 compulsory GCSE exams even after adjustment for socioeconomic background and cognitive ability; pupils who reported enjoying school scored on average 14.4 (95% CI: 6.9, 21.9) more points (equivalent to almost a 3-grade increase across all subjects) and were 29% more likely to obtain 5 + A*-C GCSE’s including Maths and English (OR: 1.29; 95% CI: 0.99, 1.7) than those who did not enjoy school. These results highlight the importance of school enjoyment for educational achievement. As a potentially more modifiable factor than socioeconomic background, cognitive ability or sex, school enjoyment may represent a promising intervention target for improving educational outcomes.
The role of abnormalities of lipoproteins and HDL functionality in small fibre dysfunction in people with severe obesity
Authors: Azmi Shazli , Ferdousi Maryam , Liu Yifen , Adam Safwaan , Siahmansur Tarza , Ponirakis Georgios , Marshall Andrew , Petropoulos Ioannis N. , Ho Jan Hoong , Syed Akheel A. , Gibson John M. , Ammori Basil J. , Durrington Paul N. , Malik Rayaz A. , Soran Handrean
Published: June 2021

Obesity and associated dyslipidemia may contribute to increased cardiovascular disease. Obesity has also been associated with neuropathy. We have investigated presence of peripheral nerve damage in patients with severe obesity without type 2 diabetes and the status of metabolic syndrome and lipoprotein abnormalities. 47participants with severe obesity and 30 age-matched healthy controls underwent detailed phenotyping of neuropathy and an assessment of lipoproteins and HDL-functionality. Participants with severe obesity had a higher neuropathy symptom profile, lower sural and peroneal nerve amplitudes, abnormal thermal thresholds, heart rate variability with deep breathing and corneal nerve parameters compared to healthy controls. Circulating apolipoprotein A1 (P = 0.009), HDL cholesterol (HDL-C) (P < 0.0001), cholesterol efflux (P = 0.002) and paroxonase-1 (PON-1) activity (P < 0.0001) were lower, and serum amyloid A (SAA) (P < 0.0001) was higher in participants with obesity compared to controls. Obese participants with small nerve fibre damage had higher serum triglycerides (P = 0.02), lower PON-1 activity (P = 0.002) and higher prevalence of metabolic syndrome (58% vs. 23%, P = 0.02) compared to those without. However, HDL-C (P = 0.8), cholesterol efflux (P = 0.08), apoA1 (P = 0.8) and SAA (P = 0.8) did not differ significantly between obese participants with and without small nerve fibre damage. Small nerve fibre damage occurs in people with severe obesity. Patients with obesity have deranged lipoproteins and compromised HDL functionality compared to controls. Obese patients with evidence of small nerve fibre damage, compared to those without, had significantly higher serum triglycerides, lower PON-1 activity and a higher prevalence of metabolic syndrome.
Dielectric response of nitrogen in soil amended with chicken litter biochar and urea under Oryza sativa L. cultivation
Authors: Maru Ali , Ahmed Osumanu Haruna , Primus Walter Charles , Jeffary Alicia Vanessa
Published: June 2021

Unbalanced utilization of nitrogen (N) rice not economically viable neither is this practice environmental friendly. Co-application of biochar and urea could reduce the unbalanced use of this N fertilizer in rice cultivation. Thus, a field study was carried out to: (i) determine the effects of chicken litter biochar and urea fertilization on N concentration in soil solution of a cultivated rice (MR219) using dielectric measurement at a low frequency and (ii) correlate soil dielectric conductivity with rice grain yield at maturity. Dielectric response of the soil samples at 20, 40, 55, and 75 days after transplanting were determined using an inductance–capacitance–resistance meter HIOKI 3522-50 LCR HiTESTER. Selected soil chemical properties and yield were determined using standard procedures. The dielectric conductivity and permittivity of the soil samples measured before transplanting the rice seedlings were higher than those for the soil samples after transplanting. This was due to the inherent nitrogen of the chicken litter biochar and the low nitrogen uptake at the transplanting stage. The soil N response increased with increasing measurement frequency and N concentration. The permittivity of the soil samples was inversely proportional to frequency but directly proportional to N concentration in the soil solution. The estimated contents of N in the soil using the dielectric conductivity approach at 1000 Hz decreased with increasing days of fertilization and the results were similar to those of soil NH4+ determined using chemical analysis. The conductivity measured within 1000 Hz and 100,000 Hz correlated positively with the rice grain yield suggesting that nitrogen concentration of the soil can be used to estimate grain yield of the cultivated rice plants.
Plantaricin NC8 αβ prevents Staphylococcus aureus-mediated cytotoxicity and inflammatory responses of human keratinocytes
Authors: Musa Amani , Wiman Emanuel , Selegård Robert , Aili Daniel , Bengtsson Torbjörn , Khalaf Hazem
Published: June 2021

Multidrug resistance bacteria constitue an increasing global health problem and the development of novel therapeutic strategies to face this challenge is urgent. Antimicrobial peptides have been proven as potent agents against pathogenic bacteria shown by promising in vitro results. The aim of this study was to characterize the antimicrobial effects of PLNC8 αβ on cell signaling pathways and inflammatory responses of human keratinocytes infected with S. aureus. PLNC8 αβ did not affect the viability of human keratinocytes but upregulated several cytokines (IL-1β, IL-6, CXCL8), MMPs (MMP1, MMP2, MMP9, MMP10) and growth factors (VEGF and PDGF-AA), which are essential in cell regeneration. S. aureus induced the expression of several inflammatory mediators at the gene and protein level and PLNC8 αβ was able to significantly suppress these effects. Intracellular signaling events involved primarily c-Jun via JNK, c-Fos and NFκB, suggesting their essential role in the initiation of inflammatory responses in human keratinocytes. PLNC8 αβ was shown to modulate early keratinocyte responses, without affecting their viability. The peptides have high selectivity towards S. aureus and were efficient at eliminating the bacteria and counteracting their inflammatory and cytotoxic effects, alone and in combination with low concentrations of gentamicin. We propose that PLNC8 αβ may be developed to combat infections caused by Staphylococcus spp.
Inferring transcriptomic cell states and transitions only from time series transcriptome data
Authors: Jo Kyuri , Sung Inyoung , Lee Dohoon , Jang Hyuksoon , Kim Sun
Published: June 2021

Cellular stages of biological processes have been characterized using fluorescence-activated cell sorting and genetic perturbations, charting a limited landscape of cellular states. Time series transcriptome data can help define new cellular states at the molecular level since the analysis of transcriptional changes can provide information on cell states and transitions. However, existing methods for inferring cell states from transcriptome data use additional information such as prior knowledge on cell types or cell-type-specific markers to reduce the complexity of data. In this study, we present a novel time series clustering framework to infer TRAnscriptomic Cellular States (TRACS) only from time series transcriptome data by integrating Gaussian process regression, shape-based distance, and ranked pairs algorithm in a single computational framework. TRACS determines patterns that correspond to hidden cellular states by clustering gene expression data. TRACS was used to analyse single-cell and bulk RNA sequencing data and successfully generated cluster networks that reflected the characteristics of key stages of biological processes. Thus, TRACS has a potential to help reveal unknown cellular states and transitions at the molecular level using only time series transcriptome data. TRACS is implemented in Python and available at http://github.com/BML-cbnu/TRACS/.
Design and in silico validation of polymerase chain reaction primers to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Authors: Davi Maria Júlia P. , Jeronimo Selma M. B. , Lima João P. M. S. , Lanza Daniel C. F.
Published: June 2021

Accurate designing of polymerase chain reaction (PCR) primers targeting conserved segments in viral genomes is desirable for preventing false-negative results and decreasing the need for standardization across different PCR protocols. In this work, we designed and described a set of primers and probes targeting conserved regions identified from a multiple sequence alignment of 2341 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) genomes from the Global Initiative on Sharing All Influenza Data (GISAID). We subsequently validated those primers and probes in 211,833 SARS-CoV-2 whole-genome sequences. We obtained nine systems (forward primer + reverse primer + probe) that potentially anneal to highly conserved regions of the virus genome from these analyses. In silico predictions also demonstrated that those primers do not bind to nonspecific targets for human, bacterial, fungal, apicomplexan, and other Betacoronaviruses and less pathogenic sub-strains of coronavirus. The availability of these primer and probe sequences will make it possible to validate more efficient protocols for identifying SARS-CoV-2.
Lack of detectable genetic isolation in the cyclic rodent Microtus arvalis despite large landscape fragmentation owing to transportation infrastructures
Authors: Dominguez Julio C. , Calero-Riestra María , Olea Pedro P. , Malo Juan E. , Burridge Christopher P. , Proft Kirstin , Illanas Sonia , Viñuela Javier , García Jesús T.
Published: June 2021

Although roads are widely seen as dispersal barriers, their genetic consequences for animals that experience large fluctuations in population density are poorly documented. We developed a spatially paired experimental design to assess the genetic impacts of roads on cyclic voles (Microtus arvalis) during a high-density phase in North-Western Spain. We compared genetic patterns from 15 paired plots bisected by three different barrier types, using linear mixed models and computing effect sizes to assess the importance of each type, and the influence of road features like width or the age of the infrastructure. Evidence of effects by roads on genetic diversity and differentiation were lacking. We speculate that the recurrent (each 3–5 generations) episodes of massive dispersal associated with population density peaks can homogenize populations and mitigate the possible genetic impact of landscape fragmentation by roads. This study highlights the importance of developing spatially replicated experimental designs that allow us to consider the large natural spatial variation in genetic parameters. More generally, these results contribute to our understanding of the not well explored effects of habitat fragmentation on dispersal in species showing “boom-bust” dynamics.
A deep learning based approach for prediction of Chlamydomonas reinhardtii phosphorylation sites
Authors: Thapa Niraj , Chaudhari Meenal , Iannetta Anthony A. , White Clarence , Roy Kaushik , Newman Robert H. , Hicks Leslie M. , KC Dukka B.
Published: June 2021

Protein phosphorylation, which is one of the most important post-translational modifications (PTMs), is involved in regulating myriad cellular processes. Herein, we present a novel deep learning based approach for organism-specific protein phosphorylation site prediction in Chlamydomonas reinhardtii, a model algal phototroph. An ensemble model combining convolutional neural networks and long short-term memory (LSTM) achieves the best performance in predicting phosphorylation sites in C. reinhardtii. Deemed Chlamy-EnPhosSite, the measured best AUC and MCC are 0.90 and 0.64 respectively for a combined dataset of serine (S) and threonine (T) in independent testing higher than those measures for other predictors. When applied to the entire C. reinhardtii proteome (totaling 1,809,304 S and T sites), Chlamy-EnPhosSite yielded 499,411 phosphorylated sites with a cut-off value of 0.5 and 237,949 phosphorylated sites with a cut-off value of 0.7. These predictions were compared to an experimental dataset of phosphosites identified by liquid chromatography-tandem mass spectrometry (LC–MS/MS) in a blinded study and approximately 89.69% of 2,663 C. reinhardtii S and T phosphorylation sites were successfully predicted by Chlamy-EnPhosSite at a probability cut-off of 0.5 and 76.83% of sites were successfully identified at a more stringent 0.7 cut-off. Interestingly, Chlamy-EnPhosSite also successfully predicted experimentally confirmed phosphorylation sites in a protein sequence (e.g., RPS6 S245) which did not appear in the training dataset, highlighting prediction accuracy and the power of leveraging predictions to identify biologically relevant PTM sites. These results demonstrate that our method represents a robust and complementary technique for high-throughput phosphorylation site prediction in C. reinhardtii. It has potential to serve as a useful tool to the community. Chlamy-EnPhosSite will contribute to the understanding of how protein phosphorylation influences various biological processes in this important model microalga.
Association of age-related cognitive and obstacle avoidance performances
Authors: Sakurai Ryota , Kodama Kentaro , Ozawa Yu , Pieruccini-Faria Frederico , Kobayashi-Cuya Kimi Estela , Ogawa Susumu
Published: June 2021

An association between cognitive impairment and tripping over obstacles during locomotion in older adults has been suggested. However, owing to its memory-guided movement, whether this is more pronounced in the trailing limb is poorly known. We examined age-related changes in stepping over, focusing on trailing limb movements, and their association with cognitive performance. Age-related changes in obstacle avoidance were examined by comparing the foot kinematics of 105 older and 103 younger adults when stepping over an obstacle. The difference in the clearance between the leading and trailing limbs (Δ clearance) was calculated to determine the degree of decrement in the clearance of the trailing limb. A cognitive test battery was used to evaluate cognitive function among older adults to assess their association with Δ clearance. Older adults showed a significantly lower clearance of the trailing limb than young adults, resulting in greater Δ clearance. Significant correlations were observed between greater Δ clearance and scores on the Montreal Cognitive Assessment and immediate recall of the Wechsler Memory Scale-Revised Logical Memory test. Therefore, memory functions may contribute to the control of trailing limb movements, which can secure a safety margin to avoid stumbling over an obstacle during obstacle avoidance locomotion.
Varied-shaped gold nanoparticles with nanogram killing efficiency as potential antimicrobial surface coatings for the medical devices
Authors: Piktel Ewelina , Suprewicz Łukasz , Depciuch Joanna , Chmielewska Sylwia , Skłodowski Karol , Daniluk Tamara , Król Grzegorz , Kołat-Brodecka Paulina , Bijak Piotr , Pajor-Świerzy Anna , Fiedoruk Krzysztof , Parlinska-Wojtan Magdalena , Bucki Robert
Published: June 2021

Medical device-associated infections are a serious medical threat, particularly for patients with impaired mobility and/or advanced age. Despite a variety of antimicrobial coatings for medical devices being explored to date, only a limited number have been introduced for clinical use. Research into new bactericidal agents with the ability to eradicate pathogens, limit biofilm formation, and exhibit satisfactory biocompatibility, is therefore necessary and urgent. In this study, a series of varied-morphology gold nanoparticles in shapes of rods, peanuts, stars and spherical-like, porous ones with potent antibacterial activity were synthesized and thoroughly tested against spectrum of Candida albicans, Pseudomonas aeruginosa, Staphylococcus aureus clinical strains, as well as spectrum of uropathogenic Escherichia coli isolates. The optimization of gold nanoparticles synthesis allowed to develop nanomaterials, which are proved to be significantly more potent against tested microbes compared with the gold nanoformulations reported to date. Notably, their antimicrobial spectrum includes strains with different drug resistance mechanisms. Facile and cost-efficient synthesis of gold nanoparticles, remarkable bactericidal efficiency at nanogram doses, and low toxicity, underline their potential for development as a new coatings, as indicated by the example of urological catheters. The presented research fills a gap in microbial studies of non-spherical gold nanoparticles for the development of antimicrobial coatings targeting multidrug-resistant pathogens responsible for device-associated nosocomial infections.
Effect of nano-grain carbide formation on electrochemical behavior of 316L stainless steel
Authors: Boonruang Chatdanai , Sanumang Wutipong
Published: June 2021

The effect of low oxygen-partial pressured carburizing on relaxation process for 316L stainless steel is reported. Phase, morphology, and amount of compound formation during initial stage of carburizing are investigated using X-ray diffractometry (XRD) and X-ray photoelectron spectroscopy (XPS). The results show formation and development of surface multilayer with nano-grain-carbide (Cr7C3, Fe7C3, and/or Cr3C2) generation in the layer located below outermost protective layer. The relaxation process has been investigated using electrochemical impedance spectroscopy (EIS). Formation of nano-grain carbide(s) during carburizing causes deterioration effect on the electrochemical behavior of steel. However, the steel with large amount of carbide generation (carburized for 30 min) tends to have higher corrosion resistance (indicated by higher values of Rcl and Rct) than the smaller ones (10 and 20 min) due to the effect of phase, grain size, morphology, and amount of compound formation.
Long-term atomoxetine-oxybutynin combination use may be beneficial for the prevention of obstructive sleep apnea
Authors: Chen Tien-Yu , Chung Chi-Hsiang , Chang Hsin-An , Kao Yu-Chen , Chang Shan-Yueh , Kuo Terry B. J. , Yang Cheryl C. H. , Chien Wu-Chien , Tzeng Nian-Sheng
Published: June 2021

One recent study showed that atomoxetine-oxybutynin combination (AOC) use is effective in reducing obstructive sleep apnea (OSA) severity. We used a nationwide database to examine the association between AOC use and the risk of OSA incidence. This retrospective cohort study used Taiwan’s National Health Insurance Research Database between the years 2000 and 2015. The patients who used atomoxetine or oxybutynin were included as an exposed cohort. The exposed and unexposed groups were selected in a ratio of 1:3 with sex, age, and index year matching. We used the multivariate Cox proportional regression model to evaluate the association between AOC use and the risk of an incident diagnosis of OSA. The incidence rates of OSA in the exposed cohort (N = 8940) and the unexposed cohort (N = 26,820), were 21.92 and 22.93 per 100,000 person-years, respectively. The adjusted hazard ratio of oxybutynin use only and AOC with a treatment duration of ≥ 366 days were 0.307 (95% CI 0.204–0.995, P = 0.045) and 0.299 (95% CI 0.102–0.933, P = 0.002), respectively. Long-term atomoxetine-oxybutynin combination therapy may be beneficial to reduce the risk of obstructive sleep apnea. Further studies to examine these mechanisms are warranted.
Associations of fitness, motor competence, and adiposity with the indicators of physical activity intensity during different physical activities in children
Authors: Haapala Eero A. , Gao Ying , Hartikainen Jani , Rantalainen Timo , Finni Taija
Published: June 2021

We investigated the associations of peak oxygen uptake (V̇O2peak), ventilatory threshold (VT), muscle strength, motor competence (MC), and adiposity with the indicators of PA intensity during different physical activities used to create absolute PA intensity cut-offs among 35 children 7–11-years-of-age. V̇O2peakwas defined as the highest V̇O2achieved in the maximal cardiopulmonary exercise test (CPET) on a cycle ergometer, self-paced running, or running on a treadmill at 8 km/h. VT was defined from the CPET data. Peak isometric knee extensor and flexor strength was assessed by a dynamometer, MC by the Körperkoordination test für Kinder tests, and body composition by the bioelectrical impedance analysis. PA intensity was assessed using V̇O2as a % of V̇O2reserveor V̇O2at VT, mean amplitude deviation (MAD) measured by accelerometry, metabolic equivalent of task (MET), and muscle activity measured by textile electromyography during walking or running on a treadmill at 4, 6, and 8 km/h, playing hopscotch, walking up and down the stairs, self-paced walking, and self-paced running. Children with lower V̇O2peak, V̇O2at VT, and MC operated at higher intensity level during given physical task than their peers with higher fitness and MC when PA intensity was expressed using relative PA intensity using V̇O2as a % of V̇O2reserveor V̇O2at VT (p < 0.05). MAD and METs during different tasks were not able to discriminate PA intensity between children with varying levels of physical fitness or MC. Traditionally used absolute measures of PA intensity based on accelerometry or MET underestimated PA intensity in children with lower V̇O2peak, V̇O2at VT, and MC.
SETD4-expressing cells contribute to pancreatic development and response to cerulein induced pancreatitis injury
Authors: Tian Jin-Ze , Xing Sheng , Feng Jing-Yi , Yang Shu-Hua , Ding Yan-Fu , Huang Xue-Ting , Yang Jin-Shu , Yang Wei-Jun
Published: June 2021

In the adult pancreas, the presence of progenitor or stem cells and their potential involvement in homeostasis and regeneration remains unclear. Here, we identify that SET domain-containing protein 4 (SETD4), a histone lysine methyltransferase, is expressed in a small cell population in the adult mouse pancreas. Genetic lineage tracing shows that during pancreatic development, descendants of SETD4+cells make up over 70% of pancreatic cells and then contribute to each pancreatic lineage during pancreatic homeostasis. SETD4+cells generate newborn acinar cells in response to cerulein-induced pancreatitis in acinar compartments. Ablation of SETD4+cells compromises regeneration of acinar cells, in contrast to controls. Our findings provide a new cellular narrative for pancreatic development, homeostasis and response to injury via a small SETD4+cell population. Potential applications may act to preserve pancreatic function in case of pancreatic disease and/or damage.
Real-time prediction of Poisson’s ratio from drilling parameters using machine learning tools
Authors: Siddig Osama , Gamal Hany , Elkatatny Salaheldin , Abdulraheem Abdulazeez
Published: June 2021

Rock elastic properties such as Poisson’s ratio influence wellbore stability, in-situ stresses estimation, drilling performance, and hydraulic fracturing design. Conventionally, Poisson’s ratio estimation requires either laboratory experiments or derived from sonic logs, the main concerns of these methods are the data and samples availability, costs, and time-consumption. In this paper, an alternative real-time technique utilizing drilling parameters and machine learning was presented. The main added value of this approach is that the drilling parameters are more likely to be available and could be collected in real-time during drilling operation without additional cost. These parameters include weight on bit, penetration rate, pump rate, standpipe pressure, and torque. Two machine learning algorithms were used, artificial neural network (ANN) and adaptive neuro-fuzzy inference system (ANFIS). To train and test the models, 2905 data points from one well were used, while 2912 data points from a different well were used for model validation. The lithology of both wells contains carbonate, sandstone, and shale. Optimization on different tuning parameters in the algorithm was conducted to ensure the best prediction was achieved. A good match between the actual and predicted Poisson’s ratio was achieved in both methods with correlation coefficients between 0.98 and 0.99 using ANN and between 0.97 and 0.98 using ANFIS. The average absolute percentage error values were between 1 and 2% in ANN predictions and around 2% when ANFIS was used. Based on these results, the employment of drilling data and machine learning is a strong tool for real-time prediction of geomechanical properties without additional cost.
Use of skeletal muscle index as a predictor of short-term mortality in patients with acute-on-chronic liver failure
Authors: Li Tongzeng , Xu Manman , Kong Ming , Song Wenyan , Duan Zhongping , Chen Yu
Published: June 2021

Sarcopenia is a well-recognized factor affecting the prognosis of chronic liver disease, but its impact on acute decompensation underlying chronic liver disease is unknown. This study evaluated the impact of sarcopenia on short-term mortality in patients with acute-on-chronic liver failure (ACLF). One hundred and seventy-one ACLF patients who underwent abdominal CT between 2015 and 2019 were retrospectively included in this study. Skeletal muscle index at the third lumbar vertebrae (L3-SMI) was used to diagnose sarcopenia.The ACLF patients in this study had a L3-SMI of 41.2 ± 8.3 cm2/m2 and sarcopenia was present in 95/171 (55.6%) patients. Body mass index (BMI), cirrhosis, and higher serum bilirubin were independently associated with sarcopenia. Following multivariate Cox regression analysis, cirrhosis (hazard ratio (HR) 2.758, 95%CI 1.323–5.750), serum bilirubin (HR 1.049, 95%CI 1.026–1.073), and international normalized ratio (INR) (HR 1.725, 95%CI 1.263–2.355) were associated with 3-month mortality (P < 0.05), whereas L3-SMI and sarcopenia were not. A subgroup analysis of the factors related to sarcopenia showed that sarcopenia was still not predictive of short-term outcome in ACLF patients. L3-SMI and sarcopenia are not associated with short-term mortality in patients with ACLF.
Quantitative proteomics analysis of glioblastoma cell lines after lncRNA HULC silencing
Authors: Ye Shan , Wu Jing , Wang Yiran , Hu Yuchen , Yin Tiantian , He Jie
Published: June 2021

Glioblastoma multiforme (GBM) is a life-threatening brain tumor. This study aimed to identify potential targets of the long noncoding RNA (lncRNA) HULC that promoted the progression of GBM. Two U87 cell lines were constructed: HULC-siRNA and negative control (NC). Quantitative real-time PCR (qRT-PCR) was performed to validate the transfection efficiency of HULC silencing vector. Mass spectrometry (MS) was used to generate proteomic profiles for the two cell lines. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to distinguish HULC-related genes and pathway mapping. Colony formation, Transwell, and wound-healing assays were used to investigate the functional effects of HULC knockdown on GBM. We identified 112 up-regulated proteins and 24 down-regulated proteins from a total of 4360 quantified proteins. GO enrichment illustrated that these proteins were mainly involved in organelle structure, catalysis, cell movement, and material metabolism. KEGG pathway analysis indicated that some of these proteins were significantly enriched in tight junction, metabolic pathways, and arachidonic acid metabolism. In vitro experiments demonstrated that HULC knockdown inhibited GBM cell proliferation, invasion, and migration. Our KEGG analyses revealed that PLA2G4A was a shared protein in several enriched pathways. HULC silencing significantly down-regulated the expression of PLA2G4A. Knockdown of HULC changed the proteomic characteristics of GBM and altered the behaviors of GBM cells. Specifically, we identified PLA2G4A as an HULC target in GBM. This study provides a new perspective on the mechanisms and potential drug targets of GBM treatment.
Classification of caries in third molars on panoramic radiographs using deep learning
Authors: Vinayahalingam Shankeeth , Kempers Steven , Limon Lorenzo , Deibel Dionne , Maal Thomas , Hanisch Marcel , Bergé Stefaan , Xi Tong
Published: June 2021

The objective of this study is to assess the classification accuracy of dental caries on panoramic radiographs using deep-learning algorithms. A convolutional neural network (CNN) was trained on a reference data set consisted of 400 cropped panoramic images in the classification of carious lesions in mandibular and maxillary third molars, based on the CNN MobileNet V2. For this pilot study, the trained MobileNet V2 was applied on a test set consisting of 100 cropped PR(s). The classification accuracy and the area-under-the-curve (AUC) were calculated. The proposed method achieved an accuracy of 0.87, a sensitivity of 0.86, a specificity of 0.88 and an AUC of 0.90 for the classification of carious lesions of third molars on PR(s). A high accuracy was achieved in caries classification in third molars based on the MobileNet V2 algorithm as presented. This is beneficial for the further development of a deep-learning based automated third molar removal assessment in future.
Corneal transplantation for keratoconus in South Korea
Authors: Hwang Sungsoon , Chung Tae-Young , Han Jisang , Kim Kyunga , Lim Dong Hui
Published: June 2021

This nationwide population-based study investigated the incidence rate of and risk factors for the progression to corneal transplantation in patients with keratoconus in South Korea using claims data from the Health Insurance Review and Assessment service. Among the entire South Korean population, 10,612 patients newly diagnosed with keratoconus between January 2010 and June 2015 were identified and included in the study. During the study period, 124 patients (1.17%) underwent corneal transplantation, with an average follow-up period of 2.97 ± 1.59 years. The incidence rate of corneal transplantation in patients with keratoconus was 4.46 cases per 1000 person-years. The rate of corneal transplantation for keratoconus was relatively low in South Korea compared to other countries. Multivariate Cox regression analysis revealed that male sex (HR 2.37; 95% CI 1.61–3.50; P < 0.001), severe atopic dermatitis (HR 2.32; 95% CI 1.02–5.28; P = 0.044), obstructive sleep apnea (HR 9.78; 95% CI 1.36–70.10; P = 0.023), and intellectual disability (HR 4.48; 95% CI 1.33–15.11; P = 0.016) significantly increased the risk of progression to corneal transplantation. In patients with keratoconus, male sex, severe atopic dermatitis, obstructive sleep apnea, and intellectual disability were associated with an increased risk of corneal transplantation.
Association between subjective oral dysfunction and locomotive syndrome in community-dwelling older adults
Authors: Nakamura Misa , Imaoka Masakazu , Nakao Hidetoshi , Hida Mitsumasa , Tazaki Fumie , Imai Ryota , Utsunomiya Hirotoshi , Hashizume Hiroshi
Published: June 2021

The need for support and care is a major problem facing societies around the world. Locomotive syndrome (LS) refers to a condition in which people require healthcare services because of problems associated with locomotion. Oral dysfunction is also associated with various long-term care factors including activities of daily living. The purpose of this study was to determine the association between oral dysfunction and LS. The study participants were 407 elderly people living in a rural area in Japan. Evaluation of oral dysfunction was based on subjective judgment by each participant. LS was assessed using Locomo-25, which is a self-administered questionnaire and was defined by a Locomo-25 score ≥ 7 points. Those with a “decline in masticatory function” and “difficulty swallowing” had higher odds of LS than those without these dysfunctions (odds ratio (OR) = 2.134, 2.007, respectively). Furthermore, participants with a Locomo-25 score ≥ 11 had higher odds of a “decline in masticatory function” (OR = 2.657) than those with a Locomo-25 score < 11, and those with a Locomo-25 score ≥ 9 had higher odds of “difficulty swallowing” (OR = 2.411) than those with a Locomo-25 score < 9. These findings suggest that a strong relationship exists between oral dysfunction and LS.
Millimeter-sized smart sensors reveal that a solar refuge protects tree snail Partula hyalina from extirpation
Authors: Bick Cindy S. , Lee Inhee , Coote Trevor , Haponski Amanda E. , Blaauw David , Foighil Diarmaid Ó
Published: June 2021

Pacific Island land snails are highly endangered due in part to misguided biological control programs employing the alien predator Euglandina rosea. Its victims include the fabled Society Island partulid tree snail fauna, but a few members have avoided extirpation in the wild, including the distinctly white-shelled Partula hyalina. High albedo shell coloration can facilitate land snail survival in open, sunlit environments and we hypothesized that P. hyalina has a solar refuge from the predator. We developed a 2.2 × 4.8 × 2.4 mm smart solar sensor to test this hypothesis and found that extant P. hyalina populations on Tahiti are restricted to forest edge habitats, where they are routinely exposed to significantly higher solar radiation levels than those endured by the predator. Long-term survival of this species on Tahiti may require proactive conservation of its forest edge solar refugia and our study demonstrates the utility of miniaturized smart sensors in invertebrate ecology and conservation.
Dynamic relationships between spontaneous and evoked electrophysiological activity
Authors: Wainio-Theberge Soren , Wolff Annemarie , Northoff Georg
Published: June 2021

Spontaneous neural activity fluctuations have been shown to influence trial-by-trial variation in perceptual, cognitive, and behavioral outcomes. However, the complex electrophysiological mechanisms by which these fluctuations shape stimulus-evoked neural activity remain largely to be explored. Employing a large-scale magnetoencephalographic dataset and an electroencephalographic replication dataset, we investigate the relationship between spontaneous and evoked neural activity across a range of electrophysiological variables. We observe that for high-frequency activity, high pre-stimulus amplitudes lead to greater evoked desynchronization, while for low frequencies, high pre-stimulus amplitudes induce larger degrees of event-related synchronization. We further decompose electrophysiological power into oscillatory and scale-free components, demonstrating different patterns of spontaneous-evoked correlation for each component. Finally, we find correlations between spontaneous and evoked time-domain electrophysiological signals. Overall, we demonstrate that the dynamics of multiple electrophysiological variables exhibit distinct relationships between their spontaneous and evoked activity, a result which carries implications for experimental design and analysis in non-invasive electrophysiology.
The damping and structural properties of dragonfly and damselfly wings during dynamic movement
Authors: Lietz Carina , Schaber Clemens F. , Gorb Stanislav N. , Rajabi Hamed
Published: June 2021

For flying insects, stability is essential to maintain the orientation and direction of motion in flight. Flight instability is caused by a variety of factors, such as intended abrupt flight manoeuvres and unwanted environmental disturbances. Although wings play a key role in insect flight stability, little is known about their oscillatory behaviour. Here we present the first systematic study of insect wing damping. We show that different wing regions have almost identical damping properties. The mean damping ratio of fresh wings is noticeably higher than that previously thought. Flight muscles and hemolymph have almost no ‘direct’ influence on the wing damping. In contrast, the involvement of the wing hinge can significantly increase damping. We also show that although desiccation reduces the wing damping ratio, rehydration leads to full recovery of damping properties after desiccation. Hence, we expect hemolymph to influence the wing damping indirectly, by continuously hydrating the wing system.
Hypergraph reconstruction from network data
Authors: Young Jean-Gabriel , Petri Giovanni , Peixoto Tiago P.
Published: June 2021

Networks can describe the structure of a wide variety of complex systems by specifying which pairs of entities in the system are connected. While such pairwise representations are flexible, they are not necessarily appropriate when the fundamental interactions involve more than two entities at the same time. Pairwise representations nonetheless remain ubiquitous, because higher-order interactions are often not recorded explicitly in network data. Here, we introduce a Bayesian approach to reconstruct latent higher-order interactions from ordinary pairwise network data. Our method is based on the principle of parsimony and only includes higher-order structures when there is sufficient statistical evidence for them. We demonstrate its applicability to a wide range of datasets, both synthetic and empirical.
Seasonal sea ice persisted through the Holocene Thermal Maximum at 80°N
Authors: Pieńkowski Anna J. , Husum Katrine , Belt Simon T. , Ninnemann Ulysses , Köseoğlu Denizcan , Divine Dmitry V. , Smik Lukas , Knies Jochen , Hogan Kelly , Noormets Riko
Published: June 2021

The cryospheric response to climatic warming responsible for recent Arctic sea ice decline can be elucidated using marine geological archives which offer an important long-term perspective. The Holocene Thermal Maximum, between 10 and 6 thousand years ago, provides an opportunity to investigate sea ice during a warmer-than-present interval. Here we use organic biomarkers and benthic foraminiferal stable isotope data from two sediment cores in the northernmost Barents Sea (>80 °N) to reconstruct seasonal sea ice between 11.7 and 9.1 thousand years ago. We identify the continued persistence of sea-ice biomarkers which suggest spring sea ice concentrations as high as 55%. During the same period, high foraminiferal oxygen stable isotopes and elevated phytoplankton biomarker concentrations indicate the influence of warm Atlantic-derived bottom water and peak biological productivity, respectively. We conclude that seasonal sea ice persisted in the northern Barents Sea during the Holocene Thermal Maximum, despite warmer-than-present conditions and Atlantic Water inflow.