bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractPediatric 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

AbstractFor 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

AbstractQuantum 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

AbstractEducation 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

AbstractObesity 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

AbstractUnbalanced 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

AbstractMultidrug 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

AbstractCellular 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

AbstractAccurate 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

AbstractAlthough 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

AbstractProtein 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

AbstractAn 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

AbstractMedical 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.