bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning discovery of missing links that mediate alternative branches to plant alkaloids
Authors: Vavricka Christopher J. , Takahashi Shunsuke , Watanabe Naoki , Takenaka Musashi , Matsuda Mami , Yoshida Takanobu , Suzuki Ryo , Kiyota Hiromasa , Li Jianyong , Minami Hiromichi , Ishii Jun , Tsuge Kenji , Araki Michihiro , Kondo Akihiko , Hasunuma Tomohisa 
Published: March 2022

AbstractEngineering the microbial production of secondary metabolites is limited by the known reactions of correctly annotated enzymes. Therefore, the machine learning discovery of specialized enzymes offers great potential to expand the range of biosynthesis pathways. Benzylisoquinoline alkaloid production is a model example of metabolic engineering with potential to revolutionize the paradigm of sustainable biomanufacturing. Existing bacterial studies utilize a norlaudanosoline pathway, whereas plants contain a more stable norcoclaurine pathway, which is exploited in yeast. However, committed aromatic precursors are still produced using microbial enzymes that remain elusive in plants, and additional downstream missing links remain hidden within highly duplicated plant gene families. In the current study, machine learning is applied to predict and select plant missing link enzymes from homologous candidate sequences. Metabolomics-based characterization of the selected sequences reveals potential aromatic acetaldehyde synthases and phenylpyruvate decarboxylases in reconstructed plant gene-only benzylisoquinoline alkaloid pathways from tyrosine. Synergistic application of the aryl acetaldehyde producing enzymes results in enhanced benzylisoquinoline alkaloid production through hybrid norcoclaurine and norlaudanosoline pathways.
Generation of a μ-1,2-hydroperoxo FeIIIFeIII and a μ-1,2-peroxo FeIVFeIII Complex
Authors: Walleck Stephan , Zimmermann Thomas Philipp , Hachmeister Henning , Pilger Christian , Huser Thomas , Katz Sagie , Hildebrandt Peter , Stammler Anja , Bögge Hartmut , Bill Eckhard , Glaser Thorsten 
Published: March 2022

Abstractμ-1,2-Peroxo-diferric intermediates (P) of non-heme diiron enzymes are proposed to convert upon protonation either to high-valent active species or to activated P′ intermediates via hydroperoxo-diferric intermediates. Protonation of synthetic μ-1,2-peroxo model complexes occurred at the μ-oxo and not at the μ-1,2-peroxo bridge. Here we report a stable μ-1,2-peroxo complex {FeIII(μ-O)(μ-1,2-O2)FeIII} using a dinucleating ligand and study its reactivity. The reversible oxidation and protonation of the μ-1,2-peroxo-diferric complex provide μ-1,2-peroxo FeIVFeIII and μ-1,2-hydroperoxo-diferric species, respectively. Neither the oxidation nor the protonation induces a strong electrophilic reactivity. Hence, the observed intramolecular C-H hydroxylation of preorganized methyl groups of the parent μ-1,2-peroxo-diferric complex should occur via conversion to a more electrophilic high-valent species. The thorough characterization of these species provides structure-spectroscopy correlations allowing insights into the formation and reactivities of hydroperoxo intermediates in diiron enzymes and their conversion to activated P′ or high-valent intermediates.
Impaired bidirectional communication between interneurons and oligodendrocyte precursor cells affects social cognitive behavior
Authors: Fang Li-Pao , Zhao Na , Caudal Laura C. , Chang Hsin-Fang , Zhao Renping , Lin Ching-Hsin , Hainz Nadine , Meier Carola , Bettler Bernhard , Huang Wenhui , Scheller Anja , Kirchhoff Frank , Bai Xianshu 
Published: March 2022

AbstractCortical neural circuits are complex but very precise networks of balanced excitation and inhibition. Yet, the molecular and cellular mechanisms that form the balance are just beginning to emerge. Here, using conditional γ-aminobutyric acid receptor B1- deficient mice we identify a γ-aminobutyric acid/tumor necrosis factor superfamily member 12-mediated bidirectional communication pathway between parvalbumin-positive fast spiking interneurons and oligodendrocyte precursor cells that determines the density and function of interneurons in the developing medial prefrontal cortex. Interruption of the GABAergic signaling to oligodendrocyte precursor cells results in reduced myelination and hypoactivity of interneurons, strong changes of cortical network activities and impaired social cognitive behavior. In conclusion, glial transmitter receptors are pivotal elements in finetuning distinct brain functions.
Unbiasing fermionic quantum Monte Carlo with a quantum computer
Authors: Huggins William J. , O’Gorman Bryan A. , Rubin Nicholas C. , Reichman David R. , Babbush Ryan , Lee Joonho 
Published: March 2022

AbstractInteracting many-electron problems pose some of the greatest computational challenges in science, with essential applications across many fields. The solutions to these problems will offer accurate predictions of chemical reactivity and kinetics, and other properties of quantum systems1–4. Fermionic quantum Monte Carlo (QMC) methods5,6, which use a statistical sampling of the ground state, are among the most powerful approaches to these problems. Controlling the fermionic sign problem with constraints ensures the efficiency of QMC at the expense of potentially significant biases owing to the limited flexibility of classical computation. Here we propose an approach that combines constrained QMC with quantum computation to reduce such biases. We implement our scheme experimentally using up to 16 qubits to unbias constrained QMC calculations performed on chemical systems with as many as 120 orbitals. These experiments represent the largest chemistry simulations performed with the help of quantum computers, while achieving accuracy that is competitive with state-of-the-art classical methods without burdensome error mitigation. Compared with the popular variational quantum eigensolver7,8, our hybrid quantum-classical computational model offers an alternative path towards achieving a practical quantum advantage for the electronic structure problem without demanding exceedingly accurate preparation and measurement of the ground-state wavefunction.
High-resolution laser resonances of antiprotonic helium in superfluid 4He
Authors: Sótér Anna , Aghai-Khozani Hossein , Barna Dániel , Dax Andreas , Venturelli Luca , Hori Masaki 
Published: March 2022

AbstractWhen atoms are placed into liquids, their optical spectral lines corresponding to the electronic transitions are greatly broadened compared to those of single, isolated atoms. This linewidth increase can often reach a factor of more than a million, obscuring spectroscopic structures and preventing high-resolution spectroscopy, even when superfluid helium, which is the most transparent, cold and chemically inert liquid, is used as the host material1–6. Here we show that when an exotic helium atom with a constituent antiproton7–9 is embedded into superfluid helium, its visible-wavelength spectral line retains a sub-gigahertz linewidth. An abrupt reduction in the linewidth of the antiprotonic laser resonance was observed when the liquid surrounding the atom transitioned into the superfluid phase. This resolved the hyperfine structure arising from the spin–spin interaction between the electron and antiproton with a relative spectral resolution of two parts in 106, even though the antiprotonic helium resided in a dense matrix of normal matter atoms. The electron shell of the antiprotonic atom retains a small radius of approximately 40 picometres during the laser excitation7. This implies that other helium atoms containing antinuclei, as well as negatively charged mesons and hyperons that include strange quarks formed in superfluid helium, may be studied by laser spectroscopy with a high spectral resolution, enabling the determination of the particle masses9. The sharp spectral lines may enable the detection of cosmic-ray antiprotons10,11 or searches for antideuterons12 that come to rest in liquid helium targets.
Tumor cell identification and classification in esophageal adenocarcinoma specimens by hyperspectral imaging
Authors: Maktabi Marianne , Wichmann Yannis , Köhler Hannes , Ahle Henning , Lorenz Dietmar , Bange Michael , Braun Susanne , Gockel Ines , Chalopin Claire , Thieme René 
Published: March 2022

AbstractEsophageal cancer is the sixth leading cause of cancer-related death worldwide. Histopathological confirmation is a key step in tumor diagnosis. Therefore, simplification in decision-making by discrimination between malignant and non-malignant cells of histological specimens can be provided by combination of new imaging technology and artificial intelligence (AI). In this work, hyperspectral imaging (HSI) data from 95 patients were used to classify three different histopathological features (squamous epithelium cells, esophageal adenocarcinoma (EAC) cells, and tumor stroma cells), based on a multi-layer perceptron with two hidden layers. We achieved an accuracy of 78% for EAC and stroma cells, and 80% for squamous epithelium. HSI combined with machine learning algorithms is a promising and innovative technique, which allows image acquisition beyond Red–Green–Blue (RGB) images. Further method validation and standardization will be necessary, before automated tumor cell identification algorithms can be used in daily clinical practice.
Caller ID for Risso’s and Pacific White-sided dolphins
Authors: Al-Badrawi Mahdi H. , Liang Yue , Seger Kerri D. , Foster Christopher M. , Kirsch Nicholas J. 
Published: March 2022

AbstractTracking species with expanding ranges is crucial to conservation efforts and some typically temperate marine species are spreading northward into the Arctic Ocean. Risso’s (Gg) and Pacific white-sided (Lo) dolphins have been documented spreading poleward. Further, they make very similar sounds, so it is difficult for both human analysts and classification algorithms to tell them apart. Using automatic detectors and classifiers on large acoustic datasets would improve the efficiency of monitoring these species. variational mode decomposition (VMD) provides both an easier visualization tool for human analysts and exhibited robustness to background noise while extracting features in pulsed signals with very similar spectral properties. The goal of this work was to develop a new visualization tool using VMD and a statistics-based classification algorithm to differentiate similar pulsed signals. The proposed VMD method achieved 81% accuracy, even when using audio files with low SNR that did not have concurrent visual survey data. While many dolphins whistle, pulsed signals are one of the more useful vocalizations to use in detection and classification because of their species-specific acoustic features. Automating the VMD method and expanding it to other dolphin species that have very similar pulsed signals would complement current detection and classification methods and lead to a more complete understanding of ecosystem dynamics under a changing climate.
Sleep phase and pre-sleep arousal predicted co-developmental trajectories of pain and insomnia within adolescence
Authors: Arnison Tor , Schrooten Martien G. S. , Bauducco Serena , Jansson-Fröjmark Markus , Persson Jonas 
Published: March 2022

AbstractThe onset of both chronic pain and insomnia is high during adolescence. Although a bidirectional relationship between pain and insomnia has support, how pain and sleep co-develop throughout adolescence remains unknown. Sleep–wake patterns, pre-sleep behavior and pre-sleep arousal may influence the co-development of pain and insomnia. Four waves of longitudinal self-report data were used (Nbaseline = 2767, Agebaseline M = 13.65 years, SD = 0.65). Multidimensional growth mixture modeling was used to identify four subgroups of adolescents with different concurrent trajectories of pain and insomnia. The trajectories followed each other across time in all classes: one class of consistently low pain and insomnia (68.7%), one class with persistent high symptoms (4.9%), as well as one class of increasing (13.9%), and one of decreasing (12.5%), trajectories. Later sleep–wake patterns and more pre-sleep cognitive-emotional arousal predicted both increasing and decreasing trajectories of concurrent pain and insomnia. The current study showed that developmental trajectories of pain and insomnia follow each other within adolescents and across adolescence. Both sleep-phase focused interventions as well as psychological interventions that focus on pre-sleep cognitive-emotional arousal may prove beneficial for adolescents with comorbid pain and insomnia.
Looking beyond community structure leads to the discovery of dynamical communities in weighted networks
Authors: Nathe Chad , Gambuzza Lucia Valentina , Frasca Mattia , Sorrentino Francesco 
Published: March 2022

AbstractA fundamental question is whether groups of nodes of a complex network can possibly display long-term cluster-synchronized behavior. While this question has been addressed for the restricted classes of unweighted and labeled graphs, it remains an open problem for the more general class of weighted networks. The emergence of coordinated motion of nodes in natural and technological networks is directly related to the network structure through the concept of an equitable partition, which determines which nodes can show long-term synchronized behavior and which nodes cannot. We provide a method to detect the presence of nearly equitable partitions in weighted networks, based on minimal information about the network structure. With this approach we are able to discover the presence of dynamical communities in both synthetic and real technological, biological, and social networks, to a statistically significant level. We show that our approach based on dynamical communities is better at predicting the emergence of synchronized behavior than existing methods to detect community structure.
The surgical outcome of multilevel anterior cervical discectomy and fusion in myelopathic elderly and younger patients
Authors: Luo Chi-An , Lim Austin Samuel , Lu Meng-Ling , Chiu Ping-Yeh , Lai Po-Liang , Niu Chi-Chien 
Published: March 2022

AbstractThe elderly population has an increased risk of degenerative cervical myelopathy due to multilevel disease, causing motor and sensory dysfunctions and a poor quality of life. Multilevel anterior cervical discectomy and fusion (ACDF) is an alternative surgical treatment option, but has a perceived higher risk of complications. The goal of this study is to report the outcome. We retrospectively reviewed patients from 2006 to 2019 undergoing multilevel ACDF for degenerative cervical myelopathy and compared outcomes and complications between elder patients (aged 70 and above) and younger patients (below 70). The patients’ comorbidities, and postoperative complications, radiographic parameters such as C2–C7 Cobb angle, C2–C7 sagittal vertical axis, inter-body height of surgical levels and fusion rate were recorded. Japanese Orthopaedic Association (JOA) score and modified Odom’s score were collected. Included were 18 elderly (mean age 74, range 70–87) and 45 young patients (mean age 56, range 43–65) with a follow-up of 43.8 and 55.5 months respectively. Three-level ACDF was the most common. The ratios of ASA class III patients were 94.4% and 48.9% (p < 0.001). The Charlson comorbidity indexes were 4.3 ± 1.03 and 2.1 ± 1.11 (p < 0.001). The average lengths of hospital stays were 4.9 and 4.6 days. Eleven patients (61.1%) in the elderly group experienced at least one short-term complication, compared with 16 patients (35.6%) in the younger group (p < 0.05). The middle-term complications were comparable (22.2% and 20.0%). The JOA score, recovery rate and modified Odom score showed comparable result between groups. Despite its extensiveness, multilevel ACDF is feasible for the elder patients with good clinical outcome and fusion rate. When compared to younger cohort, there is a trend of lower preoperative JOA score and recovery rate. The short-term complication rate is higher in the elderly group.
Generalized ComBat harmonization methods for radiomic features with multi-modal distributions and multiple batch effects
Authors: Horng Hannah , Singh Apurva , Yousefi Bardia , Cohen Eric A. , Haghighi Babak , Katz Sharyn , Noël Peter B. , Shinohara Russell T. , Kontos Despina 
Published: March 2022

AbstractRadiomic features have a wide range of clinical applications, but variability due to image acquisition factors can affect their performance. The harmonization tool ComBat is a promising solution but is limited by inability to harmonize multimodal distributions, unknown imaging parameters, and multiple imaging parameters. In this study, we propose two methods for addressing these limitations. We propose a sequential method that allows for harmonization of radiomic features by multiple imaging parameters (Nested ComBat). We also employ a Gaussian Mixture Model (GMM)-based method (GMM ComBat) where scans are split into groupings based on the shape of the distribution used for harmonization as a batch effect and subsequent harmonization by a known imaging parameter. These two methods were evaluated on features extracted with CapTK and PyRadiomics from two public lung computed tomography datasets. We found that Nested ComBat exhibited similar performance to standard ComBat in reducing the percentage of features with statistically significant differences in distribution attributable to imaging parameters. GMM ComBat improved harmonization performance over standard ComBat (− 11%, − 10% for Lung3/CAPTK, Lung3/PyRadiomics harmonizing by kernel resolution). Features harmonized with a variant of the Nested method and the GMM split method demonstrated similar c-statistics and Kaplan–Meier curves when used in survival analyses.
Ingroup favoritism overrides fairness when resources are limited
Authors: Chae Jihwan , Kim Kunil , Kim Yuri , Lim Gahyun , Kim Daeeun , Kim Hackjin 
Published: March 2022

AbstractIngroup favoritism and fairness are two potentially competing motives guiding intergroup behaviors in human. Here, we investigate if and how limited resources can modulate the way these two motives affect individuals’ decisions in intergroup situation. In the present study, participants (N = 58) were asked to accept or reject three types of resource allocation proposals generated by a computer: the ingroup advantageous condition, outgroup advantageous condition, and neutral condition. In general, participants were more willing to accept the proposals in the ingroup advantageous condition than the outgroup advantageous or the neutral conditions, and also in the moderate inequality than the extreme inequality condition. This may indicate that people sought a careful balance between ingroup favoritism and fairness, although we also found marked individual differences in their preferences for ingroup favoritism or fairness. Importantly, as predicted, participants were more likely to show ingroup favoritism only when limited resources affect the well-being of ingroup members. The present study provides novel insights into the situational and personality factors affecting human intergroup behaviors, shedding light on motives underlying intergroup conflicts prevalent in human societies.
Expanding the clinical spectrum of COL2A1 related disorders by a mass like phenotype
Authors: Demal Till Joscha , Scholz Tasja , Schüler Helke , Olfe Jakob , Fröhlich Anja , Speth Fabian , von Kodolitsch Yskert , Mir Thomas S. , Reichenspurner Hermann , Kubisch Christian , Hempel Maja , Rosenberger Georg 
Published: March 2022

AbstractMASS phenotype is a connective tissue disorder clinically overlapping with Marfan syndrome and caused by pathogenic variants in FBN1. We report four patients from three families presenting with a MASS-like phenotype consisting of tall stature, arachnodactyly, spinal deformations, dural ectasia, pectus and/or feet deformations, osteoarthritis, and/or high arched palate. Gene panel sequencing was negative for FBN1 variants. However, it revealed likely pathogenic missense variants in three individuals [c.3936G > T p.(Lys1312Asn), c.193G > A p.(Asp65Asn)] and a missense variant of unknown significance in the fourth patient [c.4013G > A p.(Ser1338Asn)] in propeptide coding regions of COL2A1. Pathogenic COL2A1 variants are associated with type II collagenopathies comprising a remarkable clinical variablility. Main features include skeletal dysplasia, ocular anomalies, and auditory defects. A MASS-like phenotype has not been associated with COL2A1 variants before. Thus, the identification of likely pathogenic COL2A1 variants in our patients expands the phenotypic spectrum of type II collagenopathies and suggests that a MASS-like phenotype can be assigned to various hereditary disorders of connective tissue. We compare the phenotypes of our patients with related disorders of connective tissue and discuss possible pathomechanisms and genotype–phenotype correlations for the identified COL2A1 variants. Our data recommend COL2A1 sequencing in FBN1-negative patients suggestive for MASS/Marfan-like phenotype (without aortopathy).
The role of the right prefrontal cortex in the retrieval of weak representations
Authors: Yi Kyongmyon , Heo Juyeon , Hong Jiyun , Kim Chobok 
Published: March 2022

AbstractAlthough recent studies have shown the importance of control in creative problem solving, the neural mechanisms of control processes engaged in retrieval of weak representations, which is closely linked to creative problem solving, remain unclear. The current study aimed to examine the neural mechanisms associated with retrieval of weak representations using functional magnetic resonance imaging and their potential relationships with creativity task performance. For this purpose, participants performed an experimental task that enabled us to directly compare between retrieval of previously unattended-and-weak representations and attended-and-strong representations. Imaging results indicated that the right anterior dorsolateral prefrontal cortex (aDLPFC) was selectively engaged in retrieval of weak representations. Moreover, the right aDLPFC activations were positively correlated with individuals’ creativity task performance but independent of attention-demanding task performance. We therefore suggest that the right aDLPFC plays a key role in retrieval of weak representations and may support creative problem solving.
Risk of colloidal and pseudo-colloidal transport of actinides in nitrate contaminated groundwater near a radioactive waste repository after bioremediation
Authors: Safonov Alexey , Lavrinovich Elena , Emel’yanov Alexander , Boldyrev Kirill , Kuryakov Vladimir , Rodygina Natalia , Zakharova Elena , Novikov Alexander 
Published: March 2022

AbstractThe possible role of biogeochemical processes in the transport of colloidal and pseudo-colloidal U, Np, and Pu during bioremediation of radionuclide- and nitrate-contaminated groundwater was investigated. In two laboratory experiments with water samples taken from contaminated aquifers before and post bioremediation, we found that microbial processes could cause clayed, ferruginous, and actinide colloids to coagulate. The main mechanisms are biogenic insoluble ferrous iron species formations (goethite, pyrrhotite, siderite, troilite, and ferrihydrite), the aggregation of clay particles by microbial metabolites, and the immobilization of actinides in the bacterial cells, large polymers, and iron and clayed sediments. This process decreases the risk of colloidal and pseudo-colloidal transport of actinides.