bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incidence of invasive Group B Streptococcal infection and the risk of infant death and cerebral palsy: a Norwegian Cohort Study
Authors: Mynarek Maren , Bjellmo Solveig , Lydersen Stian , Afset Jan E. , Andersen Guro L. , Vik Torstein 
Published: July 2020

AbstractBackgroundGroup B Streptococcus (GBS) is the leading cause of invasive neonatal infection worldwide. In high-income countries mortality rates are 4–10%, and among survivors of GBS meningitis 30–50% have neurodevelopmental impairments. We hypothesized that invasive GBS infection was associated with increased risk of infant mortality and cerebral palsy (CP).MethodsAll children born alive in Norway during 1996–2012 were included. Data were collected from three national registers. Invasive GBS infection during infancy was categorized into early-onset disease (EOD), late-onset disease (LOD), and very late-onset disease (VLOD). Primary outcomes were infant mortality and CP.ResultsInvasive GBS infection was diagnosed in 625 children (incidence: 0.62 per 1000 live births; 95% confidence interval (CI): 0.57–0.67). The incidence of EOD was 0.41 (0.37–0.45), of LOD 0.20 (0.17–0.23), and of VLOD 0.012 (0.007–0.021). The annual incidence of LOD increased slightly. Among infected infants, 44 (7%) died (odds ratio (OR): 24.5; 95% CI: 18.0–33.3 compared with the background population). Among survivors, 24 (4.1%) children were later diagnosed with CP, compared with 1887 (0.19%) in the background population (OR: 22.9; 95% CI: 15.1–34.5).ConclusionDespite a relatively low incidence of invasive GBS infection in Norway, the risk of death and CP remains high. Improvements in prevention strategies are needed.ImpactDuring the first decade of the twenty-first century, invasive GBS disease in infancy is still associated with high mortality.Despite the overall low incidence of invasive GBS disease, the incidence of LOD increased during the study period.The finding that invasive GBS infection in the neonatal period or during infancy is associated with an excess risk of CP, comparable to the risk following moderate preterm birth and moderate low Apgar scores, adds to the existing literature.The results of this study emphasize the importance of adhering to guidelines and the need for better prevention strategies.
The model of cytokine release syndrome in CAR T-cell treatment for B-cell non-Hodgkin lymphoma
Authors: Wei Jianshu , Liu Yang , Wang Chunmeng , Zhang Yajing , Tong Chuan , Dai Guanghai , Wang Wei , Rasko John E. J. , Melenhorst J. Joseph , Qian Wenbin , Liang Aibin , Han Weidong 
Published: July 2020

AbstractChimeric antigen receptor T (CAR T) cell therapy has demonstrated efficacy in the treatment of haematologic malignancies. However, the accompanying adverse events, the most common of which is cytokine release syndrome (CRS), substantially limit its wide application. Due to its unique physiological characteristics, CRS in CAR T-cell treatment for B-cell non-Hodgkin lymphoma (B-NHL) may exhibit some special features. Although existing guidelines had greatly promoted the recognition and management of CRS, many recommendations are not fully applicable to B-NHL. Therefore, it is imperative to identify responses that are specific to CRS observed following CAR T treatment for B-NHL. Based on underlying biological processes and known pathophysiological mechanisms, we tentatively propose a new model to illustrate the occurrence and evolution of CAR T-cell-therapy-related CRS in B-NHL. In this model, tumour burden and bone marrow suppression are considered determinants of CRS. Novel phenomena after CAR T-cell infusion (such as local inflammatory response) are further identified. The proposed model will help us better understand the basic biology of CRS and recognize and manage it more rationally.
Facilitating patient-centred care for special care dentistry patients: A Quality Improvement Project in the Community Dental Service
Authors: Nic Iomhair Aoife , John Miriam 
Published: July 2020

Abstract
Aim
A Quality Improvement Project in one of the Special Care Dentistry (SCD) specialist centres in the School of Dentistry in Belfast aimed to improve the identification of the specific dental care needs of SCD patients from information available in the clinical record.

Methods
The Model for Improvement was used to define project objectives and subsequently implement changes to practice aimed at achieving those objectives through Plan-Do-Study-Act (PDSA) cycles. Continuous data collection to monitor performance was undertaken throughout.

Design
A Patient Needs Assessment Tool to be used during new SCD patient assessments was designed and introduced, with subsequent changes to the defined process for use following analysis of the success of the initial intervention.

Results
The amount of information on relevant dental care needs identifiable from clinical records following new SCD patient assessments increased from 30 to 90%, whereas the time taken to identify the relevant information decreased from 2 min and 31 s to 17 s.

Conclusion
The use of a Patient Needs Assessment pro-forma can achieve significant improvements in the extent and accessibility of information available to assist in the planning and delivery of appropriate and equitable care for SCD patients.
CircATRNL1 promotes epithelial–mesenchymal transition in endometriosis by upregulating Yes-associated protein 1 in vitro
Authors: Wang Dandan , Luo Yajuan , Wang Guangwei , Yang Qing 
Published: July 2020

AbstractEndometriosis is a common and benign gynecological disorder but exhibits malignant features. However, the underlying pathogenesis and pathophysiology of endometriosis remain unclear. Circular RNAs have been demonstrated to participate in the occurrence and progression of multiple diseases. This study was aimed to explore the roles of circATRNL1 in endometriosis in vitro. Based on the results of reverse transcription-quantitative polymerase chain reaction analysis, we found significant upregulation of circATRNL1 and Yes-associated protein 1 (YAP1), while downregulation of miR-141-3p and miR-200a-3p in ectopic tissues compared to eutopic tissues. The immunohistochemistry and western blot analysis showed differentially expressed epithelial–mesenchymal transition (EMT) markers between EuEM and EcEM tissues. The in vitro assays indicated that overexpression of circATRNL1 could promote the proliferation, migration, and invasion of Ishikawa cells, and induce EMT process, while circATRNL1 silencing showed the opposite effect. The mechanical investigation indicated that circATRNL1 upregulated YAP1 by sponging miR-141-3p and miR-200a-3p. Gain-of-function assays validated the inhibitory function of miR-141-3p and miR-200a-3p in endometriosis. The results of rescue assays confirmed the function of circATRNL1–miR-141-3p/miR-200a-3p–YAP1 axis on Ishikawa cells. Our findings demonstrate that abnormal upregulation of circATRNL1 regulates cell proliferation and motility and promotes EMT process via the miR-141-3p/miR-200a-3p–YAP1 axis in vitro, which could contribute to the progression of endometriosis.
An integrative ENCODE resource for cancer genomics
Authors: Zhang Jing , Lee Donghoon , Dhiman Vineet , Jiang Peng , Xu Jie , McGillivray Patrick , Yang Hongbo , Liu Jason , Meyerson William , Clarke Declan , Gu Mengting , Li Shantao , Lou Shaoke , Xu Jinrui , Lochovsky Lucas , Ung Matthew , Ma Lijia , Yu Shan , Cao Qin , Harmanci Arif , Yan Koon-Kiu , Sethi Anurag , Gürsoy Gamze , Schoenberg Michael Rutenberg , Rozowsky Joel , Warrell Jonathan , Emani Prashant , Yang Yucheng T. , Galeev Timur , Kong Xiangmeng , Liu Shuang , Li Xiaotong , Krishnan Jayanth , Feng Yanlin , Rivera-Mulia Juan Carlos , Adrian Jessica , Broach James R , Bolt Michael , Moran Jennifer , Fitzgerald Dominic , Dileep Vishnu , Liu Tingting , Mei Shenglin , Sasaki Takayo , Trevilla-Garcia Claudia , Wang Su , Wang Yanli , Zang Chongzhi , Wang Daifeng , Klein Robert J. , Snyder Michael , Gilbert David M. , Yip Kevin , Cheng Chao , Yue Feng , Liu X. Shirley , White Kevin P. , Gerstein Mark 
Published: July 2020

AbstractENCODE comprises thousands of functional genomics datasets, and the encyclopedia covers hundreds of cell types, providing a universal annotation for genome interpretation. However, for particular applications, it may be advantageous to use a customized annotation. Here, we develop such a custom annotation by leveraging advanced assays, such as eCLIP, Hi-C, and whole-genome STARR-seq on a number of data-rich ENCODE cell types. A key aspect of this annotation is comprehensive and experimentally derived networks of both transcription factors and RNA-binding proteins (TFs and RBPs). Cancer, a disease of system-wide dysregulation, is an ideal application for such a network-based annotation. Specifically, for cancer-associated cell types, we put regulators into hierarchies and measure their network change (rewiring) during oncogenesis. We also extensively survey TF-RBP crosstalk, highlighting how SUB1, a previously uncharacterized RBP, drives aberrant tumor expression and amplifies the effect of MYC, a well-known oncogenic TF. Furthermore, we show how our annotation allows us to place oncogenic transformations in the context of a broad cell space; here, many normal-to-tumor transitions move towards a stem-like state, while oncogene knockdowns show an opposing trend. Finally, we organize the resource into a coherent workflow to prioritize key elements and variants, in addition to regulators. We showcase the application of this prioritization to somatic burdening, cancer differential expression and GWAS. Targeted validations of the prioritized regulators, elements and variants using siRNA knockdowns, CRISPR-based editing, and luciferase assays demonstrate the value of the ENCODE resource.
Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors
Authors: Gordon Sean P. , Contreras-Moreira Bruno , Levy Joshua J. , Djamei Armin , Czedik-Eysenberg Angelika , Tartaglio Virginia S. , Session Adam , Martin Joel , Cartwright Amy , Katz Andrew , Singan Vasanth R. , Goltsman Eugene , Barry Kerrie , Dinh-Thi Vinh Ha , Chalhoub Boulos , Diaz-Perez Antonio , Sancho Ruben , Lusinska Joanna , Wolny Elzbieta , Nibau Candida , Doonan John H. , Mur Luis A. J. , Plott Chris , Jenkins Jerry , Hazen Samuel P. , Lee Scott J. , Shu Shengqiang , Goodstein David , Rokhsar Daniel , Schmutz Jeremy , Hasterok Robert , Catalan Pilar , Vogel John P. 
Published: July 2020

AbstractOur understanding of polyploid genome evolution is constrained because we cannot know the exact founders of a particular polyploid. To differentiate between founder effects and post polyploidization evolution, we use a pan-genomic approach to study the allotetraploid Brachypodium hybridum and its diploid progenitors. Comparative analysis suggests that most B. hybridum whole gene presence/absence variation is part of the standing variation in its diploid progenitors. Analysis of nuclear single nucleotide variants, plastomes and k-mers associated with retrotransposons reveals two independent origins for B. hybridum, ~1.4 and ~0.14 million years ago. Examination of gene expression in the younger B. hybridum lineage reveals no bias in overall subgenome expression. Our results are consistent with a gradual accumulation of genomic changes after polyploidization and a lack of subgenome expression dominance. Significantly, if we did not use a pan-genomic approach, we would grossly overestimate the number of genomic changes attributable to post polyploidization evolution.
Developmental GABA polarity switch and neuronal plasticity in Bioengineered Neuronal Organoids
Authors: Zafeiriou Maria-Patapia , Bao Guobin , Hudson James , Halder Rashi , Blenkle Alica , Schreiber Marie-Kristin , Fischer Andre , Schild Detlev , Zimmermann Wolfram-Hubertus 
Published: July 2020

AbstractBrain organoids are promising tools for disease modeling and drug development. For proper neuronal network formation excitatory and inhibitory neurons as well as glia need to co-develop. Here, we report the directed self-organization of human induced pluripotent stem cells in a collagen hydrogel towards a highly interconnected neuronal network at a macroscale tissue format. Bioengineered Neuronal Organoids (BENOs) comprise interconnected excitatory and inhibitory neurons with supportive astrocytes and oligodendrocytes. Giant depolarizing potential (GDP)-like events observed in early BENO cultures mimic early network activity of the fetal brain. The observed GABA polarity switch and reduced GDPs in >40 day BENO indicate progressive neuronal network maturation. BENOs demonstrate expedited complex network burst development after two months and evidence for long-term potentiation. The similarity of structural and functional properties to the fetal brain may allow for the application of BENOs in studies of neuronal plasticity and modeling of disease.
Quantum advantage in postselected metrology
Authors: Arvidsson-Shukur David R. M. , Yunger Halpern Nicole , Lepage Hugo V. , Lasek Aleksander A. , Barnes Crispin H. W. , Lloyd Seth 
Published: July 2020

AbstractIn every parameter-estimation experiment, the final measurement or the postprocessing incurs a cost. Postselection can improve the rate of Fisher information (the average information learned about an unknown parameter from a trial) to cost. We show that this improvement stems from the negativity of a particular quasiprobability distribution, a quantum extension of a probability distribution. In a classical theory, in which all observables commute, our quasiprobability distribution is real and nonnegative. In a quantum-mechanically noncommuting theory, nonclassicality manifests in negative or nonreal quasiprobabilities. Negative quasiprobabilities enable postselected experiments to outperform optimal postselection-free experiments: postselected quantum experiments can yield anomalously large information-cost rates. This advantage, we prove, is unrealizable in any classically commuting theory. Finally, we construct a preparation-and-postselection procedure that yields an arbitrarily large Fisher information. Our results establish the nonclassicality of a metrological advantage, leveraging our quasiprobability distribution as a mathematical tool.
Molecular mechanisms underlying menthol binding and activation of TRPM8 ion channel
Authors: Xu Lizhen , Han Yalan , Chen Xiaoying , Aierken Aerziguli , Wen Han , Zheng Wenjun , Wang Hongkun , Lu Xiancui , Zhao Zhenye , Ma Cheng , Liang Ping , Yang Wei , Yang Shilong , Yang Fan 
Published: July 2020

AbstractMenthol in mints elicits coolness sensation by selectively activating TRPM8 channel. Although structures of TRPM8 were determined in the apo and liganded states, the menthol-bounded state is unresolved. To understand how menthol activates the channel, we docked menthol to the channel and systematically validated our menthol binding models with thermodynamic mutant cycle analysis. We observed that menthol uses its hydroxyl group as a hand to specifically grab with R842, and its isopropyl group as legs to stand on I846 and L843. By imaging with fluorescent unnatural amino acid, we found that menthol binding induces wide-spread conformational rearrangements within the transmembrane domains. By Φ analysis based on single-channel recordings, we observed a temporal sequence of conformational changes in the S6 bundle crossing and the selectivity filter leading to channel activation. Therefore, our study suggested a ‘grab and stand’ mechanism of menthol binding and how menthol activates TRPM8 at the atomic level.
Placebos without deception reduce self-report and neural measures of emotional distress
Authors: Guevarra Darwin A. , Moser Jason S. , Wager Tor D. , Kross Ethan 
Published: July 2020

AbstractSeveral recent studies suggest that placebos administered without deception (i.e., non-deceptive placebos) can help people manage a variety of highly distressing clinical disorders and nonclinical impairments. However, whether non-deceptive placebos represent genuine psychobiological effects is unknown. Here we address this issue by demonstrating across two experiments that during a highly arousing negative picture viewing task, non-deceptive placebos reduce both a self-report and neural measure of emotional distress, the late positive potential. These results show that non-deceptive placebo effects are not merely a product of response bias. Additionally, they provide insight into the neural time course of non-deceptive placebo effects on emotional distress and the psychological mechanisms that explain how they function.
An improved symmetry-based approach to reciprocal space path selection in band structure calculations
Authors: Munro Jason M. , Latimer Katherine , Horton Matthew K. , Dwaraknath Shyam , Persson Kristin A. 
Published: July 2020

AbstractBand structures for electrons, phonons, and other quasiparticles are often an important aspect of describing the physical properties of periodic solids. Most commonly, energy bands are computed along a one-dimensional path of high-symmetry points and line segments in reciprocal space (the “k-path”), which are assumed to pass through important features of the dispersion landscape. However, existing methods for choosing this path rely on tabulated lists of high-symmetry points and line segments in the first Brillouin zone, determined using different symmetry criteria and unit cell conventions. Here we present a new “on-the-fly” symmetry-based approach to obtaining paths in reciprocal space that attempts to address the previous limitations of these conventions. Given a unit cell of a magnetic or nonmagnetic periodic solid, the site symmetry groups of points and line segments in the irreducible Brillouin zone are obtained from the total space group. The elements in these groups are used alongside general and maximally inclusive high-symmetry criteria to choose segments for the final k-path. A smooth path connecting each segment is obtained using graph theory. This new framework not only allows for increased flexibility and user convenience but also identifies notable overlooked features in certain electronic band structures. In addition, a more intelligent and efficient method for analyzing magnetic materials is also enabled through proper accommodation of magnetic symmetry.
Robust energy-selective tunneling readout of singlet-triplet qubits under large magnetic field gradient
Authors: Jang Wonjin , Kim Jehyun , Cho Min-Kyun , Chung Hwanchul , Park Sanghyeok , Eom Jaeun , Umansky Vladimir , Chung Yunchul , Kim Dohun 
Published: July 2020

AbstractFast and high-fidelity quantum state detection is essential for building robust spin-based quantum information processing platforms in semiconductors. The Pauli spin blockade (PSB)-based spin-to-charge conversion and its variants are widely used for the spin state discrimination of two-electron singlet–triplet (ST0) qubits; however, the single-shot measurement fidelity is limited by either the low signal contrast, or the short lifetime of the triplet state at the PSB energy detuning, especially due to strong mixing with singlet states at large magnetic field gradients. Ultimately, the limited single-shot measurement fidelity leads to low visibility of quantum operations. Here, we demonstrate an alternative method to achieve spin-to-charge conversion of ST0 qubit states using energy-selective tunneling between doubly occupied quantum dots (QDs) and electron reservoirs. We demonstrate a single-shot measurement fidelity of 90% and an S–T0 oscillation visibility of 81% at a field gradient of 100 mT (~500 MHz h (g*·μB)−1); this allows single-shot readout with full electron charge signal contrast and, at the same time, long and tunable measurement time with negligible effect of relaxation even at strong magnetic field gradients. Using an rf-sensor positioned opposite to the QD array, we apply this method to two ST0 qubits and show high-visibility readout of two individual single-qubit gate operations is possible with a single rf single-electron transistor sensor. We expect our measurement scheme for two-electron spin states can be applied to various hosting materials and provides a simplified and complementary route for multiple qubit state detection with high accuracy in QD-based quantum computing platforms.
Mathematical model of blood glucose dynamics by emulating the pathophysiology of glucose metabolism in type 2 diabetes mellitus
Authors: López-Palau Nelida Elizabeth , Olais-Govea José Manuel 
Published: July 2020

AbstractMathematical modelling has established itself as a theoretical tool to understand fundamental aspects of a variety of medical-biological phenomena. The predictive power of mathematical models on some chronic conditions has been helpful in its proper prevention, diagnosis, and treatment. Such is the case of the modelling of glycaemic dynamics in type 2 diabetes mellitus (T2DM), whose physiology-based mathematical models have captured the metabolic abnormalities of this disease. Through a physiology-based pharmacokinetic-pharmacodynamic approach, this work addresses a mathematical model whose structure starts from a model of blood glucose dynamics in healthy humans. This proposal is capable of emulating the pathophysiology of T2DM metabolism, including the effect of gastric emptying and insulin enhancing effect due to incretin hormones. The incorporation of these effects lies in the implemented methodology since the mathematical functions that represent metabolic rates, with a relevant contribution to hyperglycaemia, are adjusting individually to the clinical data of patients with T2DM. Numerically, the resulting model successfully simulates a scheduled graded intravenous glucose test and oral glucose tolerance tests at different doses. The comparison between simulations and clinical data shows an acceptable description of the blood glucose dynamics in T2DM. It opens the possibility of using this model to develop model-based controllers for the regulation of blood glucose in T2DM.
Oral administration of Cystine and Theanine ameliorates oxaliplatin-induced chronic peripheral neuropathy in rodents
Authors: Kawashiri Takehiro , Kobayashi Daisuke , Egashira Nobuaki , Tsuchiya Takashi , Shimazoe Takao 
Published: July 2020

AbstractOxaliplatin frequently causes severe peripheral neuropathy as a dose-limiting toxicity. However, this toxicity lacks a strategy for prevention. Cystine/Theanine is a supplement, which includes precursors for the biosynthesis of glutathione. In this study, we investigated the effects of Cystine/Theanine on oxaliplatin-induced peripheral neuropathy using an in vivo model. Repeated injection of oxaliplatin (4 mg/kg intraperitoneally twice a week for 2 weeks) caused mechanical allodynia, cold hyperalgesia and axonal degeneration of the sciatic nerve in rats. Mechanical allodynia and axonal degeneration, but not cold hyperalgesia, were ameliorated by daily co-administration of Cystine [200 mg/kg orally (p.o.)] and Theanine (80 mg/kg p.o.). Moreover, co-administration of Cystine and Theanine to rats significantly increased the glutathione level in the sciatic nerve compared with the oxaliplatin group. Furthermore, Cystine and Theanine did not attenuate the tumour cytotoxicity of oxaliplatin in C-26 tumour cell-bearing mice. These findings suggest that Cystine and Theanine may be beneficial for preventing oxaliplatin-induced peripheral neuropathy.