bluuebunny/crossref_metadata_2025_split huggingface dataset:
Function-adaptive clustered nanoparticles reverse Streptococcus mutans dental biofilm and maintain microbiota balance
Authors: Ostadhossein Fatemeh , Moitra Parikshit , Altun Esra , Dutta Debapriya , Sar Dinabandhu , Tripathi Indu , Hsiao Shih-Hsuan , Kravchuk Valeriya , Nie Shuming , Pan Dipanjan 
Published: July 2021

AbstractDental plaques are biofilms that cause dental caries by demineralization with acidogenic bacteria. These bacteria reside inside a protective sheath which makes any curative treatment challenging. We propose an antibiotic-free strategy to disrupt the biofilm by engineered clustered carbon dot nanoparticles that function in the acidic environment of the biofilms. In vitro and ex vivo studies on the mature biofilms ofStreptococcus mutansrevealed >90% biofilm inhibition associated with the contact-mediated interaction of nanoparticles with the bacterial membrane, excessive reactive oxygen species generation, and DNA fragmentation. An in vivo examination showed that these nanoparticles could effectively suppress the growth ofS. mutans. Importantly, 16S rRNA analysis of the dental microbiota showed that the diversity and richness of bacterial species did not substantially change with nanoparticle treatment. Overall, this study presents a safe and effective approach to decrease the dental biofilm formation without disrupting the ecological balance of the oral cavity.
Systems biology informed neural networks (SBINN) predict response and novel combinations for PD-1 checkpoint blockade
Authors: Przedborski Michelle , Smalley Munisha , Thiyagarajan Saravanan , Goldman Aaron , Kohandel Mohammad 
Published: July 2021

AbstractAnti-PD-1 immunotherapy has recently shown tremendous success for the treatment of several aggressive cancers. However, variability and unpredictability in treatment outcome have been observed, and are thought to be driven by patient-specific biology and interactions of the patient’s immune system with the tumor. Here we develop an integrative systems biology and machine learning approach, built around clinical data, to predict patient response to anti-PD-1 immunotherapy and to improve the response rate. Using this approach, we determine biomarkers of patient response and identify potential mechanisms of drug resistance. We develop systems biology informed neural networks (SBINN) to calculate patient-specific kinetic parameter values and to predict clinical outcome. We show how transfer learning can be leveraged with simulated clinical data to significantly improve the response prediction accuracy of the SBINN. Further, we identify novel drug combinations and optimize the treatment protocol for triple combination therapy consisting of IL-6 inhibition, recombinant IL-12, and anti-PD-1 immunotherapy in order to maximize patient response. We also find unexpected differences in protein expression levels between response phenotypes which complement recent clinical findings. Our approach has the potential to aid in the development of targeted experiments for patient drug screening as well as identify novel therapeutic targets.
DeepEMhancer: a deep learning solution for cryo-EM volume post-processing
Authors: Sanchez-Garcia Ruben , Gomez-Blanco Josue , Cuervo Ana , Carazo Jose Maria , Sorzano Carlos Oscar S. , Vargas Javier 
Published: July 2021

AbstractCryo-EM maps are valuable sources of information for protein structure modeling. However, due to the loss of contrast at high frequencies, they generally need to be post-processed to improve their interpretability. Most popular approaches, based on global B-factor correction, suffer from limitations. For instance, they ignore the heterogeneity in the map local quality that reconstructions tend to exhibit. Aiming to overcome these problems, we present DeepEMhancer, a deep learning approach designed to perform automatic post-processing of cryo-EM maps. Trained on a dataset of pairs of experimental maps and maps sharpened using their respective atomic models, DeepEMhancer has learned how to post-process experimental maps performing masking-like and sharpening-like operations in a single step. DeepEMhancer was evaluated on a testing set of 20 different experimental maps, showing its ability to reduce noise levels and obtain more detailed versions of the experimental maps. Additionally, we illustrated the benefits of DeepEMhancer on the structure of the SARS-CoV-2 RNA polymerase.
Large-scale phenotyping of 1,000 fungal strains for the degradation of non-natural, industrial compounds
Authors: Navarro David , Chaduli Delphine , Taussac Sabine , Lesage-Meessen Laurence , Grisel Sacha , Haon Mireille , Callac Philippe , Courtecuisse Régis , Decock Cony , Dupont Joëlle , Richard-Forget Florence , Fournier Jacques , Guinberteau Jacques , Lechat Christian , Moreau Pierre-Arthur , Pinson-Gadais Laetitia , Rivoire Bernard , Sage Lucile , Welti Stéphane , Rosso Marie-Noëlle , Berrin Jean-Guy , Bissaro Bastien , Favel Anne 
Published: July 2021

AbstractFungal biotechnology is set to play a keystone role in the emerging bioeconomy, notably to address pollution issues arising from human activities. Because they preserve biological diversity, Biological Resource Centres are considered as critical infrastructures to support the development of biotechnological solutions. Here, we report the first large-scale phenotyping of more than 1,000 fungal strains with evaluation of their growth and degradation potential towards five industrial, human-designed and recalcitrant compounds, including two synthetic dyes, two lignocellulose-derived compounds and a synthetic plastic polymer. We draw a functional map over the phylogenetic diversity ofBasidiomycotaandAscomycota, to guide the selection of fungal taxa to be tested for dedicated biotechnological applications. We evidence a functional diversity at all taxonomic ranks, including between strains of a same species. Beyond demonstrating the tremendous potential of filamentous fungi, our results pave the avenue for further functional exploration to solve the ever-growing issue of ecosystems pollution.
Essential roles of plexin-B3+ oligodendrocyte precursor cells in the pathogenesis of Alzheimer’s disease
Authors: Nihonmatsu-Kikuchi Naomi , Yu Xiu-Jun , Matsuda Yoshiki , Ozawa Nobuyuki , Ito Taeko , Satou Kazuhito , Kaname Tadashi , Iwasaki Yasushi , Akagi Akio , Yoshida Mari , Toru Shuta , Hirokawa Katsuiku , Takashima Akihiko , Hasegawa Masato , Uchihara Toshiki , Tatebayashi Yoshitaka 
Published: July 2021

AbstractThe role of oligodendrocyte lineage cells, the largest glial population in the adult central nervous system (CNS), in the pathogenesis of Alzheimer’s disease (AD) remains elusive. Here, we developed a culture method for adult oligodendrocyte progenitor cells (aOPCs). Fibroblast growth factor 2 (FGF2) promotes survival and proliferation of NG2+ aOPCs in a serum-free defined medium; a subpopulation (~5%) of plexin-B3+ aOPCs was also found. FGF2 withdrawal decreased NG2+, but increased plexin-B3+ aOPCs and Aβ1-42 secretion. Plexin-B3+ aOPCs were distributed throughout the adult rat brain, although less densely than NG2+ aOPCs. Spreading depolarization induced delayed cortical plexin-B3+ aOPC gliosis in the ipsilateral remote cortex. Furthermore, extracellular Aβ1-42 accumulation was occasionally found around plexin-B3+ aOPCs near the lesions. In AD brains, virtually all cortical SPs were immunostained for plexin-B3, and plexin-B3 levels increased significantly in the Sarkosyl-soluble fractions. These findings suggest that plexin-B3+ aOPCs may play essential roles in AD pathogenesis, as natural Aβ-secreting cells.
Resonating dimer–monomer liquid state in a magnetization plateau of a spin-$$\frac{1}{2}$$ kagome-strip Heisenberg chain
Authors: Morita Katsuhiro , Sota Shigetoshi , Tohyama Takami 
Published: July 2021

AbstractHighly frustrated spin systems such as the kagome lattice are a treasure trove of new quantum states with large entanglements. Herein, we study the spin-$$\frac{1}{2}$$

1

2

Heisenberg model on a kagome-strip chain, which is a one-dimensional kagome lattice, using the density matrix renormalization group method. Calculating the central charge and entanglement spectrum for the kagome-strip chain, we find a gapless spin liquid state with doubly degenerate entanglement spectra in a 1/5 magnetization plateau. We also obtain a gapless low-lying continuum in the dynamic spin structure calculated using the dynamical density matrix renormalization group method. We then propose a resonating dimer–monomer liquid state that meets these features.
Observation-based selection of climate models projects Arctic ice-free summers around 2035
Authors: Docquier David , Koenigk Torben 
Published: July 2021

AbstractArctic sea ice has been retreating at an accelerating pace over the past decades. Model projections show that the Arctic Ocean could be almost ice free in summer by the middle of this century. However, the uncertainties related to these projections are relatively large. Here we use 33 global climate models from the Coupled Model Intercomparison Project 6 (CMIP6) and select models that best capture the observed Arctic sea-ice area and volume and northward ocean heat transport to refine model projections of Arctic sea ice. This model selection leads to lower Arctic sea-ice area and volume relative to the multi-model mean without model selection and summer ice-free conditions could occur as early as around 2035. These results highlight a potential underestimation of future Arctic sea-ice loss when including all CMIP6 models.
A novel dynamic dual‐path routing for end‐to‐end communication security in wide area networks
Authors: Zhang Rongbo , Li Xin , Chen Shanzhi 
Published: July 2021

AbstractDynamic multipath routing gives users flexibility over the transmitting path to deliver messages for security. Several protocols have already presented, such as multipath TCP, random routing mutation. However, they often limited to scalability, which mainly reflects on two aspects of network resource consumption and compossibility with other main transfer protocols. In this paper, to enhance the security of data delivery in wide area networks, a novel multipath routing scheme for end‐to‐end communication is proposed. The basic idea is concurrently using two paths (a fixed path and a changing path) to deliver the data of a pair, the fixed routing path undertakes the main delivery tasks, and the continually changing routing path only transfers a little data of the flow during the whole communication period. For systematically achieving security, Information Dispersal Algorithm disperses the flow data over the two paths for resisting anyone routing path compromised. Further, the method can maintain more routing path change since the burst network resource requirement decreases significantly at the routing mutation moment. Meanwhile, it brings a small amount of bandwidth disturbance over the traffic statuses of the network, thus alleviating instead of worsening the compossibility with other protocols.
Euclidean space data alignment approach for multi‐channel LSTM network in EEG based fatigue driving detection
Authors: Tang Jiahao , Li Xueping , Yang Yuan , Zhang Wan 
Published: July 2021

AbstractFatigue driving is the main reason of traffic accidents. The electroencephalograph (EEG) signal can accurately reflect the changes of human physiological state, so EEG is considered as a reliable method to detect fatigue driving. In this letter, the Euclidean space data alignment approach is adopted to reduce individual differences. Then, to consider the spatial correlation between multiple channels EEG signals and further improve the accuracy, an efficient long short‐term memory (LSTM) network structure is designed to detect the fatigue state of drivers. The experimental result shows that the method improves the generalisation capability and achieves the performance with an average accuracy of 95.70% for three categories. Evaluation of the algorithm performance in comparison with other traditional methods indicates that the method has higher accuracy and lower standard deviation. Generally speaking, the proposed method is promising for the application of fatigue driving monitoring.
Synthesis of chitosan functionalized magnetic carbon nanotubes for dispersive solid‐phase extraction of bromocresol green
Authors: Abniki Milad , Moghimi Ali 
Published: July 2021

AbstractAbstractThis study presents a new and rapid method for preconcentration, measurement, and removal of trace amounts of coloured wastewater using chitosan functionalized magnetic carbon nanotubes in aqueous samples. This method involves a two‐phase system in which the donor phase contains an aqueous phase with bromocresol green, and the acceptor phase contains functionalized magnetic carbon nanotubes with chitosan. Experiments were carried out in two stages of extraction of bromocresol green from aqueous solution and desorption of bromocresol green using ethanol solvent. The samples were analysed by UV–Vis spectrophotometer. Extraction parameters were investigated such as the effect of organic solvent, pH of the donor and acceptor phases, extraction time, interference species, and volume of elution solvent. The isotherm of bromocresol green adsorption was fine described by the Langmuir model, and the adsorption capacity in the maximum was 28.49 mg g−1. The preconcentration factor and limit of detection for bromocresol green were 14.3 and 7.5 μg L−1, respectively. A linear range is observed between 0.1 and 20 mg L−1. Finally, the chitosan functionalized magnetic carbon nanotubes (Fe3O4@MWCNT‐CN) exhibited a high potential for removing the bromocresol green from aqueous samples.
Two‐dimensional adaptive beamforming for large planar array antennas based on weight matrix reconstruction
Authors: Gao Wei , Li Xiaoming , Liu Zheng , Meng Ziqiang , Ran Lei 
Published: July 2021

AbstractAdaptive beamformers at the element level usually require a great number of training samples and the computational cost for calculating the weight vector for large phased array antennas is very high, which make it difficult for real‐time applications. To address this problem, a two‐dimensional (2‐D) adaptive beamformer applicable to large planar array antennas that have low computational complexity and low training sample requirement is proposed. In the proposed method, the weight matrix is first reconstructed as a matrix that has the same or close columns and rows by utilising the special Kronecker property of the array steering matrix. Then, the weight vector is determined by adopting a bi‐quadratic cost function and a bi‐iterative algorithm. Experimental results show that the proposed method can achieve fairly good performance even when the training samples are small.
Preparation of Functionalized Diorganomagnesium Reagents in Toluene via Bromine or Iodine/Magnesium-Exchange Reactions
Authors: Desaintjean Alexandre , Danton Fanny , Knochel Paul 
Published: July 2021

AbstractA wide range of polyfunctionalized di(hetero)aryl- and dialkenyl-magnesium reagents are prepared in toluene within 10 to 120 minutes between –78 °C and 25 °C via an I/Mg- or Br/Mg-exchange reaction using reagents of the general formula R2Mg (R = sBu, Mes). Highly sensitive functional groups, such as triazene or nitro, are tolerated in these exchange reactions, enabling the synthesis of various functionalized (hetero)arene and alkene derivatives after quenching with several electrophiles including allyl bromides, acyl chlorides, aldehydes, ketones, and aryl iodides.
Lhermitte–Duclos Disease Mimicking Cerebellopontine Angle Tumor: A Case Report
Authors: Abbasoglu Bilal , Zaimoglu Murat , Eroglu Umit , Ersoz Cevriye Cansiz , Attar Ayhan 
Published: July 2021

AbstractLhermitte-Duclos disease (LDD) is dysplastic gangliocytoma of the cerebellum, which is rare, tends to grow slowly, usually has good prognosis, and wherein the cerebellar cortex becomes thick and the central white matter is not observed. On MRI of the brain, it has hyperintense and hypointense presentations on T2- and T1-weighted scans, respectively. It has nonhomogenous contrasting pattern on T1-contrast scans. LDD can be seen unilaterally or bilaterally in the cerebellum. When the disease is located at the cerebellopontine angle, it can be mistaken for the tumors located in this region. Recurrence can occur postoperatively, which is rare. The present case is a rare one because the tumor was located at the cerebellopontine angle and radiologically mimicked cerebellopontine angle tumors.
Simple Removal of Ventriculoatrial Shunt and Simultaneous Ventriculoperitoneal Shunt Revision: Short Communication
Authors: Oike Ryo , Inoue Yasuaki , Matsuzawa Kazuhito 
Published: July 2021

Abstract
Background  Ventriculoatrial shunt (VAS) is a common alternative treatment option for hydrocephalus in patients with ventriculoperitoneal shunt (VPS) failure. Most previous reports on VAS discuss the atrial-related complications and none focus on simple removal (i.e., without specialized equipment). We report a case of simple VAS removal and simultaneous VPS revision, with no obvious shunt-related cardiac complications.
Case presentation  The patient was an 87-year-old female who had received a VAS for idiopathic normal pressure hydrocephalus 6 years prior. She developed a right thalamic hemorrhage with intraventricular hemorrhage and was admitted to our hospital. She had a recurrence of the hydrocephalus and was diagnosed with shunt malfunction, due to simple obstruction without obvious shunt-related cardiac complications. The VAS was simply and safely removed, and a VPS was simultaneously placed, as per the usual procedure in our institution. She remains well with no evidence of complications on postoperative day 10.
Discussion  Since VAS is mostly used in pediatric cases that are difficult to treat with VPS, the duration of time elapsed allows VAS catheters to form strong adhesions with the surrounding cardiac tissue. Therefore, the simple removal of VAS is usually not straightforward.
Conclusion  If the follow-up period is short and there are no specific cardiac complications at the time of replacement, VAS can be safely removed and VPS can be spontaneously placed, without any specialized surgical techniques or equipment.
Tendon: Principles of Healing and Repair
Authors: Chartier Christian , ElHawary Hassan , Baradaran Aslan , Vorstenbosch Joshua , Xu Liqin , Efanov Johnny Ionut 
Published: July 2021

AbstractTendon stores, releases, and dissipates energy to efficiently transmit contractile forces from muscle to bone. Tendon injury is exceedingly common, with the spectrum ranging from chronic tendinopathy to acute tendon rupture. Tendon generally develops according to three main steps: collagen fibrillogenesis, linear growth, and lateral growth. In the setting of injury, it also repairs and regenerates in three overlapping steps (inflammation, proliferation, and remodeling) with tendon-specific durations. Acute injury to the flexor and extensor tendons of the hand are of particular clinical importance to plastic surgeons, with tendon-specific treatment guided by the general principle of minimum protective immobilization followed by hand therapy to overcome potential adhesions. Thorough knowledge of the underlying biomechanical principles of tendon healing is required to provide optimal care to patients presenting with tendon injury.
Wound Healing: A Comprehensive Review
Authors: Almadani Yasser H. , Vorstenbosch Joshua , Davison Peter G. , Murphy Amanda M. 
Published: July 2021

AbstractWound healing is an intricate, tightly regulated process that is critical to maintaining the barrier function of skin along with preserving all other skin functions. This process can be influenced by a variety of modifiable and nonmodifiable factors. As wound healing takes place in all parts of the human body, this review focuses on cutaneous wound healing and highlights the classical wound healing phases. Alterations in any of these phases can promote chronic wound development and may impede wound healing.
A Rare Case of Dissemination of Primary Spinal Glioblastoma
Authors: Sirinoglu Deniz , Sarigul Buse , Baskurt Ozan , Aydin Mehmet Volkan 
Published: July 2021

Abstract
Background Primary spinal glioblastoma is a rare lesion which constitutes only 1.5% of all spinal tumors. Diagnosis is challenging due to absence of any radiological hallmark of the disease. Even though surgery combined with chemoradiotherapy is the optimal management for these tumors, prognosis is still poor. Dissemination of glioblastoma is reported several times in the literature, which is correlated with worse prognosis and outcome. This case report that we are presenting is the first case where dissemination of primary spinal glioblastoma dissemination is limited only to spinal cord, without intracranial invasion, and regression was achieved with chemoradiotherapy.
Case Report In this article, a patient with primary spinal glioblastoma who presented with paraparesia is presented. Patient underwent surgery for resection of the tumor and received adjuvant radiotherapy. However, 9 months postoperatively, dissemination was detected in epidural and subdural spaces of spinal canal, with concomitant compression of spinal cord. There was no radiographically detected lesion in cranial MRI. He underwent second session of radiotherapy, combined with chemotherapy and steroid. Five months later, regression of metastatic disseminated lesions was observed.
Conclusion Primary spinal glioblastoma is a rare pathology and known to have a poor prognosis, notably with dissemination of the disease. Even though further biomolecular studies are necessary to explain the pathophysiology better, chemotherapy and radiotherapy may be effective in regression of disseminated lesions.
Interface and optical properties of Zn1−xMgxO films with Mg content of more than 70% grown on the (12̄10)-ZnO substrates
Authors: Liang Xin , Zhou Hua , Wang Hui-Qiong , Zhang Lihua , Kisslinger Kim , Kang Junyong 
Published: July 2021

Fabricating Zn1−xMgxO films with a high Mg content is key to their applications in deep-ultraviolet optoelectronic devices. In this work, we report the preparation of Zn1−xMgxO films on (12̄10)-ZnO substrates by molecular beam epitaxy. The Zn1−xMgxO/(12̄10)-ZnO structure is revealed by x-ray diffraction and high-resolution transmission electron microscopy. Remarkably, no cubic MgO is observed for films with 74.6% Mg content; the film shows mainly the wurtzite structure with some intermediate phases at the interface. Photoluminescence spectra show that the film exhibits good optoelectronic properties with a bandgap of 4.6 eV. This work provides a new avenue for the fabrication of deep-ultraviolet Zn1−xMgxO films.