bluuebunny/crossref_metadata_2025_split huggingface dataset:
Catalytic trajectory of a dimeric nonribosomal peptide synthetase subunit with an inserted epimerase domain
Authors: Wang Jialiang , Li Dandan , Chen Lu , Cao Wei , Kong Liangliang , Zhang Wei , Croll Tristan , Deng Zixin , Liang Jingdan , Wang Zhijun 
Published: February 2022

AbstractNonribosomal peptide synthetases (NRPSs) are modular assembly-line megaenzymes that synthesize diverse metabolites with wide-ranging biological activities. The structural dynamics of synthetic elongation has remained unclear. Here, we present cryo-EM structures of PchE, an NRPS elongation module, in distinct conformations. The domain organization reveals a unique “H”-shaped head-to-tail dimeric architecture. The capture of both aryl and peptidyl carrier protein-tethered substrates and intermediates inside the heterocyclization domain and l-cysteinyl adenylate in the adenylation domain illustrates the catalytic and recognition residues. The multilevel structural transitions guided by the adenylation C-terminal subdomain in combination with the inserted epimerase and the conformational changes of the heterocyclization tunnel are controlled by two residues. Moreover, we visualized the direct structural dynamics of the full catalytic cycle from thiolation to epimerization. This study establishes the catalytic trajectory of PchE and sheds light on the rational re-engineering of domain-inserted dimeric NRPSs for the production of novel pharmaceutical agents.
Inhibition of base editors with anti-deaminases derived from viruses
Authors: Liu Zhiquan , Chen Siyu , Lai Liangxue , Li Zhanjun 
Published: February 2022

AbstractCytosine base editors (CBEs), combining cytidine deaminases with the Cas9 nickase (nCas9), enable targeted C-to-T conversions in genomic DNA and are powerful genome-editing tools used in biotechnology and medicine. However, the overexpression of cytidine deaminases in vivo leads to unexpected potential safety risks, such as Cas9-independent off-target effects. This risk makes the development of deaminase off switches for modulating CBE activity an urgent need. Here, we report the repurpose of four virus-derived anti-deaminases (Ades) that efficiently inhibit APOBEC3 deaminase-CBEs. We demonstrate that they antagonize CBEs by inhibiting the APOBEC3 catalytic domain, relocating the deaminases to the extranuclear region or degrading the whole CBE complex. By rationally engineering the deaminase domain, other frequently used base editors, such as CGBE, A&CBE, A&CGBE, rA1-CBE and ABE8e, can be moderately inhibited by Ades, expanding the scope of their applications. As a proof of concept, the Ades in this study dramatically decrease both Cas9-dependent and Cas9-independent off-target effects of CBEs better than traditional anti-CRISPRs (Acrs). Finally, we report the creation of a cell type-specific CBE-ON switch based on a microRNA-responsive Ade vector, showing its practicality. In summary, these natural deaminase-specific Ades are tools that can be used to regulate the genome-engineering functions of BEs.
Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant
Authors: Suzuki Rigel , Yamasoba Daichi , Kimura Izumi , Wang Lei , Kishimoto Mai , Ito Jumpei , Morioka Yuhei , Nao Naganori , Nasser Hesham , Uriu Keiya , Kosugi Yusuke , Tsuda Masumi , Orba Yasuko , Sasaki Michihito , Shimizu Ryo , Kawabata Ryoko , Yoshimatsu Kumiko , Asakura Hiroyuki , Nagashima Mami , Sadamasu Kenji , Yoshimura Kazuhisa ,   The Genotype to Phenotype Japan (G2P-Japan) Consortium, Suganami Mai , Oide Akiko , Chiba Mika , Ito Hayato , Tamura Tomokazu , Tsushima Kana , Kubo Haruko , Ferdous Zannatul , Mouri Hiromi , Iida Miki , Kasahara Keiko , Tabata Koshiro , Ishizuka Mariko , Shigeno Asako , Tokunaga Kenzo , Ozono Seiya , Yoshida Isao , Nakagawa So , Wu Jiaqi , Takahashi Miyoko , Kaneda Atsushi , Seki Motoaki , Fujiki Ryoji , Nawai Bahityar Rahmutulla , Suzuki Yutaka , Kashima Yukie , Abe Kazumi , Imamura Kiyomi , Shirakawa Kotaro , Takaori-Kondo Akifumi , Kazuma Yasuhiro , Nomura Ryosuke , Horisawa Yoshihito , Nagata Kayoko , Kawai Yugo , Yanagida Yohei , Tashiro Yusuke , Takahashi Otowa , Kitazato Kazuko , Hasebe Haruyo , Motozono Chihiro , Toyoda Mako , Tan Toong Seng , Ngare Isaac , Ueno Takamasa , Saito Akatsuki , Butlertanaka Erika P. , Tanaka Yuri L. , Morizako Nanami , Sawa Hirofumi , Ikeda Terumasa , Irie Takashi , Matsuno Keita , Tanaka Shinya , Fukuhara Takasuke , Sato Kei 
Published: February 2022

AbstractThe emergence of the Omicron variant of SARS-CoV-2 is an urgent global health concern1. In this study, our statistical modelling suggests that Omicron has spread more rapidly than the Delta variant in several countries including South Africa. Cell culture experiments showed Omicron to be less fusogenic than Delta and than an ancestral strain of SARS-CoV-2. Although the spike (S) protein of Delta is efficiently cleaved into two subunits, which facilitates cell–cell fusion2,3, the Omicron S protein was less efficiently cleaved compared to the S proteins of Delta and ancestral SARS-CoV-2. Furthermore, in a hamster model, Omicron showed decreased lung infectivity and was less pathogenic compared to Delta and ancestral SARS-CoV-2. Our multiscale investigations reveal the virological characteristics of Omicron, including rapid growth in the human population, lower fusogenicity and attenuated pathogenicity.
RETRACTED ARTICLE: The Hopewell airburst event, 1699–1567 years ago (252–383 CE)
Authors: Tankersley Kenneth Barnett , Meyers Stephen D. , Meyers Stephanie A. , Jordan James A. , Herzner Louis , Lentz David L. , Zedaker Dylan 
Published: February 2022

AbstractMeteorites, Fe and Si-rich microspherules, positive Ir and Pt anomalies, and burned charcoal-rich Hopewell habitation surfaces demonstrate that a cosmic airburst event occurred over the Ohio River valley during the late Holocene. A comet-shaped earthwork was constructed near the airburst epicenter. Twenty-nine radiocarbon ages establish that the event occurred between 252 and 383 CE, a time when 69 near-Earth comets were documented. While Hopewell people survived the catastrophic event, it likely contributed to their cultural decline. The Hopewell airburst event expands our understanding of the frequency and impact of cataclysmic cosmic events on complex human societies.
Tetrahydroxy stilbene glycoside attenuates endothelial cell premature senescence induced by H2O2 through the microRNA-34a/SIRT1 pathway
Authors: Zhang Lixuan , Guo Yan , Shi Shennan , Zhuge Yani , Chen Nipi , Ding Zhishan , Jin Bo 
Published: February 2022

AbstractNumerous studies have demonstrated that endothelial cell senescence plays a decisive role in the development and progression of cardiovascular diseases (CVD). Our previous results confirmed that Tetrahydroxy stilbene glycoside (TSG) can alleviate the human umbilical vein endothelial cells (HUVECs) senescence induced by H2O2 through SIRT1. It has been reported that miR-34a is a translational suppressor of SIRT1. In this study, we aimed to explore whether TSG regulates SIRT1 through miR-34a to ameliorate HUVECs senescence. H2O2 was used to induce premature senescence in HUVECs, and miR-34a mimic or inhibitor were transfected to over-express or suppress the expression level of miR-34a. Results revealed that TSG apparently decreased the miR-34a expression level in H2O2-induced premature senescence of HUVECs. When SIRT1 expression was inhibited by EX527, the attenuation of TSG on the expression level of miR-34a were abolished. When miR-34a expression was knockdown, the effect of TSG on HUVECs senescence could be enhanced. While miR-34a mimic could reverse the effect of TSG on HUVECs senescence. In conclusion, we demonstrated that TSG could attenuated endothelial cell senescence by targeting miR-34a/SIRT1 pathway.
Effect of mass variation on vibration properties of the tooth in drilling operation
Authors: Vujkov Sanja , Cveticanin Livija 
Published: February 2022

AbstractDental cavity represent one of the widespread illness of the tooth. Method for treating of the tooth is to drill the cavity and to fill the hole with suitable material. Measurements show that during drilling the tooth vibrates with increasing mass that causes unpleasant feeling for patient. The aim of the paper is to give the theoretical explanation for this phenomena and to give suggestion for vibration elimination. During drilling, mass of the tooth is decreasing and the so called ‘reactive force’ occurs. Drilling and reactive force cause tooth vibration. The system is modeled as a nonlinear time variable system. An analytical procedure for solving of the equation of vibration is developed. The solution is assumed in the form of the generalized trigonometric function with time variable amplitude and phase. It is obtained that not only the amplitude but also the frequency of tooth vibration in drilling are increased. In addition to reactive force the drilling velocity, diameter of the drill tool and spindle speed affect the vibration level. The appropriate values of these parameters would eliminate or decrease the patient bad feeling.
Implementation Science Research in Communication Sciences and Disorders: A Scoping Review
Authors: Douglas Natalie F. , Feuerstein Julie L. , Oshita Jennifer Y. , Schliep Megan E. , Danowski Margaret L. 
Published: February 2022

Purpose:
The purpose of this study was to complete a scoping review of implementation science (IS) research in communication sciences and disorders (CSD) over time and to determine characteristics of IS research in CSD.

Method:
A scoping review was conducted of PubMed and Education Resources Information Center for sources published in English that (a) included CSD practitioners, (b) addressed IS research, and (c) identified a specific evidence-based practice. Resulting sources were systematically examined for study aim, patient populations, implementation framework utilized, setting of the study, implementation strategy examined, and implementation outcome measured.

Results:
The majority of the 82 studies that underwent a full-text review (80.5%) were published in 2014 or later. One fourth of the studies were concept papers, and another one fourth focused on context assessment (25.6% of studies, each), 11% focused on designing implementation strategies, and 36.6% focused on testing implementation strategies. The patient population most frequently represented aphasia (21.3%), and most studies (34.4%) were conducted in inpatient medical settings. Nearly half (42.6%) of the nonconcept studies lacked an IS framework. Among implementation strategies identified, approximately one third of studies focused on education and/or training plus another strategy and one fourth focused on education and/or training alone. Implementation outcomes measured typically represented early stages of implementation.

Conclusions:
This scoping review of IS research in CSD described the landscape of IS studies in CSD. IS is intersecting with CSD at a rapid rate, especially since 2014. Future IS research in CSD should adopt an implementation framework a priori and consider the broad range of implementation strategies and outcomes to support the uptake of research into typical practice settings.
Network anomaly detection using deep learning techniques
Authors: Hooshmand Mohammad Kazim , Hosahalli Doreswamy 
Published: February 2022

AbstractConvolutional neural networks (CNNs) are the specific architecture of feed‐forward artificial neural networks. It is the de‐facto standard for various operations in machine learning and computer vision. To transform this performance towards the task of network anomaly detection in cyber‐security, this study proposes a model using one‐dimensional CNN architecture. The authors' approach divides network traffic data into transmission control protocol (TCP), user datagram protocol (UDP), and OTHER protocol categories in the first phase, then each category is treated independently. Before training the model, feature selection is performed using the Chi‐square technique, and then, over‐sampling is conducted using the synthetic minority over‐sampling technique to tackle a class imbalance problem. The authors' method yields the weighted average f‐score 0.85, 0.97, 0.86, and 0.78 for TCP, UDP, OTHER, and ALL categories, respectively. The model is tested on the UNSW‐NB15 dataset.
Triggered finite‐time consensus of first‐order multi‐agent systems with input saturation
Authors: Zheng Kanghua , Fan Huijin , Liu Lei , Cheng Zhongtao 
Published: February 2022

AbstractInput saturation, which brings input non‐linearity to systems and limits the closed‐loop systems' performances severely, is an ubiquitous problem in practice. Here, triggered finite‐time consensus problem of disturbed leader‐follower multi‐agent systems is addressed under input saturation constraint. To overcome the coupling of the non‐linearity and finite‐time convergence together with input saturation, non‐linear triggered control protocol has been proposed, which is confirmed through a two‐step stabilization procedure. First, the saturated closed‐loop system is designed to be asymptotically stable, under which the systems converge into a desaturated region in finite time. Then in the second step, with the proposed control protocol, the desaturated closed‐loop multi‐agent systems can achieve practical finite‐time consensus. In addition, to get rid of continuous communication in the monitoring of event‐triggered condition, a self‐triggered approach is further proposed. With rigorous analyses, practical finite‐time consensus can be achieved for the overall closed‐loop systems and Zeno behavior is also excluded. Simulations are carried out in detail to illustrate the theoretical results in this study.
High‐gain and low‐cost circularly polarized antenna array for 5G MMW applications
Authors: Xiao Jun , Li Hongmei , Luo Delin , Jin Hui , Ding Tongyu , Ye Qiubo 
Published: February 2022

AbstractA high‐gain, low‐cost empty substrate integrated waveguide (ESIW)‐fed circularly polarized (CP) antenna array is demonstrated for millimetre‐wave 5G applications in this letter. The ESIW is formed by metallized FR4 printed circuit boards. By stacking the metallic aluminium z‐shaped radiating slots atop the ESIW feeding network, CP radiation is achieved. The proposed 1 × 8 antenna array offers a high measured gain of 17.8 dBic and high measured radiation efficiency of 89.1%. The measured impedance bandwidth for |S11| ≤ −10 dB and measured axial ratio (AR) bandwidth for AR ≤ 3 of the proposed 1 × 8 array are 11.4% (36.5–40.9 GHz) and 7.8% (37–40 GHz), respectively.
On the design of an optimal coherent multistatic radar network configuration
Authors: Berry Paul Edward , Dahal Nabaraj , Venkataraman Krishna 
Published: February 2022

AbstractThe purpose of operating a radar system multistatically is to acquire information about targets of interest more quickly and reliably than would be possible using disparate radars, which fuse data and track post‐detection. This paper identifies and addresses the critical issues for designing a coherent multistatic radar system using conventional coherent radars and proposes a set of design principles for configuring a coherent multistatic radar network with the aim of maximising the utility of information while constraining system cost and complexity. The issues discussed are as follows: the localisation of targets in three dimensions; eliminating the inevitable spatial ambiguities arising from sparse spatial sampling while exploiting the large aperture for high resolution; the achievement of spatial coherent processing gain for target detection; the effect of phase centre localisation, phase and frequency errors on synchronisation; the incorporation of three‐dimensional Doppler estimation for slow‐time coherent integration. The arguments presented are physically‐based and complemented by mathematical analysis and numerical experimentation using non‐linear sparse estimation, the sparse algorithm being critically important for resolving spatial ambiguities. An optimal configuration is identified, which has sufficiently many nodes to overcome spatial ambiguities and achieves significant spatial coherent processing gain, while simultaneously constraining the overheads of inter‐node synchronisation and communication.
Ultrastructural and molecular study of the microsporidianToguebayea baccigerin. gen., n. sp., a hyperparasite of the digenean trematodeBacciger israelensis(Faustulidae), a parasite ofBoops boops(Teleostei, Sparidae)
Authors: Miquel Jordi , Kacem Hichem , Baz-González Edgar , Foronda Pilar , Marchand Bernard 
Published: February 2022

A new microsporidianToguebayea baccigerin. gen., n. sp., hyperparasite ofBacciger israelensis(Digenea, Faustulidae), parasite ofBoops boops(Teleostei, Sparidae) is described by means of transmission electron microscopy. The phylogenetic analysis, based on the SSU rDNA gene, places the new species in the clade containing mainly crustacean-infecting microsporidia of the genusCucumispora, within superclade V (Marinosporidia)sensuVossbrinck et al., 2014. Mature spores ofT. baccigeriare ovoid, uninucleated and measure 2.5 × 1.4 μm. The number of coils of the polar tube is 8–10. The polaroplast is composed of an external lamellar part and an internal vesicular or granular part. The main differences that distinguish the new genus and new species from the closely related microsporidia include hyperparasitism in a digenean host infecting a marine fish, the geographic distribution (coast of Tunisia), presence of one nucleus at all developmental stages, disporoblastic sporogony, and the absence of sporophorous vacuoles.
Efficacy of Repair for ACL Injury: A Meta‑analysis of Randomized
Controlled Trials
Authors: Li Zhuoyang 
Published: February 2022

AbstractWe aim to compare the curative effect of primary repair for anterior cruciate
ligament (ACL) injury with reconstruction and provide the reliable evidence for
its clinical application. The literatures were searched in PubMed, EMBASE,
Springer, and other medical literature databases published between January 1970
and June 2021. Basic characteristics, surgery technique, clinical outcome scores
and physical examination results were recorded and evaluated. Seven randomized
controlled trials (RCT) were eligible for inclusion. The results showed that
there were no statistically significant differences between arthroscopic ACL
repair and ACL reconstruction for Tegner, Lysholm, Lachman, KT-1000, range of
motion (ROM), functional outcomes and reoperation rate (P>0.05), even
the result of IKDC scores showed that arthroscopic repair was better than
reconstruction (P=0.04). However, through the subgroup analysis, it was
found that the short-term follow-up results of arthroscopic ACL repair were
indeed better than those of open ACL repair. Therefore, we can assume that the
arthroscopic ACL repair technique is an optional and promising surgical method
to treat ACL injury.
Antiproliferative and Microtubule-stabilizing Activities of Two Iboga-vobasine Bisindoles Alkaloids from Tabernaemontana corymbosa in Colorectal Adenocarcinoma HT-29
Cells
Authors: Tan Chun Hoe , Sim Dawn Su Yin , Lim Siew Huah , Mohd Mohidin Taznim Begam , Mohan Gokula , Low Yun Yee , Kam Toh Seok , Sim Kae Shin 
Published: February 2022

AbstractTwo iboga-vobasine bisindoles, 16′-decarbomethoxyvoacamine (1) and its 19,20-dihydro derivative, 16′-decarbomethoxydihydrovoacamine (2) from Tabernaemontana corymbosa
exhibited potent cytotoxicity against the human colorectal adenocarcinoma HT-29 cells in our previous studies. Bisindoles 1 and 2 selectively inhibited the growth of HT-29
cells without significant cytotoxicity to normal human colon fibroblasts CCD-18Co. Treatment with bisindoles 1 and 2 suppressed the formation of HT-29 colonies via G0/G1 cell
cycle arrest and induction of mitochondrial apoptosis. Owing to its higher antiproliferative activity, bisindole 2 was chosen for the subsequent studies. Bisindole 2 inhibited
the formation of HT-29 spheroids (tumor-like cell aggregates) in 3D experiments in a dose-dependent manner, while an in vitro tubulin polymerization assay and molecular docking
analysis showed that bisindole 2 is a microtubule-stabilizing agent which is predicted to bind at the β-tubulin subunit at the taxol-binding site. The binding resulted in the
generation of ROS, which consequently activated the oxidative stress-related cell cycle arrest and apoptotic pathways, viz., JNK/p38, p21Cip1/Chk1, and p21Cip1/Rb/E2F,
as shown by microarray profiling.
Viral Ventilator-Associated Pneumonia/Hospital-Acquired Pneumonia
Authors: Luyt Charles-Edouard , Hékimian Guillaume , Bréchot Nicolas , Chastre Jean 
Published: February 2022

AbstractAmong the viruses possibly responsible for hospital-acquired and ventilator-associated pneumonia, herpes simplex virus (HSV) is probably the most often involved: HSV reactivation is frequent in intensive care unit patients, and lung parenchymal infection (HSV bronchopneumonitis) has been well described, either using cytological signs of parenchymal involvement in cells obtained during bronchoalveolar lavage or using HSV virus load in the lower respiratory tract. Although treating patients with HSV bronchopneumonitis may be recommended, based on expert opinion, prophylactic or preemptive treatment of HSV reactivation should be avoided. Ventilator-associated pneumonia due to cytomegalovirus (CMV) is less frequent than HSV bronchopneumonitis, and more difficult to diagnose. No data exists on the impact of antiviral treatment on CMV pneumonia. The involvement of respiratory viruses has been described in patients with healthcare-associated pneumonia and hospital-acquired pneumonia, but their role in ventilator-associated pneumonia is not clear.
Real-time pandemic surveillance using hospital admissions and mobility data
Authors: Fox Spencer J. , Lachmann Michael , Tec Mauricio , Pasco Remy , Woody Spencer , Du Zhanwei , Wang Xutong , Ingle Tanvi A. , Javan Emily , Dahan Maytal , Gaither Kelly , Escott Mark E. , Adler Stephen I. , Johnston S. Claiborne , Scott James G. , Meyers Lauren Ancel 
Published: February 2022

Significance
Forecasting COVID-19 healthcare demand has been hindered by poor data throughout the pandemic. We introduce a robust model for predicting COVID-19 transmission and hospitalizations based on COVID-19 hospital admissions and cell phone mobility data. This approach was developed by a municipal COVID-19 task force in Austin, TX, which includes civic leaders, public health officials, healthcare executives, and scientists. The model was incorporated into a dashboard providing daily healthcare forecasts that have raised public awareness, guided the city’s staged alert system to prevent unmanageable ICU surges, and triggered the launch of an alternative care site to accommodate hospital overflow.
Leucine retention in lysosomes is regulated by starvation
Authors: Bandyopadhyay Urmi , Todorova Pavlina , Pavlova Natalya N. , Tada Yuma , Thompson Craig B. , Finley Lydia W.S. , Overholtzer Michael 
Published: February 2022

Significance
Cells can respond to starvation by up-regulating stress responses that promote the recycling or scavenging of essential nutrients. We identify a starvation response that allows cells to store the essential amino acid leucine within lysosomes when extracellular amino acids are scarce. This “storage” response allows cells to sequester an essential amino acid in support of protein synthesis. We find that numerous essential amino acids are trafficked through lysosomes even when extracellular concentrations are high, suggesting that constitutive flux through lysosomes is related to starvation-induced storage.