bluuebunny/crossref_metadata_2025_split huggingface dataset:
High hydrostatic pressure shapes the development and production of secondary metabolites of Mariana Trench sediment fungi
Authors: Peng Qingqing , Li Yongqi , Deng Ludan , Fang Jiasong , Yu Xi 
Published: June 2021

AbstractThe hadal biosphere is one of the least understood ecosystems on our planet. Recent studies have revealed diverse and active communities of prokaryotes in hadal sediment. However, there have been few studies on fungi in hadal sediment. Here we report the first isolation and cultivation of 8 fungi from the Mariana Trench sediment. The individual colonies were isolated and identified as Stemphylium sp., Cladosporium sp., Arthrinium sp., Fusarium sp., Alternaria sp., and Aspergillus sp. High hydrostatic pressure (HHP) test was carried out to identify the piezophily of these hadal fungi. Among them, 7 out of the 8 fungal isolates exhibited the ability of germination after incubation under 40 MPa for 7 days. Vegetative growth of the isolates was also affected by HHP. Characterization of secondary metabolites under different pressure conditions was also performed. The production of secondary metabolites was affected by the HHP treatment, improving the potential of discovering novel natural products from hadal fungi. The antibacterial assay revealed the potential of discovering novel natural products. Our results suggest that fungal growth pressure plays an important role in the development and production of secondary metabolites of these hadal fungi under the extreme environment in the Mariana Trench.
Bones geometric morphometrics illustrate 10th millennium cal. BP domestication of autochthonous Cypriot wild boar (Sus scrofa circeus nov. ssp)
Authors: Cucchi Thomas , Domont Auriale , Harbers Hugo , Evin Allowen , Alcàntara Fors Roger , Saña Maria , Leduc Charlotte , Guidez Aurélie , Bridault Anne , Hongo Hitomi , Price Max , Peters Joris , Briois François , Guilaine Jean , Vigne Jean-Denis 
Published: June 2021

AbstractEpipaleolithic hunter-gatherers from the Near East introduced wild boars (Sus scrofa) to Cyprus, with the Early Pre-Pottery Neolithic (PPN) settlers hunting the wild descendants of these boars. However, the geographic origin of the Cypriot boar and how they were integrated into the earliest forms of pig husbandry remain unsolved. Here, we present data on 11,000 to 9000 cal. BP Sus scrofa from the PPN sites of Klimonas and Shillourokambos. We compared them to contemporaneous populations from the Near East and to Neolithic and modern populations in Corsica, exploring their origin and evolution using biosystematic signals from molar teeth and heel bones (calcanei), using 2D and 3D geometric morphometrics. We found that the Cypriot PPN lineage of Sus scrofa originates from the Northern Levant. Yet, their phenotypic idiosyncrasy suggest that they evolved into an insular sub-species that we named Sus scrofa circeus, referring to Circe, the metamorphosis goddess that changed Ulysses companions into pigs. The phenotypic homogeneity among PPNA Klimonas wild boars and managed populations of PPNB Shillourokambos suggests that local domestication has been undertaken on the endemic S. s. circeus, strengthening the idea that Cyprus was integrated into the core region of animal domestication.
Comparative analysis of tuberous root metabolites between cultivated and wild varieties of Rehmannia glutinosa by widely targeted metabolomics
Authors: Zhou Yanqing , Shao Luying , Zhu Jialin , Li Huimin , Duan Hongying 
Published: June 2021

AbstractDifferential metabolites between tuberous roots from cultivated variety (ZP) and wild variety (YS) of Rehmannia glutinosa were analyzed by widely targeted metabolomics, and annotated to KEGG pathways. 228 secondary metabolites (SM) in ZP and YS were detected, of which 58 were differential metabolites (DM), including 41 flavonoids, 10 phenolic acids, 3 terpenoids, 2 alkaloids and 2 others, and 170 were unchanged; Among 58 DMs, 44 (75.9%) were up-regulated in YS, of which 30 were unique to YS, while 14 (24.1%) were down-regulated in YS, of which 10 were unique to ZP; Among flavonoids, 33 (80.5%) were more highly expressed in YS than in ZP; Among phenolic acids, 7 (70%) were more highly expressed in YS than in ZP; 12 of 58 DMs were annotated into 17 types of KEGG pathways. Among them, benzoic acid and p-Coumaryl alcohol were up-regulated in YS, and annotated into 10 pathways (58.8%) and 4 pathways (23.5%), respectively. In addition, much of DMs possess various pharmacological effects. These results indicated better quality of YS than ZP and the necessity of YS domestication. Taken together, this study will provide a reference for the scientific introduction, comprehensive development and utilization of wild Rehmannia glutinosa.
Stable duplex-linked antisense targeting miR-148a inhibits breast cancer cell proliferation
Authors: Okumura Sho , Hirano Yu , Komatsu Yasuo 
Published: June 2021

AbstractMicroRNAs (miRNAs) regulate cancer cell proliferation by binding directly to the untranslated regions of messenger RNA (mRNA). MicroRNA-148a (miR-148a) is expressed at low levels in breast cancer (BC). However, little attention has been paid to the sequestration of miR-148a. Here, we performed a knockdown of miR-148a using anti-miRNA oligonucleotides (AMOs) and investigated the effect on BC cell proliferation. BC cell proliferation was significantly suppressed by AMO flanked by interstrand cross-linked duplexes (CL-AMO), whereas single-stranded and commercially available AMOs had no effect. The suppression was caused by sequestering specifically miR-148a. Indeed, miR-148b, another member of the miR-148 family, was not affected. Importantly, the downregulation of miR-148a induced a greater and longer-lasting inhibition of BC cell proliferation than the targeting of oncogenic microRNA-21 (miR-21) did. We identified thioredoxin-interacting protein (TXNIP), a tumor suppressor gene, as a target of miR-148a and showed that CL-AMO provoked an increase in TXNIP mRNA expression. This study provide evidence that lowly expressed miRNAs such as miR-148a have an oncogenic function and might be a promising target for cancer treatment.
Interferon-induced protein with tetratricopeptide repeats 3 may be a key factor in primary biliary cholangitis
Authors: Sasaki Motoko , Sato Yasunori , Nakanuma Yasuni 
Published: June 2021

AbstractAccumulating studies suggest that senescent biliary epithelial cells (BECs) produce senescence-associated secretory phenotypes (SASPs) and play various roles in the pathogenesis of primary biliary cholangitis (PBC) and other cholangiopathies. We examined comprehensive profiles of senescent BECs and its contribution to the pathogenesis of PBC taking advantage of microarray analysis. cDNA microarray analysis revealed that 1841 genes including CCL2, IFIT3, CPQ were commonly up-regulated in senescent BECs cultured in serum depleted media or media with glycochenodeoxycholic acid. Knockdown of IFIT3 significantly suppressed cellular senescence (p < 0.01) and significantly increased apoptosis (p < 0.01) in BECs treated with serum depletion or glycochenodeoxycholic acid. Significantly increased expression of IFIT3 was seen in senescent BECs in small bile ducts showing cholangitis and in ductular reactions in PBC, compared to control livers (p < 0.01). An inadequate response to UDCA was inversely correlated to the increased expression of IFIT3 in small bile duct in PBC (p < 0.05). In conclusion, the expression of various genes related to immunity and inflammation including SASPs were increased in senescent BECs. Upregulated IFIT3 in senescent BECs may be associated with the pathogenesis of PBC and may be a possible therapeutic target in PBC.
Ab initio description of oxygen vacancies in epitaxially strained $$\hbox {SrTiO}_{{3}}$$ at finite temperatures
Authors: Zhou Zizhen , Chu Dewei , Cazorla Claudio 
Published: June 2021

AbstractEpitaxially grown $$\hbox {SrTiO}_{{3}}$$

SrTiO
3

(STO) thin films are material enablers for a number of critical energy-conversion and information-storage technologies like electrochemical electrode coatings, solid oxide fuel cells and random access memories. Oxygen vacancies ($${\mathrm{V}_{{\mathrm{O}}}}$$

V
O

), on the other hand, are key defects to understand and tailor many of the unique functionalities realized in oxide perovskite thin films. Here, we present a comprehensive and technically sound ab initio description of $${\mathrm{V}_{{\mathrm{O}}}}$$

V
O

in epitaxially strained (001) STO thin films. The novelty of our first-principles study lies in the incorporation of lattice thermal excitations on the formation energy and diffusion properties of $${\mathrm{V}_{{\mathrm{O}}}}$$

V
O

over wide epitaxial strain conditions ($$-4 \le \eta \le +4$$

-
4
≤
η
≤
+
4

%). We found that thermal lattice excitations are necessary to obtain a satisfactory agreement between first-principles calculations and the available experimental data for the formation energy of $${\mathrm{V}_{{\mathrm{O}}}}$$

V
O

. Furthermore, it is shown that thermal lattice excitations noticeably affect the energy barriers for oxygen ion diffusion, which strongly depend on $$\eta $$
η
and are significantly reduced (increased) under tensile (compressive) strain. The present work demonstrates that for a realistic theoretical description of oxygen vacancies in STO thin films is necessary to consider lattice thermal excitations, thus going beyond standard zero-temperature ab initio approaches.
Plant debris are hotbeds for pathogenic bacteria on recreational sandy beaches
Authors: Suzuki Yoshihiro , Shimizu Hiroki , Kuroda Takahiro , Takada Yusuke , Nukazawa Kei 
Published: June 2021

AbstractOn recreational sandy beaches, there are guidelines for the management of bacterial pollution in coastal waters regarding untreated sewage, urban wastewater, and industrial wastewater. However, terrestrial plant debris on coastal beaches can be abundant especially after floods and whilst it has rarely been considered a concern, the bacterial population associated with this type of pollution from the viewpoint of public health has not been adequately assessed. In this study, microbes associated with plant debris drifting onto Kizaki Beach in Japan were monitored for 8 months throughout the rainy season, summer, typhoon season, and winter. Here we show that faecal-indicator bacteria in the plant debris and sand under the debris were significantly higher than the number of faecal bacteria in the sand after a 2015 typhoon. When we focused on specific pathogenic bacteria, Brevundimonas vesicularis and Pseudomonas alcaligenes were commonly detected only in the plant debris and sand under the debris during the survey period. The prompt removal of plant debris would therefore help create safer beaches.
Combination of consensus and ensemble docking strategies for the discovery of human dihydroorotate dehydrogenase inhibitors
Authors: Chilingaryan Garri , Abelyan Narek , Sargsyan Arsen , Nazaryan Karen , Serobian Andre , Zakaryan Hovakim 
Published: June 2021

AbstractThe inconsistencies in the performance of the virtual screening (VS) process, depending on the used software and structural conformation of the protein, is a challenging issue in the drug design and discovery field. Varying performance, especially in terms of early recognition of the potential hit compounds, negatively affects the whole process and leads to unnecessary waste of the time and resources. Appropriate application of the ensemble docking and consensus-scoring approaches can significantly increase reliability of the VS results. Dihydroorotate dehydrogenase (DHODH) is a key enzyme in the pyrimidine biosynthesis pathway. It is considered as a valuable therapeutic target in cancer, autoimmune and viral diseases. Based on the conducted benchmark study and analysis of the effect of different combinations of the applied methods and approaches, here we suggested a structure-based virtual screening (SBVS) workflow that can be used to increase the reliability of VS.
Association of hemodynamic factors and progressive aortic dilatation following type A aortic dissection surgical repair
Authors: Zhu Yu , Mirsadraee Saeed , Asimakopoulos George , Gambaro Alessia , Rosendahl Ulrich , Pepper John , Xu Xiao Yun 
Published: June 2021

AbstractType A aortic dissection (TAAD) involves the ascending aorta or the arch. Acute TAAD usually requires urgent replacement of the ascending aorta. However, a subset of these patients develops aortic rupture due to further dilatation of the residual dissected aorta. There is currently no reliable means to predict the risk of dilatation following TAAD repair. In this study, we performed a comprehensive morphological and hemodynamic analysis for patients with and without progressive aortic dilatation following surgical replacement of the ascending aorta. Patient-specific models of repaired TAAD were reconstructed from post-surgery computed tomography images for detailed computational fluid dynamic analysis. Geometric and hemodynamic parameters were evaluated and compared between patients with stable aortic diameters (N = 9) and those with aortic dilatation (N = 8). Our results showed that the number of re-entry tears and true/false lumen pressure difference were significantly different between the two groups. Patients with progressive aortic dilatation had higher luminal pressure difference (6.7 [4.6, 10.9] vs. 0.9 [0.5, 2.3] mmHg; P = 0.001) and fewer re-entry tears (1.5 [1, 2.8] vs. 5 [3.3, 7.5]; P = 0.02) compared to patients with stable aortic diameters, suggesting that these factors may serve as potential predictors of aneurysmal dilatation following surgical repair of TAAD.
Homogeneous material based acoustic concentrators and rotators with linear coordinate transformation
Authors: Wang Huaping , Zhang Lei , Shah Shahnawaz , Zhu Rongrong , Zheng Bin 
Published: June 2021

AbstractWith the ability to focus and rotate the acoustic field in a given region while keeping the outside region unchanged, the acoustic concentrator and rotator has been developed for the versatile manipulations of acoustic wave. In this letter, we report the design of acoustic concentrator and rotator facilitated by linear coordinate transformation. Compared with the previous ones that have inhomogeneous parameter distributions, the designed devices are composed of several parts with homogeneous parameters, which can be achieved with the help of few homogeneous layered structures. Simulations are also performed to verify the functions of the designed device. The proposed acoustic concentrators and rotators would be useful in numerous applications such as acoustic sensing and communication.
Predictive analysis of the number of human brucellosis cases in Xinjiang, China
Authors: Zheng Yanling , Zhang Liping , Wang Chunxia , Wang Kai , Guo Gang , Zhang Xueliang , Wang Jing 
Published: June 2021

AbstractBrucellosis is one of the major public health problems in China, and human brucellosis represents a serious public health concern in Xinjiang and requires a prediction analysis to help making early planning and putting forward science preventive and control countermeasures. According to the characteristics of the time series of monthly reported cases of human brucellosis in Xinjiang from January 2008 to June 2020, we used seasonal autoregressive integrated moving average (SARIMA) method and nonlinear autoregressive regression neural network (NARNN) method, which are widely prevalent and have high prediction accuracy, to construct prediction models and make prediction analysis. Finally, we established the SARIMA((1,4,5,7),0,0)(0,1,2)12 model and the NARNN model with a time lag of 5 and a hidden layer neuron of 10. Both models have high fitting performance. After comparing the accuracies of two established models, we found that the SARIMA((1,4,5,7),0,0)(0,1,2)12 model was better than the NARNN model. We used the SARIMA((1,4,5,7),0,0)(0,1,2)12 model to predict the number of monthly reported cases of human brucellosis in Xinjiang from July 2020 to December 2021, and the results showed that the fluctuation of the time series from July 2020 to December 2021 was similar to that of the last year and a half while maintaining the current prevention and control ability. The methodology applied here and its prediction values of this study could be useful to give a scientific reference for prevention and control human brucellosis.
Clinical evolution of ST11 carbapenem resistant and hypervirulent Klebsiella pneumoniae
Authors: Xie Miaomiao , Yang Xuemei , Xu Qi , Ye Lianwei , Chen Kaichao , Zheng Zhiwei , Dong Ning , Sun Qiaoling , Shu Lingbin , Gu Danxia , Chan Edward Wai-Chi , Zhang Rong , Chen Sheng 
Published: June 2021

AbstractCarbapenem-resistant and hypervirulent K. pneumoniae (CR-HvKP) strains that have emerged recently have caused infections of extremely high mortality in various countries. In this study, we discovered a conjugative plasmid that encodes carbapenem resistance and hypervirulence in a clinical ST86 K2 CR-HvKP, namely 17ZR-91. The conjugative plasmid (p17ZR-91-Vir-KPC) was formed by fusion of a non-conjugative pLVPK-like plasmid and a conjugative blaKPC-2-bearing plasmid and is present dynamically with two other non-fusion plasmids. Conjugation of p17ZR-91-Vir-KPC to other K. pneumoniae enabled them to rapidly express the carbapenem resistance and hypervirulence phenotypes. More importantly, genome analysis provided direct evidence that p17ZR-91-Vir-KPC could be directly transmitted from K2 CR-HvKP strain, 17ZR-91, to ST11 clinical K. pneumoniae strains to convert them into ST11 CR-HvKP strains, which explains the evolutionary mechanisms of recently emerged ST11 CR-HvKP strains.
Ammonia-oxidizing archaea are integral to nitrogen cycling in a highly fertile agricultural soil
Authors: Huang Laibin , Chakrabarti Seemanti , Cooper Jennifer , Perez Ana , John Sophia M , Daroub Samira H , Martens-Habbena Willm 
Published: June 2021

Abstract
Nitrification is a central process in the global nitrogen cycle, carried out by a complex network of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Nitrification is responsible for significant nitrogen leaching and N2O emissions and thought to impede plant nitrogen use efficiency in agricultural systems. However, the actual contribution of each nitrifier group to net rates and N2O emissions remain poorly understood. We hypothesized that highly fertile agricultural soils with high organic matter mineralization rates could allow a detailed characterization of N cycling in these soils. Using a combination of molecular and activity measurements, we show that in a mixed AOA, AOB, and comammox community, AOA outnumbered low diversity assemblages of AOB and comammox 50- to 430-fold, and strongly dominated net nitrification activities with low N2O yields between 0.18 and 0.41 ng N2O–N per µg NOx–N in cropped, fallow, as well as native soil. Nitrification rates were not significantly different in plant-covered and fallow plots. Mass balance calculations indicated that plants relied heavily on nitrate, and not ammonium as primary nitrogen source in these soils. Together, these results imply AOA as integral part of the nitrogen cycle in a highly fertile agricultural soil.
Sublethal hyperthermia enhances anticancer activity of doxorubicin in chronically hypoxic HepG2 cells through ROS-dependent mechanism
Authors: Wang Qi , Zhang Hui , Ren Qian-qian , Ye Tian-he , Liu Yi-ming , Zheng Chuan-sheng , Zhou Guo-feng , Xia Xiang-wen 
Published: June 2021

Abstract
Thermal ablation in combination with transarterial chemoembolization (TACE) has been reported to exert a more powerful antitumor effect than thermal ablation alone in hepatocellular carcinoma patients. However, the underlying mechanisms remain unclear. The purpose of the present study was to evaluate whether sublethal hyperthermia encountered in the periablation zone during thermal ablation enhances the anticancer activity of doxorubicin in chronically hypoxic (encountered in the tumor area after TACE) liver cancer cells and to explore the underlying mechanisms. In the present study, HepG2 cells precultured under chronic hypoxic conditions (1% oxygen) were treated in a 42°C water bath for 15 or 30 min, followed by incubation with doxorubicin. Assays were then performed to determine intracellular uptake of doxorubicin, cell viability, apoptosis, cell cycle, mitochondrial membrane potential (MMP), reactive oxygen species (ROS), and total antioxidant capacity. The results confirmed that sublethal hyperthermia enhanced the intracellular uptake of doxorubicin into hypoxic HepG2 cells. Hyperthermia combined with doxorubicin led to a greater inhibition of cell viability and increased apoptosis in hypoxic HepG2 cells as compared with hyperthermia or doxorubicin alone. In addition, the combination induced apoptosis by increasing ROS and causing disruption of MMP. Pretreatment with the ROS scavenger N-acetyl cysteine significantly inhibited the apoptotic response, suggesting that cell death is ROS-dependent. These findings suggested that sublethal hyperthermia enhances the anticancer activity of doxorubicin in hypoxic HepG2 cells via a ROS-dependent mechanism.
Adopting a Conceptual Validity Framework for Testing in Speech-Language Pathology
Authors: Daub Olivia , Cunningham Barbara Jane , Bagatto Marlene P. , Johnson Andrew M. , Kwok Elaine Y. , Smyth Rachael E. , Cardy Janis Oram 
Published: June 2021

Purpose
Limited evidence-based guidelines for test selection continue to result in inconsistency in test use and interpretation in speech-language pathology. A major barrier is the lack of explicit and consistent adoption of a validity framework by our field. In this viewpoint, we argue that adopting the conceptual validity framework in the Standards for Educational and Psychological Testing (American Educational Research Association et al., 2014) would support both the development of more meaningful and feasible clinical tests and more appropriate use and interpretation of tests in speech-language pathology.

Method

We describe and evaluate the
Standards for Educational and Psychological Testing
(American Educational Research Association et al., 2014) validity framework and consider its relevance to speech-language pathology. We describe how the validity framework could be integrated into clinical practice and include examples of how it could be applied to support common clinical decisions. We evaluate the costs and benefits of adopting this framework, from the perspectives of speech-language pathologists, clients, and test developers.

Results

The
Standards'
validity framework clarifies complex validity issues by shifting the focus of validity from tests to the decisions speech-language pathologists make based on test results. By focusing on decisions, the framework requires critical evaluation of test use, rather than evaluating tests against sets of criteria. Adopting this framework has the potential for appreciable improvement in the way tests are used and valued across our profession.

Conclusions
Speech-language pathologists, test developers, and clients will benefit from improved evidence-based assessment practices. It is recommended that regulators, test developers, professional associations, universities, and researchers adopt the framework and endorse it as best practice moving forward. This viewpoint proposes a series of first steps toward supporting uptake of the framework into research and practice.