bluuebunny/crossref_metadata_2025 huggingface dataset:
Studying the Changes in the Hydro‐Meteorological Components of Water Budget in Lake Urmia
Authors: Vaheddoost Babak , Fathian Farshad , Gul Enes , Safari Mir Jafar Sadegh
Published: June 2022

Abrupt changes in the Lake Urmia water level have been addressed in many studies, and yet the link between the water level decline and hydro‐meteorological variables in the basin is a major topic for debate between researchers. In this study, a set of data‐driven techniques is used to investigate the components of the water budget in Lake Urmia. Then, the rate of monthly depth differences (DD), precipitation (P), evaporation (E), potential groundwater head (G), and streamflow (Q) time series between 1974 and 2014 are used in the analysis. Several scenarios and strategies are developed by considering the major changes in the year‐2000, which is believed to be the initiation of the hydrological encroachment in the basin. Simple water budget (WB), dynamic regression (DR), and symbolic regression (SR) techniques are used to simulate the DD with consideration to P, E, G, and Q. Alternatively, the effect of the year 1997 as the potential base‐line for the initiation of significant meteorological trends in the basin is investigated. Conducted analysis showed that the DR models of an autoregressive moving average together with multiple exogenous inputs provide an approximate R2: 0.7 as the best alternative among the selected models. It is shown that the Q and G depict abrupt changes compared to the P and E, while either the year 1997 (climate effect) or the year 2000 (encroachment effect) is considered as the baseline in the study.
Ovarian carcinosarcoma is a distinct form of ovarian cancer with poorer survival compared to tubo-ovarian high-grade serous carcinoma
Authors: Hollis Robert L. , Croy Ian , Churchman Michael , Bartos Clare , Rye Tzyvia , Gourley Charlie , Herrington C. Simon
Published: June 2022

Background

Ovarian carcinosarcoma (OCS) is an uncommon, biphasic and highly aggressive ovarian cancer type, which has received relatively little research attention.

Methods

We curated the largest pathologically confirmed OCS cohort to date, performing detailed histopathological characterisation, analysis of features associated with survival and comparison against high-grade serous ovarian carcinoma (HGSOC).

Results

Eighty-two OCS patients were identified; overall survival was poor (median 12.7 months). In all, 79% demonstrated epithelial components of high-grade serous (HGS) type, while 21% were endometrioid. Heterologous elements were common (chondrosarcoma in 32%, rhabdomyosarcoma in 21%, liposarcoma in 2%); chondrosarcoma was more frequent in OCS with endometrioid carcinomatous components. Earlier stage, complete resection and platinum-containing adjuvant chemotherapy were associated with prolonged survival; however, risk of relapse and mortality was high across all patient groups. Histological subclassification did not identify subgroups with distinct survival. Compared to HGSOC, OCS patients were older (P < 0.0001), more likely to be FIGO stage I (P = 0.025), demonstrated lower chemotherapy response rate (P = 0.001) and had significantly poorer survival (P < 0.0001).

Conclusion

OCS represents a distinct, highly lethal form of ovarian cancer for which new treatment strategies are urgently needed. Histological subclassification does not identify patient subgroups with distinct survival. Aggressive adjuvant chemotherapy should be considered for all cases, including those with early-stage disease.
Emerging nanomedical strategies for direct targeting of pediatric and adult diffuse gliomas
Authors: Kolsteeg Christy , Hulleman Esther , Bianco John
Published: June 2022

High-grade gliomas, in particularly diffuse midline glioma, H3K27-altered in children and glioblastoma in adults, are the most lethal brain tumour with a dismal prognosis. Developments in modern medicine are constantly being applied in the search for a cure, although finding the right strategy remains elusive. Circumventing the blood–brain barrier is one of the biggest challenges when it comes to treating brain tumours. The cat and mouse game of finding the Trojan horse to traverse this barrier and deliver therapeutics to the brain has been a long and hard-fought struggle. Research is ongoing to find new and feasible ways to reach specific targets in the brain, with a special focus on inoperable or recurring brain tumours. Many options and combinations of options have been tested to date and continue to be so in the search to find the most effective and least toxic treatment paradigm. Although improvements are often small and slow, some of these strategies have already shown promise, shining a light of hope that finding the cure is feasible. In this review, we discuss recent findings that elucidate promising but atypical strategies for targeting gliomas and the implications that this work has on developing new treatment regimens.
Identification of an Epi-metabolic dependency on EHMT2/G9a in T-cell acute lymphoblastic leukemia
Authors: Montanaro Anna , Kitara Samuel , Cerretani Elisa , Marchesini Matteo , Rompietti Chiara , Pagliaro Luca , Gherli Andrea , Su Angela , Minchillo Maria Laura , Caputi Mariafrancesca , Fioretzaki Rodanthi , Lorusso Bruno , Ross Linda , Alexe Gabriela , Masselli Elena , Marozzi Marina , Rizzi Federica Maria Angela , La Starza Roberta , Mecucci Cristina , Xiong Yan , Jin Jian , Falco Angela , Knoechel Birgit , Aversa Franco , Candini Olivia , Quaini Federico , Sportoletti Paolo , Stegmaier Kimberly , Roti Giovanni
Published: June 2022

Genomic studies have identified recurrent somatic alterations in genes involved in DNA methylation and post-translational histone modifications in acute lymphoblastic leukemia (ALL), suggesting new opportunities for therapeutic interventions. In this study, we identified G9a/EHMT2 as a potential target in T-ALL through the intersection of epigenome-centered shRNA and chemical screens. We subsequently validated G9a with low-throughput CRISPR-Cas9-based studies targeting the catalytic G9a SET-domain and the testing of G9a chemical inhibitors in vitro, 3D, and in vivo T-ALL models. Mechanistically we determined that G9a repression promotes lysosomal biogenesis and autophagic degradation associated with the suppression of sestrin2 (SESN2) and inhibition of glycogen synthase kinase-3 (GSK-3), suggesting that in T-ALL glycolytic dependent pathways are at least in part under epigenetic control. Thus, targeting G9a represents a strategy to exhaust the metabolic requirement of T-ALL cells.
Adipocyte-derived kynurenine promotes obesity and insulin resistance by activating the AhR/STAT3/IL-6 signaling
Authors: Huang Teng , Song Jia , Gao Jia , Cheng Jia , Xie Hao , Zhang Lu , Wang Yu-Han , Gao Zhichao , Wang Yi , Wang Xiaohui , He Jinhan , Liu Shiwei , Yu Qilin , Zhang Shu , Xiong Fei , Zhou Qing , Wang Cong-Yi
Published: June 2022

Aberrant amino acid metabolism is a common event in obesity. Particularly, subjects with obesity are characterized by the excessive plasma kynurenine (Kyn). However, the primary source of Kyn and its impact on metabolic syndrome are yet to be fully addressed. Herein, we show that the overexpressed indoleamine 2,3-dioxygenase 1 (IDO1) in adipocytes predominantly contributes to the excessive Kyn, indicating a central role of adipocytes in Kyn metabolism. Depletion of Ido1 in adipocytes abrogates Kyn accumulation, protecting mice against obesity. Mechanistically, Kyn impairs lipid homeostasis in adipocytes via activating the aryl hydrocarbon receptor (AhR)/Signal transducer and activator of transcription 3 /interleukin-6 signaling. Genetic ablation of AhR in adipocytes abolishes the effect of Kyn. Moreover, supplementation of vitamin B6 ameliorated Kyn accumulation, protecting mice from obesity. Collectively, our data support that adipocytes are the primary source of increased circulating Kyn, while elimination of accumulated Kyn could be a viable strategy against obesity.
RIViT-seq enables systematic identification of regulons of transcriptional machineries
Authors: Otani Hiroshi , Mouncey Nigel J.
Published: June 2022

Transcriptional regulation is a critical process to ensure expression of genes necessary for growth and survival in diverse environments. Transcription is mediated by multiple transcription factors including activators, repressors and sigma factors. Accurate computational prediction of the regulon of target genes for transcription factors is difficult and experimental identification is laborious and not scalable. Here, we demonstrate regulon identification by in vitro transcription-sequencing (RIViT-seq) that enables systematic identification of regulons of transcription factors by combining an in vitro transcription assay and RNA-sequencing. Using this technology, target genes of 11 sigma factors were identified inStreptomyces coelicolorA3(2). The RIViT-seq data expands the transcriptional regulatory network in this bacterium, discovering regulatory cascades and crosstalk between sigma factors. Implementation of RIViT-seq with other transcription factors and in other organisms will improve our understanding of transcriptional regulatory networks across biology.
Context-dependent enhancer function revealed by targeted inter-TAD relocation
Authors: Bolt Christopher Chase , Lopez-Delisle Lucille , Hintermann Aurélie , Mascrez Bénédicte , Rauseo Antonella , Andrey Guillaume , Duboule Denis
Published: June 2022

The expression of some genes depends on large, adjacent regions of the genome that contain multiple enhancers. These regulatory landscapes frequently align with Topologically Associating Domains (TADs), where they integrate the function of multiple similar enhancers to produce a global, TAD-specific regulation. We asked if an individual enhancer could overcome the influence of one of these landscapes, to drive gene transcription. To test this, we transferred an enhancer from its native location, into a nearby TAD with a related yet different functional specificity. We used the biphasic regulation of Hoxd genes during limb development as a paradigm. These genes are first activated in proximal limb cells by enhancers located in one TAD, which is then silenced when the neighboring TAD activates its enhancers in distal limb cells. We transferred a distal limb enhancer into the proximal limb TAD and found that its new context suppresses its normal distal specificity, even though it is bound by HOX13 transcription factors, which are responsible for the distal activity. This activity can be rescued only when a large portion of the surrounding environment is removed. These results indicate that, at least in some cases, the functioning of enhancer elements is subordinated to the host chromatin context, which can exert a dominant control over its activity.
Multifunctional biomimetic tactile system via a stick-slip sensing strategy for human–machine interactions
Authors: Li Yue , Zhao Manjun , Yan Yadong , He Luanxi , Wang Yingyi , Xiong Zuoping , Wang Shuqi , Bai Yuanyuan , Sun Fuqin , Lu Qifeng , Wang Yu , Li Tie , Zhang Ting
Published: June 2022

A tactile sensor system enables natural interaction between humans and machines; this interaction is crucial for dexterous robotic hands, interactive entertainment, and other smart scenarios. However, the lack of sliding friction detection significantly limits the accuracy and scope of interactions due to the absence of sophisticated information, such as slippage, material and roughness of held objects. Here, inspired by the stick-slip phenomena in the sliding process, we have developed a multifunctional biomimetic tactile system based on the stick-slip sensing strategy, which is a universal method to detect slippage and estimate the surface properties of objects by sliding. This system consists of a flexible fingertip-inspired tactile sensor, a read-out circuit and a machine-learning module. Based on the stick-slip sensing strategy, our system was endowed with high recognition rates for slippage detection (100.0%), material classification (93.3%) and roughness discrimination (92.8%). Moreover, robotic hand manipulation, interactive games and object classification are demonstrated with this multifunctional system for comprehensive and promising human–machine interactions.
Better force fields start with better data: A data set of cation dipeptide interactions
Authors: Hu Xiaojuan , Lenz-Himmer Maja-Olivia , Baldauf Carsten
Published: June 2022

We present a data set from a first-principles study of amino-methylated and acetylated (capped) dipeptides of the 20 proteinogenic amino acids – including alternative possible side chain protonation states and their interactions with selected divalent cations (Ca2+, Mg2+ and Ba2+). The data covers 21,909 stationary points on the respective potential-energy surfaces in a wide relative energy range of up to 4 eV (390 kJ/mol). Relevant properties of interest, like partial charges, were derived for the conformers. The motivation was to provide a solid data basis for force field parameterization and further applications like machine learning or benchmarking. In particular the process of creating all this data on the same first-principles footing, i.e. density-functional theory calculations employing the generalized gradient approximation with a van der Waals correction, makes this data suitable for first principles data-driven force field development. To make the data accessible across domain borders and to machines, we formalized the metadata in an ontology.
PISCOeo_pm, a reference evapotranspiration gridded database based on FAO Penman-Monteith in Peru
Authors: Huerta Adrian , Bonnesoeur Vivien , Cuadros-Adriazola José , Gutierrez Leonardo , Ochoa-Tocachi Boris F. , Román-Dañobeytia Francisco , Lavado-Casimiro Waldo
Published: June 2022

A new FAO Penman-Monteith reference evapotranspiration gridded dataset is introduced, called PISCOeo_pm. PISCOeo_pm has been developed for the 1981–2016 period at ~1 km (0.01°) spatial resolution for the entire continental Peruvian territory. The framework for the development of PISCOeo_pm is based on previously generated gridded data of meteorological subvariables such as air temperature (maximum and minimum), sunshine duration, dew point temperature, and wind speed. Different steps, i.e., (i) quality control, (ii) gap-filling, (iii) homogenization, and (iv) spatial interpolation, were applied to the subvariables. Based on the results of an independent validation, on average, PISCOeo_pm exhibits better precision than three existing gridded products (CRU_TS, TerraClimate, and ERA5-Land) because it presents a predictive capacity above the average observed using daily and monthly data and has a higher spatial resolution. Therefore, PISCOeo_pm is useful for better understanding the terrestrial water and energy balances in Peru as well as for its application in fields such as climatology, hydrology, and agronomy, among others.
A study of triple-mass diffusion species and energy transfer in Carreau–Yasuda material influenced by activation energy and heat source
Authors: Sohail Muhammad , Nazir Umar , El-Zahar Essam R. , Alrabaiah Hussam , Kumam Poom , Mousa Abd Allah A. , Sitthithakerngkiet Kanokwan , Park Choonkil
Published: June 2022

The mechanism of thermal transport can be enhanced by mixing the nanoparticles in the base liquid. This research discusses the utilization of nanoparticles (tri-hybrid) mixture into Carreau–Yasuda material. The flow is assumed to be produced due to the stretching of vertical heated surface. The phenomena of thermal transport are modeled by considering Joule heating and heat generation or absorption involvement. Additionally, activation energy is engaged to enhance heat transfer rate. The mathematical model composing transport of momentum, heat and mass species is developed in Cartesian coordinate system under boundary layer investigation in the form of coupled nonlinear partial differential equations. The complex partial differential equations are converted into coupled nonlinear ordinary differential equations by using the appropriate similarity transformation. The conversion of PDEs into ODEs make the problem easy to handle and it overcome the difficulties to solve the PDEs. The transformed ordinary differential equations are solved with the help of help of finite element scheme. The obtained solution is plotted against numerous involved parameters and comparative study is established for the reliability of method and accuracy of obtained results. An enhancement in fluid temperature is recorded against magnetic parameter and Eckert number. Also, decline in velocity is recorded for Weissenberg number and concentration is controlled against higher values of Schmidt number. Furthermore, it is recommended that the finite element scheme can be implemented to handle complex coupled nonlinear differential equation arising in modeling of several phenomena occurs in mathematical physics.
Mebendazole, an anti-helminth drug, suppresses inflammation, oxidative stress and injury in a mouse model of ulcerative colitis
Authors: Eskandari Moein , Asgharzadeh Fereshteh , Askarnia-faal Mohammad Mostafa , Naimi Hamideh , Avan Amir , Ahadi Mitra , Vossoughinia Hassan , Gharib Masoumeh , Soleimani Atena , Naghibzadeh Niloufar , Ferns Gordon , Ryzhikov Mikhail , Khazaei Majid , Hassanian Seyed Mahdi
Published: June 2022

Mebendazole (MBZ) is an efficacious anthelmintic with known anti-inflammatory and fibrinolytic properties. In this study, we aimed to explore the protective effects of this FDA-approved drug against DSS-induced colitis in a murine model either alone or in combination with Sulfasalazine (SSZ), a standard therapy for ulcerative colitis. We found that MBZ significantly improved colitis disease activity index as assessed by changes in body weight, degree of stool consistency, rectal bleeding, and prolapse. We also found that MBZ ameliorated the colon histopathological score by attenuating crypt loss, mucosal damage, and inflammation score in colitis tissues. Similarly, DSS-induced colon shortening, colon weight loss, and increase in spleen weight were all abrogated in the presence of MBZ. Moreover, MBZ decreased inflammation, possibly by reducing oxidative stress markers, suppressing inflammatory cell infiltration, and down-regulation of inflammatory genes in colon tissues. Furthermore, MBZ potently reduced fibrosis by decreasing collagen deposition and down-regulating pro-fibrotic genes including Col 1a1 and Col 1a2 in colitis tissue homogenates. In conclusion, our study showed that this broad-spectrum anthelminthic could be repurposed as a novel therapy for ulcerative colitis without any observed side effects, however, regarding the concerns about the potential toxicity of MBZ in UC patients, future experiments on MBZ therapy in other models of UC is needed to completely address the toxicity concerns.
Social capital building interventions and self-reported post-disaster recovery in Ofunato, Japan
Authors: Lee Juheon , Aldrich Daniel P. , Kiyota Emi , Yasuhiro Tanaka , Sawada Yasuyuki
Published: June 2022

Evidence shows that communal resources, cohesion, and social infrastructure can mitigate shocks and enhance resilience. However, we know less about how specific social capital building interventions facilitate recovery in post-disaster environments. Using a survey of over 1000 residents of Ofunato, Japan after the 2011 Tohoku earthquake and tsunami, this study demonstrates that the individuals who actively participated in a community center—created for and led by neighborhood elders—reported higher levels of family and neighborhood recovery than similar individuals who did not participate. Results from ordinal logistic regression analyses, propensity score matching (PSM) and coarsened exact matching (CEM) show arguably stronger causal links between bottom-up, microlocal programs to boost connections in post-disaster areas and post-disaster outcomes. Community-based programs that strengthen social ties even among elderly residents can measurably improve their recoveries.
A novel approach GRNTSTE to reconstruct gene regulatory interactions applied to a case study for rat pineal rhythm gene
Authors: Liu Zhenyu , Gao Jing , Li Tao , Jing Yi , Xu Cheng , Zhu Zhengtong , Zuo Dongshi , Chen Junjie
Published: June 2022

Accurate inference and prediction of gene regulatory network are very important for understanding dynamic cellular processes. The large-scale time series genomics data are helpful to reveal the molecular dynamics and dynamic biological processes of complex biological systems. Firstly, we collected the time series data of the rat pineal gland tissue in the natural state according to a fixed sampling rate, and performed whole-genome sequencing. The large-scale time-series sequencing data set of rat pineal gland was constructed, which includes 480 time points, the time interval between adjacent time points is 3 min, and the sampling period is 24 h. Then, we proposed a new method of constructing gene expression regulatory network, named the gene regulatory network based on time series data and entropy transfer (GRNTSTE) method. The method is based on transfer entropy and large-scale time-series gene expression data to infer the causal regulatory relationship between genes in a data-driven mode. The comparative experiments prove that GRNTSTE has better performance than dynamical gene network inference with ensemble of trees (dynGENIE3) and SCRIBE, and has similar performance to TENET. Meanwhile, we proved that the performance of GRNTSTE is slightly lower than that of SINCERITIES method and better than other gene regulatory network construction methods in BEELINE framework, which is based on the BEELINE data set. Finally, the rat pineal rhythm gene expression regulatory network was constructed by us based on the GRNTSTE method, which provides an important reference for the study of the pineal rhythm mechanism, and is of great significance to the study of the pineal rhythm mechanism.
Synthetic applications of hydride abstraction reactions by organic oxidants
Authors: Miller Jenna L. , Lawrence Jean-Marc I. A. , Rodriguez del Rey Freddy O. , Floreancig Paul E.
Published: June 2022

Organic oxidants, including quinones, oxoammonium ions, and trityl cations, abstract hydride ions to form carbocations. This review describes the mechanistic foundations for these processes and the vast array of their applications in synthesis.
Simultaneous monitoring of HIV viral load and screening of SARS-CoV-2 employing a low-cost RT-qPCR test workflow
Authors: Gulati Gaurav K. , Panpradist Nuttada , Stewart Samuel W. A. , Beck Ingrid A. , Boyce Ceejay , Oreskovic Amy K. , García-Morales Claudia , Avila-Ríos Santiago , Han Peter D. , Reyes-Terán Gustavo , Starita Lea M. , Frenkel Lisa M. , Lutz Barry R. , Lai James J.
Published: June 2022

This new workflow enables co-extraction of HIV and SARS-CoV2 RNAs from clinical pooled plasma/nasal secretion samples that allows sensitive detection of SARS-CoV-2 and HIV infections in the patients-living with HIV.
Use of MALDI-TOF mass spectrometry for virus identification: a review
Authors: Do Tomas , Guran Roman , Adam Vojtech , Zitka Ondrej
Published: June 2022

The possibilities of virus identification, including SARS-CoV-2, by MALDI-TOF mass spectrometry are discussed in this review.
Appropriate aggregation is needed for highly active Pt/Al2O3 to enable hydrogenation of chlorinated nitrobenzene
Authors: Gu Rongtian , Meng Deming , She Minyi , Wang Yibo , Yang Hua , Guo Xiangke , Xue Nianhua , Ding Weiping
Published: June 2022

Access to aggregated Pt particles on the non-reducing support Al2O3 is essential for selective hydrogenation of chlorinated nitrobenzene to aniline chloride, whereas atomic platinum is nearly inactive.
Controllable sensitization of Zr-MOFs by using CdS and its application for photoelectrochemical detection of alkaline phosphatase
Authors: Ying Ying , Wu Wenying , He Guihua , Deng Wenfang , Tan Yueming , Xie Qingji
Published: June 2022

Sensitive photoelectrochemical detection of alkaline phosphatase activity is achieved based on controllable sensitization of Zr-MOFs by using CdS QDs.
Transition between growth of dense and porous films: theory of dual-layer SEI
Authors: von Kolzenberg Lars , Werres Martin , Tetzloff Jonas , Horstmann Birger
Published: June 2022

The film-growth model predicts a morphology-driven dual-layer structure due to slowing down of electron diffusion through the SEI.
Topology detection in cavity QED
Authors: Pérez-González Beatriz , Gómez-León Álvaro , Platero Gloria
Published: June 2022

We explore the physics of topological lattice models immersed in c-QED architectures for arbitrary coupling strength with the photon field, and investigate the use of the cavity transmission as a topology detector.
Cellular imaging properties of phosphorescent iridium(iii) complexes substituted with ester or amide groups
Authors: Dai Peiling , Li Jiangshan , Tang Man , Yan Dong , Xu Zihan , Li Yonghua , Chen Zejing , Liu Shujuan , Zhao Qiang , Zhang Kenneth Yin
Published: June 2022

A phosphorescent iridium(iii) complex substituted with two ester groups revealed whole-cell staining. The nuclear uptake of the complex was mediated by clathrin and microtubules. The nuclear uptake efficiency was related to the cell division cycle.
Facile in situ construction of a covalent adaptable network polyester vitrimer with advanced performance in repairability, foamability and recyclability
Authors: Li Pengzhi , Lan Bin , Zhang Xutao , Lei Siyuan , Yang Qi , Gong Pengjian , Park Chul B. , Li Guangxian
Published: June 2022

An environmentally friendly polyester vitrimer was prepared through an efficient one-pot method. The vitrimer possesses advanced recyclability,  foamability, creep resistance and self-healing performance.
Biobased thin-film composite membranes comprising priamine–genipin selective layer on nanofibrous biodegradable polylactic acid support for oil and solvent-resistant nanofiltration
Authors: Yang Cong , Topuz Fuat , Park Sang-Hee , Szekely Gyorgy
Published: June 2022

A robust and sustainable thin-film composite membrane, using green raw materials on a highly porous, electrospun and biodegradable support, was developed for molecular sieving.
Improving performance of monolayer arsenene tunnel field-effect transistors by defects
Authors: Song Shun , Gong Jian , Wen Hongyu , Yang Shenyuan
Published: June 2022

Suitable defect at the source-channel interface can significantly improve the performance of arsenene TFETs.
A metal–oxide interface enhances the methane oxidative coupling reaction in a solid oxide electrolyzer
Authors: Xu Yihong , Zhang Youkai , Huang Lingwei , Gan Lizhen
Published: June 2022

The reaction mechanism for the oxidative coupling of methane.
Metal-free polychloromethyl radical-initiated cyclization of unactivated N-allylindoles towards pyrrolo[1,2-a]indoles
Authors: Shan Yujia , Yang Zixian , Yu Jin-Tao , Pan Changduo
Published: June 2022

A polychloromethylation-initiated cyclization of N-allyl-indoles towards pyrrolo[1,2-a]indoles was developed using CH2Cl2 and CHCl3 as the di- and trichloromethyl radical sources.
Stiffening of under-constrained spring networks under isotropic strain
Authors: Lee Cheng-Tai , Merkel Matthias
Published: June 2022

We study strain stiffening of sub-isostatic spring networks, numerically testing analytical predictions of the elastic network properties, e.g., a linear scaling of the shear modulus with isotropic tension. We also probe how our results depend on system size.
Construction of a competing endogenous RNA network to analyse glucose-6-phosphate dehydrogenase dysregulation in hepatocellular carcinoma
Authors: Wang Pengyu , Yang Xitong , Liu Dan , Yang Yunhui , Zhang Yuanyuan , Wang Guangming
Published: June 2022

Hepatocellular carcinoma (HCC) is a common malignant tumour with high rates of morbidity and mortality worldwide. Therefore, it is of great significance to find new molecular markers for HCC diagnosis and treatment. G6PD is known to be dysregulated in a variety of tumours. In addition, the ceRNA network plays a crucial role in the occurrence and development of HCC. However, the mechanism by which the ceRNA network regulates G6PD in HCC remains unclear. We used TCGA-LIHC data to analyse the possibility of using G6PD as an independent prognostic marker. Univariate Cox proportional hazards regression, multivariate Cox proportional hazards regression, and receiver operating characteristic curve analysis were used to analyse the influence of G6PD overexpression on the prognosis of HCC patients. We also analysed the biological function of G6PD, its effect on the immune microenvironment, and drug sensitivity. Finally, we constructed a ceRNA network of lncRNAs/miR-122-5p/G6PD to explore the regulatory mechanism of G6PD. G6PD was highly expressed in HCC, was related to pathological stage and poor prognosis, and could be used as an independent prognostic indicator of HCC. The expression of G6PD was closely related to the immune microenvironment of HCC. In addition, the expression of G6PD in HCC could be regulated by the ceRNA network. Therefore, G6PD can be used as an immunotherapy target to improve the survival and prognosis of HCC patients, and the ceRNA regulatory network of G6PD has potential diagnostic and therapeutic value for HCC.
Fully Bayesian analysis of the relevance vector machine classification for imbalanced data problem
Authors: Wang Wenyang , Sun Yanna , Li Keran , Wang Jinglin , He Chong , Sun Dongchu
Published: June 2022

Relevance Vector Machine (RVM) is a supervised learning algorithm extended from Support Vector Machine based on the Bayesian sparsity model. Relevance Vector Machine classification suffers from theoretical limitations and computational inefficiency mainly because there is no closed‐form solution for the posterior of the weight parameters. We propose two advanced Bayesian approaches for RVM classification, namely the Enhanced RVM and the Reinforced RVM, to perfect the theoretic framework of RVM and extend the algorithm to the imbalanced data problem, which has an arresting skew in data size between classes. First, the Enhanced RVM conducts a strict Bayesian sampling process instead of the approximation method in the original one to remedy its theoretic limitations, especially the non‐convergence of the iterations. Secondly, we conjecture that the hierarchical prior makes the Reinforced RVM achieve consistent estimations of the quantities of interest compared with the non‐consistent estimations of the original RVM. Consistency is necessary for RVM classification since it makes the model more stable and localises the relevant vectors more accurately in the imbalanced data problem. The two‐level prior also renders the Reinforced one competitive in the imbalanced data problem by building the inner connection of parameter dimensions and alloting a more vital relevance to the small class data weight parameter. The theoretic proofs and several numeric studies demonstrate the merits of our two proposed algorithms.
Gaia EDR3 comparative study of protoplanetary disk fractions in young stellar clusters
Authors: Mendigutía I. , Solano E. , Vioque M. , Balaguer-Nuñez L. , Ribas A. , Huélamo N. , Rodrigo C.
Published: June 2022

Context. The lifetime of protoplanetary disks around young stars limits the timescale of planet formation. A disk dissipation timescale ≤10 Myr was inferred from surveys that count the relative number of stars with disks – the disk fraction – in young stellar clusters with different ages. However, most previous surveys focused on the compact region within ∼2 pc of the clusters’ centers, for which the disk fraction information about the outer part is practically absent.

Aims. We aim to test if disk fraction estimates change when inferred from an extended region around the clusters’ centers.

Methods.Gaia EDR3 data and a best-suited, Virtual Observatory (VO)-based tool – Clusterix – are used to identify member stars for a representative sample of 19 young stellar clusters considering two concentric fields of view (FOVs) with radii of ∼20 pc and ∼2 pc. Inner-disk fractions associated with each FOV are identically derived from 2MASS color-color diagrams and compared to each other.

Results. Although the density of members is smaller in the periphery, the absolute number of member stars is typically ∼5 times larger at distances farther than ∼2 pc from the clusters’ centers. In turn, our analysis reveals that the inner disk fractions inferred from the compact and the extended regions are equal within ∼±10%. A list of member and disk stars identified in each cluster is provided and stored in a VO-compliant archive, along with their membership probabilities, angular distances to the center, and Gaia and near-infrared data. Averaged values and plots that characterize the whole clusters are also provided, including Hertzsprung-Russell diagrams based on Gaia colors and absolute magnitudes for the sources with known extinction.

Conclusions. Our results cover the largest fields ever probed when dealing with disk fractions for all clusters analyzed, and imply that their complete characterization requires the use of wide FOVs. However, the comparative study does not support a previous hypothesis that disk fractions should be significantly larger when extended regions are considered. The resulting database is a benchmark for future detailed studies of young clusters, whose disk fractions must be accurately determined by using multiwavelength analysis potentially combined with data from upcoming Gaia releases.
Effect of multi-angle parameter on fluid flow characteristics of swirl-type oxygen lance
Authors: Wang Xi , Han Peng , Liu Kun
Published: June 2022

The supersonic jet characteristics of the oxygen lance nozzle play an important role in converter melting. In this study, the jet characteristics of swirl-type oxygen lance were investigated by numerical simulation. The velocity field, jet coalescence behavior and jet impact cavity area of swirl-type oxygen lance with different inclination and swirl angles were analyzed. The results demonstrate that compared with the traditional oxygen lance, the swirl angle accelerates the attenuation of the jet. However, the tangential velocity of jet is conducive to the rapid melting of the slag in the steelmaking process. With the increase of swirl angle and inclination angle, the velocity of jet decreases, the temperature of jet increases and the independence between jets is improved. With the increase of the swirl angle, the tangential velocity of the swirl-type oxygen lance increases, but the possibility of slag adhering to the nozzle surface increases. The effective impact area varies non-monotonically with the swirl angle. The optimum inclination and swirl angle of the swirl-type oxygen lance for a 260 t converter are 15° and 10° respectively. When the oxygen flow rate increases, the decay of jet velocity decreases and the effective impact area increases.
Bounds on the disjunctive domination number of a tree
Authors: Zhuang Wei
Published: June 2022

A set D of vertices in a graph G is a disjunctive dominating set in G if every vertex not in D is adjacent to a vertex of D or has at least two vertices in D at distance 2 from it in G. The disjunctive domination number, γd2(G), of G is the minimum cardinality of a disjunctive dominating set in G. We show that if T is a tree of order n with l leaves and s support vertices, then n-l+3/4≤γd2(T)≤n+l+s/4. Moreover, we characterize the families of trees which attain these bounds.
Focal Muscle Vibration Reduces Spasticity and Improves Functional
Level in Incomplete Spinal Cord Injury: A Case Report
Authors: Alashram Anas R. , Annino Giuseppe
Published: June 2022

Background Spasticity is a common impairment following spinal cord injury
(SCI) that negatively affects the activity of daily livings (ADLs). Focal muscle
vibration (FMV) has beneficial effects in reducing spasticity post-stroke.

Objectives This case report aimed to investigate the effects of 8-week FMV
on spasticity and ADLs in a single patient with an incomplete spinal cord
injury.

Case description The patient was a 26-year-old man with 6-month post-SCI.
Twenty-four sessions of FMV were provided for 15 minutes per session.
Outcome measures included the Modified Ashworth Scale (MAS) and the Barthel
Index (BI).

Findings The FMV treatment resulted in spasticity reduction of biceps
muscle (reduction from 2 to 1+point median), quadriceps (reduction from
2 to 1 point median), and dorsiflexors (reduction from 3 to 1+point
median) as measured by the Modified Ashworth Scale. The activity of daily
livings assessed by the Barthel Index (improved from 67 to 79 points median)
postintervention and at follow-up.

Conclusions This case report demonstrates that FMV reduces spasticity and
improves the activity of daily livings in patients with incomplete spinal cord
injury. Further research is needed in a larger patient population to verify our
findings.
Improvement of the Pain of Temporomandibular Disorder in Parts of the
Human Body through Temporomandibular Joint Correction Treatment
Authors: Park Bo-Ra , Gim Jeong-An , Baek Kyung-Wan
Published: June 2022

Background and Aim Patients with temporomandibular disorder often
experience pain in various parts of the body. However, the degree of improvement
of patients’ pain through temporomandibular joint correction has not
been identified in an independent study. This study aimed to identify the
symptoms most frequently reported by patients with temporomandibular disorder
and determine the degree of pain improvement and structural changes through
temporomandibular joint correction.

Methodology Patients who complained of temporomandibular disorder and
visited a dental clinic and agreed to participate were included in the study
(n=85). The patients were divided into a nontreatment group
(Control, n=35) and treatment group (Treatment,
n=50) of the temporomandibular joint, and the treatment group
received more than 10 correction treatments. All reported locations of pain were
recorded preintervention and postintervention of temporomandibular joint
correction treatment, and the degree of pain, which measured using a visual
analog scale, was also recorded. Simultaneously, X-ray imaging was performed to
confirm the structural difference between the pre-temporomandibular joint and
post-temporomandibular joint correction treatment.

Result Most of the patients with temporomandibular disorder complained of
temporomandibular joint pain (n=66/85), but the majority
complained of neck pain (n=61/85) and shoulder pain
(n=60/85). In addition, there were many cases of
headache (n=26/85), back pain (n=25/85),
and lockjaw (n=22/85). In rare cases, complaints of
facial pain (n=2/85), tinnitus
(n=2/85), hip joint pain (n=4/85),
knee pain (n=5/85), xeroma
(n=1/85), and ear pain (n=1/85)
have been reported. After temporomandibular joint correction treatment, the
treatment group had significantly lower visual analog scale scores than
pretreatment for TMJ pain, headache, shoulder pain, neck pain, back pain, and
lockjaw (p<.0001). Furthermore, it was confirmed that the balance
of the cranial bone and mandibular condyle symmetry in the X-ray image was
significantly improved in the TMJ correction treatment group (pretreatment vs.
posttreatment, p<.001). In the control group, no significant
differences were observed pre-and post-intervention in all symptoms and X-ray
images.

Conclusion Temporomandibular disorders can cause pain in other parts of
the body with an unknown cause. Therefore, these results show that if the pain
in other parts of the body cannot be fundamentally resolved, temporomandibular
joint correction treatment through the diagnosis of temporomandibular disorder
may need to be performed in dental clinics.
Oligomeric Proanthocyanidin Complex from Avocado Seed as A Promising α-glucosidase Inhibitor: Characteristics and Mechanisms
Authors: Nguyen Thien Huu , Amen Yhiya , Wang Dongmei , Othman Ahmed , Matsumoto Masako , Nagata Maki , Shimizu Kuniyoshi
Published: June 2022

Although considered an abundant source of agricultural by-products, avocado (Persea americana Mill.) seed, with several biological activities and bioactive components, might become a promising resource for phytopharmaceutical development. In this study, through bioassay-guided isolation of the main α-glucosidase inhibitors in avocado seed, we discovered the major α-glucosidase inhibitor to be avocado seed oligomeric proanthocyanidin complex (ASOPC). Thiolysis and UPLC-DAD-HRESIMS showed the presence of A- and B-type procyanidins, and B-type propelargonidin with (epi)afzelechin as extension unit. Mean degree of polymerization (mDP) of ASOPC was calculated as 7.3 ± 1. Furthermore, ASOPC appeared to be a strong, reversible, competitive inhibitor of α-glucosidase, with IC50 value of 0.1 µg/mL, which was significantly lower than Acarbose (IC50 = 75.6 µg/mL), indicated that ASOPC is a potential natural α-glucosidase inhibitor. These findings would contribute to the direction of utilizing avocado seed bioactive components with the possibility to be used as natural anti-diabetic agents.
Increased Opioid Consumption following DIEP Flap Breast Reconstruction: Effect of Depression and Anxiety
Authors: Rodnoi Pope , Dickey Ryan M. , Teotia Sumeet S. , Haddock Nicholas T.
Published: June 2022

Background Enhanced Recovery After Surgery (ERAS) protocols have decreased postoperative opioid consumption and hospital length of stay in deep inferior epigastric perforator (DIEP) flap breast reconstruction. We aim to evaluate whether there needs to be further adjustments to best improve outcomes specifically in patients with a preexisting psychiatric condition.

Methods A retrospective review was performed of all patients that underwent DIEP flap breast reconstruction between October 2018 and September 2020. This includes all patients with the most recent ERAS protocol implementation of intraoperative transverse abdominal plane blocks with liposomal bupivacaine. We looked at patients with a psychiatric diagnosis at the time of surgery. Specifically, forms of depression and anxiety were the psychiatric diagnoses for these patients. We divided these patients into three groups: those with no diagnoses, those with a single diagnosis, and those with both diagnoses. Primary outcomes observed were postoperative opioid consumption and length of stay. A one-way analysis of variance determined whether there was a difference between the three groups and a Tukey post hoc analysis made pairwise comparisons. A p-value of < 0.05 was significant.

Results A total of 176 patients were analyzed in this study: 59 (33.5%) of our study population had a diagnosis of either depression, anxiety, or both. Postoperative opioid consumption was higher in patients with a psychiatric diagnosis compared with those without (123.8 to 91.5; p < 0.0005). A multiple regression model consisting of operating time, hospital length of stay, whether the patient has a psychiatric diagnosis, and history of chemotherapy statistically significantly predicted opioid consumption (p < 0.0005).

Conclusion With similar hospital length of stay postoperatively, it is notable that patients with a psychiatric diagnosis had significantly higher amounts of postoperative opioid consumption. This study highlights the need to further improve multidisciplinary integrated care for patients with psychiatric comorbidities to improve pain management postoperatively.
Perforator Characteristics and Impact on Postoperative Outcomes in DIEP Flap Breast Reconstruction: A Systematic Review and Meta-Analysis
Authors: Aravind Pathik , Colakoglu Salih , Bhoopalam Myan , Ibrahim Ahmed , Mathes David , Kaoutzanis Christodoulos , Mureau Marc , Reddy Sashank
Published: June 2022

Background High-quality evidence on perforator selection in deep inferior epigastric perforator (DIEP) flap harvesting is lacking, making preoperative planning and choice of perforators “surgeon-specific.” This lack of consensus is a subject of continuous debate among microsurgeons. We aimed to systematically review perforator characteristics and their impact on DIEP flap breast reconstruction outcomes.

Methods We conducted a systematic review and meta-analysis across six databases: ClinicalTrials.gov, Cochrane Library, Medline, Ovid Embase, PubMed, and Web of Science for all studies on DIEP flap breast reconstruction focused on perforator characteristics—caliber, number, and location. The primary goal was to analyze the impact of perforator characteristics on partial and/or total flap failure and fat necrosis. Data was analyzed using RevMan V5.3.

Results Initial search gave us 2,768 articles of which 17 were included in our review. Pooled analysis did not show any statistically significant correlations between partial and/or total flap failure and perforator number, or perforator location. Sensitivity analysis accounting for heterogeneity across studies showed that, the risk for fat necrosis was significantly higher if single perforators (relative risk [RR] = 2.0, 95% confidence interval [CI] = 1.5–2.6, I
2 = 39%) and medial row perforators (RR = 2.7, 95% CI = 1.8–3.9, I
2 = 0%) were used.

Conclusion Our findings suggest that a single dominant perforator and medial row perforators may be associated with higher risk of fat necrosis after DIEP flap breast reconstruction. Adopting a standardized perforator selection algorithm may facilitate operative decision making, shorten the learning curve for novice surgeons, and optimize postoperative outcomes by minimizing the burden of major complications. This in turn would help improve patient satisfaction and quality of life.
Detecting contact in language trees: a Bayesian phylogenetic model with horizontal transfer
Authors: Neureiter Nico , Ranacher Peter , Efrat-Kowalsky Nour , Kaiping Gereon A. , Weibel Robert , Widmer Paul , Bouckaert Remco R.
Published: June 2022

Phylogenetic trees are a central tool for studying language evolution and have wide implications for understanding cultural evolution as a whole. For example, they have been the basis of studies on the evolution of musical instruments, religious beliefs and political complexity. Bayesian phylogenetic methods are transparent regarding the data and assumptions underlying the inference. One of these assumptions—that languages change independently—is incompatible with the reality of language evolution, particularly with language contact. When speakers interact, languages frequently borrow linguistic traits from each other. Phylogenetic methods ignore this issue, which can lead to errors in the reconstruction. More importantly, they neglect the rich history of language contact. A principled way of integrating language contact in phylogenetic methods is sorely missing. We present , a Bayesian phylogenetic model with horizontal transfer for language evolution. The model efficiently infers the phylogenetic tree of a language family and contact events between its clades. The implementation is available as a package for the phylogenetics software BEAST 2. We apply in a simulation study and a case study on a subset of well-documented Indo-European languages. The simulation study demonstrates that correctly reconstructs the history of a simulated language family, including simulated contact events. Moreover, it shows that ignoring contact can lead to systematic errors in the estimated tree height, rate of change and tree topology, which can be avoided with . The case study confirms that reconstructs known contact events in the history of Indo-European and finds known loanwords, demonstrating its practical potential. The model has a higher statistical fit to the data than a conventional phylogenetic reconstruction, and the reconstructed tree height is significantly closer to well-attested estimates. Our method closes a long-standing gap between the theoretical and empirical models of cultural evolution. The implications are especially relevant for less documented language families, where our knowledge of past contacts and linguistic borrowings is limited. Since linguistic phylogenies have become the backbone of many studies of cultural evolution, the addition of this integral piece of the puzzle is crucial in the endeavour to understand the history of human culture.