bluuebunny/crossref_metadata_2025_split huggingface dataset:
DDX39B drives colorectal cancer progression by promoting the stability and nuclear translocation of PKM2
Authors: Zhao Gang , Yuan Hang , Li Qin , Zhang Jie , Guo Yafei , Feng Tianyu , Gu Rui , Ou Deqiong , Li Siqi , Li Kai , Lin Ping 
Published: August 2022

AbstractMetastasis is a major cause of colorectal cancer (CRC) mortality, but its molecular mechanisms are still not fully understood. Here, we show that upregulated DDX39B correlates with liver metastases and aggressive phenotypes in CRC. DDX39B is an independent prognostic factor associated with poor clinical outcome in CRC patients. We demonstrate that Sp1 potently activates DDX39B transcription by directly binding to the GC box of the DDX39B promoter in CRC cells. DDX39B overexpression augments the proliferation, migration, and invasion of CRC cells, while the opposite results are obtained in DDX39B-deficient CRC cells. Mechanistically, DDX39B interacts directly with and stabilizes PKM2 by competitively suppressing STUB1-mediated PKM2 ubiquitination and degradation. Importantly, DDX39B recruits importin α5 to accelerate the nuclear translocation of PKM2 independent of ERK1/2-mediated phosphorylation of PKM2, leading to the transactivation of oncogenes and glycolysis-related genes. Consequently, DDX39B enhances glucose uptake and lactate production to activate Warburg effect in CRC. We identify that Arg319 of DDX39B is required for PKM2 binding as well as PKM2 nuclear accumulation and for DDX39B to promote CRC growth and metastasis. In addition, blocking PKM2 nuclear translocation or treatment with glycolytic inhibitor 2-deoxy-D-glucose efficiently abolishes DDX39B-triggered malignant development in CRC. Taken together, our findings uncover a key role for DDX39B in modulating glycolytic reprogramming and aggressive progression, and implicate DDX39B as a potential therapeutic target in CRC.
Intrinsic cell rheology drives junction maturation
Authors: Sri-Ranjan K. , Sanchez-Alonso J. L. , Swiatlowska P. , Rothery S. , Novak P. , Gerlach S. , Koeninger D. , Hoffmann B. , Merkel R. , Stevens M. M. , Sun S. X. , Gorelik J. , Braga Vania M. M. 
Published: August 2022

AbstractA fundamental property of higher eukaryotes that underpins their evolutionary success is stable cell-cell cohesion. Yet, how intrinsic cell rheology and stiffness contributes to junction stabilization and maturation is poorly understood. We demonstrate that localized modulation of cell rheology governs the transition of a slack, undulated cell-cell contact (weak adhesion) to a mature, straight junction (optimal adhesion). Cell pairs confined on different geometries have heterogeneous elasticity maps and control their own intrinsic rheology co-ordinately. More compliant cell pairs grown on circles have slack contacts, while stiffer triangular cell pairs favour straight junctions with flanking contractile thin bundles. Counter-intuitively, straighter cell-cell contacts have reduced receptor density and less dynamic junctional actin, suggesting an unusual adaptive mechano-response to stabilize cell-cell adhesion. Our modelling informs that slack junctions arise from failure of circular cell pairs to increase their own intrinsic stiffness and resist the pressures from the neighbouring cell. The inability to form a straight junction can be reversed by increasing mechanical stress artificially on stiffer substrates. Our data inform on the minimal intrinsic rheology to generate a mature junction and provide a springboard towards understanding elements governing tissue-level mechanics.
Flexible unimodal strain sensors for human motion detection and differentiation
Authors: Jin Lu , Li Zhenhong , Liu Zekun , Richardson Bethany , Zheng Yan , Xu Lulu , Chen Zhongda , Zhai Heng , Kim Hongdoo , Song Qingwen , Yue Pengfei , Xie Sheng Quan , Kim Kap Jin , Li Yi 
Published: August 2022

AbstractMultiple strain sensors are required to identify individual forces/stresses on human joints and recognize how they work together in order to determine the motion’s direction and trajectory. However, current sensors cannot detect and differentiate the individual forces/stresses and their contributions to the motion from the sensors’ electrical signals. To address this critical issue, we propose a concept of unimodal tension, bend, shear, and twist strain sensors with piezoelectric poly L-lactic acid films. We then construct an integrated unimodal sensor (i-US) using the unimodal sensors and prove that the i-US can detect and differentiate individual strain modes, such as tensioning, bending, shearing, and twisting in complex motion. To demonstrate the potential impact of unimodal sensors, we design a sleeve and a glove with the i-US that can capture wrist motions and finger movements. Therefore, we expect unimodal strain sensors to provide a turning point in developing motion recognition and control systems.
High-temperature oxidation performance of Ni-based GH3536 superalloy fabricated by laser powder bed fusion
Authors: Min Shiling , Liu Hui , Yang Mengmeng , Zhang Huawei , Hou Juan , Zhang Kai , Liang Jingjing , Li Jinguo , Wang Hao , Wang Jianqiu , Huang Aijun 
Published: August 2022

AbstractThis study investigates the effect of microstructure on short-term and long-term oxidation behaviours of GH3536 superalloy fabricated by laser powder bed fusion (LPBF), in which the superalloy is isothermally oxidised at 950 °C for 6 h and 500 h in air. The LPBF sample exhibits improved oxidation resistance compared with a wrought counterpart after long-term exposure. The effect of microstructure diversity between LPBF and wrought samples on oxidation behaviour is discussed. The cellular structure produced during the LPBF process acts as a rapid diffusion path to accelerate the formation of a protective film in the initial stage, leading to an enhancement in oxidation resistance for extended exposure.
Lightweight Distributed Provenance Model for Complex Real–world Environments
Authors: Wittner Rudolf , Mascia Cecilia , Gallo Matej , Frexia Francesca , Müller Heimo , Plass Markus , Geiger Jörg , Holub Petr 
Published: August 2022

AbstractProvenance is information describing the lineage of an object, such as a dataset or biological material. Since these objects can be passed between organizations, each organization can document only parts of the objects life cycle. As a result, interconnection of distributed provenance parts forms distributed provenance chains. Dependant on the actual provenance content, complete provenance chains can provide traceability and contribute to reproducibility and FAIRness of research objects. In this paper, we define a lightweight provenance model based on W3C PROV that enables generation of distributed provenance chains in complex, multi-organizational environments. The application of the model is demonstrated with a use case spanning several steps of a real-world research pipeline — starting with the acquisition of a specimen, its processing and storage, histological examination, and the generation/collection of associated data (images, annotations, clinical data), ending with training an AI model for the detection of tumor in the images. The proposed model has become an open conceptual foundation of the currently developed ISO 23494 standard on provenance for biotechnology domain.
Global data on fertilizer use by crop and by country
Authors: Ludemann Cameron I. , Gruere Armelle , Heffer Patrick , Dobermann Achim 
Published: August 2022

AbstractUnderstanding how much inorganic fertilizer (referred to as fertilizer) is applied to different crops at national, regional and global levels is an essential component of fertilizer consumption analysis and demand projection. Good information on fertilizer use by crop (FUBC) is rarely available because it is difficult to collect and time-consuming to process and validate. To fill this gap, a first global FUBC report was published in 1992 for the 1990/1991 period, based on an expert survey conducted jointly by the Food and Agriculture Organization (FAO) of the UN, the International Fertilizer Development Center (IFDC) and the International Fertilizer Association (IFA). Since then, similar expert surveys have been carried out and published every two to four years in the main fertilizer-consuming countries. Since 2008 IFA has led these efforts and, to our knowledge, remains the only globally available data set on FUBC. This dataset includes data (in CSV format) from a survey carried out by IFA to represent the 2017–18 period as well as a collation of all historic FUBC data.
China economy-wide material flow account database from 1990 to 2020
Authors: Chen Chuke , Qi Jianchuan , Li Nan , Ji Tiantian , Wang Heming , Huang Yuanyi , Guo Jing , Lu Xiaohui , Han Ruru , Wei Jianlimin , Chen Wei-Qiang 
Published: August 2022

AbstractMaterial utilisation has been playing a fundamental role in economic development, but meanwhile, it may have environmental and social consequences. Given China’s rapid economic growth, understanding China’s material utilisation patterns would inform decisions for researchers and policymakers. However, fragmented data from multiple statistical sources hinder us from comprehensively portraying China’s material utilisation dynamics. This study harmonised China-specific official statistics and constructed a China economy-wide material flow accounts database. This database covers hundreds of materials and more than 30 years (1990–2020) from thousands of data sources, which is comprehensive, long-term, up-to-date, and publicly accessed. This database would provide insights into the historical metabolic dynamics of China’s economy with elaboration on the production, consumption, and end-of-life disposal of materials. This database also allows for international analyses since it is developed based on an internationally standardised analytical framework. Furthermore, this study would benefit studies on policy impact evaluation, environmental pressure assessment, and sustainable development strategies.
Discrimination of human papillomavirus genotypes using innovative technique nested-high resolution melting
Authors: Alirezaei Melika , Mosawi Sayed Hussain , Afgar Ali , Zarean Mehdi , Movahhed Tahereh Komeili , Abbasi Vajiheh , Fotouhi-Ardakani Reza 
Published: August 2022

AbstractThe prompt detection of human papillomavirus and discrimination of its genotypes by combining conventional methods in new molecular laboratories is essential to achieve the global call of eliminating cervical cancer. After predicting the melting temperature of an approximately 221 bp region of the L1 gene from different HPV genotypes by bioinformatics software, an innovative technique based on the nested- high resolution melting was designed with three approaches and using conventional PCR, qPCR, and diagnostic standards. HPV-positive samples identified by microarray along with diagnostic standards were evaluated by qPCR-HRM and discordant results were subjected to sequencing and analyzed in silico using reference types. In addition to screening for human papillomavirus, nested-qPCR-HRM is one of the modified HRM techniques which can discriminate some genotypes, including 6, 16, 18, 52, 59, 68 and 89. Despite the differences in diagnostic capabilities among HRM, microarray and sequencing, a number of similarities between HRM, and sequencing were diagnostically identified as the gold standard method. However, the bioinformatics analysis and melting temperature studies of the selected region in different HPV genotypes showed that it could be predicted. With numerous HPV genotypes and significant genetic diversity among them, determining the virus genotype is important. Therefore, our goal in this design was to use the specific molecular techniques with several specific primers to increase sensitivity and specificity for discriminating a wide range of HPV genotypes. This approach led to new findings to evaluate the ability of different approaches and procedures in accordance with bioinformatics.
Human milk oligosaccharide 2'-fucosyllactose promotes melanin degradation via the autophagic AMPK–ULK1 signaling axis
Authors: Heo Hyojin , Cha Byungsun , Jang Dongmin , Park Chaewon , Park Gunwoo , Kwak Byeong-Mun , Bin Bum-Ho , Park Ji-Hwan , Lee Mi-Gi 
Published: August 2022

AbstractThere is still an unmet need for development of safer antimelanogenic or melanin-degrading agents for skin hyperpigmentation, induced by intrinsic or extrinsic factors including aging or ultraviolet irradiation. Owing to the relatively low cytotoxicity compared with other chemical materials, several studies have explored the role of 2'-fucosyllactose (2'-FL), the most dominant component of human milk oligosaccharides. Here, we showed that 2'-FL reduced melanin levels in both melanocytic cells and a human skin equivalent three-dimensional in vitro model. Regarding the cellular and molecular mechanism, 2'-FL induced LC3I conversion into LC3II, an autophagy activation marker, followed by the formation of LC3II+/PMEL+ autophagosomes. Comparative transcriptome analysis provided a comprehensive understanding for the up- and downstream cellular processes and signaling pathways of the AMPK–ULK1 signaling axis triggered by 2'-FL treatment. Moreover, 2'-FL activated the phosphorylation of AMPK at Thr172 and of ULK1 at Ser555, which were readily reversed in the presence of dorsomorphin, a specific AMPK inhibitor, with consequent reduction of the 2'-FL-mediated hypopigmentation. Taken together, these findings demonstrate that 2'-FL promotes melanin degradation by inducing autophagy through the AMPK–ULK1 axis. Hence, 2'-FL may represent a new natural melanin-degrading agent for hyperpigmentation.
An FPGA-based system for generalised electron devices testing
Authors: Foster Patrick , Huang Jinqi , Serb Alex , Stathopoulos Spyros , Papavassiliou Christos , Prodromakis Themis 
Published: August 2022

AbstractElectronic systems are becoming more and more ubiquitous as our world digitises. Simultaneously, even basic components are experiencing a wave of improvements with new transistors, memristors, voltage/current references, data converters, etc, being designed every year by hundreds of R &D groups world-wide. To date, the workhorse for testing all these designs has been a suite of lab instruments including oscilloscopes and signal generators, to mention the most popular. However, as components become more complex and pin numbers soar, the need for more parallel and versatile testing tools also becomes more pressing. In this work, we describe and benchmark an FPGA system developed that addresses this need. This general purpose testing system features a 64-channel source-meter unit, and $$2\times $$

2
×

banks of 32 digital pins for digital I/O. We demonstrate that this bench-top system can obtain $${170}\,\hbox {pA}$$

170

pA

current noise floor, $${40}\,\hbox {ns}$$

40

ns

pulse delivery at $$\pm {13.5}\,\hbox {V}$$

±

13.5

V

and $${12}\,\hbox {mA}$$

12

mA

maximum current drive/channel. We then showcase the instrument’s use in performing a selection of three characteristic measurement tasks: (a) current–voltage characterisation of a diode and a transistor, (b) fully parallel read-out of a memristor crossbar array and (c) an integral non-linearity test on a DAC. This work introduces a down-scaled electronics laboratory packaged in a single instrument which provides a shift towards more affordable, reliable, compact and multi-functional instrumentation for emerging electronic technologies.
Znhit1 and HIF-2α are correlated with cancer stem cell markers in breast cancer patients
Authors: Ebeid Samia A. , Abd El Moneim Nadia A. , El-Benhawy Sanaa A. , Ramadan Rabie , Ismail Samah E. 
Published: August 2022

AbstractEpigenetic alterations have emerged as fundamental players in development and progression of breast cancer (BC). A hypoxic tumour microenvironment regulates the stemness phenotype in breast cancer stem cells (BCSCs). The aim of this study was to investigate Znhit1 and HIF-2α gene expression in breast cancer tissues as well as their relation to CSCs markers LGR5, ALDH1A1 and β-catenin in tissue and serum of BC patients. The present study included 160 females divided into two groups, group I: 80 healthy females served as control group and group II: 80 breast cancer patients. Gene expression of tissue Znhit1 and HIF-2α was determined by qRT-PCR. Tissue and serum ALDH1A1, LGR5 and β-catenin levels were determined by ELISA. We found that gene expression of Znhit1 was significantly downregulated in BC tissues. Moreover, it was significantly negatively correlated with clinical stage and β-catenin levels in BC patients. Regarding HIF-2α, gene expression of HIF-2α was significantly upregulated in BC tissues. Moreover, it was significantly positively correlated with Her-2/neu expression and β-catenin levels in BC patients. Based upon our results, Znhit1 and HIF-2α may serve as novel therapeutic targets for BC therapy. Additionally, each of serum ALDH1A1, LGR5 and β-catenin may play a crucial role in non-invasive detection of BC with a high specificity and sensitivity.
Femtosecond laser hierarchical surface restructuring for next generation neural interfacing electrodes and microelectrode arrays
Authors: Amini Shahram , Seche Wesley , May Nicholas , Choi Hongbin , Tavousi Pouya , Shahbazmohamadi Sina 
Published: August 2022

AbstractLong-term implantable neural interfacing devices are able to diagnose, monitor, and treat many cardiac, neurological, retinal and hearing disorders through nerve stimulation, as well as sensing and recording electrical signals to and from neural tissue. To improve specificity, functionality, and performance of these devices, the electrodes and microelectrode arrays—that are the basis of most emerging devices—must be further miniaturized and must possess exceptional electrochemical performance and charge exchange characteristics with neural tissue. In this report, we show for the first time that the electrochemical performance of femtosecond-laser hierarchically-restructured electrodes can be tuned to yield unprecedented performance values that significantly exceed those reported in the literature, e.g. charge storage capacity and specific capacitance were shown to have improved by two orders of magnitude and over 700-fold, respectively, compared to un-restructured electrodes. Additionally, correlation amongst laser parameters, electrochemical performance and surface parameters of the electrodes was established, and while performance metrics exhibit a relatively consistent increasing behavior with laser parameters, surface parameters tend to follow a less predictable trend negating a direct relationship between these surface parameters and performance. To answer the question of what drives such performance and tunability, and whether the widely adopted reasoning of increased surface area and roughening of the electrodes are the key contributors to the observed increase in performance, cross-sectional analysis of the electrodes using focused ion beam shows, for the first time, the existence of subsurface features that may have contributed to the observed electrochemical performance enhancements. This report is the first time that such performance enhancement and tunability are reported for femtosecond-laser hierarchically-restructured electrodes for neural interfacing applications.
Longitudinal proteomics study of serum changes after allogeneic HSCT reveals potential markers of metabolic complications related to aGvHD
Authors: Wong Sing Ying , Kato Seiko , Rodenburg Frans , Tojo Arinobu , Hayashi Nobuhiro 
Published: August 2022

AbstractEven though hematopoietic stem cell transplantation (HSCT) allows successful treatment for many malignant and non-malignant disorders, its curative potential remains limited by severe side effects, including infections and other transplant-related complications such as graft-versus-host disease (GvHD). This study examined changes in serum proteome via high-performance two-dimensional gel electrophoresis (2-DE) during HSCT to search for diagnostic biomarkers for post-HSCT complications. Longitudinal proteomic analysis revealed proteins related to metabolic complications and hemolytic anemia. Retinol-binding protein 4 (RBP4), a reliable marker of insulin resistance, was identified, and is possibly associated with the onset mechanism of acute graft-versus-host disease (aGvHD) and/or skin GvHD. Although the cause of insulin resistance is not fully understood, it is thought to be associated with adipocytes inflammation induced by RBP4, iron overload and hemolytic anemia after HSCT, as observed in this study. The present study has demonstrated that insulin resistance and metabolic complications could be immediate complications after transplantation and are associated with aGvHD. The biomarkers revealed in this study are promising tools to be used for improving the early diagnosis of HSCT-associated complications, especially aGvHD, possibly even before clinical manifestations.
Streptococcus suis TrpX is part of a tryptophan uptake system, and its expression is regulated by a T-box regulatory element
Authors: Dresen Muriel , Schaaf Desirée , Arenas Jesús , de Greeff Astrid , Valentin-Weigand Peter , Nerlich Andreas 
Published: August 2022

AbstractStreptococcus suis, a common member of the porcine respiratory microbiota, can cause life-threatening diseases in pigs as well as humans. A previous study identified the gene trpX as conditionally essential for in vivo survival by intrathecal infection of pigs with a transposon library of S. suis strain 10. Here, we characterized trpX, encoding a putative tryptophan/tyrosine transport system substrate-binding protein, in more detail. We compared growth capacities of the isogenic trpX-deficient mutant derivative strain 10∆trpX with its parent. Growth experiments in chemically defined media (CDM) revealed that growth of 10∆trpX depended on tryptophan concentration, suggesting TrpX involvement in tryptophan uptake. We demonstrated that trpX is part of an operon structure and co-transcribed with two additional genes encoding a putative permease and ATPase, respectively. Bioinformatics analysis identified a putative tryptophan T-box riboswitch in the 5′ untranslated region of this operon. Finally, qRT-PCR and a reporter activation assay revealed trpX mRNA induction under tryptophan-limited conditions. In conclusion, our study showed that TrpX is part of a putative tryptophan ABC transporter system regulated by a T-box riboswitch probably functioning as a substrate-binding protein. Due to the tryptophan auxotrophy of S. suis, TrpX plays a crucial role for metabolic adaptation and growth during infection.
Fitting of TC model according to key parameters affecting Parkinson's state based on improved particle swarm optimization algorithm
Authors: Yuan Chunhua , Li Xiangyu 
Published: August 2022

AbstractBiophysical models contain a large number of parameters, while the spiking characteristics of neurons are related to a few key parameters. For thalamic neurons, relay reliability is an important characteristic that affects Parkinson's state. This paper proposes a method to fit key parameters of the model based on the spiking characteristics of neurons, and improves the traditional particle swarm optimization algorithm. That is, a nonlinear concave function and a Logistic chaotic mapping are combined to adjust the inertia weight of particles to avoid the particle falling into a local optimum in the search process or appearing premature convergence. In this paper, three parameters that play an important role in Parkinson's state of the thalamic cell model are selected and fitted by the improved particle swarm optimization algorithm. Using the fitted parameters to reconstruct the neuron model can predict the spiking trajectories well, which verifies the effectiveness of the fitting method. By comparing the fitting results with other particle swarm optimization algorithms, it is shown that the proposed particle swarm optimization algorithm can better avoid local optima and converge to the optimal values quickly.