bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conceptual framework of smart fertilization management for oil palm tree based on IOT and deep learning
Authors: Mohd Adib N A N , Daliman S 
Published: September 2021

Abstract
Oil palm trees contribute economic income to the national and community by generating various types of productions. This will cause an expansion of the area for the plantation of oil palm seeds, then contributes to the stability in distributing good quality oil to accommodate the growing population. Furthermore, degradation occurs when the planting of oil palm trees increases rapidly, especially the occurrence of uncontrolled oil palm cultivation. The degradation can cause loss of soil nutrients due to soil erosion. The lack of macronutrients, Nitrogen (N), Phosphorus (P), Potassium (K) and Magnesium (Mg) on oil palm tree may impact on its growth which includes the quality of crops. Traditional approach to detect macronutrients, can also lead to some improper control in turn leads results in reduction in yield. The existing system has given limited information of dataset and slower classification performance due to limited functions. With the adaptability of Internet of Things (IoT) technologies, oil palm tree growth data and fertilization management can be utilizing effortlessly and effectively. The context of conceptual framework comprises the IoT technologies, image processing, machine learning and deep learning which focuses on environmental factors that affecting the young oil palm tree growth that involve temperature, humidity, soil moisture content, light and nutrient. Thus, a study of IoT, machine learning and deep learning for smart fertilization management of oil palm trees is suggested helping and raise the efficiency of oil palm trees management in Malaysia.
Evaluation on mechanical properties of plywood from two fast growing species: Neolamarckia cadamba and Paraserianthes falcataria
Authors: Rahman W M N W A , Yunus N Y , Sa’ad M F , Amin M F M , Mohamad M A N , Chotikhan A , Ahmad M I , Rasat M S M 
Published: September 2021

Abstract

Neolamarckia cadamba (Laran@Kelampayan) and Paraserianthes falcataria (Batai) are both fast growing species known to be planted in Malaysia for their high growth rate, therefore made as reforestation species. This study had been done in evaluating the mechanical properties of these species as a new wood material for plywood production as an alternative and discovering used for the depleting supply of big diameter log from virgin forest. The tree samples were harvested from trial plot in UiTM Pahang, Bandar Tun Razak Jengka, Pahang, Malaysia and sent to plywood mills nearby for plywood production. Plywood was composed in five layers and seven layers with 12 mm thickness and used melamine urea formaldehyde (MUF) as their binder based on commercial industry production. Panels were cut and tested according to Japanese Agriculture Standard for plywood (JAS 2014) at Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia. Based on minimum standard requirement, results show that both species were suitable to be used in plywood production for general use and structural (decorative) purpose. In addition, increased veneer layers were improved the panel strength. This study shows those species had potential to be an alternative wood material for plywood industry in Malaysia thus can reduce independency of wood species from virgin forest.
BleTIES: annotation of natural genome editing in ciliates using long read sequencing
Authors: Seah Brandon K B , Swart Estienne C 
Published: September 2021

Abstract

Summary
Ciliates are single-celled eukaryotes that eliminate specific, interspersed DNA sequences (internally eliminated sequences, IESs) from their genomes during development. These are challenging to annotate and assemble because IES-containing sequences are typically much less abundant in the cell than those without, and IES sequences themselves often contain repetitive and low-complexity sequences. Long-read sequencing technologies from Pacific Biosciences and Oxford Nanopore have the potential to reconstruct longer IESs than has been possible with short reads but require a different assembly strategy. Here we present BleTIES, a software toolkit for detecting, assembling, and analyzing IESs using mapped long reads.

Availability and implementation
BleTIES is implemented in Python 3. Source code is available at https://github.com/Swart-lab/bleties (MIT license) and also distributed via Bioconda.

Supplementary information
Supplementary data are available at Bioinformatics online.
Analysis of tripartite motif (TRIM) family gene expression in prostate cancer bone metastases
Authors: Offermann Anne , Kang Duan , Watermann Christian , Weingart Anika , Hupe Marie C , Saraji Alireza , Stegmann-Frehse Janine , Kruper Rosemarie , Schüle Roland , Pantel Klaus , Taubert Helge , Duensing Stefan , Culig Zoran , Aigner Achim , Klapper Wolfram , Jonigk Danny , Philipp Kühnel Mark , Merseburger Axel S , Kirfel Jutta , Sailer Verena , Perner Sven 
Published: September 2021

Abstract
Tripartite motif (TRIM) family proteins are post-translational protein modifiers with E3-ubiquitin ligase activity, thereby involved in various biological processes. The molecular mechanisms driving prostate cancer (PCa) bone metastasis (BM) are incompletely understood, and targetable genetic alterations are lacking in the majority of cases. Therefore, we aimed to explore the expression and potential functional relevance of 71 TRIM members in bone metastatic PCa. We performed transcriptome analysis of all human TRIM family members and 770 cancer-related genes in 29 localized PCa and 30 PCa BM using Nanostring. KEGG, STRING and Ubibrowser were used for further bioinformatic gene correlation and pathway enrichment analyses. Compared to localized tumors, six TRIMs are under-expressed while nine TRIMs are over-expressed in BM. The differentially expressed TRIM proteins are linked to TNF-, TGFβ-, PI3K/AKT- and HIF-1-signaling, and to features such as proteoglycans, platelet activation, adhesion and ECM-interaction based on correlation to cancer-related genes. The identification of TRIM-specific E3-ligase-substrates revealed insight into functional connections to oncogenes, tumor suppressors and cancer-related pathways including androgen receptor- and TGFβ signaling, cell cycle regulation and splicing. In summary, this is the first study that comprehensively and systematically characterizes the expression of all TRIM members in PCa BM. Our results describe post-translational protein modification as an important regulatory mechanism of oncogenes, tumor suppressors, and pathway molecules in PCa progression. Therefore, this study may provide evidence for novel therapeutic targets, in particular for the treatment or prevention of BM.
Pradefovir Treatment in Patients With Chronic Hepatitis B: Week 24 Results From a Multicenter, Double-Blind, Randomized, Noninferiority, Phase 2 Trial
Authors: Gao Yanhang , Kong Fei , Song Xinwen , Shang Jia , Yao Lvfeng , Xia Jinyu , Peng Yanzhong , Liu Weidong , Gong Huanyu , Mu Mao , Cui Hesong , Han Tao , Chen Wen , Wu Xiaolu , Yang Yongfeng , Yan Xuebing , Jin Zhenjing , Wang Peng , Zhu Qingjing , Chen Liang , Zhao Caiyan , Zhang Dengke , Jin Weili , Wang Daidi , Wen Xiuhong , Liu Chunmei , Jia Jidong , Mao Qing , Ding Yanhua , Jin Xueyuan , Zhang Zong , Mao Qianguo , Li Guangming , Niu Junqi 
Published: September 2021

Abstract

Background
Pradefovir is a liver-targeted prodrug of adefovir, a nucleoside/nucleotide analogue with antiviral activity against hepatitis B virus (HBV) DNA polymerase. This phase 2 study compared the efficacy and safety of oral pradefovir (30, 45, 60, or 75 mg) versus tenofovir disoproxil fumarate (TDF; 300 mg) and aimed to identify the most appropriate dose of pradefovir for the forthcoming phase 3 study.

Methods
Treatment-naive and experienced (not on treatment &gt;6 months) patients with chronic hepatitis B were eligible.

Results
A total of 240 participants were randomized and treated in the study (48 per group). Approximately 80% were hepatitis B e antigen (HBeAg) positive, and 10% had liver cirrhosis. The reductions from baseline in HBV DNA levels achieved at week 24 were 5.40, 5.34, 5.33, and 5.40 log10 IU/mL, with pradefovir doses of 30-, 45-, 60-, and 75-mg, respectively, compared with 5.12 log10 IU/mL with TDF. However, HBeAg loss was attained by more participants who received 45-, 60-, or 75-mg pradefovir than by those receiving TDF (12%, 6%, and 9% vs 3%). The TDF group exhibited a more significant increase in serum creatinine than the pradefovir 30- and 45-mg groups, and serum phosphate levels were comparable among all groups. Most adverse events (AEs) were mild (grade 1). No treatment-related severe AEs were reported. Overall, AEs and laboratory abnormalities were comparable to those in the TDF group.

Conclusions
Pradefovir and TDF exhibited comparable reductions in HBV DNA levels. All treatments were safe and well tolerated.

Clinical Trials registration
NCT00230503 and China Drug Trials CTR2018042
Patterns of bacterial diversity in embryonic capsules of the spotted salamanderAmbystoma maculatum: an expanding view of a symbiosis
Authors: Bishop Cory , Jurga Emil , Graham Lori 
Published: September 2021

ABSTRACTThe unicellular green alga, Oophila amblystomatis, populates egg capsules of the spotted salamander Ambystoma maculatum. This nutrient-exchange mutualism is widely perceived as a bipartite interaction, but the presence and contributing effects of bacteria to this symbiosis are unknown. We used standard cultivation techniques and amplicon sequencing of the V4/V5 region of 16S rRNA gene to identify and compare diversity of bacterial taxa in embryonic capsules with that in the aquatic breeding habitat. Our sampling regime allowed us to investigate diversity among individual capsules of an egg mass and between two ponds and sampling years. Capsules contain much lower diversity of bacteria than pond water, and spatial and temporal variation in intracapsular and pond bacterial diversity was observed. Despite this variation, sequences corresponding to species in the orders Burkholderiales and Oligoflexales were either prevalent or abundant, or both. Isolates most commonly recovered from capsules were closely related to species in the genus Herbaspirillum (Burkholderiaceae); other isolates were pseudomonads, but in all cases are closely related to known vascular plant-associated species. We conclude that, despite observed variation, there are bacterial taxa whose presence is held in common spatially and temporally among capsules and that the symbiosis between O. amblystomatis and A. maculatum may involve these taxa.
Development of an Haa1-based biosensor for acetic acid sensing in Saccharomyces cerevisiae
Authors: Mormino Maurizio , Siewers Verena , Nygård Yvonne 
Published: September 2021

ABSTRACT
Acetic acid is one of the main inhibitors of lignocellulosic hydrolysates and acetic acid tolerance is crucial for the development of robust cell factories for conversion of biomass. As a precursor of acetyl-coenzyme A, it also plays an important role in central carbon metabolism. Thus, monitoring acetic acid levels is a crucial aspect when cultivating yeast. Transcription factor-based biosensors represent useful tools to follow metabolite concentrations. Here, we present the development of an acetic acid biosensor based on the Saccharomyces cerevisiae transcription factor Haa1 that upon binding to acetic acid relocates to the nucleus. In the biosensor, a synthetic transcription factor consisting of Haa1 and BM3R1 from Bacillus megaterium was used to control expression of a reporter gene under a promoter containing BM3R1 binding sites. The biosensor did not drive expression under a promoter containing Haa1 binding sites and responded to acetic acid over a linear range spanning from 10 to 60 mM. To validate its applicability, the biosensor was integrated into acetic acid-producing strains. A direct correlation between biosensor output and acetic acid production was detected. The developed biosensor enables high-throughput screening of strains producing acetic acid and could also be used to investigate acetic acid-tolerant strain libraries.
Microtremor surveys based on rotational seismology: theoretical analysis with focus on separation of Rayleigh and Love waves in general wavefield of microtremors
Authors: Cho I , Yoshida K , Uebayashi H 
Published: September 2021

SUMMARYThe applicability of rotational seismology to the general wavefield of microtremors is theoretically demonstrated based on a random process model of a 2-D wavefield. We show the effectiveness of taking the rotations (i.e. spatial differentiation) of microtremor waveforms in separating the Rayleigh and Love waves in a wavefield where waves are simultaneously arriving from various directions with different intensities. This means that a method based on rotational seismology (a rotational method) is capable of separating Rayleigh and Love waves without adopting a specific array geometry or imposing a specific assumption on the microtremor wavefield. This is an important feature of a rotational method because the spatial autocorrelation (SPAC) method, a conventional approach for determining phase velocities in microtremor array surveys, requires either the use of a circular array or the assumption of an isotropic wavefield (i.e. azimuthal averaging of correlations is required). Derivatives of the SPAC method additionally require the assumption that Rayleigh and Love waves are uncorrelated. We also show that it is possible to apply a rotational method to determine the characteristics of Love waves based on a simple three-point microtremor array that consists of translational (i.e. ordinary) three-component sensors. In later sections, we assume realistic data processing for microtremor arrays with translational sensors to construct a theoretical model to evaluate the effects of approximating spatial differentiation via finite differencing (i.e. array-derived rotation, ADR) and the effects of incoherent noise on analysis results. Using this model, it is shown that in a short-wavelength range compared to the distance for finite differencing (e.g. $\lambda &lt; 3h$, where $\lambda $ and $h$ are the wavelength and distance for finite differencing, respectively), the leakage of unwanted wave components can determine the analysis limit. It is also shown that in a long-wavelength range (e.g. $\lambda &gt; 3h$), the signal intensity gradually decreases, and thus the effects of incoherent noise increase (i.e. the signal-to-noise ratio, SNR decreases) and determine the analysis limit. We derive the relation between the SNR and wavelength. Although the analysis results quantitatively depend on the array geometry used for finite differencing, the qualitative understanding supported by mathematical expressions with a physically clear meaning can serve as a guideline for the treatment of data obtained from ADR.
Assessing the role of selected constraints in Bayesian dynamic source inversion: application to the 2017Mw 6.3 Lesvos earthquake
Authors: Kostka Filip , Zahradník Jiří , Sokos Efthimios , Gallovič František 
Published: September 2021

SUMMARYA dynamic finite-fault source inversion for stress and frictional parameters of the Mw 6.3 2017 Lesvos earthquake is carried out. The main shock occurred on June 12, offshore the southeastern coast of the Greek island of Lesvos in the north Aegean Sea. It caused 1 fatality, 15 injuries, and extensive damage to the southern part of the island. Dynamic rupture evolution is modelled on an elliptic patch, using the linear slip-weakening friction law. The inversion is posed as a Bayesian problem and the Parallel Tempering Markov Chain Monte Carlo algorithm is used to obtain posterior probability distributions by updating the prior distribution with progressively more constraints. To calculate the first posterior distribution, only the constraint that the model should expand beyond the nucleation patch is used. Then, we add the constraint that the model should reach a moment magnitude similar to that obtained from our centroid moment tensor inversion. For the final posterior distribution, 15 acceleration records from Greek and Turkish strong motion networks at near regional distances (≈ 30–150 km) in the frequency range of 0.05–0.15 Hz are used. The three posterior distributions are compared to understand how much each constraint contributes to resolving different quantities. The most probable values and uncertainties of individual parameters are also calculated, along with their mutual trade-offs. The features best determined by seismograms in the final posterior distribution include the position of the nucleation region, the mean direction of rupture (towards WNW), the mean rupture speed (with 68 per cent of the distribution lying between 1.4 and 2.6 km s–1), radiated energy (12–65 TJ), radiation efficiency (0.09–0.38) and the mean stress drop (2.2–6.5 MPa).
Understanding the ‘crisis of the institution’ in the liberal trade order at the WTO
Authors: Sinha Aseema 
Published: September 2021

Abstract
The liberal trade order is in crisis. I argue that the origins of the current crises lie in the underlying tension which exists in the World Trade Organization (WTO), magnified by a churning in global power dynamics. A dilemma at the heart of the WTO between two important goals of representativeness and effectiveness means that both goals cannot be pursued at the same time. Now, this inherent tension is being magnified by power shifts in the global economy most evident in the rise of emerging powers within the WTO, who demand more representation, and the retreat by the US towards a more inward-looking orientation; both together damage effectiveness. Simultaneously, new powers such as China and India are defending a ‘reformed multilateralism’ combined with selective protectionism with varying capacity. These shifts are transforming previous ‘crises within institutions’ into a ‘crisis of institutions’ at the WTO, wherein the rules of the game, ideas of free trade and the legitimacy of the WTO are under threat. Global trade politics is seeing new coalitions at the WTO, as emerging powers craft their own rise, US defends sovereignty and trade protections, and launches a challenge to China's rise, and some established powers (the EU for example) seek to reform it. The new global trade politics is walking on two uneven legs and creating winners and losers and new ways of managing the transitional trading order as did the creation of the post-world war order.
Globalization, deglobalization and the liberal international order
Authors: Kornprobst Markus , Paul T V 
Published: September 2021

Abstract
For decades, globalization and the liberal international order evolved side by side. Recently, however, deglobalizing forces have been on the rise and the liberal international order has come to be increasingly beleaguered. The special issue ‘Deglobalization? The future of the liberal international order’ examines the interconnectedness of globalization and deglobalization processes on the one hand and the trajectory of the liberal international order on the other. This introduction provides a conceptual frame for the articles to follow. It discusses globalization and deglobalization processes, compares how they have been intertwined with the liberal international order in the past and presently, and explores how these differences are likely to affect the future of world politics. The special issue makes three important contributions. First, we examine globalization and deglobalization processes systematically. Second, we break new ground in studying the future of international order. Third, we generate novel insights into epochal change.
Seeing Red: representing a mark consisting of a colour combination
Authors: Martin Stefan , Boyd Jonathan 
Published: September 2021

Abstract
General Court, T-193/18, Andreas Stihl v EUIPO, EU:T:2021:163, 24 March 2021
In its first judgment since the decision of the Court of Justice of the European Union (‘CJEU’) in the Red Bull case (C-124/18 P), the General Court has clarified its approach to colour marks and Article 4 of the EU Trade Mark Regulation 2017/1001 (‘EUTMR’).
Persuasive Message Pretesting Using Non-Behavioral Outcomes: Differences in Attitudinal and Intention Effects as Diagnostic of Differences in Behavioral Effects
Authors: O’Keefe Daniel J 
Published: September 2021

Abstract
Persuasive message designers would like to be able to pretest messages to see which will be more effective in influencing behavioral outcomes, but pretesting using behavioral measures is commonly not practical. Examination of within-study effect size comparisons from 317 studies of 22 message variations suggests that persuasive messages’ relative effectiveness is strikingly similar across attitudinal, intention, and behavioral outcomes—with messages’ relative persuasiveness with respect to intention outcomes especially indicative of relative persuasiveness with respect to behavioral outcomes. Intention measures thus provide a convenient and accurate means of persuasive message pretesting.
The Distorting Prism of Social Media: How Self-Selection and Exposure to Incivility Fuel Online Comment Toxicity
Authors: Kim Jin Woo , Guess Andrew , Nyhan Brendan , Reifler Jason 
Published: September 2021

Abstract
Though prior studies have analyzed the textual characteristics of online comments about politics, less is known about how selection into commenting behavior and exposure to other people’s comments changes the tone and content of political discourse. This article makes three contributions. First, we show that frequent commenters on Facebook are more likely to be interested in politics, to have more polarized opinions, and to use toxic language in comments in an elicitation task. Second, we find that people who comment on articles in the real world use more toxic language on average than the public as a whole; levels of toxicity in comments scraped from media outlet Facebook pages greatly exceed what is observed in comments we elicit on the same articles from a nationally representative sample. Finally, we demonstrate experimentally that exposure to toxic language in comments increases the toxicity of subsequent comments.
The small GTPase NtRHO1 negatively regulates tobacco defense response to tobacco mosaic virus by interacting with NtWRKY50
Authors: Han Hongyan , Zou Jialing , Zhou Jingya , Zeng Mengyuan , Zheng Dongchao , Yuan Xuefeng , Xi Dehui 
Published: September 2021

Abstract
Small GTPases play critical roles in the regulation of plant growth and development. However, the mechanism of action of small GTPases in plant response to virus infection remains largely unknown. Here, the gene encoding a Rho-type GTPase, NtRHO1, was identified as one of the genes up-regulated after tobacco mosaic virus (TMV) infection. Subcellular localization of NtRHO1 showed that it was located in the cytoplasm, plasma membrane, and nucleus. Transient overexpression of NtRHO1 in Nicotiana benthamiana accelerated TMV reproduction and led to the production of reactive oxygen species. By contrast, silencing of NtRHO1 reduced the sensitivity of N. benthamiana to TMV-GFP. Further exploration revealed a direct interaction between NtRHO1 and NtWRKY50, a positive regulator of the N. benthamiana response to virus infection. Yeast one-hybrid and electrophoretic mobility shift assays showed that this regulation was related to the capacity of NtWRKY50 to bind to the WK-box of the PR1 promoter, which was weakened by the interaction between NtRHO1 and NtWRKY50. Thus, our results indicate that the small GTPase NtRHO1 plays a negative role in tobacco response to TMV infection by interacting with transcription factor NtWRKY50, resulting in reduced plant immunity.