Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Dissection of Azuki Bean Weevil (Callosobruchus chinensis L.) Resistance in Moth Bean (Vigna aconitifolia [Jaqc.] Maréchal)

The azuki bean weevil (Callosobruchus chinensis L.) is an insect pest responsible for serious postharvest seed loss in leguminous crops. In this study, we performed quantitative trait locus (QTL) mapping of seed resistance to C. chinensis in moth bean (Vigna aconitifolia [Jaqc.] Maréchal). An F2 population of 188 plants developed by crossing resistant accession ‘TN67’ (wild type from India; male parent) and susceptible accession ‘IPCMO056’ (cultivated type from India; female parent) was used for mapping. Seeds of the F2 population from 2014 and F2:3 populations from 2016 and 2017 were bioassayed with C. chinensis, and the percentage of damaged seeds and progress of infestation severity were measured. Segregation analysis suggested that C. chinensis resistance in TN176 is controlled by a single dominant gene, designated as Rcc. QTL analysis revealed one principal and one modifying QTL for the resistance, named qVacBrc2.1 and qVacBrc5.1, respectively. qVacBrc2.1 was located on linkage group 2 between simple sequence repeat markers CEDG261 and DMB-SSR160 and accounted for 50.41% to 64.23% of resistance-related traits, depending on the trait and population. Comparative genomic analysis suggested that qVacBrc2.1 is the same as QTL Brc2.1 conferring C. chinensis resistance in wild azuki bean (V. nepalensis Tateishi and Maxted). Markers CEDG261 and DMB-SSR160 should be useful for marker-assisted selection for C. chinensis resistance in moth bean.
Machine learning with remote sensing data to locate uncontacted indigenous villages in Amazonia

Background The world’s last uncontacted indigenous societies in Amazonia have only intermittent and often hostile interactions with the outside world. Knowledge of their locations is essential for urgent protection efforts, but their extreme isolation, small populations, and semi-nomadic lifestyles make this a challenging task. Methods Remote sensing technology with Landsat satellite sensors is a non-invasive methodology to track isolated indigenous populations through time. However, the small-scale nature of the deforestation signature left by uncontacted populations clearing villages and gardens has similarities to those made by contacted indigenous villages. Both contacted and uncontacted indigenous populations often live in proximity to one another making it difficult to distinguish the two in satellite imagery. Here we use machine learning techniques applied to remote sensing data with a training dataset of 500 contacted and 25 uncontacted villages. Results Uncontacted villages generally have smaller cleared areas, reside at higher elevations, and are farther from populated places and satellite-detected lights at night. A random forest algorithm with an optimally-tuned detection cutoff has a leave-one-out cross-validated sensitivity and specificity of over 98%. A grid search around known uncontacted villages led us to identify three previously-unknown villages using predictions from the random forest model. Our efforts can improve policies toward isolated populations by providing better near real-time knowledge of their locations and movements in relation to encroaching loggers, settlers, and other external threats to their survival.
Thermal Stress Relaxation and High-Temperature Corrosion of Cr-Mo Steel Processed Using Multifunction Cavitation

This research investigated high-temperature corrosion (500 °C) of Cr-Mo steel processed using water jet peening or multifunction cavitation (MFC), and the suitability of such steel for high-temperature boilers and reaction vessels. High-temperature corrosion was induced using an embedment test and a coating test using sulfide-type K2SO4-Na2SO4 powder. To measure the relaxation of the residual stress due to the decrease in work hardening caused by an increase in specimen temperature and the difference in thermal shrinkage between the surface and interior of the specimen, a thermal cycling test was conducted. For the MFC-processed specimen, the oxide film that formed on the surface suppressed mass loss, prevented crack formation, and reduced the compressive residual stress caused by high-temperature corrosion. MFC-processed Cr-Mo steel is thus suitable for a high-temperature corrosion environment.
BRCA1 represses DNA replication initiation through antagonizing estrogen signaling and maintains genome stability in parallel with WEE1‐MCM2 signaling during pregnancy

Abstract The mammary gland undergoes fast cell proliferation during early pregnancy, yet the mechanism to ensure genome integrity during this highly proliferative stage is largely unknown. We show that pregnancy triggers replicative stresses leading to genetic instability in mice carrying a mammary specific disruption of breast cancer associated gene‐1 (BRCA1). The fast cell proliferation was correlated with enhanced expression of most genes encoding replisomes, which are positively regulated by estrogen/ER&agr; signaling but negatively regulated by BRCA1. Our further analysis revealed two parallel signaling pathways, which are mediated by ATR‐CHK1 and WEE1‐MCM2 and are responsible for regulating DNA replication checkpoint. Upon DNA damage, BRCA1 deficiency markedly enhances DNA replication initiation and preferably impairs DNA replication checkpoint mediated by ATR and CHK1. Meanwhile, DNA damage also activates WEE1‐MCM2 signaling, which inhibits DNA replication initiation and enables BRCA1‐deficient cells to avoid further genomic instability. Finally, we demonstrated that overriding this defense by WEE1 inhibition in combination with cisplatin, which causes DNA damage, serves as a promising therapeutic approach for killing BRCA1‐deficient cancer cells.
Towards a Secure and Borderless Collaboration between Organizations: An Automated Enforcement Mechanism

During the last decade, organizations have been more and more aware of the benefits of engaging in collaborative activities. To attain a required collaborative objective, they are obligated to share sensitive resources such as data, services, and knowledge. However, sharing sensitive and private resources and exposing them for an external usage may prevent the organizations involved from collaborating. Therefore, this usage requires more preoccupation with security issues. Access control is one of these required security concerns. Several access control models are defined in the literature and this multitude of models creates heterogeneity of access control policies between the collaborating organizations. In this paper, we propose Access Control in Cross-Organizational coLLABoration ACCOLLAB, a solution for automatic mapping between heterogeneous access control policies in cross-organizational collaboration. To carry out this mapping, we suggest a mechanism founded mainly on XACML profiles and on a generic language derivative of XACML we define as Generic-XACML. We also formally prove that the mapping does not affect decision evaluation of policies. Thereby the proposed contribution ACCOLLAB allows each collaborating organization to communicate their access control policies and adopt other’s policies without affecting their existing access control systems.
Caught red-handed: behaviour of brood thieves in an Indian ant

ABSTRACT Theft of resources is ubiquitous in the animal kingdom. An evolutionary arms race between thieves and their victims is expected. Although several studies have documented inter- and intraspecific theft of resources in different taxa, studies that delve into the behaviour of thieves and the factors that influence their behaviour have not been undertaken. In the current study on the primitively eusocial ant Diacamma indicum, we caught brood thieves red-handed: we observed them in the act of stealing brood and examined their behaviour. Thieves were persistent in their attempts despite facing aggression in the victim colony. Experiencing aggression or failure to steal in the previous attempt negatively impacted a thief's drive to reattempt. To avoid the risks associated with theft, successful thieves exited from victim nests about three times faster than others who were procuring brood from unguarded nests. In a series of experiments examining factors that caused thieves to increase their exit speed, we found that indirect cues of a foreign colony's presence, such as odour or the presence of foreign ants, did not induce these changes in thieves. Thus, we conclude that these ant thieves only respond to the direct threat posed by aggressive foreign ants. In this comprehensive study using behavioural experiments, we reveal the simple rules of engagement between victims and brood thieves. Summary: The simple rules of engagement between victims and thieves are revealed by catching ant thieves red-handed and investigating their behaviour.
Changes of gene expression but not cytosine methylation are associated with male parental care reflecting behavioural state, social context and individual flexibility

ABSTRACT Behaviour is often a front line response to changing environments. Recent studies show behavioural changes are associated with changes of gene expression; however, these studies have primarily focused on discrete behavioural states. We build on these studies by addressing additional contexts that produce qualitatively similar behavioural changes. We measured levels of gene expression and cytosine methylation, which is hypothesized to regulate the transcriptional architecture of behavioural transitions, within the brain during male parental care of the burying beetle Nicrophorus vespilloides in a factorial design. Male parenting is a suitably plastic behaviour because although male N. vespilloides typically do not provide direct care (i.e. feed offspring) when females are present, levels of feeding by a male equivalent to the female can be induced by removing the female. We examined three different factors: behavioural state (caring versus non-caring), social context (with or without a female mate) and individual flexibility (if a male switched to direct care after his mate was removed). The greatest number of differentially expressed genes were associated with behavioural state, followed by social context and individual flexibility. Cytosine methylation was not associated with changes of gene expression in any of the factors. Our results suggest a hierarchical association between gene expression and the different factors, but that this process is not controlled by cytosine methylation. Our results further suggest that the extent a behaviour is transient plays an underappreciated role in determining its underpinning molecular mechanisms. Summary: Behavioural state has more influence on gene expression than social context or individual flexibility during a transition to parental care, whereas cytosine methylation is not associated with differential gene expression.
An Improved Permission Management Scheme of Android Application Based on Machine Learning

The Android permission mechanism prevents malicious application from accessing the mobile multimedia data and invoking the sensitive API. However, there are still lots of deficiencies in the current permission management, which results in the permission mechanism being unable to protect users’ private data properly. In this paper, a dynamic management scheme of Android permission based on machine learning is proposed to solve the problem of the existing permission mechanism. In order to accomplish the dynamic management, the proposed scheme maintains a dynamic permission management database which records the state of permissions for each application. Only the permission which is granted state in the database can be used in this application. In the whole process, the scheme first classifies the application by means of machine learning, then retrieves the corresponding permission information from databases, and issues the dangerous permission warning to users. Finally, the scheme updates the dynamic management database according to the users’ decisions. Through this scheme, users can prevent malicious behaviour of accessing private data and invoking sensitive API in time. The solution increases the flexibility of permission management and improves the security and reliability of multimedia data in Android devices.
Rescuing ocular development in an anophthalmic pig by blastocyst complementation

Porcine‐derived xenogeneic sources for transplantation are a promising alternative strategy for providing organs for treatment of end‐stage organ failure in human patients because of the shortage of human donor organs. The recently developed blastocyst or pluripotent stem cell (PSC) complementation strategy opens a new route for regenerating allogenic organs in miniature pigs. Since the eye is a complicated organ with highly specialized constituent tissues derived from different primordial cell lineages, the development of an intact eye from allogenic cells is a challenging task. Here, combining somatic cell nuclear transfer technology (SCNT) and an anophthalmic pig model (MITFL247S/L247S), allogenic retinal pigmented epithelium cells (RPEs) were retrieved from an E60 chimeric fetus using blastocyst complementation. Furthermore, all structures were successfully regenerated in the intact eye from the injected donor blastomeres. These results clearly demonstrate that not only differentiated functional somatic cells but also a disabled organ with highly specialized constituent tissues can be generated from exogenous blastomeres when delivered to pig embryos with an empty organ niche. This system may also provide novel insights into ocular organogenesis.
Antioxidant potential and phytochemical composition of extracts obtained from Phyllanthus phillyreifolius by different extraction methods

Abstract Phyllanthus phillyreifolius (Euphorbiaceae), poorly studied plant species, was fractionated using conventional and high pressure extraction techniques such as supercritical fluid and pressurized liquid extractions. Lipophilic substances were extracted with n-hexane and supercritical CO2 with or without co-solvent ethanol, meanwhile higher polarity fractions were recovered with acetone and 70% ethanol. Antioxidant potential was assessed by various chemical assays, which revealed that 70% ethanol was the most effective solvent for recovery of antioxidants. UPLC-MS phytochemical analysis of hydrophilic extracts confirmed geraniin as the main constituent of P. phillyreifolius. Other quantitatively important compounds were phyllanthusiin D and elaeocarpusin. Three isomers of tocopherol (α, β and γ) were quantified by HPLC in lipofhilic extracts. Generally, the results from this study revealed high antioxidant potential of P. phillyreifolius; consequently the plant may be considered as a promising source of antioxidants for functional foods, nutraceuticals and pharmaceutical formulations.
Chemogenetic Manipulations of Ventral Tegmental Area Dopamine Neurons Reveal Multifaceted Roles in Cocaine Abuse

Ventral tegmental area (VTA) dopamine (DA) neurons perform diverse functions in motivation and cognition, but their precise roles in addiction-related behaviors are still debated. Here, we targeted VTA DA neurons for bidirectional chemogenetic modulation during specific tests of cocaine reinforcement, demand, and relapse-related behaviors in male rats, querying the roles of DA neuron inhibitory and excitatory G-protein signaling in these processes. Designer receptor stimulation of Gq signaling, but not Gs signaling, in DA neurons enhanced cocaine seeking via functionally distinct projections to forebrain limbic regions. In contrast, engaging inhibitory Gi/o signaling in DA neurons blunted the reinforcing and priming effects of cocaine, reduced stress-potentiated reinstatement, and altered behavioral strategies for cocaine seeking and taking. Results demonstrate that DA neurons play several distinct roles in cocaine seeking, depending on behavioral context, G-protein-signaling cascades, and DA neuron efferent targets, highlighting their multifaceted roles in addiction. SIGNIFICANCE STATEMENT G-protein-coupled receptors are crucial modulators of ventral tegmental area (VTA) dopamine neuron activity, but how this metabotropic signaling impacts the complex roles of dopamine in reward and addiction is poorly understood. Here, we bidirectionally modulate dopamine neuron G-protein signaling with DREADDs (designer receptors exclusively activated by designer drugs) during a variety of cocaine-seeking behaviors, revealing nuanced, pathway-specific roles in cocaine reward, effortful seeking, and relapse-like behaviors. Gq and Gs stimulation activated dopamine neurons, but only Gq stimulation robustly enhanced cocaine seeking. Gi/o inhibitory signaling reduced some, but not all, types of cocaine seeking. Results show that VTA dopamine neurons modulate numerous distinct aspects of cocaine addiction- and relapse-related behaviors, and point to potential new approaches for intervening in these processes to treat addiction.
BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures

Motivation Modern bioinformatics tools for analyzing large-scale NGS datasets often need to include fast implementations of core sequence alignment algorithms in order to achieve reasonable execution times. We address this need by presenting the BGSA toolkit for optimized implementations of popular bit-parallel global pairwise alignment algorithms on modern microprocessors. Results BGSA outperforms Edlib, SeqAn, and BitPAl for pairwise edit distance computations and Parasail, SeqAn, and BitPAl when using more general scoring schemes for pairwise alignments of a batch of sequence reads on both standard multi-core CPUs and Xeon Phi many-core CPUs. Furthermore, banded edit distance performance of BGSA on a Xeon Phi-7210 outperforms the highly optimized NVBio implementation on a Titan X GPU for the seed verification stage of a read mapper by a factor of 4.4. Availability BGSA is open-source and available at https://github.com/sdu-hpcl/BGSA. Supplementary information Supplementary data are available at Bioinformatics online.
A prospective Phase II study for the efficacy of radiotherapy in combination with zoledronic acid in treating painful bone metastases from gastrointestinal cancers

Abstract We investigated the efficacy of combined radiotherapy (RT) and zoledronic acid in treating painful bone metastases from gastrointestinal cancers. Sixty patients were prospectively enrolled between November 2014 and July 2016. The most common primary cancer type was hepatocellular carcinoma (HCC, n = 25), followed by colorectal cancer (n = 6). Patients received external beam RT of 30–54 Gy in 10–17 fractions or 20 Gy in 5 fractions for symptomatic bone metastases. On the first day of RT, patients received 4 mg intravenous zoledronic acid, which was repeated monthly for a total of six cycles. The mean pain score before treatment was 6.7, and it decreased to 2.8 at 1 month and 2.1 at 3 months (P < 0.001). The overall pain response rates at 1 and 3 months were 95% and 96%, respectively. Among the 24 patients who underwent magnetic resonance imaging, 71% were responders, with a complete response in 1 patient and partial in 16 patients. Combined treatment significantly decreased levels of macrophage inflammatory protein-1α and matrix metalloproteinase (MMP)-2 and -3 compared with baseline (all P < 0.05). In HCC patients, IL-6 and MMP-9 levels were significantly lower 1 month after treatment (P < 0.05). The mean quality of life (QOL) score improved from 66 to 56 at 1 month (P < 0.001) and 55 at 3 months (P = 0.016). The median survival was 7 months. In conclusion, RT with zoledronic acid decreased bone pain and improved QOL in patients with painful bone metastases from gastrointestinal cancers. Radiographic findings and serum biomarker measurements were closely correlated with therapeutic responses.
Evolutionary Hierarchical Sparse Extreme Learning Autoencoder Network for Object Recognition

Extreme learning machine (ELM), characterized by its fast learning efficiency and great generalization ability, has been applied to various object recognition tasks. When extended to the stacked autoencoder network, which is a typical symmetrical representation learning model architecture, ELM manages to realize hierarchical feature extraction and classification, which is what deep neural networks usually do, but with much less training time. Nevertheless, the input weights and biases of the hidden nodes in ELM are generated according to a random distribution and may lead to the occurrence of non-optimal and redundant parameters that deteriorate discriminative features, which will have a bad influence on the final classification effect. In this paper, a novel sparse autoencoder derived from ELM and differential evolution is proposed and integrated into a hierarchical hybrid autoencoder network to accomplish the end-to-end learning with raw visible light camera sensor images and applied to several typical object recognition problems. Experimental results show that the proposed method is able to obtain competitive or better performance than current relevant methods with acceptable or less time consumption.
Comparison of Quantitative Exposure Models for Occupational Exposure to Organic Solvents in Korea

This study aims to evaluate the accuracy, precision and conservatism of three models (ECETOC TRA 3.1, Stoffenmanager 7.0 and ART 1.5) by comparing model predictions and repeated exposure measurements in Korea. We collected the exposure measurements (n = 390) and detailed contextual information extracted from 10 survey reports published by Ministry of Employment and Labour in the mid-2000s. Using these three models, seven occupational health professionals predicted inhalation exposure to 10 solvents used for cleaning tasks in 51 situations at 33 companies in 15 industries. We applied four comparison approaches previously used by several European studies and calculated the lack of agreement (bias, relative bias, precision), Pearson correlation coefficients (r), level of conservatism, and residuals between the log-transformed predicted estimates and measured exposures on both individual and situation levels. The overall bias and precision were -0.53 ± 2.11 with ART, -1.32 ± 5.88 with Stoffenmanager, and -1.03 ± 8.88 with ECETOC TRA. Pearson correlation coefficients were significantly high in ART (r = 0.95) and Stoffenmanager (r = 0.82), but moderate in ECETOC TRA (r = 0.58). We found ART to be the most accurate model, and Stoffenmanager was the most balanced model in terms of good accuracy, high correlation, and medium conservatism in the model predictions. However, ECETOC TRA showed less accurate outcomes and lower level of conservatism but still had moderate correlations. We observed a systematic tendency to overestimate low exposures and underestimate higher exposures in all models, similar to previous studies. Therefore, our findings suggest that these European models can be used to predict occupational exposure to solvents in Korea.