Miracle-dz/UniFAR-FTUs huggingface dataset:
Plant condensin II is required for the correct spatial relationship between centromeres and rDNA arrays

ABSTRACT Plants possess the structural maintenance of chromosome (SMC) protein complexes cohesin, condensin, and SMC5/6, which function in fundamental biological processes such as sister chromatid cohesion, chromosome condensation and segregation, and damaged DNA repair. Recently, increasing evidence in several organisms has suggested that condensin is involved in chromatin organizations during interphase. In Arabidopsis thaliana, condensin II is localized in the nucleus throughout interphase and is suggested to be required for keeping centromeres apart and the assembly of euchromatic chromosome arms. However, it remains unclear how condensin II organizes chromatin associations. Here, we first showed the high possibility that the function of condensin II as a complex is required for the disassociation of centromeres. Analysis of the rDNA array distribution revealed that condensin II is also indispensable for the association of centromeres with rDNA arrays. Reduced axial compaction of chromosomes and impaired genome integrity in condensin II mutants are not related to the disruption of chromatin organization. In contrast, the axial compaction of chromosomes by condensin II produces the force leading to the disassociation of heterologous centromeres in Drosophila melanogaster. Taken together, our data imply that the condensin II function in chromatin organization differs among eukaryotes.
A New Computer Self-immune Model against Malicious Codes

A new computer self-immune model against malicious codes is addressed. Instead of detecting or recognizing the exact characters of malicious codes, the model gives computer system the self-immune ability against malicious codes by getting rid of the prerequisites for malicious codes to spread and do harm directly. Because the model needs no character of malicious codes, the heavy work of character code computing and detecting will be avoided and the large amount of storage space for character codes will be saved.
K2 DISCOVERS A BUSY BEE: AN UNUSUAL TRANSITING NEPTUNE FOUND IN THE BEEHIVE CLUSTER

Open clusters have been the focus of several exoplanet surveys, but only a few planets have so far been discovered. The Kepler spacecraft revealed an abundance of small planets around small cool stars, therefore, such cluster members are prime targets for exoplanet transit searches. Kepler's new mission, K2, is targeting several open clusters and star-forming regions around the ecliptic to search for transiting planets around their low-mass constituents. Here, we report the discovery of the first transiting planet in the intermediate-age (800 Myr) Beehive cluster (Praesepe). K2-95 is a faint ( ) dwarf from K2's Campaign 5 with an effective temperature of , approximately solar metallicity and a radius of . We detected a transiting planet with a radius of and an orbital period of 10.134 days. We combined photometry, medium/high-resolution spectroscopy, adaptive optics/speckle imaging, and archival survey images to rule out any false-positive detection scenarios, validate the planet, and further characterize the system. The planet’s radius is very unusual as M-dwarf field stars rarely have Neptune-sized transiting planets. The comparatively large radius of K2-95b is consistent with the other recently discovered cluster planets K2-25b (Hyades) and K2-33b (Upper Scorpius), indicating systematic differences in their evolutionary states or formation. These discoveries from K2 provide a snapshot of planet formation and evolution in cluster environments and thus make excellent laboratories to test differences between field-star and cluster planet populations.
Artemisinin alleviates atherosclerotic lesion by reducing macrophage inflammation via regulation of AMPK/NF-κB/NLRP3 inflammasomes pathway

Abstract There is increasing evidence that atherosclerosis is the significant risk factor for cardiovascular diseases, which are the leading causes of morbidity and mortality worldwide. Artemisinin is a natural endoperoxides quiterpene lactone compound in Artemisia annua L with vasculoprotective effects. The primary aim of this study was to investigate whether artemisinin could be conferred an anti-atherosclerotic effect in high-fat diet (HFD)-fed ApoE–/– mice and explore the possible mechanism. We found that treatment with artemisinin (50 and 100 mg/kg) effectively ameliorated atherosclerotic lesions, such as foam cell formation, hyperplasia and fibrosis in the aortic intima. Atherosclerotic mice treated with artemisinin showed reduced inflammation by up-regulating adenosine 5′-monophosphate (AMP) activated protein kinase (AMPK) activation and by down-regulating nuclear factor-κB (NF-κB) phosphorylation and nod-like receptor family pyrin domain containing 3 (NLRP3) inflammasome expression in the aortas. In addition, artemisinin was found to promote AMPK activity in macrophages and its anti-inflammatory effect was neutralised by AMPK silence using specific siRNA. In conclusion, we demonstrate that artemisinin may protect the aortas from atherosclerotic lesions by suppression of inflammatory reaction via AMPK/NF-κB/NLRP3 inflammasomes signalling in macrophages.
Identification of an Immunogenic Broadly Inhibitory Surface Epitope of the Plasmodium vivax Duffy Binding Protein Ligand Domain

Vivax malaria is the second leading cause of malaria worldwide and the major cause of non-African malaria. Unfortunately, efforts to develop antimalarial vaccines specifically targeting Plasmodium vivax have been largely neglected, and few candidates have progressed into clinical trials. The Duffy binding protein is considered a leading blood-stage vaccine candidate because this ligand’s recognition of the Duffy blood group reticulocyte surface receptor is considered essential for infection. This study identifies a new target epitope on the ligand’s surface that may serve as the target of vaccine-induced binding-inhibitory antibody (BIAb). Understanding the potential targets of vaccine protection will be important for development of an effective vaccine. ABSTRACT The Plasmodium vivax Duffy binding protein region II (DBPII) is a vital ligand for the parasite’s invasion of reticulocytes, thereby making this molecule an attractive vaccine candidate against vivax malaria. However, strain-specific immunity due to DBPII allelic variation in Bc epitopes may complicate vaccine efficacy, suggesting that an effective DBPII vaccine needs to target conserved epitopes that are potential targets of strain-transcending neutralizing immunity. The minimal epitopes reactive with functionally inhibitory anti-DBPII monoclonal antibody (MAb) 3C9 and noninhibitory anti-DBPII MAb 3D10 were mapped using phage display expression libraries, since previous attempts to deduce the 3C9 epitope by cocrystallographic methods failed. Inhibitory MAb 3C9 binds to a conserved conformation-dependent epitope in subdomain 3, while noninhibitory MAb 3D10 binds to a linear epitope in subdomain 1 of DBPII, consistent with previous studies. Immunogenicity studies using synthetic linear peptides of the minimal epitopes determined that the 3C9 epitope, but not the 3D10 epitope, could induce functionally inhibitory anti-DBPII antibodies. Therefore, the highly conserved binding-inhibitory 3C9 epitope offers the potential as a component in a broadly inhibitory, strain-transcending DBP subunit vaccine. IMPORTANCE Vivax malaria is the second leading cause of malaria worldwide and the major cause of non-African malaria. Unfortunately, efforts to develop antimalarial vaccines specifically targeting Plasmodium vivax have been largely neglected, and few candidates have progressed into clinical trials. The Duffy binding protein is considered a leading blood-stage vaccine candidate because this ligand’s recognition of the Duffy blood group reticulocyte surface receptor is considered essential for infection. This study identifies a new target epitope on the ligand’s surface that may serve as the target of vaccine-induced binding-inhibitory antibody (BIAb). Understanding the potential targets of vaccine protection will be important for development of an effective vaccine.
Studies on the mechanism of peptidoglycan- and lipopolysaccharide-induced polyclonal activation

Peptidoglycan (PG) and lipopolysaccharide (LPS) are T cell-independent B cell mitogens and polyclonal activators in mice. The mechanism of in vitro proliferation and polyclonal activation of mouse splenocytes induced by PG from Staphylococcus aureus and LPS from Escherichia coli was further studied by using [3H]thymidine incorporation and protein A hemolytic plaque assays. Concanavalin A-generated suppressor cells suppressed both polyclonal and proliferative responses induced by PG, LPS, and pokeweed mitogen. The suppression of the proliferative responses was similar for all these mitogens, but was significantly less pronounced than the suppression of the polyclonal antibody response. Polyclonal activation induced by LPS was the most susceptible to suppression by concanavalin A-generated suppressor cells, and the suppression was significantly greater than in the PG-induced polyclonal response. Also, PG-induced polyclonal activation was not susceptible to inhibition by polymyxin B, which is an inhibitor of other B cell mitogens and polyclonal activators. For optimal generation of immunoglobulin-secreting cells, PG of LPS had to be present for at least 48 h after the initiation of the cultures. Removal of the mitogens after 4 or 24 h of incubation resulted in a suboptimal response. For effective induction of the proliferative response, the mitogens had to be present in cultures for over 24 h. Polyclonal-activating properties of staphylococcal cell wall components were also compared. PG was by far the most potent inducer of polyclonal antibodies. Teichoic acid was not active as a polyclonal activator, whereas purified cell wall and protein A were very weak inducers of polyclonal antibodies. These studies demonstrate that PG, in addition to LPS, can be a useful probe for studies on polyclonal activation.
Enabling Massive XML-Based Biological Data Management in HBase

Publishing biological data in XML formats is attractive for organizations who would like to provide their bioinformatics resources in an extensible and machine-readable format. In the era of big data, massive XML-based biological data management is emerged as a challengeable issue. With the continuous growth of the XML-based biological data sets, it is usually frustrating to use traditional declarative query languages to provide efficient query capabilities in terms of processing speed and scale. In this study, we report a novel platform to store and query massive XML-based biological data collections. A prototype tool for constructing HBase tables from XML-based biological data collections is first developed, and then a formal approach to transform the XML query model into the MapReduce query model is proposed. Finally, an evaluation of the query performance of the proposed approach on the existing XML-based biological databases is presented, showing that the performance advantages of the proposed solution. The source code of the massive XML-based biological data management platform is freely available at https://github.com/lyotvincent/X2H.
Vascular Risk Prediction in Ischemic Stroke Patients Undergoing in-patient Rehabilitation – Insights from the Investigation of Patients with Ischemic Stroke in Neurologic Rehabilitation (INSIGHT) Registry

Background In-patient rehabilitation following ischemic stroke offers a unique opportunity for risk factor and lifestyle modification. Quantification of risk in this setting may help to tailor therapy, increase physician awareness and patient compliance and thus to reduce recurrent vascular events. Aims To validate the predictive value of established secondary stroke risk scores. Methods One thousand one hundred sixty-three patients undergoing in-patient rehabilitation following recent ischemic stroke in 15 German neurologic rehabilitation centers were included 0·9 ± 0·5 months after the index event. Outcome information was available for 846 participants (72·7%) after a mean follow-up of 13 ± 2·3 months. Results Patients' mean age was 66·3 ± 12·3 years and 42·5% were women. The National Institutes of Health Stroke Scale (mean 4·0 ± 3·9), modified Rankin scale (median 2, range 0–5), and Barthel Index (median 90, range 0–100) indicated good functional status. A recurrent fatal or nonfatal stroke during follow-up occurred in 6·7% and combined vascular events (stroke, myocardial infarction, vascular death) in 10·9%. The predictive accuracy for recurrent stroke was slightly higher on the Essen Stroke Risk Score than on the Stroke Prognostis Instrument II (area under the curve 0·62 vs. 0·56), while both scores had a similar predictive accuracy for combined vascular events. Conclusions Risk stratification on the Essen Stroke Risk Score and Stroke Prognostis Instrument II provides a moderate accuracy for the prediction of recurrent stroke and vascular events in patients undergoing neurologic inpatient rehabilitation. Although individual risk prediction may remain imprecise, the use of these scores should be encouraged.
Immuno-Imaging to Predict Treatment Response in Infection, Inflammation and Oncology

Background: Molecular nuclear medicine plays a pivotal role for diagnosis in a preclinical phase, in genetically susceptible patients, for radio-guided surgery, for disease relapse evaluation, and for therapy decision-making and follow-up. This is possible thanks to the development of new radiopharmaceuticals to target specific biomarkers of infection, inflammation and tumour immunology. Methods: In this review, we describe the use of specific radiopharmaceuticals for infectious and inflammatory diseases with the aim of fast and accurate diagnosis and treatment follow-up. Furthermore, we focus on specific oncological indications with an emphasis on tumour immunology and visualizing the tumour environment. Results: Molecular nuclear medicine imaging techniques get a foothold in the diagnosis of a variety of infectious and inflammatory diseases, such as bacterial and fungal infections, rheumatoid arthritis, and large vessel vasculitis, but also for treatment response in cancer immunotherapy. Conclusion: Several specific radiopharmaceuticals can be used to improve diagnosis and staging, but also for therapy decision-making and follow-up in infectious, inflammatory and oncological diseases where immune cells are involved. The identification of these cell subpopulations by nuclear medicine techniques would provide personalized medicine for these patients, avoiding side effects and improving therapeutic approaches.
Strategies for oral delivery of metal-saturated lactoferrin.

Lactoferrin was isolated and purified for the first time over 50-years ago. Since then, extensive studies on the structure and function of this protein have been performed and the research is still being continued. In this mini-review we focus on presenting recent scientific efforts towards the elucidation of the role and therapeutic potential of lactoferrin saturated with iron(III) or manganese(III) ions. The difference in biological activity of metal-saturated lactoferrin vs. the unmetalated one is emphasized. The strategies for oral delivery of lactoferrin, are also reviewed, with particular attention to the metalated protein.
Mechanical and electrical reliability assessment of bump-less wafer-on-wafer integration with one-time bottom-up TSV filling

Three-dimensional (3D) stacked memory module based on TSV is becoming an attractive alternative. Chips are assembled through micro bumps, which will bring additional thermo-mechanical stress, as well as the channel resistance and interconnection reliability problem. In this paper, we leverage thermal cycles to assess the mechanical and electrical reliability of a bump-less wafer-on-wafer integration approach with one-time bottom-up TSV filling we reported. Resistance was measured by four-point probes test after 10, 20, 40, 80, 160, 240, 320. , until 640 thermal cycles. Part of fixed TSVs' morphology was observed through scanning electron micro-scope (SEM) and stress was qualitative characterized by an infrared photo elastic system during thermal cycles. What's more, a thermo-mechanical finite element model (FEM) simulation was discussed, which showed that there was little difference in stress, strain, and copper extrusion values at lower temperature. All test results supported the good mechanical and electrical behavior of this bump-less wafer-on-wafer integration approach.
First Report on a Solvent-Free Preparation of Polymer Inclusion Membranes with an Ionic Liquid

A novel and environmentally-friendly procedure for the preparation of polymer inclusion membranes (PIMs) containing an ionic liquid is presented for the first time. Traditionally, PIMs are prepared by a solvent casting method with the use of harmful organic solvents. Here we report a new solvent-free procedure based on a thermal-compression technique which involve the melting of the components of the PIM and the application of a high pressure to the melted specimen to form a flat-sheet film. In our study, we have tested different polymers, such as two cellulose derivatives as well as two thermoplastic polymers, polyurethane (TPU) and poli ε-caprolactone (PCL). The ionic liquid (IL) trioctylmethylammonium chloride (Aliquat 336) has been used to produce PIMs with a fixed composition of 70% polymer–30% IL (w/w). Both TPU and PCL polymers provide successful membranes, which have been thoroughly characterized. PIMs based on the polymer PCL showed a high stability. To test whether the properties of the IL were affected by the preparation conditions, the extraction ability of Aliquat 336 was investigated for both PCL and TPU membranes in terms of Cr(VI) extraction. Satisfactory values (90% extraction) were obtained for both membranes tested, showing this novel procedure as a green alternative for the preparation of PIMs with ILs.
Intensification of smallholder agriculture in Rwanda: scenarios and challenges towards a sustainable transformation

This paper clarifies the path that Rwanda took in the quest for a modern, intensive, productive and market-oriented agriculture. The facts presented here have been collected by means of documentation that led to the review of different publications including published papers and government and development partners’ reports. The paper shows that an adequate policy and institutional environment has been created by various socio-economic, institutional and agriculture-led reforms launched since the early 2000s. The literature review reveals that impressive results have been recorded in regard to smallholder agriculture intensification. In addition, the theoretical model for progressive smallholder agriculture transformation helped to show that most of the smallholders grouped in cooperatives are at the 'semi-commercial smallholders' stage while only a few are at the 'commercial smallholders' and 'advanced farmers' stages. This study also examines various challenges that hamper the sustainable intensification of smallholder agriculture at both institutional, community and smallholder level. It suggests some policy actions to be put forward by the government and other agriculture sector development partners to address those challenges.
Human Attitude toward Reptiles: A Relationship between Fear, Disgust, and Aesthetic Preferences

Simple Summary Although there are many articles about reptiles, no one has ever studied the human perception of reptiles as a whole, a group that would include representatives of different taxonomic clades. Thus, we designed a study of human perception of all reptiles focusing on the relationship between perceived fear, disgust, and aesthetic preferences. Respondents evaluated various reptile images and the results revealed that people tend to perceive them as two clearly distinct groups based on their similar morphotype—legless reptiles (incl. snakes) and other reptiles with legs. In the case of snakes, the most feared species also tend to be perceived as beautiful. Compared to the most feared reptiles with legs (lizards, turtle, crocodiles), the legless once tend to be perceived as more disgusting. In both groups, species perceived as the least beautiful were the same as those rated as the most disgusting. Thus, reptiles cannot be rated as both beautiful and disgusting at the same time. Abstract Focusing on one group of animals can bring interesting results regarding our attitudes toward them and show the key features that our evaluation of such animals is based on. Thus, we designed a study of human perception of all reptiles focusing on the relationship between perceived fear, disgust, and aesthetic preferences and differences between snakes and other reptiles. Two sets containing 127 standardized photos of reptiles were developed, with one species per each subfamily. Respondents were asked to rate the animals according to fear, disgust, and beauty on a seven-point Likert scale. Evaluation of reptile species shows that people tend to perceive them as two clearly distinct groups based on their similar morphotype. In a subset of lizards, there was a positive correlation between fear and disgust, while disgust and fear were both negatively correlated with beauty. Surprisingly, a positive correlation between fear and beauty of snakes was revealed, i.e., the most feared species also tend to be perceived as beautiful. Snakes represent a distinct group of animals that is also reflected in the theory of attentional prioritization of snakes as an evolutionary relevant threat.
An Exploratory Factor Analysis of Sensor-Based Physical Capability Assessment

Physical capability (PC) is conventionally evaluated through performance-based clinical assessments. We aimed to transform a battery of sensor-based functional tests into a clinically applicable assessment tool. We used Exploratory Factor Analysis (EFA) to uncover the underlying latent structure within sensor-based measures obtained in a population-based study. Three hundred four community-dwelling older adults (163 females, 80.9 ± 6.4 years), underwent three functional tests (Quiet Stand, QS, 7-meter Walk, 7MW and Chair Stand, CST) wearing a smartphone at the lower back. Instrumented tests provided 73 sensor-based measures, out of which EFA identified a fifteen-factor model. A priori knowledge and the associations with health-related measures supported the functional interpretation and construct validity analysis of the factors, and provided the basis for developing a conceptual model of PC. For example, the “Walking Impairment” domain obtained from the 7MW test was significantly associated with measures of leg muscle power, gait speed, and overall lower extremity function. To the best of our knowledge, this is the first time that a battery of functional tests, instrumented through a smartphone, is used for outlining a sensor-based conceptual model, which could be suitable for assessing PC in older adults and tracking its changes over time.