Miracle-dz/UniFAR-FTUs huggingface dataset:
Lack of Detection of Bt Sugarcane Cry1Ab and NptII DNA and Proteins in Sugarcane Processing Products Including Raw Sugar

Brazil is the largest sugarcane producer and the main sugar exporter in the world. The industrial processes applied by Brazilian mills are very efficient in producing highly purified sugar and ethanol. Literature presents evidence of lack of DNA/protein in these products, regardless of the nature of sugarcane used as raw material. Recently CTNBio, the Brazilian biosafety authority, has approved the first biotechnology-derived sugarcane variety for cultivation, event CTC175-A, which expresses the Cry1Ab protein to control the sugarcane borer (Diatraea saccharalis). The event also expresses neomycin-phosphotransferase type II (NptII) protein used as selectable marker during the transformation process. Because of the high purity of sugar and ethanol produced from genetically modified sugarcane, these end-products should potentially be classified as “pure substances, chemically defined,” by Brazilian Biosafety Law No. 11.105. If this classification is to be adopted, these substances are not considered as “GMO derivatives” and fall out of the scope of Law No. 11.105. In order to assess sugar composition and quality, we evaluate Cry1Ab and NptII expression in several sugarcane tissues and in several fractions from laboratory-scale processing of event CTC175-A for the presence of these heterologous proteins as well as for the presence of traces of recombinant DNA. The results of these studies show that CTC175-A presents high expression of Cry1Ab in leaves and barely detectable expression of heterologous proteins in stalks. We also evaluated the presence of ribulose-1,5-bisphosphate carboxylase/oxygenase protein and DNA in the fractions of the industrial processing of conventional Brazilian sugarcane cultivars. Results from both laboratory and industrial processing were concordant, demonstrating that DNA and protein are not detected in the clarified juice and downstream processed fractions, including ethanol and raw sugar, indicating that protein and DNA are removed and/or degraded during processing. In conclusion, the processing of conventional sugarcane and CTC175-A Bt event results in downstream products with no detectable concentrations of heterologous DNA or new protein. These results help in the classification of sugar and ethanol derived from CTC175-A event as pure, chemically defined substances in Brazil and may relieve regulatory burdens in countries that import Brazilian sugar.
Simultaneous 6300 Å airglow and radar observations of ionospheric irregularities and dynamics at the geomagnetic equator

Abstract. In March 2014 an all-sky imager (ASI) was installed at the Jicamarca Radio Observatory (11.95 ∘ S, 76.87 ∘ W; 0.3 ∘ S MLAT). We present results of equatorial spread F (ESF) characteristics observed at Jicamarca and at low latitudes. Optical 6300 and 7774 A airglow observations from the Jicamarca ASI are compared with other collocated instruments and with ASIs at El Leoncito, Argentina (31.8 ∘ S, 69.3 ∘ W; 19.8 ∘ S MLAT), and Villa de Leyva, Colombia (5.6 ∘ N, 73.52 ∘ W; 16.4 ∘ N MLAT). We use Jicamarca radar data, in incoherent and coherent modes, to obtain plasma parameters and detect echoes from irregularities. We find that ESF depletions tend to appear in groups with a group-to-group separation around 400–500 km and within-group separation around 50–100 km. We combine data from the three ASIs to investigate the conditions at Jicamarca that could lead to the development of high-altitude, or topside, plumes. We compare zonal winds, obtained from a Fabry–Perot interferometer, with plasma drifts inferred from the zonal motion of plasma depletions. In addition to the ESF studies we also investigate the midnight temperature maximum and its effects at higher latitudes, visible as a brightness wave at El Leoncito. The ASI at Jicamarca along with collocated and low-latitude instruments provide a clear two-dimensional view of spatial and temporal evolution of ionospheric phenomena at equatorial and low latitudes that helps to explain the dynamics and evolution of equatorial ionospheric/thermospheric processes. Keywords. Ionosphere (equatorial ionosphere; ionospheric irregularities; plasma temperature and density)
Hydrothermal Synthesis of Tetragonal Phase CuInS2 Nanoparticles

The tetragonal phase CuInS2 nanoparticles were synthesized by the reaction of Cu(Ac)2, InCl3·4H2O and thioacetamide by hydrothermal method at 200 °C for 6 h in pH 1. The products were characterized by X-ray diffraction, energy-dispersive X-ray spectrum, X-ray photoelectron spectroscopy, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) techniques. Experimental results indicate that reaction temperature and the pH of solution are the important factors in the formation of CuInS2. The SEM and TEM results illuminated that the CuInS2 was composed of so many nanoparticles.
Worst-Case Optimal Join Algorithms: Techniques, Results, and Open Problems

Worst-case optimal join algorithms are the class of join algorithms whose runtime match the worst-case output size of a given join query. While the first provably worse-case optimal join algorithm was discovered relatively recently, the techniques and results surrounding these algorithms grow out of decades of research from a wide range of areas, intimately connecting graph theory, algorithms, information theory, constraint satisfaction, database theory, and geometric inequalities. These ideas are not just paperware: in addition to academic project implementations, two variations of such algorithms are the work-horse join algorithms of commercial database and data analytics engines. This paper aims to be a brief introduction to the design and analysis of worst-case optimal join algorithms. We discuss the key techniques for proving runtime and output size bounds. We particularly focus on the fascinating connection between join algorithms and information theoretic inequalities, and the idea of how one can turn a proof into an algorithm. Finally, we conclude with a representative list of fundamental open problems in this area.
Too much of a good thing

Abstract Background There has been an increased usage of metallic antimicrobial materials to control pathogenic and multi-drug resistant bacteria. Yet, there is a corresponding need to know if this usage leads to genetic adaptations that could produce more harmful strains. Methodology Experimental evolution was used to adapt Escherichia coli K-12 MG1655 to excess iron (II) with subsequent genomic analysis. Phenotypic assays and gene expression studies were conducted to demonstrate pleiotropic effects associated with this adaptation and to elucidate potential cellular responses. Results After 200 days of adaptation, populations cultured in excess iron (II), showed a significant increase in 24-h optical densities compared to controls. Furthermore, these populations showed increased resistance toward other metals [iron (III) and gallium (III)] and to traditional antibiotics (bacitracin, rifampin, chloramphenicol and sulfanilamide). Genomic analysis identified selective sweeps in three genes; fecA, ptsP and ilvG unique to the iron (II) resistant populations, and gene expression studies demonstrated that their cellular response may be to downregulate genes involved in iron transport (cirA and fecA) while increasing the oxidative stress response (oxyR, soxS and soxR) prior to FeSO4 exposure. Conclusions and implications Together, this indicates that the selected populations can quickly adapt to stressful levels of iron (II). This study is unique in that it demonstrates that E. coli can adapt to environments that contain excess levels of an essential micronutrient while also demonstrating the genomic foundations of the response and the pleiotropic consequences. The fact that adaptation to excess iron also causes increases in general antibiotic resistance is a serious concern. Lay summary: The evolution of iron resistance in E. coli leads to multi-drug and general metal resistance through the acquisition of mutations in three genes (fecA, ptsP and ilvG) while also initiating cellular defenses as part of their normal growth process.
Vitamin D supplements: a novel therapeutic approach for Alzheimer patients

Alzheimer disease (AD) is the main cause of dementia and loss of functional independence in the elderly (Aisen, 2010; Vellas and Aisen, 2010). AD is a chronic neurodegenerative disease characterized by a progressive decline of cognitive performance with a deleterious impact on social activities. AD is a worldwide big concern because of its adverse consequences and its expanding prevalence and incidence (Aisen, 2010; Vellas and Aisen, 2010). In order to reduce AD impact at an individual level and in terms of health and social costs, the development of efficient therapeutic strategies proves necessary. Regrettably, the development of all current specific medications is unsuccessful in clinical development phases (Birks, 2006; McShane et al., 2006; Anand et al., 2014). However, an interesting fact is that the prevalence of dementia in the general population might still be subject to changes. Indeed, a reduction in the prevalence of dementia is reported among English community-dwellers over the past two decades (Matthews et al., 2013). So, even if some factors, such as the increased life expectancy beyond 80 years, are unavoidable and augment the global prevalence of dementia, others may instead reduce its prevalence. For instance, efficient primary prevention of cardio-vascular disease is suspected to explain the reduced prevalence of dementia in England (Matthews et al., 2013). In the same vein, vitamin D, an “old” molecule primarily known for its effects on the bone, has been singled out in the last decade as an important biological component able to influence the natural history of AD. Here, we wish to highlight the difficulties experienced by the research on curative treatments and, in contrast, the prospects offered by multi-target drugs, especially those based on vitamin D.
Health literacy, literacy, numeracy and nutrition label understanding and use: a scoping review of the literature

BACKGROUND Low health literacy, literacy and numeracy have been identified as barriers to consumer understanding and the interpretation of nutrition-related information. To inform policy and dietetic practice, we examined the extent, range and nature of research on empirical relationships between health literacy, literacy or numeracy and the understanding and use of nutrition labels. METHODS A scoping review of the literature was conducted. A search of eight databases on 15 April 2014 and 26 May 2016 returned 651 and 173 records, respectively. After de-duplication and two levels of relevance screening, 16 studies were deemed eligible for inclusion in the present review. RESULTS The majority of studies were conducted in the USA and focused primarily on the use of back-of-pack nutrition labels. Empirical relationships reported between health literacy and nutrition label use were inconsistent and, in some cases, contradictory. The findings from studies examining empirical relationships between literacy, numeracy and nutrition label use suggest that consumers with lower literacy and numeracy: (i) differ from those with higher levels in some of the judgements that they make about food and (ii) may benefit from interventions designed to improve their understanding and use of nutrition label information. Measurement-related issues were identified, such as a reliance on self-reports of nutrition label use, as well as a lack of independence between some measures of health literacy and nutrition label understanding and use. CONCLUSIONS The empirical relationships between health literacy, literacy, numeracy and nutrition label understanding and use have not been well-studied. Additional attention is needed regarding the measurement-related issues identified in the present review.
An optimized FAIRE procedure for low cell numbers in yeast

We report an optimized low‐input FAIRE‐seq (Formaldehyde‐Assisted Isolation of Regulatory Elements‐sequencing) procedure to assay chromatin accessibility from limited amounts of yeast cells. We demonstrate that the method performs well on as little as 4 mg of cells scraped directly from a few colonies. Sensitivity, specificity and reproducibility of the scaled‐down method are comparable with those of regular, higher input amounts, and allow the use of 100‐fold fewer cells than existing procedures. The method enables epigenetic analysis of chromatin structure without the need for cell multiplication of exponentially growing cells in liquid culture, thus opening the possibility of studying colony cell subpopulations, or those that can be isolated directly from environmental samples.
Robot portrait rendering based on multi-features fusion method inspired by human painting

Traditionally, image drawing robot draws a portrait only by generated image, without concerning the certain order of people's facial features. Therefore, to make a portrait, a robot drawing model was proposed. Through geometric and textural features generating algorithm, lines to represent the geometric contours and texture features of human face are captured. Besides, a fusion method is proposed to better strengthen the feature integrity of partial region. The lines represent geometric features and textural features are fused so that a face sketch which is more suitable for robot rendering is obtained. Experimental results show that with our rendering model, robot draws a portrait more effectively. Comparing with the previous robot drawing method, the drawn image contains more information of facial features.
TGVisor: A Tiny Hypervisor-Based Trusted Geolocation Framework for Mobile Cloud Clients

In cloud computing, geographic location of data is one of major security concerns of cloud users. To resolve this problem, most of previous work has been done on trusted relocation service in cloud service providers. For example, users are allowed to determine the physical location of their cloud servers and ensured about their requirements of relocation-based restrictions. However, it is also essential to handle trusted relocation service at cloud users' devices in mobile cloud computing. As mobile cloud tenants use cloud services everywhere, trusted relocation of cloud users arises a new security issue. Thus, in this paper, we present a novel trusted relocation system named Devisor for cloud user devices. The key mechanism of Devisor is providing a trusted channel between the relocation server and the GPS module in each mobile client device. We leverage Trusted Platform Module (TPM) and tiny hyper visor in order to securely perform the attestation of the relocation of client devices. To prove the practicality of Devisor, we design and implement a cloud word processor with trusted relocation service based on Ether pad. We also evaluate the performance of Devisor in cloud devices and show that it causes only 8.3% overhead in JavaScript benchmark, which indicates the feasibility of TGVisor.
Deformation of a Beam with Partially Debonded Piezoelectric Actuators

A linear and a non-linear mathematical models for analyzing the deformation behavior of a beam with a pair of partially debonded piezoelectric actuators are developed on the basis of the Timoshenko beam theory. Effect of buckling is considered in the linear model, where the debonded actuator region is assumed to generate the Euler buckling load when the axial force in the region is larger than the load. The static behavior of the beam is investigated for extension and bending deformation. When the actuator debonds from its edge, the performance deteriorates; in contrast, the debonding in the middle of the actuator does not show any performance degradation until the debonded region buckles. The deformation behavior obtained from the linear model has been found to have good agreement with that from the non-linear model. The non-linear analysis shows that after the buckling the debonded actuator region maintains an axial force of the order of the Euler buckling load of a fix—fix column for the extending actuation, although for the bending actuation, it retains nearly 75% of the Euler buckling load. Further, the strain distribution in the debonded region shows that the buckling may occur before cracks begin in the actuator.
Smooth Muscle Cell

P = 0.041, P = 0.028, and P = 0.002, respectively). Expression was observed in macrophages, foam cells, endothelial cells, and smooth muscle cells. Moreover, unstable plaques from men demonstrated greater features of plaque instability compared to unstable plaques from women, including hemorrhage, large lipid core, abundance of inflammatory cells, and fibrous cap infiltration by inflamma- tory cells ( P < 0.05 for all). Conclusion: Our preliminary findings indicate a possible association between androgens and the androgen receptor pathway and plaque instability. With further investigations, our ongoing work will unravel the underlying mechanisms
Centralisation of acute stroke services in London: Impact evaluation using two treatment groups

The bundling of clinical expertise in centralised treatment centres is considered an effective intervention to improve quality and efficiency of acute stroke care. In 2010, 8 London Trusts were converted into Hyper Acute Stroke Units. The intention was to discontinue acute stroke services in 22 London hospitals. However, in reality, provision of services declined only gradually, and 2 years later, 15% of all patients were still treated in Trusts without a Hyper Acute Stroke Unit. This study evaluates the impact of centralising London's stroke care on 7 process and outcome indicators using a difference-in-difference analysis with two treatment groups, Hyper Acute and discontinued London Trusts, and data on all stroke patients recorded in the hospital episode statistics database from April 2006 to April 2014. The policy resulted in improved thrombolysis treatment and lower rates of pneumonia in acute units. However, 6 indicators worsened in the Trusts that were meant to discontinue services, including deaths within 7 and 30 days, readmissions, brain scan rates, and thrombolysis treatment. The reasons for these results are difficult to uncover and could be related to differences in patient complexity, data recording, or quality of care. The findings highlight that actual implementation of centralisation policies needs careful monitoring and evaluation.
Human corneal fibrosis: an in vitro model.

PURPOSE Corneal injury may ultimately lead to a scar by way of corneal fibrosis, which is characterized by the presence of myofibroblasts and improper deposition of extracellular matrix (ECM) components. TGF-beta1 is known to stimulate overproduction and deposition of ECM components. Previously, an in vitro three-dimensional (3-D) model of a corneal stroma was developed by using primary human corneal fibroblasts (HCFs) stimulated with stable vitamin C (VitC). This model mimics corneal development. The authors postulate that with the addition of TGF-beta1, a 3-D corneal scar model can be generated. METHODS HCFs were grown in four media conditions for 4 or 8 weeks: VitC only; VitC+TGF-beta1 for the entire time; VitC+TGF-beta1 for 1 week, then VitC only for 3 or 7 weeks; and VitC for 4 weeks, then VitC+TGF-beta1 for 4 weeks. Cultures were analyzed with TEM and indirect immunofluorescence. RESULTS Compared with the control, addition of TGF-beta1 increased construct thickness significantly, with maximum increase in constructs with TGF-beta1 present for the entire time-2.1- to 3.2-fold at 4 and 8 weeks, respectively. In all TGF-beta-treated cultures, cells became long and flat, numerous filamentous cells were seen, collagen levels increased, and long collagen fibrils were visible. Smooth muscle actin, cellular fibronectin, and type III collagen expression all appeared to increase. Cultures between weeks 4 and 8 showed minimal differences. CONCLUSIONS Human corneal fibroblasts stimulated by VitC and TGF-beta1 appear to generate a model that resembles processes observed in human corneal fibrosis. This model should be useful in examining matrix deposition and assembly in a wound-healing situation.
Green Massive MIMO Scheduling for 5G Traffic with Fairness

The emergence features of 5G networks will be concentrated on an enhancement of quality of experience in conformity with SLA service contracts. Most previous massive MIMO schedulers do not take into account the traffic characteristics of 5G (different packet lengths and the arrival process parameters) and QoS (Quality of Service) requirements; consequently, they fall short of simultaneously providing fairness and a low average packet transmission delay for users. The paper addresses an important problem related to scheduling of 5G traffic in a fair and energy efficient way using a state-of-the art formulation of energy efficient scheduling. It is based on an OFDM multicarrier scheme in which all users use all subcarriers. The proposed scheme is backed by an extensive set of simulations.
Hidden alternate structures of proline isomerase essential for catalysis

A longstanding challenge is to understand at the atomic level how protein dynamics contribute to enzyme catalysis. X-ray crystallography can provide snapshots of conformational substates sampled during enzymatic reactions1, while NMR relaxation methods reveal the rates of interconversion between substates and the corresponding relative populations1,2. However, these current methods cannot simultaneously reveal the detailed atomic structures of the rare states and rationalize the finding that intrinsic motions in the free enzyme occur on a time scale similar to the catalytic turnover rate. Here we introduce dual strategies of ambient-temperature X-ray crystallographic data collection and automated electron-density sampling to structurally unravel interconverting substates of the human proline isomerase, cyclophilin A (CypA). A conservative mutation outside the active site was designed to stabilize features of the previously hidden minor conformation. This mutation not only inverts the equilibrium between the substates, but also causes large, parallel reductions in the conformational interconversion rates and the catalytic rate. These studies introduce crystallographic approaches to define functional minor protein conformations and, in combination with NMR analysis of the enzyme dynamics in solution, show how collective motions directly contribute to the catalytic power of an enzyme. It has become widely accepted that not only the chemical steps of an enzymatic reaction, but also protein conformational rearrangements contribute to the rate acceleration of enzymes1,3-6. For human CypA, a peptidyl-prolyl cis/trans isomerase, NMR relaxation experiments revealed that millisecond motions during catalysis occur in a “dynamic Users may view, print, copy, download and text and datamine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature. com/authors/editorial_policies/license.html#terms Corresponding authors: (T.A.) tom@ucxray.berkeley. edu, 510-642-8758 (V), 510-666-2768 (FAX) and (D.K.) dkern@brandeis.edu, 781-736-2354 (V), 781-736-2316 (FAX). JSF, SD, and RE performed the X-ray experiments, MWC performed the NMR experiments, and MWC and JSF performed the activity and binding assays. JSF, MWC, DK, and TA analyzed data and wrote the paper. All authors contributed to data interpretation and commented on the manuscript. Supplementary Information accompanies the paper. Atomic coordinates and structure factors for the reported crystal structures have been deposited in the PDB under accession codes (3K0M, 3K0N, 3K0O, 3K0P, 3K0Q, and 3K0R). The authors declare no competing financial interest. HHS Public Access Author manuscript Nature. Author manuscript; available in PMC 2010 June 03. Published in final edited form as: Nature. 2009 December 3; 462(7273): 669–673. doi:10.1038/nature08615. A uhor M anscript