Miracle-dz/UniFAR-FTUs huggingface dataset:
Generation and Characterization of a Defective HIV-1 Virus as an Immunogen for a Therapeutic Vaccine

Background The generation of new immunogens able to elicit strong specific immune responses remains a major challenge in the attempts to obtain a prophylactic or therapeutic vaccine against HIV/AIDS. We designed and constructed a defective recombinant virus based on the HIV-1 genome generating infective but non-replicative virions able to elicit broad and strong cellular immune responses in HIV-1 seropositive individuals. Results Viral particles were generated through transient transfection in producer cells (293-T) of a full length HIV-1 DNA carrying a deletion of 892 base pairs (bp) in the pol gene encompassing the sequence that codes for the reverse transcriptase (NL4-3/ΔRT clone). The viral particles generated were able to enter target cells, but due to the absence of reverse transcriptase no replication was detected. The immunogenic capacity of these particles was assessed by ELISPOT to determine γ-interferon production in a cohort of 69 chronic asymptomatic HIV-1 seropositive individuals. Surprisingly, defective particles produced from NL4-3/ΔRT triggered stronger cellular responses than wild-type HIV-1 viruses inactivated with Aldrithiol-2 (AT-2) and in a larger proportion of individuals (55% versus 23% seropositive individuals tested). Electron microscopy showed that NL4-3/ΔRT virions display immature morphology. Interestingly, wild-type viruses treated with Amprenavir (APV) to induce defective core maturation also induced stronger responses than the same viral particles generated in the absence of protease inhibitors. Conclusions We propose that immature HIV-1 virions generated from NL4-3/ΔRT viral clones may represent new prototypes of immunogens with a safer profile and stronger capacity to induce cellular immune responses than wild-type inactivated viral particles.
A Cation-Chloride Cotransporter Gene Is Required for Cell Elongation and Osmoregulation in Rice1[OPEN]

OsCCC1 functions as a K+, Na+, and Cl− cotransporter in rice to maintain osmotic potential for cell elongation through increasing internal solute concentrations. Rice (Oryza sativa) is characterized by having fibrous root systems; however, the molecular mechanisms underlying the root development are not fully understood. Here, we isolated a rice mutant with short roots and found that the mutant had a decreased cell size of the roots and shoots compared with wild-type rice. Map-based cloning combined with whole-genome sequencing revealed that a single nucleotide mutation occurred in a gene, which encodes a putative cation-chloride cotransporter (OsCCC1). Introduction of OsCCC1 cDNA into the mutant rescued the mutant growth, indicating that growth defects of both the roots and shoots are caused by loss of function of OsCCC1. Physiological analysis showed that the mutant had a lower concentration of Cl− and K+ and lower osmolality in the root cell sap than the wild type at all KCl supply conditions tested; however, the mutant only showed a lower Na+ concentration at high external Na+. Expression of OsCCC1 in yeast increased accumulation of K+, Na+, and Cl−. The expression of OsCCC1 was found in both the roots and shoots, although higher expression was found in the root tips. Furthermore, the expression in the roots did not respond to different Na+, K+, and Cl− supply. OsCCC1 was expressed in all cells of the roots, leaf, and basal node. Immunoblot analysis revealed that OsCCC1 was mainly localized to the plasma membrane. These results suggest that OsCCC1 is involved in the cell elongation by regulating ion (Cl−, K+, and Na+) homeostasis to maintain cellular osmotic potential.
Requirements and Specifications for Robots, Linked Data and all the REST

The use of autonomous robots in both industry and every day life has increased significantly in the recent years. A growing number of robots is connected to and operated from networks, including the World Wide Web. Consequently, the Robotics community is exploring and adopting REST (Representational State Transfer) architectural principles and considers the use of Linked Data technologies as fruitful next step. However, we observe a lack of concise and stable specifications of how to properly leverage the RESTful paradigm and Linked Data concepts in the Robotics domain. Introducing the notion of Linked Robotic Things, we provide a minimalistic, yet well-defined specification covering a minimal set of requirements with respect to the use of HTTP and RDF.
Detailed Source-Specific Molecular Composition of Ambient Aerosol Organic Matter Using Ultrahigh Resolution Mass Spectrometry and 1H NMR

Organic aerosols (OA) are universally regarded as an important component of the atmosphere that have far-ranging impacts on climate forcing and human health. Many of these impacts are related to OA molecular characteristics. Despite the acknowledged importance, current uncertainties related to the source apportionment of molecular properties and environmental impacts make it difficult to confidently predict the net impacts of OA. Here we evaluate the specific molecular compounds as well as bulk structural properties of total suspended particulates in ambient OA collected from key emission sources (marine, biomass burning, and urban) using ultrahigh resolution mass spectrometry (UHR-MS) and proton nuclear magnetic resonance spectroscopy (1H NMR). UHR-MS and 1H NMR show that OA within each source is structurally diverse, and the molecular characteristics are described in detail. Principal component analysis (PCA) revealed that (1) aromatic nitrogen species are distinguishing components for these biomass burning aerosols; (2) these urban aerosols are distinguished by having formulas with high O/C ratios and lesser aromatic and condensed aromatic formulas; and (3) these marine aerosols are distinguished by lipid-like compounds of likely marine biological origin. This study provides a unique qualitative approach for enhancing the chemical characterization of OA necessary for molecular source apportionment.
Advanced Copper Composites Against Copper-Tolerant Xanthomonas perforans and Tomato Bacterial Spot.

Bacterial spot, caused by Xanthomonas spp. , is a widespread and damaging bacterial disease of tomato (Solanum lycopersicum). For disease management, growers rely on copper bactericides, which are often ineffective due to the presence of copper-tolerant Xanthomonas strains. This study evaluated the antibacterial activity of the new copper composites core-shell copper (CS-Cu), multivalent copper (MV-Cu), and fixed quaternary ammonium copper (FQ-Cu) as potential alternatives to commercially available micron-sized copper bactericides for controlling copper-tolerant Xanthomonas perforans. In vitro, metallic copper from CS-Cu and FQ-Cu at 100 μg/ml killed the copper-tolerant X. perforans strain within 1 h of exposure. In contrast, none of the micron-sized copper rates (100 to 1,000 μg/ml) from Kocide 3000 significantly reduced copper-tolerant X. perforans populations after 48 h of exposure compared with the water control (P < 0.05). All copper-based treatments killed the copper-sensitive X. perforans strain within 1 h. Greenhouse studies demonstrated that all copper composites significantly reduced bacterial spot disease severity when compared with copper-mancozeb and water controls (P < 0.05). Although there was no significant impact on yield, copper composites significantly reduced disease severity when compared with water controls, using 80% less metallic copper in comparison with copper-mancozeb in field studies (P < 0.05). This study highlights the discovery that copper composites have the potential to manage copper-tolerant X. perforans and tomato bacterial spot.
A Step towards Advanced Metering for the Smart Grid: A Survey of Energy Monitors

-The smart grid initiative has encouraged utility companies worldwide to rollout new and smarter versions of energy meters. Before an extensive rollout, which is both laborintensive and incurs high capital costs, consumers need to be incentivized to reap the long-term benefits of smart grid. Off-theshelf energy monitors can provide consumers with an insight of such potential benefits. Since energy monitors are owned by the consumer, the consumer has greater control over data which significantly reduces privacy and data confidentiality concerns. We evaluate several existing energy monitors using an online technical survey and online product literature. For consumers, the use of different off-the-shelf energy monitors can help demonstrate the potential gains of smart grid. Our survey indicates a trend towards incorporation of state-of-the-art capabilities, like appliance level monitoring through load disaggregation in energy monitors, which can encourage effective consumer participation. Multiple sensor types and ratings allow some monitors to operate in various configurations and environments.
Epitope Mapping of Metuximab on CD147 Using Phage Display and Molecular Docking

Metuximab is the generic name of Licartin, a new drug for radioimmunotherapy of hepatocellular carcinoma. Although it is known to be a mouse monoclonal antibody against CD147, the complete epitope mediating the binding of metuximab to CD147 remains unknown. We panned the Ph.D.-12 phage display peptide library against metuximab and got six mimotopes. The following bioinformatics analysis based on mimotopes suggested that metuximab recognizes a conformational epitope composed of more than 20 residues. The residues of its epitope may include T28, V30, K36, L38, K57, F74, D77, S78, D79, D80, Q81, G83, S86, N98, Q100, L101, H102, G103, P104, V131, P132, and K191. The homology modeling of metuximab and the docking of CD147 to metuximab were also performed. Based on the top one docking model, the epitope was predicted to contain 28 residues: AGTVFTTV (23–30), I37, D45, E84, V88, EPMGTANIQLH (92–102), VPP (131–133), Q164, and K191. Almost half of the residues predicted on the basis of mimotope analysis also appear in the docking result, indicating that both results are reliable. As the predicted epitopes of metuximab largely overlap with interfaces of CD147-CD147 interactions, a structural mechanism of metuximab is proposed as blocking the formation of CD147 dimer.
TumorNext: A comprehensive tumor profiling assay that incorporates high resolution copy number analysis and germline status to improve testing accuracy

The development of targeted therapies for both germline and somatic DNA mutations has increased the need for molecular profiling assays to determine the mutational status of specific genes. Moreover, the potential of off-label prescription of targeted therapies favors classifying tumors based on DNA alterations rather than traditional tissue pathology. Here we describe the analytical validation of a custom probe-based NGS tumor panel, TumorNext, which can detect single nucleotide variants, small insertions and deletions in 142 genes that are frequently mutated in somatic and/or germline cancers. TumorNext also detects gene fusions and structural variants, such as tandem duplications and inversions, in 15 frequently disrupted oncogenes and tumor suppressors. The assay uses a matched control and custom bioinformatics pipeline to differentiate between somatic and germline mutations, allowing precise variant classification. We tested 170 previously characterized samples, of which > 95% were formalin-fixed paraffin embedded tissue from 8 different cancer types, and highlight examples where lack of germline status may have led to the inappropriate prescription of therapy. We also describe the validation of the Affymetrix OncoScan platform, an array technology for high resolution copy number variant detection for use in parallel with the NGS panel that can detect single copy amplifications and hemizygous deletions. We analyzed 80 previously characterized formalin-fixed paraffin-embedded specimens and provide examples of hemizygous deletion detection in samples with known pathogenic germline mutations. Thus, the TumorNext combined approach of NGS and OncoScan potentially allows for the identification of the “second hit” in hereditary cancer patients.
A Comparison of Honey Bee-Collected Pollen From Working Agricultural Lands Using Light Microscopy and ITS Metabarcoding

Abstract Taxonomic identification of pollen has historically been accomplished via light microscopy but requires specialized knowledge and reference collections, particularly when identification to lower taxonomic levels is necessary. Recently, next-generation sequencing technology has been used as a cost-effective alternative for identifying bee-collected pollen; however, this novel approach has not been tested on a spatially or temporally robust number of pollen samples. Here, we compare pollen identification results derived from light microscopy and DNA sequencing techniques with samples collected from honey bee colonies embedded within a gradient of intensive agricultural landscapes in the Northern Great Plains throughout the 2010–2011 growing seasons. We demonstrate that at all taxonomic levels, DNA sequencing was able to discern a greater number of taxa, and was particularly useful for the identification of infrequently detected species. Importantly, substantial phenological overlap did occur for commonly detected taxa using either technique, suggesting that DNA sequencing is an appropriate, and enhancing, substitutive technique for accurately capturing the breadth of bee-collected species of pollen present across agricultural landscapes. We also show that honey bees located in high and low intensity agricultural settings forage on dissimilar plants, though with overlap of the most abundantly collected pollen taxa. We highlight practical applications of utilizing sequencing technology, including addressing ecological issues surrounding land use, climate change, importance of taxa relative to abundance, and evaluating the impact of conservation program habitat enhancement efforts.
Recessive TAF1A mutations reveal ribosomopathy in siblings with end-stage pediatric dilated cardiomyopathy

Non-ischemic dilated cardiomyopathy (DCM) has been recognized as a heritable disorder for over 25 years, yet clinical genetic testing is non-diagnostic in >50% of patients, underscoring the ongoing need for DCM gene discovery. Here, whole exome sequencing uncovered a novel molecular basis for idiopathic end-stage heart failure in two sisters who underwent cardiac transplantation at three years of age. Compound heterozygous recessive mutations in TAF1A, encoding an RNA polymerase I complex protein, were associated with marked fibrosis of explanted hearts and gene-specific nucleolar segregation defects in cardiomyocytes, indicative of impaired ribosomal RNA synthesis. Knockout of the homologous gene in zebrafish recapitulated a heart failure phenotype with pericardial edema, decreased ventricular systolic function, and embryonic mortality. These findings expand the clinical spectrum of ribosomopathies to include pediatric DCM.
The Clustered, Regularly Interspaced, Short Palindromic Repeats-associated Endonuclease 9 (CRISPR/Cas9)-created MDM2 T309G Mutation Enhances Vitreous-induced Expression of MDM2 and Proliferation and Survival of Cells*

The G309 allele of SNPs in the mouse double minute (MDM2) promoter locus is associated with a higher risk of cancer and proliferative vitreoretinopathy (PVR), but whether SNP G309 contributes to the pathogenesis of PVR is to date unknown. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonuclease (Cas) 9 from Streptococcus pyogenes (SpCas9) can be harnessed to manipulate a single or multiple nucleotides in mammalian cells. Here we delivered SpCas9 and guide RNAs using dual adeno-associated virus-derived vectors to target the MDM2 genomic locus together with a homologous repair template for creating the mutation of MDM2 T309G in human primary retinal pigment epithelial (hPRPE) cells whose genotype is MDM2 T309T. The next-generation sequencing results indicated that there was 42.51% MDM2 G309 in the edited hPRPE cells using adeno-associated viral CRISPR/Cas9. Our data showed that vitreous induced an increase in MDM2 and subsequent attenuation of p53 expression in MDM2 T309G hPRPE cells. Furthermore, our experimental results demonstrated that MDM2 T309G in hPRPE cells enhanced vitreous-induced cell proliferation and survival, suggesting that this SNP contributes to the pathogenesis of PVR.
Applications of Combinatorial Testing Methods for Breakthrough Results in Software Testing

In last three decades, lot of research work has been done by statisticians and academicians (D. Richard Kuhn, Raghu N. Kacker, Vu Lei, Ljubomir Lazic, Sloane, Neil J. A., Madhav Phadke, D. M. Cohen, James Bach and others) in the field of Combinatorial testing (CT) and its use in software testing. However, its tremendous potential in terms of test optimization and fault detection is yet to be exploited to its fullest. This paper showcases some of the real-world examples from iGATE Corporation, where CT has been used successfully to achieve breakthrough results in software testing. The paper, through three case studies taken from different domains describes the challenges faced by testing teams in terms of test scenario complexities, schedule and budget constraints; and how CT helped resolve those challenges successfully. Our experience shows 60 to 70 percent benefits in terms of optimization of test efforts while enhancing test case coverage. In the end, the paper highlights some learnings from our experiences in implementing CT approach which may be of help to fellow practitioners.
DTA and p VT Measurements on 4-cyanobenzyI-5- (4-n-octyloxybenzoyloxy)-2-undecyloxybenzoate up to 250 MPa and 383 K

Abstract The phase diagram of 4-cyanobenzyl-5-(4-«-octyloxybenzoyloxy)-2-undecyloxybenzoate (4CNOUB) has been established with differential thermal analysis (DTA). The pressure range for the smectic A phase is limited, resulting in a triple point at 165 MPa and 378.26 K. p, Vm, T data have been measured for the smectic and istotropic phases of 4CNOUB between 243 and 383 K and up to 250 MPa. The volume changes accompanying the crystal - smectic and scmectic - isotropic transitions have been deter-mined. The corresponding enthalpy changes have been calculated using the Clausius-Clapeyron equation. The p, Vm, T data enable also to estimate the volume entropy for the smectic - isotropic transition and the volume dependence of the clearing temperature.
Graph Similarity and Approximate Isomorphism

The graph similarity problem, also known as approximate graph isomorphism or graph matching problem, has been extensively studied in the machine learning community, but has not received much attention in the algorithms community: Given two graphs $G,H$ of the same order $n$ with adjacency matrices $A_G,A_H$, a well-studied measure of similarity is the Frobenius distance \[ \mathrm{dist}(G,H):=\min_{\pi}\|A_G^\pi-A_H\|_F, \] where $\pi$ ranges over all permutations of the vertex set of $G$, where $A_G^\pi$ denotes the matrix obtained from $A_G$ by permuting rows and columns according to $\pi$, and where $\|M\|_F$ is the Frobenius norm of a matrix $M$. The (weighted) graph similarity problem, denoted by SIM (WSIM), is the problem of computing this distance for two graphs of same order. This problem is closely related to the notoriously hard quadratic assignment problem (QAP), which is known to be NP-hard even for severely restricted cases. It is known that SIM (WSIM) is NP-hard; we strengthen this hardness result by showing that the problem remains NP-hard even for the class of trees. Identifying the boundary of tractability for WSIM is best done in the framework of linear algebra. We show that WSIM is NP-hard as long as one of the matrices has unbounded rank or negative eigenvalues: hence, the realm of tractability is restricted to positive semi-definite matrices of bounded rank. Our main result is a polynomial time algorithm for the special case where one of the matrices has a bounded clustering number, a parameter arising from spectral graph drawing techniques.
Effect of central corneal thickness on intraocular pressure and comparison of Topcon CT‐80 non‐contact tonometry with Goldmann applanation tonometry

To compare intraocular pressure (IOP) measurements obtained with the Topcon CT‐80 non‐contact tonometer (NCT) and Goldmann applanation tonometer (GAT), in different ranges of IOP in normal and glaucoma subjects, and to assess the influence of central corneal thickness (CCT) on the IOP measurements in Asian Indian eyes.
Privacy Policy Inference for Social Images

Social networking has become an indivisible part of the modern lifestyle. It plays a crucial role in our daily lives. It allows us to communicate with numerous individuals.Popular social networking sites such as Facebook1, LinkedIn2 allow people to get connected from diverse geographic locations. Existing and the emerging social media sites empower users to utilize various interesting features such as sharing photos or information with as many friends as they want, commenting on a text or picture, creating groups and so on. Privacy settings offered by these sites come into picture when a user may not want to share his profile globally or with certain people. Privacy violation is an important issue that needs to be addressed while being active on any social networking site. If the privacy settings provided by the respective site are inadequate, then people may invade your privacy and misuse your information. Going towards this need, utilizing system to compose privacy settings for user’s images is important. Further, the privacy inference policies should be maintained with respect to user profile. Hence, we have decided to develop a system that will help the user to maintain security for images he/she has uploaded on a content sharing site.
Decreased TCL6 expression is associated with poor prognosis in patients with clear cell renal cell carcinoma

One-third of clear cell renal cell carcinoma (ccRCC) patients present with metastasis at the time of diagnosis. The prognosis of these patients is poor. To identify potential prognostic biomarkers and therapeutic targets for ccRCC, we re-evaluated published long non-coding RNA (lncRNA) expression profiling data from the Gene Expression Omnibus and ArrayExpress database. We found that five lncRNAs were differentially expressed in ccRCC and adjacent tissues. These lncRNAs were assessed in an independent cohort of 71 paired patient samples using real-time PCR. Differences in expression of three of the lncRNAs (ENSG00000177133, TCL6, and ENSG00000244020) were validated in this analysis. Kaplan-Meier analysis indicated that low expression of ENSG00000177133 and TCL6 was associated with a poor prognosis. Univariate and multivariate regression analyses demonstrated that TCL6 but not ENSG00000177133 expression was an independent predictor of ccRCC aggressiveness and had hazard ratios predictive of clinical outcome. TCL6 expression was negatively correlated with pTNM stage. Overexpression of TCL6 in 786-O and Caki-1 ccRCC cells decreased proliferation and increased apoptosis compared to controls. Our results indicate that lncRNA expression is altered in ccRCC and that decreased TCL6 expression may be an independent adverse prognostic factor in ccRCC patients.
Event triggered control scheme for power converters

The work aims to leverage event triggered controller for power converters to achieve better performance and to improve overall efficiency of the system. It presents a control implementation scheme which is event based and can be applied to nonlinear systems with a stabilizing feedback. In this scheme, the control input signal is held constant, not periodically, but while the performance is satisfactory. In this paper, an existing classical Sliding Mode Control (SMC), which regulates a Buck converter, is made event-triggered to demonstrate the effectiveness of the proposed strategy. Complete analysis is done to prove the feasibility of the technique for practical application and simulations have been carried out to support the theoretical claims.