Miracle-dz/UniFAR-FTUs huggingface dataset:
Detargeting Lentiviral-Mediated CFTR Expression in Airway Basal Cells Using miR-106b

Lentiviral-mediated integration of a CFTR transgene cassette into airway basal cells is a strategy being considered for cystic fibrosis (CF) cell-based therapies. However, CFTR expression is highly regulated in differentiated airway cell types and a subset of intermediate basal cells destined to differentiate. Since basal stem cells typically do not express CFTR, suppressing the CFTR expression from the lentiviral vector in airway basal cells may be beneficial for maintaining their proliferative capacity and multipotency. We identified miR-106b as highly expressed in proliferating airway basal cells and extinguished in differentiated columnar cells. Herein, we developed lentiviral vectors with the miR-106b-target sequence (miRT) to both study miR-106b regulation during basal cell differentiation and detarget CFTR expression in basal cells. Given that miR-106b is expressed in the 293T cells used for viral production, obstacles of viral genome integrity and titers were overcome by creating a 293T-B2 cell line that inducibly expresses the RNAi suppressor B2 protein from flock house virus. While miR-106b vectors effectively detargeted reporter gene expression in proliferating basal cells and following differentiation in the air–liquid interface and organoid cultures, the CFTR-miRT vector produced significantly less CFTR-mediated current than the non-miR-targeted CFTR vector following transduction and differentiation of CF basal cells. These findings suggest that miR-106b is expressed in certain airway cell types that contribute to the majority of CFTR anion transport in airway epithelium.
Feasibility of management of hemodynamically stable patients with acute myocardial infarction following primary percutaneous coronary intervention in the general ward settings

Background Although current guidelines recommend admission to the intensive/coronary care unit (ICU/CCU) for patients with ST-segment elevation myocardial infarction (MI), routine use of the CCU in uncomplicated patients with acute MI remains controversial. We aimed to evaluate the safety of management in the general ward (GW) of hemodynamically stable patients with acute MI after primary percutaneous coronary intervention (PCI). Methods Using a large nationwide administrative database, a cohort of 19426 patients diagnosed with acute MI in 52 hospitals where a CCU was available were retrospectively analyzed. Patients with mechanical cardiac support and Killip classification 4, and those without primary PCI on admission were excluded. A total of 5736 patients were included and divided into the CCU (n = 3488) and GW (n = 2248) groups according to the type of hospitalization room after primary PCI. Propensity score matching was performed, and 1644 pairs were matched. The primary endpoint was in-hospital mortality at 30 days. Results The CCU group had a higher rate of Killip classification 3 and ambulance use than the GW group. There was no significant difference in the incidence of in-hospital mortality within 30 days among the matched subjects. Multivariable Cox proportional hazard model analysis among unmatched patients supported the findings (hazard ratio 1.12, 95% confidence interval 0.66–1.91, p = 0.67). Conclusions The use of the GW was not associated with higher in-hospital mortality in hemodynamically stable patients with acute MI after primary PCI. It may be feasible for the selected patients to be directly admitted to the GW after primary PCI.
New technologies in developing recombinant‐attenuated bacteria for cancer therapy

Cancer has always been a global problem, with more cases of cancer patients being diagnosed every year. Conventional cancer treatments, including radiotherapy, chemotherapy, and surgery, are still unable to bypass their obvious limitations, and developing effective targeted therapies is still required. More than one century ago, the doctor William B. Coley discovered that cancer patients had tumor regression by injection of Streptococcus bacteria. The studies of cancer therapy using bacterial microorganisms are now very widespread. In particular, the facultative anaerobic bacteria Salmonella typhimurium is widely investigated as it can selectively colonize different types of tumors, locally deliver various antitumor drugs, and inhibit tumor growth. The exciting antitumor efficacy and safety observed in animal tumor models prompted the well‐known attenuated Salmonella bacterial strain VNP20009 to be tested in human clinical trials in the early 21st century. Regrettably, no patients showed significant therapeutic effects and even bacterial colonization in tumor tissue was undetectable in most patients. Salmonella bacteria are still considered as a promising agent or vehicle for cancer therapy. Recent efforts have been focused on the generation of attenuated bacterial strains with higher targeting for tumor tissue, and optimization of the delivery of therapeutic antitumor cargoes into the tumor microenvironment. This review will summarize new technologies or approaches that may improve bacteria‐mediated cancer therapy.
Identification of key features required for efficient S-acylation and plasma membrane targeting of sprouty-2

ABSTRACT Sprouty-2 is an important regulator of growth factor signalling and a tumour suppressor protein. The defining feature of this protein is a cysteine-rich domain (CRD) that contains twenty-six cysteine residues and is modified by S-acylation. In this study, we show that the CRD of sprouty-2 is differentially modified by S-acyltransferase enzymes. The high specificity/low activity zDHHC17 enzyme mediated restricted S-acylation of sprouty-2, and cysteine-265 and -268 were identified as key targets of this enzyme. In contrast, the low specificity/high activity zDHHC3 and zDHHC7 enzymes mediated more expansive modification of the sprouty-2 CRD. Nevertheless, S-acylation by all enzymes enhanced sprouty-2 expression, suggesting that S-acylation stabilises this protein. In addition, we identified two charged residues (aspartate-214 and lysine-223), present on opposite faces of a predicted α-helix in the CRD, which are essential for S-acylation of sprouty-2. Interestingly, mutations that perturbed S-acylation also led to a loss of plasma membrane localisation of sprouty-2 in PC12 cells. This study provides insight into the mechanisms and outcomes of sprouty-2 S-acylation, and highlights distinct patterns of S-acylation mediated by different classes of zDHHC enzymes. Highlighted Article: S-acylation of the tumour suppressor protein sprouty-2 requires specific cysteine and charged residues in the cysteine-rich domain, and regulates plasma membrane targeting.
The role and economics of immunotherapy in solid tumour management

Cancer therapeutics is a rapidly changing field which offers patients the prospect of a better quality of life and cure. Immunotherapy has become a unique approach for select metastatic solid tumours. While initial results do show durable responses in select patients, there are concerns on how best to utilise this expensive resource which can result in costly side effects and in whom the use of biomarkers to stratify patients is still in its infancy. Given the ageing population and extreme challenges on healthcare, economic modelling with regards to immunotherapy is imperative especially now when it is being considered for further cancer types.
Kerberos: An Authentication Service for Open Network Systems

In an open network computing environment, a workstation cannot be trusted to identify its users correctly to network services. Kerberos provides an alternative approach whereby a trusted third-party authentication service is used to verify users' identities. This paper gives an overview of the Kerberos authentication model as imple- mented for MIT's Project Athena. It describes the protocols used by clients, servers, and Kerberos to achieve authentication. It also describes the management and replication of the database required. The views of Kerberos as seen by the user, programmer, and administrator are described. Finally, the role of Kerberos in the larger Athena picture is given, along with a list of applications that presently use Kerberos for user authentica- tion. We describe the addition of Kerberos authentication to the Sun Network File Sys- tem as a case study for integrating Kerberos with an existing application.
Wine Yeast Peroxiredoxin TSA1 Plays a Role in Growth, Stress Response and Trehalose Metabolism in Biomass Propagation

Peroxiredoxins are a family of peroxide-degrading enzymes for challenging oxidative stress. They receive their reducing power from redox-controlling proteins called thioredoxins, and these, in turn, from thioredoxin reductase. The main cytosolic peroxiredoxin is Tsa1, a moonlighting protein that also acts as protein chaperone a redox switch controlling some metabolic events. Gene deletion of peroxiredoxins in wine yeasts indicate that TSA1, thioredoxins and thioredoxin reductase TRR1 are required for normal growth in medium with glucose and sucrose as carbon sources. TSA1 gene deletion also diminishes growth in molasses, both in flasks and bioreactors. The TSA1 mutation brings about an expected change in redox parameters but, interestingly, it also triggers a variety of metabolic changes. It influences trehalose accumulation, lowering it in first molasses growth stages, but increasing it at the end of batch growth, when respiratory metabolism is set up. Glycogen accumulation at the entry of the stationary phase also increases in the tsa1Δ mutant. The mutation reduces fermentative capacity in grape juice, but the vinification profile does not significantly change. However, acetic acid and acetaldehyde production decrease when TSA1 is absent. Hence, TSA1 plays a role in the regulation of metabolic reactions leading to the production of such relevant enological molecules.
Is the Secret of VDAC Isoforms in Their Gene Regulation? Characterization of Human VDAC Genes Expression Profile, Promoter Activity, and Transcriptional Regulators

VDACs (voltage-dependent anion-selective channels) are pore-forming proteins of the outer mitochondrial membrane, whose permeability is primarily due to VDACs’ presence. In higher eukaryotes, three isoforms are raised during the evolution: they have the same exon–intron organization, and the proteins show the same channel-forming activity. We provide a comprehensive analysis of the three human VDAC genes (VDAC1–3), their expression profiles, promoter activity, and potential transcriptional regulators. VDAC isoforms are broadly but also specifically expressed in various human tissues at different levels, with a predominance of VDAC1 and VDAC2 over VDAC3. However, an RNA-seq cap analysis gene expression (CAGE) approach revealed a higher level of transcription activation of VDAC3 gene. We experimentally confirmed this information by reporter assay of VDACs promoter activity. Transcription factor binding sites (TFBSs) distribution in the promoters were investigated. The main regulators common to the three VDAC genes were identified as E2F-myc activator/cell cycle (E2FF), Nuclear respiratory factor 1 (NRF1), Krueppel-like transcription factors (KLFS), E-box binding factors (EBOX) transcription factor family members. All of them are involved in cell cycle and growth, proliferation, differentiation, apoptosis, and metabolism. More transcription factors specific for each VDAC gene isoform were identified, supporting the results in the literature, indicating a general role of VDAC1, as an actor of apoptosis for VDAC2, and the involvement in sex determination and development of VDAC3. For the first time, we propose a comparative analysis of human VDAC promoters to investigate their specific biological functions. Bioinformatics and experimental results confirm the essential role of the VDAC protein family in mitochondrial functionality. Moreover, insights about a specialized function and different regulation mechanisms arise for the three isoform gene.
Questioning Cause and Effect: Children with Severe Asthma Exhibit High Levels of Inflammatory Biomarkers Including Beta-Hexosaminidase, but Low Levels of Vitamin A and Immunoglobulins

Asthma affects over 8% of the pediatric population in the United States, and Memphis, Tennessee has been labeled an asthma capital. Plasma samples were analyzed for biomarker profiles from 95 children with severe asthma and 47 age-matched, hospitalized nonasthmatic controls at Le Bonheur Children’s Hospital in Memphis, where over 4000 asthmatics are cared for annually. Asthmatics exhibited significantly higher levels of periostin, surfactant protein D, receptor for advanced glycation end products and β-hexosaminidase compared to controls. Children with severe asthma had lower levels of IgG1, IgG2 and IgA, and higher levels of IgE compared to controls, and approximately half of asthmatics exhibited IgG1 levels that were below age-specific norms. Vitamin A levels, measured by the surrogate retinol-binding protein, were insufficient or deficient in most asthmatic children, and correlated positively with IgG1. Which came first, asthma status or low levels of vitamin A and immunoglobulins? It is likely that inflammatory disease and immunosuppressive drugs contributed to a reduction in vitamin A and immunoglobulin levels. However, a nonmutually exclusive hypothesis is that low dietary vitamin A caused reductions in immune function and rendered children vulnerable to respiratory disease and consequent asthma pathogenesis. Continued attention to nutrition in combination with the biomarker profile is recommended to prevent and treat asthma in vulnerable children.
High‐throughput evolutionary optimization of the induction medium towards recombinant protein production in BY‐2 tobacco

Bright yellow (BY‐2) tobacco cells combined with the XVE chemically inducible system are one of the most promising plant‐based platforms for recombinant protein production. This offers a range of benefits, including the separation of the cell growth and heterologous gene expression, lack of risk of infecting the end product with prions and human viruses or appropriate protein glycosylation and folding. However, low protein productivity remains a major obstacle that limits the extensive commercialization of bioproduction in plants. A number of molecular, cell culture and down processing approaches have been made to overcome this problem. Media development for the specific nutritional and hormonal requirements of transgenic plant cells is one of the most efficient cell‐culture approaches. We optimized the induction medium towards recombinant protein production in BY‐2 and demonstrated the usefulness of evolutionary medium optimization for high‐yield protein production in liquid plant cultures. A reliable XVE/GFP model, parallel conducting experiments in a microscale on 96‐well plates, and dedicated Gene Game evolutionary optimization software allowed for an effective search of 7611 possible solutions of 11‐component media. Within the 4608 formulations tested, the Induct X medium was found with a significant 107.14% increase in protein expression in relation to the standard BY‐2 medium.
Constitutive Expression of Arabidopsis Senescence Associated Gene 101 in Brachypodium distachyon Enhances Resistance to Puccinia brachypodii and Magnaporthe oryzae

Brachypodium distachyon, as an effective model of cereal grains, is susceptible to most destructive cereal pathogens. Senescence associated gene 101 (SAG101) has been studied extensively in Arabidopsis. SAG101 is one of the important regulators of plant immunity. However, no homologous genes of AtSAG101 were found in B. distachyon. In this study, the AtSAG101 gene was transformed into B. distachyon. Three transgenic plant lines containing the AtSAG101 gene were confirmed by PCR and GUS gene activity. There were fewer Puccinia brachypodii urediospores in the AtSAG101-overexpressing plants compared to wild type plants. P. brachypodii biomass was obviously decreased in AtSAG101 transgenic plants. The length of infection hyphae and infection unit areas of P. brachypodii were significantly limited in transgenic plants. Moreover, there were small lesions in AtSAG101 transgenic plants challenged by Magnaporthe oryzae. Salicylic acid accumulation was significantly increased, which led to elevated pathogenesis-related gene expression in transgenic B. distachyon inoculated by P. brachypodii or M. oryzae compared to wild type plants. These results were consistent with infected phenotypes. Overexpression of AtSAG101 in B. distachyon caused resistance to M. oryzae and P. brachypodii. These results suggest that AtSAG101 could regulate plant resistance in B. distachyon.
Distinguishing Features of High- and Low-Dose Vaccine against Ocular HSV-1 Infection Correlates with Recognition of Specific HSV-1–Encoded Proteins

The protective efficacy of a live-attenuated HSV type 1 (HSV-1) vaccine, HSV-1 0∆ nuclear location signal (NLS), was evaluated in mice prophylactically in response to ocular HSV-1 challenge. Mice vaccinated with the HSV-1 0∆NLS were found to be more resistant to subsequent ocular virus challenge in terms of viral shedding, spread, the inflammatory response, and ocular pathology in a dose-dependent fashion. Specifically, a strong neutralizing Ab profile associated with low virus titers recovered from the cornea and trigeminal ganglia was observed in vaccinated mice in a dose-dependent fashion with doses ranging from 1 × 103 to 1 × 105 PFU HSV-1 0∆NLS. This correlation also existed in terms of viral latency in the trigeminal ganglia, corneal neovascularization, and leukocyte infiltration and expression of inflammatory cytokines and chemokines in infected tissue with the higher doses (1 × 104–1 × 105 PFU) of the HSV-1 0∆NLS–vaccinated mice, displaying reduced viral latency, ocular pathology, or inflammation in comparison with the lowest dose (1 × 103 PFU) or vehicle vaccine employed. Fifteen HSV-1–encoded proteins were uniquely recognized by antisera from high-dose (1 × 105 PFU)–vaccinated mice in comparison with low-dose (1 × 103 PFU)– or vehicle-vaccinated animals. Passive immunization using high-dose–vaccinated, but not low-dose–vaccinated, mouse sera showed significant efficacy against ocular pathology in HSV-1–challenged animals. In summary, we have identified the minimal protective dose of HSV-1 0∆NLS vaccine in mice to prevent HSV-mediated disease and identified candidate proteins that may be useful in the development of a noninfectious prophylactic vaccine against the insidious HSV-1 pathogen.
Genetic Variability in Morus alba L by Biochemical and Bioassay Methods for increased Silk Productivity

The object of this study is to screen biochemical content of six varieties of mulberry leaves viz S13, S30, S36, ML, V1 and RFS-135 to find out nutritively richer one. Among six varieties V1 is the best one containing highest total sugar (16.72%), total protein (26.72%) and total phenol (4.56%) content compare to other five varieties, so V1 is the highly recommendable feed for silkworm (Bombyx mori L) to increase their silk productivity. Silkworms feeded with nutritively richer V1 variety were taken for the following biochemical and bioassay. Protein estimation in larval, pupal haemolymph and also in silkgland, enzymatic (amylase, protease) analysis of different (II to V) instars larvae. Likewise fibroin sericin ratios in cocoon were also done. The all the above parameters of silkworm (Bombyx mori L) feeded with V1 variety was found to be high and silk productivity was also high, which will fulfill existing market demand.
BALANCED SCORECARD AS A STRATEGIC TOOL FOR MANAGEMENT OF PUBLIC ADMINISTRATION

Balanced Scorecard is one of the modern methods of management currently being applied mainly by progressive organizations of the private sector. The subjected method was recently implemented into financial management, which is the key to the process of organizational management in relation to the achievement of the business goals. This suggests that the Balanced Scorecard could help improve management process in public administration, which should lead to improved efficiency. The aim of this article was to highlight the possibility of using the Balanced Scorecard in the management of public administration. This article defines and describes the Balanced Scorecard method and observation of its application in public administration in the Slovak Republic. JEL Classification Numbers: H73, H83, M19, DOI: http://dx.doi. org/10.12955/cbup.v3. 650
Information-theoretic approach for detection of differential splicing from RNA-seq data

The computational prediction of alternative splicing from high-throughput sequencing data is inherently difficult and necessitates robust statistical measures because the differential splicing signal is overlaid by influencing factors such as gene expression differences and simultaneous expression of multiple isoforms among others. In this work we describe ARH-seq, a discovery tool for differential splicing in case-control studies that is based on the information-theoretic concept of entropy.
Identification of novel transcription start sites and distinct proximal promoter regions for pregnane X receptor (PXR) isoforms PXR 1 and PXR 2.

TOMPKINS, LESLIE MEREDITH. Identification of Novel Transcription Start Sites and Alternative Proximal Promoters for Pregnane X Receptor (PXR) Isoforms PXR 1 and PXR 2. (Under the direction of Dr. Robert C. Smart and Dr. Andrew D. Wallace.) The identification and characterization of the orphan group of nuclear receptors has revolutionized our collective understanding of signaling pathways responsible for xenobiotic metabolism. Discovery of the pregnane X receptor (PXR) provided the mechanistic explanation to decades of research that documented xenobiotic metabolic regulation and hepatic protection through enzyme induction without a known mediator. PXR, known as the xenosensing receptor, coordinately regulates metabolic genes in response to diverse xenobiotic challenges. In particular, the ability of PXR to regulate CYP3A4, the enzyme capable of metabolizing more than 60% of all pharmaceuticals, defines its metabolic importance. Currently, the list of PXR ligands and target genes is extensive, yet investigations into the regulation and expression of PXR itself are few. After an initial review of available sequence data, we discovered discrepancies in the 5’ untranslated region (UTR) and transcription start site (TSS) characterizations of the PXR gene, so we endeavored to define TSSs and proximal promoters for the wellknown PXR 1 isoform and the lesser-known PXR 2 isoform. The PXR 2 isoform is the product of a unique first exon responsible for the 39 amino acid amino-terminal addition and is therefore regulated by a distinct proximal promoter. RT-PCR and primer extension experiments performed using total RNA from human liver samples identified two TSSs for each receptor isoform. These results extended the 5’UTR sequence of each isoform and defined new proximal promoters for both PXR isoforms. Separate promoter regions for receptor isoforms suggests the possibility that PXR isoforms are differential regulated or expressed in a tissue-specific fashion. Candidate response elements for liver-enriched transcription factors and other nuclear receptors were found in both promoters. Quantitative PCR illustrated PXR 2 expression as a modest but consistent 2-5% of total PXR expression with much less variability among individuals. In addition, transfection experiments demonstrated comparable transcriptional activity of PXR 2 when compared to that of PXR 1. In total, these data present a starting point from which to investigate the regulation of multiple isoforms of PXR and evaluate individual isoform contributions to the cumulative function of this important nuclear receptor in xenobiotic metabolism. Identification of Novel Transcription Start Sites and Distinct Proximal Promoter Regions for Pregnane X Receptor (PXR) Isoforms PXR 1 and PXR 2