Miracle-dz/UniFAR-FTUs huggingface dataset:
Alphavirus vectors and vaccination

Alphaviruses are positive‐stranded RNA viruses that have a broad host range and therefore are capable of replicating in many vertebrate and invertebrate cells. The single‐stranded alphavirus genome is divided into two ORFs. The first ORF encodes the nonstructural proteins that are translated upon entry of the virus into the cytoplasm and are responsible for transcription and replication of viral RNA. The second ORF is under the control of a subgenomic promoter and normally encodes the structural proteins, which are responsible for encapsidation of viral RNA and final assembly into enveloped particles. Expression vectors have been engineered from at least three alphaviruses in which the structural protein gene region has been replaced by heterologous genes and have been shown to express high levels of the heterologous protein in cultured cells. These RNA vectors, known as replicons, are capable of replicating on their own but are not packaged into virus‐like particles unless the structural proteins are provided in trans. Thus, replicons are single cycle vectors incapable of spreading from infected to noninfected cells. Because of these features, alphavirus replicon vectors are being developed as a platform vaccine technology for numerous viral, bacterial, protozoan and tumour antigens where they have been shown to be efficient inducers of both humoral and T cell responses. In addition, as the alphavirus structural proteins are not expressed in vaccine recipients, antivector immune responses are generally minimal, allowing for multiple effective immunisations of the same individual. Copyright © 2002 John Wiley & Sons, Ltd.
Epidemiology and Diagnosis of Myopic Choroidal Neovascularization in Asia

Background: This article aims to review recent advances in the understanding of epidemiology and risk factors for the development of myopic choroidal neovascularization (CNV) and highlight the diagnostic features of myopic CNV and signs seen on the noninvasive optical coherence tomography technology, which may be particularly useful for the purpose of screening. Choroidal neovascularization is a sight-threatening complication of pathologic myopia. Because myopic CNV frequently affects individuals during their working life, its socioeconomic impact is significant, especially in Asian countries where the prevalence of pathologic myopia is high. Epidemiology: Pathological myopia is the most common cause of CNV in patients less than 50 years old, and it is estimated that 5.2% to 11.3% of individuals with pathologic myopia develop myopic CNV. Risk Factors: The risk of developing myopic CNV increases with the severity of myopia and macular changes, such as diffuse atrophy, lacquer cracks, and patchy atrophy, which progress to myopic CNV in a significant proportion. Vascular endothelial growth factor (VEGF) may contribute to the development of myopic CNV. Natural Course and Prognosis: Untreated myopic CNV carries a poor visual prognosis, with an estimated 89% of the patients having marked visual impairment within 5 years of onset. Treatment: Anti-VEGF therapy is efficacious in treating myopic CNV. Although this significantly improves the short-term prognosis of myopic CNV, the long-term visual loss due to the sequela of myopic CNV including macular atrophy and scarring remains.
Community Detection in Twitter

Twitter has recently evolved into a source of social, political and real time information in addition to being a means of mass-communication and marketing. Monitoring and analyzing information on Twitter can lead to invaluable insights, which might otherwise be hard to get using conventional media resources. An important task in analyzing highly networked information sources like twitter is to identify communities that are formed. A community on twitter can be defined as a set of users that have more links within the set than outside it. We present a technique to devise a similarity metric between any two users on twitter based on the similarity of their content, links and metadata. The link structure on Twitter can be characterized using the twitter notion of followers, being followed and the @Mentions, @Reply and @RT tags in tweets. Content similarity is characterized by the words in the tweets combined with the hash-tags they are annotated with. Meta-data similarity includes similarity based on other sources of user information such as location, age and gender. We then use this similarity metric to cluster users into communities using spectral and bottom-up agglomerative hierarchical clustering. We evaluate the performance of clustering using different similarity measures on different types of datasets. We also present a heuristic to find communities in twitter that take advantage of the network characteristics of twitter.
Asymmetric Cancer Hallmarks in Breast Tumors on Different Sides of the Body

During the last decades it has been established that breast cancer arises through the accumulation of genetic and epigenetic alterations in different cancer related genes. These alterations confer the tumor oncogenic abilities, which can be resumed as cancer hallmarks (CH). The purpose of this study was to establish the methylation profile of CpG sites located in cancer genes in breast tumors so as to infer their potential impact on 6 CH: i.e. sustained proliferative signaling, evasion of growth suppressors, resistance to cell death, induction of angiogenesis, genome instability and invasion and metastasis. For 51 breast carcinomas, MS-MLPA derived-methylation profiles of 81 CpG sites were converted into 6 CH profiles. CH profiles distribution was tested by different statistical methods and correlated with clinical-pathological data. Unsupervised Hierarchical Cluster Analysis revealed that CH profiles segregate in two main groups (bootstrapping 90–100%), which correlate with breast laterality (p = 0.05). For validating these observations, gene expression data was obtained by RealTime-PCR in a different cohort of 25 tumors and converted into CH profiles. This analyses confirmed the same clustering and a tendency of association with breast laterality (p = 0.15). In silico analyses on gene expression data from TCGA Breast dataset from left and right breast tumors showed that they differed significantly when data was previously converted into CH profiles (p = 0.033). We show here for the first time, that breast carcinomas arising on different sides of the body present differential cancer traits inferred from methylation and expression profiles. Our results indicate that by converting methylation or expression profiles in terms of Cancer Hallmarks, it would allow to uncover veiled associations with clinical features. These results contribute with a new finding to the better understanding of breast tumor behavior, and can moreover serve as proof of principle for other bilateral cancers like lung, testes or kidney.
Biodegradation Of Tebuconazole By Bacteria Isolated From Contaminated Soils

The objective of this work was to isolate bacteria from soil historically exposed to tebuconazole and to evaluate the biodegradation of this fungicide by them. Tebuconazole is a commonly used systemic fungicide of the triazol group, which inhibits the sterol C-14 α -demethylation of 24-methylenedihydrolanosterol, a precursor of ergosterol, a cell membrane component in fungi. Microorganisms were isolated by different methods of soil sampling and the screening of degrading bacteria was performed in bioreactors cultivations, with some isolates showing the ability to degrade up to 42.76 mg L− 1 of tebuconazole (51% of the initial concentration). These strains were identified by standard biochemical procedures as being Enterobacter sakazakii and Serratia sp. These bacteria present some important characteristics for potential uses on environmental bioremediation, considering that tebucanozale is an extremely recalcitrant chemical.
Body size, dialysis dose and death risk relationships among hemodialysis patients.

BACKGROUND The normalized treatment ratio, Kt/V derived from urea kinetic models (UKM), is a commonly used measure of dialysis dose. This measure assumes that smaller patients with low volume of urea distribution (V) require proportionately less total treatment (Kt) than larger patients. The conclusion has been questioned because the UKM use assumptions that could make them invalid for accurately predicting a clinical outcome like survival. It is possible that a relationship exists between Kt and body size whereby a different Kt is required for different sizes. This study therefore explored the relationships among body size, Kt, and death risk focusing on possible interactions between Kt and size. METHODS The sample included 43,334 patients treated on January 1, 1999. Survival time was modeled using Kt or body size groups to evaluate the shape of the risk profiles. Kt and the size measures were then evaluated together as continuous functions both in main effects (that is, Kt and size) and interaction models to see if the association of Kt with risk might be different for different sizes. The size measures were body weight, weight adjusted statistically for height, body surface area (BSA), weight divided by height (wt/ht) and the body mass index (BMI). RESULTS The log of risk decreased in rough linear fashion for Kt, weight, weight for height, and BSA. The log-risk relationships were "reverse J-shaped" for wt/ht and BMI. The main effects models suggested improved survival with increasing Kt and all of the size measures. Adding an interaction term increased the benefit associated with increasing Kt and for weight, weight for height and BSA at low values of Kt and size. A significant, positive interaction term mitigated those effects at higher values. Thus, the death risk penalties associated with reducing Kt among small patients were as great as or greater than they were among large patients. A similar pattern was observed for V. Adding the interaction to the BMI model destroyed the main effects, so that there was no significant association between risk and either Kt or BMI. A cross-categorical model of BMI and Kt, however, revealed improving survival with increasing Kt among both low and high BMI patients throughout the range of Kt. CONCLUSIONS Evidence supporting the intuition that smaller patients require proportionately lower dialysis dose than larger patients was not found. To the contrary, smaller patients suffer as much risk as or more risk than larger patients from reducing Kt. Deciding dialysis treatment using a Kt/V based intuition may lead to avoidable under-dialysis particularly among small patients.
Effect Of Copper And Cadmium On Germination And Anatomical Structure Of Leaf And Root Seedling In Maize ( Zea mays L )

The aim of this work was to study the effect of copper (Cu) and/or cadmium (Cd) on grain germination and anatomical structure of Maize (Zea mays cv. Giza 2) seedling. The results indicated that Cu and/or Cd caused reduced the grain germination indices (FGP final germination percentage, MDG mean daily germination, GI germination index and CVG coefficient of velocity of germination), root anatomical traits as root diameter, central cylinder diameter, cortex thickness, cross section area of root and cross section area of central cylinder and leaf structures traits as thickness of midrib, upper epidermis and parenchyma and vascular bundle, in contrast they increased mean germination time MGT. The most inhibitory effect on grain germination indices and root anatomical traits was seen in Cd (150 μmol/L), but the highest increase in MGT was seen in a combination between Cu and Cd. The combination between Cu and Cd leads to a reduction in Cd toxicity when compared with the same concentration in Cd alone. It can concluded that both Cu and Cd either each alone or combined are toxic on maize, Cd is more toxic than Cu and the combination of Cu with Cd decreased its toxicity.
Selling Tourism Products through the Opaque Channels

This paper analyses the properties of the advanced Opaque booking systems used by online travel agencies in conjunction with their traditional transparent booking system. In section 2 an updated literature review is presented. This review underlines the interest and the specificities of Opaque goods in the Tourism Industry. It also characterises properties of the Name-Your-Own-Price channel introduced by Priceline and the Opaque channel developed by Hotwire. Then, in section 3, the possibility of joint-implementation of more than one opaque booking system by an online intermediary is discussed. Finally, in section 4, intuitions and preliminary results are presented.
Dosage-dependent modulation of glucose repression by MSN3 (STD1) in Saccharomyces cerevisiae

The SNF1 protein kinase of Saccharomyces cerevisiae is required to relieve glucose repression of transcription. To identify components of the SNF1 pathway, we isolated multicopy suppressors of defects caused by loss of SNF4, an activator of the SNF1 kinase. Increased dosage of the MSN3 gene restored invertase expression in snf4 mutants and also relieved glucose repression in the wild type. Deletion of MSN3 caused no substantial phenotype, and we identified a homolog, MTH1, encoding a protein 61% identical to MSN3. Both are also homologous to chicken fimbrin, human plastin, and yeast SAC6 over a 43-residue region. Deletion of MSN3 and MTH1 together impaired derepression of invertase in response to glucose limitation. Finally, MSN3 physically interacts with the SNF1 protein kinase, as assayed by a two-hybrid system and by in vitro binding studies. MSN3 is the same gene as STD1, a multicopy suppressor of defects caused by overexpression of the C terminus of TATA-binding protein (R. W. Ganster, W. Shen, and M. C. Schmidt, Mol. Cell. Biol. 13:3650-3659, 1993). Taken together, these data suggest that MSN3 modulates the regulatory response to glucose and may couple the SNF1 pathway to transcription.
Development of a hybrid cardiovascular graft using a tissue engineering approach 1

Tissue engineering of endothelial cells (EC) and chemical engineering with anticoagulant moieties has been undertaken in order to improve prosthetic graft patency and thrombogenicity. This was done by covalently bonding a compliant poly(carbonate‐urea)urethane graft (MyoLink™) with with arginine‐glycine‐aspartate (RGD) or/and heparin (Hep) to ascertain whether EC retention could be improved. The retention of these moieties and EC was assessed after exposure to pulsatile flow. We covalently bonded RGD, Hep, and RGD/Hep onto the luminal surface of MyoLink using spacer arm technology. Narrow‐beam X‐ray photoelectron spectroscopy was carried out to check the efficiency of the bonding. EC were radiolabeled and seeded onto native MyoLink and with 1) RGD‐, 2) Hep‐, and 3) RGD/Hep‐bonded grafts and exposed to shear stress in a physiological flow circuit for 6 h, which reproduces femoral artery flow waveforms and pulsatility. Results were recorded on a gamma camera imaging system. Viability of cells was tested with a modified Alamar Blue assay (ABA) and scanning electron microscopy for morphological appearance of seeded cells. Experiments were repeated (n=6). RGD, Hep, and RGD/Hep were bonded together in a uniform distribution on the luminal surface of each graft type, and bioactivity of each moiety covalently bonded was very high. In the flow circuit, there was exponential cell retention for the first 60 min of flow for all the grafts, but after 6 h of exposure to pulsatile flow the RGD/Hep‐bonded graft had a significantly better cell retention rate than native MyoLink (75.7%±2.3 vs. 60.5±10.1, P<0.05). ABA test showed that all the seeded cells postexposure to flow were viable, and significantly higher metabolic activity was recorded on a RGD/Hep‐bonded graft than with MyoLink‐seeded graft (P<0.01). Using RGD/Hep covalently bonded onto graft surfaces improves cell retention and provides an antithrombogenic surface for initial blood flow in vivo until full EC activity develops postseeding. This would allow the development and further improvement of hybrid grafts. —Tiwari, A. , Salacinski, H. J., Punshon, G. , Hamilton, G. , Seifalian, A. M. Development of a hybrid cardiovascular graft using a tissue engineering approach. FASEB J. 16, 791–796 (2002)
Risk factors for conversion of laparoscopic to open cholecystectomy.

BACKGROUND Laparoscopic cholecystectomy (LC) has become the treatment of choice for symptomatic gallstones; however conversion to open cholecystectomy (OC) remains a possibility. Unfortunately, preoperative factors indicating risk of conversion are unclear. Therefore, we aimed to identify risk factors associated with conversion of LC to OC. PATIENTS AND MATERIALS Records of 564 patients undergoing LC in 1995 and 1996 were reviewed. Patients were assigned to one of two groups: (1) acute cholecystitis defined by the presence of gallstones, fever, leukocyte count >10(4), and inflammation on ultrasound or histology; (2) chronic cholecystitis that included all other symptomatic patients. Demographics, history, and physical, laboratory, and radiology data, operative note, and the pathology report were reviewed. RESULTS 161 of 564 patients, had acute and 403 patients had chronic cholecystitis; 16 acute cholecystitis patients (10%) were converted from LC to OC and 17 chronic cholecystitis patients (4%) had LC converted to OC. Patients having open conversion were significantly older, had greater prevalence of cardiovascular disease, and were more likely to be males. LC conversion to OC in acute cholecystitis patients was associated with a greater leukocyte count; in gangrenous cholecystitis patients, 29% had open conversion. CONCLUSIONS Importantly, these risk factors-older men, presence of cardiovascular disease, male gender, acute cholecystitis, and severe inflammation-are determined preoperatively, permitting the surgeon to better inform patients about the conversion risk from LC to OC. While acute cholecystitis was associated with more than a twofold increased conversion rate, only 10% of these patients could not be completed laparoscopically. Therefore, acute cholecystitis alone should not preclude an attempt at laparoscopic cholecystectomy.
A High-Speed Low-Cost Millimeter Wave System with Dual Pulse Shaping Transmission and Symbol Rate Equalization Techniques

A millimeter wave system with commercially available and affordable data conversion devices is presented in this paper for achieving high-speed and low-cost wireless communications. By adopting the proposed dual pulse shaping (DPS) transmission scheme, the system can achieve full Nyquist rate transmission with only half of the sampling rate required by conventional Nyquist pulse shaping. Structures of the DPS transmitter and receiver are described and effective symbol rate equalization techniques suitable for DPS transmission are presented. Simulation results with two sets of practical dual spectral shaping pulses are also provided to compare system performance with the conventional Nyquist pulse shaping system.
Section 337 and the Protection of Intellectual Property in the United States: The Complainants and the Impact

Under Section 337 of the Tariff Act of 1930 a firm can challenge imports that infringe its U.S. intellectual property rights, such as patents, copyrights and trademarks. Based on publicly available information this paper examines the characteristics of firms that file complaints under Section 337 and also evaluates how firms are affected by the outcomes. We find a complaining firm, compared with peer firms in the same industry, is typically larger, produces a more diverse range of products, has invested more in intangibles and is no less profitable. A finding of no violation significantly depresses the filing firm's profits compared to peers. Section 337 appears to protect innovators, but its effectiveness in promoting more innovation cannot be demonstrated so clearly. Copyright 1996 by MIT Press.
Predicting future trends in the burden of pertussis in the 21st century: implications for infant pertussis and the success of maternal immunization

Support is growing for maternal immunization using acellular pertussis (aP) vaccines to prevent severe pertussis disease and deaths among very young, unvaccinated infants. Vaccine effectiveness of maternal immunization is 91% in preventing laboratory-confirmed pertussis in infants aged <3 months. To date, most mothers were primed in childhood with whole-cell pertussis vaccines. Soon, the generation of aP-primed individuals will become the new mothers-to-be. The shorter duration of protection afforded by aP vaccines, which is more pronounced with repeated aP boosters, may lead to increased pertussis circulation among aP-primed parents. Maternal Tdap immunization in aP-primed mothers-to-be may become less effective. Additional measures to protect young infants may eventually be needed, along with new vaccines that induce higher quality and more durable responses.
The Cathepsin L First Intron Stimulates Gene Expression in Rat Sertoli Cells1

Abstract Large amounts of cathepsin L (CTSL), a cysteine protease required for quantitatively normal spermatogenesis, are synthesized by mouse and rat Sertoli cells during stages VI to VII of the cycle of the seminiferous epithelium. We previously demonstrated that all of the regulatory elements required in vivo for both Sertoli cell- and stage-specific expression of the Ctsl gene are present within a ~3-kb genomic fragment that contains 2065 nucleotides upstream of the transcription start site and 977 nucleotides of downstream sequence. Most of the downstream region encodes the first intron. In this study, transient transfection assays using primary Sertoli cell cultures and the TM4 Sertoli cell line established that the Ctsl first intron increased reporter gene activity by ~5-fold. While the intron-mediated enhancement in reporter gene activity was not restricted to the Ctsl promoter, positioning the first intron upstream of the Ctsl promoter in either orientation abolished its stimulatory activity, suggesting that it does not contain a typical enhancer. Mutating the 5′-splice site of the Ctsl first intron or replacing the first intron by the Ctsl fourth intron abolished the stimulatory effect. Finally, the intron-dependent increase in reporter gene activity could be explained in part by an increase in the amounts of total RNA and transcript polyadenylation. Results from this study suggest that the stimulatory effect mediated by the Ctsl first intron may explain in part why Sertoli cells in seminiferous tubules at stages VI to VII produce high levels of CTSL.
Longitudinal Survey of Avian Metapneumoviruses in Poultry in Israel: Infiltration of Field Strains into Vaccinated Flocks

Abstract Avian metapneumovirus (aMPV) is a respiratory pathogen and includes four subtypes, which are differentially distributed worldwide. In Israel, two aMPV subtypes, A and B, are cocirculating in an area with a relatively high density of poultry houses. We performed a longitudinal survey in commercial flocks of turkeys and chickens (six and two flocks, respectively) with differing vaccination programs. This study revealed that all monitored flocks were infected by aMPV during the sampling period, as detected either by serology or by molecular methods. Moreover, to identify the subtypes infecting the birds and to distinguish between field and vaccine strains, we sequenced fragments of the attachment glycoprotein gene. This analysis revealed that both vaccine and field strains of both aMPV-A and -B could be recovered from the birds. In four out of six turkey flocks, aMPV field strains were recovered, emphasizing the broad distribution of this highly contagious pathogen. Importantly, in two out of four vaccinated turkey flocks, homologous field subtypes of aMPV-A or -B were detected even after boost administration, suggesting failure of the vaccine to protect the flocks from secondary infection. Overall, the results of this longitudinal study call for a more efficient vaccination program against aMPV, which is critical for an area of intensive commercial poultry farming.