Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete genomic sequence and phylogenetic relatedness of hepatitis B virus isolates from Iran

Hepatitis B virus (HBV) is one of the main etiological agents of acute and chronic liver disease that is still a major public health problem in the world. Numerous HBV isolates have grouped into eight genotypes, A to H, based on the complete genome sequence. To date, no study has been carried out on the complete HBV genome sequence in Iran. The objective of this study was to investigate the complete genome sequence organization and phylogenetic analysis of the five HBV strains, which obtained from Iranian chronic infected patients. Results showed that Iranian strains were closely related to each other, with 97–100% nucleotide similarity. Phylogenetic analysis based on the complete genome sequences and the precore/core gene sequences revealed that all strains were of genotype D, sub‐genotype D1 with bootstrap value 100 and 99%, respectively. The S gene encoded Arg122, Pro127, and Lys160 corresponding to subtype ayw2. Iranian HBV isolates had closely related with Turkish HBV strains. All strains had a nucleotide length of 3,182 base pair (bp) except IR‐P4 strain, with a 3,185 bp in length and with a unique Phe89 insertion in the X gene. The intragenotypic divergence of the complete genome sequence of Iranian strains was 1.8% and the intergenotypic in genotype D was 3.8% and with the other genotypes was 7.9–15.4%. In conclusion, this study revealed that the HBV genotype D, sub‐genotype D1, subtype ayw2 dominates in the Iranian infected patients. A single Phe89 insertion in the X gene of the one Iranian strain with an unforeseen length of 3185 bp was identified. J. Med. Virol. 76:318–326, 2005. © 2005 Wiley‐Liss, Inc.
Swimming behaviour and magnetotaxis function of the marine bacterium strain MO-1.

Magnetotactic bacteria (MTB) have the unique capacity to align and swim along the geomagnetic field lines downward to the oxic-anoxic interface in chemically stratified water columns and sediments. They are most abundant within the first few centimetres of sediments below the water-sediment interface. It is unknown how MTB penetrate into the sediment layer and swim in the pocket water, while their movements are restricted by the alignment along the magnetic field lines. Here we characterized the swimming behaviour of the marine fast-swimming magnetotactic ovoid bacterium MO-1.We found that it rotates around and translates along its short body axis to the magnetic north (northward). MO-1 cells swim forward constantly for a minimum of 1770 μm without apparent stopping. When encountering obstacles, MO-1 cells squeeze through or swim southward to circumvent the obstacles. The distance of southward swimming is short and inversely proportional to the magnetic field strength. Using a magnetic shielding device, we provide direct evidence that magnetotaxis is beneficial to MO-1 growth and becomes essential at low cell density. Environmental implications of the fast-swimming magnetotactic behaviour of magnetococci are discussed.
Differential Effects of Elevated Ozone on Two Hybrid Aspen Genotypes Predisposed to Chronic Ozone Fumigation. Role of Ethylene and Salicylic Acid1

The role of ethylene (ET) signaling in the responses of two hybrid aspen (Populus tremula L. × P.tremuloides Michx.) clones to chronic ozone (O3; 75 nL L−1) was investigated. The hormonal responses differed between the clones; the O3-sensitive clone 51 had higher ET evolution than the tolerant clone 200 during the exposure, whereas the free salicylic acid concentration in clone 200 was higher than in clone 51. The cellular redox status, measured as glutathione redox balance, did not differ between the clones suggesting that the O3 lesions were not a result of deficient antioxidative capacity. The buildup of salicylic acid during chronic O3 exposure might have prevented the up-regulation of ET biosynthesis in clone 200. Blocking of ET perception with 1-methylcyclopropene protected both clones from the decrease in net photosynthesis during chronic exposure to O3. After a pretreatment with low O3 for 9 d, an acute 1.5-fold O3 elevation caused necrosis in the O3-sensitive clone 51, which increased substantially when ET perception was blocked. The results suggest that in hybrid aspen, ET signaling had a dual role depending on the severity of the stress. ET accelerated leaf senescence under low O3, but under acute O3 elevation, ET signaling seemed to be required for protection from necrotic cell death.
Transscleral thermotherapy with laser-induced and conductive heating in hamster Greene melanoma

The purpose of this study was to investigate the cytotoxic effect of heat as induced by transscleral thermotherapy (TSTT), which may be of interest in the treatment of patients with choroidal melanoma. The aim of TSTT is to heat both the sclera and the tumor up to a cytotoxic temperature of about 60°C. TSTT was performed in hamsters with subcutaneously implanted Greene melanoma covered by a specimen of human donor sclera of thickness 0.5, 0.7 or 0.9 mm. A newly developed applicator, which combines conductive episcleral heating at 60°C with laser-induced heating, was used at laser powers ranging from 500 to 1500 mW delivered by an 810 nm diode laser, beam diameter 3 mm, and exposure time 1 min. Temperatures were measured at the scleral surface and at the sclera-tumor interface. The extent of tumor necrosis was examined by light microscopy and the sclera was examined by polarized light microscopy. Maximal depth of tumor necrosis without scleral damage was 4.4 (SD 1.5) mm. The temperature at the scleral surface after TSTT was 58.8 (SD 2.4) °C. The temperature at the sclera-tumor interface ranged from 56.4 (SD 3.7) °C at 500 mW to 65.3 (SD 4.4) °C at 1250 mW laser power. Structural changes to the scleral collagen started to develop at 1250 mW. TSTT with combined laser-induced and conductive heating caused cytotoxic temperatures in the tumor and the sclera, which were well tolerated by the scleral collagen.
Democracy, Governance, and Randomized Development Assistance

Can field experiments be productively employed to study the impact of development assistance on democracy and governance (DG) outcomes? A small but growing number of practitioners and scholars, often working in partnership, are inventing a new research domain at the intersection of evaluation and political science. The article reviews recent and ongoing DG field experiments, and it offers lessons about the prospects and obstacles to the future development of a useful body of experimental evidence on the political economy of development.
Phosphorylation of Serine 1106 in the Catalytic Domain of Topoisomerase IIα Regulates Enzymatic Activity and Drug Sensitivity*

Topoisomerases alter DNA topology and are vital for the maintenance of genomic integrity. Topoisomerases I and II are also targets for widely used antitumor agents. We demonstrated previously that in the human leukemia cell line, HL-60, resistance to topoisomerase (topo) II-targeting drugs such as etoposide is associated with site-specific hypophosphorylation of topo IIα. This effect can be mimicked in sensitive cells treated with the intracellular Ca2+ chelator, 1,2-bis(2-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid (BAPTA-AM). Here we identify Ser-1106 as a major phosphorylation site in the catalytic domain of topo IIα. This site lies within the consensus sequence for the acidotrophic kinases, casein kinase I and casein kinase II. Mutation of serine 1106 to alanine (S1106A) abrogates phosphorylation of phosphopeptides that were found to be hypophosphorylated in resistant HL-60 cells or sensitive cells treated with BAPTA-AM. Purified topo IIα containing a S1106A substitution is 4-fold less active than wild type topo IIα in decatenating kinetoplast DNA and also exhibits a 2–4-fold decrease in the level of etoposide-stabilized DNA cleavable complex formation.Saccharomyces cerevisiae (JN394t2-4) cells expressing S1106A mutant topo IIα protein are more resistant to the cytotoxic effects of etoposide or amsacrine. These results demonstrate that Ca2+-regulated phosphorylation of Ser-1106 in the catalytic domain of topo IIα modulates the enzymatic activity of this protein and sensitivity to topo II-targeting drugs.
Foreign Aid and Statehood in Africa

Has foreign aid destroyed state institutions in Africa? African states depend on development assistance to conduct basic government operations, yet few of these states are well governed or effective at providing public goods. The two trends, mounting foreign aid and static or diminishing state performance, raise an obvious question: Is aid dependency contributing to misrule and state failure in Africa? Many critics argue the two phenomena are related. I find they are not. My analysis fails to show a negative association between aid receipts and two measures of democracy and economic freedom. Instead, the evidence is consistent with a small, positive relationship between aid and these indicators of state performance. Since the international community seems bent on reducing foreign aid, an important issue is how African states can maintain and improve their performance with less foreign assistance.
Expression of maize KNOTTED1 related homeobox genes in the shoot apical meristem predicts patterns of morphogenesis in the vegetative shoot

In this paper we describe the expression patterns of a family of homeobox genes in maize and their relationship to organogenic domains in the vegetative shoot apical meristem. These genes are related by sequence to KNOTTED1, a gene characterized by dominant neomorphic mutations which perturb specific aspects of maize leaf development. Four members of this gene family are expressed in shoot meristems and the developing stem, but not in determinate lateral organs such as leaves or floral organs. The genes show distinct expression patterns in the vegetative shoot apical meristem that together predict the site of leaf initiation and the basal limit of the vegetative ‘phytomer’ or segmentation unit of the shoot. These genes are also expressed in the inflorescence and floral meristems, where their patterns of expression are more similar, and they are not expressed in root apical meristems. These findings are discussed in relation to other studies of shoot apical meristem organization as well as possible commonality of homeobox gene function in the animal and plant kingdoms.
Discrimination of Viable and Dead Fecal Bacteroidales Bacteria by Quantitative PCR with Propidium Monoazide

ABSTRACT Propidium monoazide (PMA) was optimized to discriminate between viable and dead Bacteroides fragilis cells and extracellular DNA at different concentrations of solids using quantitative PCR. Conditions of 100 μM PMA and a 10-min light exposure also excluded DNA from heat-treated cells of nonculturable Bacteroidales in human feces and wastewater influent and effluent.
Volume rendering methods for computational fluid dynamics visualization

The paper describes three alternative volume rendering approaches to visualizing computational fluid dynamics (CFD) data. One new approach uses realistic volumetric gas rendering techniques to produce photo-realistic images and animations from scalar CFD data. The second uses ray casting that is based an a sampler illumination model and is mainly centered around a versatile new tool for the design of transfer functions. The third method employs a simple illumination model and rapid rendering mechanisms to provide efficient preview capabilities. These tools provide a large range of volume rendering capabilities to be used by the CFD explorer to render rapidly for navigation through the data, to emphasize data features (e.g., shock waves) with a specific transfer function, or to present a realistic rendition of the model. <<ETX>>
Alarmin HNP-1 promotes pyroptosis and IL-1β release through different roles of NLRP3 inflammasome via P2X7 in LPS-primed macrophages

Defensins are the first endogenous mediators to be characterized as alarmins and play multifunctional roles in immune response. Previous studies reported that human neutrophil peptide (HNP)-1, a member of the α-defensin subfamily, could regulate the IL-1β post-translational process; however, the underlying mechanism remained unknown. Using an LPS-primed THP-1 macrophage model, we found that inhibition of P2X purinoceptor 7 (P2X7) suppressed HNP-1-initiated mature IL-1β release. Confocal microscopy and glutathione S-transferase (GST) pull-down assay demonstrated that HNP-1 bound to P2X7 directly. HNP-1 treatment increased the activated level of caspase-1, and inhibition of caspase-1 abolished IL-1β release. Incubation of LPS-primed macrophages with potassium chloride also prevented HNP-1-induced export of mature IL-1β. Likewise, an ethidium bromide uptake test showed that the P2X7-K+ efflux-caspase-1 signaling pathway triggered by HNP-1 contributed to pyroptotic pore formation. Furthermore, knock down of inflammasome adaptor Nod-like receptor family pyrin domain containing 3 (NLRP3) decreased activated caspase-1 level and reduced pore formation in macrophages, whereas IL-1β release was not significantly impaired. These findings not only illustrated the mechanism for alarmin HNP-1 in enhancing inflammatory response, but also provided therapeutic targets for certain inflammatory diseases in which defensins play important roles.
Human resources management in Spain: is it possible to speak of a typical model?

There is no shortage of literature studying the relationships between the various processes of human resources management, considered individually, and the strategy of the company. Nevertheless, studies that adopt a joint approach are scarce. In this study, working from the universalist, contingent and configurational perspectives, we seek to identify the possible existence of human resources management models and their links with the strategy of the company. Empirical analysis conducted with 130 industrial companies reveals three distinct models of human resources management but with behaviours independent of the strategies followed by the companies. At the same time we find, within each model, orientations of particular processes that are common among them and are thus characteristic of a universalist approach.
Infectivity of Moloney Murine Leukemia Virus Defective in Late Assembly Events Is Restored by Late Assembly Domains of Other Retroviruses

ABSTRACT The p12 region of the Moloney murine leukemia virus (M-MuLV) Gag protein contains a PPPY motif important for efficient virion assembly and release. To probe the function of the PPPY motif, a series of insertions of homologous and heterologous motifs from other retroviruses were introduced at various positions in a mutantgag gene lacking the PPPY motif. The assembly defects of the PPPY deletion mutant could be rescued by insertion of a wild-type PPPY motif and flanking sequences at several ectopic positions in the Gag protein. The late assembly domain (L-domain) of Rous sarcoma virus (RSV) or human immunodeficiency virus type 1 (HIV-1) could also fully or partially restore M-MuLV assembly when introduced into matrix, p12, or nucleocapsid domains of the mutant M-MuLV Gag protein lacking the PPPY motif. Strikingly, mutant viruses carrying the RSV or the HIV-1 L-domain at the original location of the deleted PPPY motif were replication competent in rodent cells. These data suggest that the PPPY motif of M-MuLV acts in a partially position-independent manner and is functionally interchangeable with L-domains of other retroviruses. Electron microscopy studies revealed that deletion of the entire p12 region resulted in the formation of tube-like rather than spherical particles. Remarkably, the PPPY deletion mutant formed chain structures composed of multiple viral particles linked on the cell surface. Many of the mutants with heterologous L-domains released virions with wild-type morphology.
How Good? The Impact of Leadership on Network Effectiveness

Michael McGuire School of Public and Environmental Affairs Indiana University – Bloomington, USA mcguirem@indiana.edu Chris Silvia School of Public and Environmental Affairs Indiana University – Bloomington, USA cesilvia@indiana.edu Paper prepared for Public Management Research Association Conference, Columbus, Ohio, October 1-3, 2009.
Public-key cryptography with joint and related-key security

The principle of key separation dictates using different keys for different cryptographic operations. We investigate the topic of joint security, where a single keypair is used in multiple primitives in a secure manner. We concentrate mainly on the case of encryption and signature under a shared keypair, giving a generic construction and a more efficient direct construction, both secure in the standard model, and show how these results relate to signcryption. We then turn our attention to security under related-key attacks (RKA), where an adversary can modify a stored secret key and observe the outputs of the system as it operates under this new key. We provide a framework enabling the construction of RKA-secure identity-based encryption (IBE) schemes, and show how specific instantiations of the framework yield IBE schemes secure against adversaries deriving new keys through affine and polynomial transformations of the master secret key. From this we obtain the first constructions of RKA-secure schemes for a variety of primitives under the same non-linear key transformations. Since achieving joint or RKA security often depends on the format of the stored keys, we introduce key-versatile signatures, where the public key is an arbitrary one-way function of the secret key, and show how these can be used to obtain further results in joint and RKA security and beyond.
How to improve organisational results through knowledge management in knowledge-intensive business services

In the future, the only sustainable competitive advantage will be the creation of collective and tacit knowledge. From a strategic point of view, and also from the directive management perspective, this is the type of knowledge that adds the greatest value to an organisation. However, it has not been easy to prove that there are positive effects when investments are made in knowledge assets and firm performance. We thus study the relationship between knowledge management and both tangible and intangible organisational results (ORs). Results are tested in 122 knowledge-intensive business services, and they confirm that this relationship is direct and positive, thereby suggesting that the introduction of this management tool improves ORs.
Protein Oxidative Damage in a Transgenic Mouse Model of Familial Amyotrophic Lateral Sclerosis

Abstract: The Gly93→Ala mutation in the Cu,Zn superoxide dismutase (Cu,Zn‐SOD) gene (SOD1) found in some familial amyotrophic lateral sclerosis (FALS) patients has been shown to result in an aberrant increase in hydroxyl radical production by the mutant enzyme that may cause oxidative injury to spinal motor neurons. In the present study, we analyzed the extent of oxidative injury to lumbar and cervical spinal cord proteins in transgenic FALS mice that overexpress the SOD1 mutation [TgN(SOD1‐G93A)G1H] in comparison with nontransgenic mice. Total protein oxidation was examined by spectrophotometric measurement of tissue protein carbonyl content by the dinitrophenylhydrazine (DNPH) assay. Four ages were investigated: 30 (pre‐motor neuron pathology and clinical disease), 60 (after initiation of pathology, but pre‐disease), 100 (∼50% loss of motor neurons and function), and 120 (near complete hindlimb paralysis) days. Protein carbonyl content in 30‐day‐old TgN(SOD1‐G93A)G1H mice was twice as high as the level found in age‐matched nontransgenic mice. However, at 60 and 100 days of age, the levels were the same. Then, between 100 and 120 days of age, the levels in the TgN(SOD1‐G93A)G1H mice increased dramatically (557%) compared with either the nontransgenic mice or transgenic animals that overexpress the wild‐type human Cu,Zn‐SOD [TgN(SOD1)N29]. The 100–120‐day increase in spinal cord protein carbonyl levels was confirmed by sodium dodecyl sulfate‐polyacrylamide gel electrophoretic separation and western blot immunoassay, which enabled the identification of heavily oxidized individual proteins using a monoclonal antibody against DNPH‐derivatized proteins. One of the more heavily oxidized protein bands (14 kDa) was identified by immunoprecipitation as largely Cu,Zn‐SOD. Western blot comparison of the extent of Cu,Zn‐SOD protein carbonylation revealed that the level in spinal cord samples from 120‐day‐old TgN(SOD1‐G93A)G1H mice was significantly higher than that found in age‐matched nontransgenic or TgN(SOD1)N29 mice. These results suggest that the increased hydroxyl radical production associated with the G93A SOD1 mutation and/or lipid peroxidation‐derived radical species (peroxyl or alkoxyl) causes extensive protein oxidative injury and that the Cu,Zn‐SOD itself is a key target, which may compromise its antioxidant function.
Suppression of the tumorigenic and metastatic abilities of murine B16-F10 melanoma cells in vivo by the overexpression of the tissue inhibitor of the metalloproteinases-1.

BACKGROUND Metalloproteinases participate in the first steps of tumor invasion and subsequent metastasis. Three distinct proteins have been identified as tissue inhibitors of metalloproteinases (TIMPs), and an imbalance between TIMPs and metalloproteinases may be an important factor in tumor progression. PURPOSE The purpose of this study was to determine if increased levels of TIMP-1 suppressed the malignant phenotype of B16-F10 melanoma cells in mice. METHODS We examined and compared the tumorigenic and metastatic behavior of B16-F10 cells, several independent clonal cell lines that were transfected to overexpress TIMP-1, and a vector-transfected control in both nude (BALB/c) and syngeneic (C56BL/6) mice. Tumor growth was assessed by subcutaneously injecting female nude mice with 10(5) cells of parental or transfected B16-F10 cell lines, and monitoring for the appearance of tumors at the injection site. Tumor size was measured every 2-3 days for 5 weeks. To evaluate the effect of elevated TIMP-1 on metastases, 3 x 10(4) cells were administered by intravenous injection into the tail vein of C57BL/6 mice, and the number of metastases counted on days 14 and 22. RESULTS Following subcutaneous injections into nude mice, TIMP-1-overexpressing cells showed a substantial decline in their primary tumor growth, characterized by a reduced tumor incidence (50%-89% versus 100% in controls) and longer periods before the appearance of tumors (15 +/- 1.0 to 19 +/- 3.3 days versus 12 +/- 0.4 days in controls). All TIMP-1 clones showed a reduction in their lung colonization ability (8.2 +/- 1.4 to 48.1 +/- 9.9 versus 59.9 +/- 6.0 metastatic nodules in controls) following intravenous injection into syngenic mice. The number of lung metastases arising from four of the five TIMP-1-overexpressing lines was significantly lower than those formed by parental or control cells. CONCLUSIONS The data demonstrate that an overexpression of TIMP-1 directly inhibits the tumorigenic as well as metastatic potential of B16-F10 cells in mice, lending further support to the importance of TIMP-1 in controlling malignancy.