Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence variations of precore/core and precore promoter regions of hepatitis B virus in patients with or without viral reactivation during cytotoxic chemotherapy

Reactivation of the hepatitis B virus (HBV) is a well‐described complication among cancer patients undergoing cytotoxic chemotherapy. Mutations in the preC/C and the preC promoter regions of HBV have been reported in some patients who developed this condition. A G‐to‐A mutation at nt 1896 in the preC/C region (HBeAg negative/anti‐HBe positive) has been associated with more severe liver disease than that caused by wild type virus. In addition, it has been suggested that patients with these mutations may be more likely to reactivate than those with the wild type virus. Whether or not such mutations were present before the commencement of or developed during the course of cytotoxic chemotherapy is not known. In this study, 28 cancer patients (consisting of 14 consecutive patients who developed HBV reactivation and another 14 who had no reactivation during cytotoxic chemotherapy) are reported. The objectives were firstly, to determine the prechemotherapy HBeAg status and nucleotide sequences of the preC/C and preC promoter regions of HBV in order to determine if these parameters affected the rate of reactivation, and secondly, for those who developed reactivation, to determine whether the mutations were present before chemotherapy or developed during, possibly as a result of, cytotoxic chemotherapy. HBV DNA was amplified by PCR and nucleotide sequencing performed on samples taken prior to chemotherapy and at the time of reactivation. Results revealed that 16 of the 28 patients were HBeAg negative/anti‐HBe positive. Of these 16, four (57%) of the seven patients who had nt 1896 mutation, but only one (17%) of the six who had the wild type HBV genome, developed reactivation. Three had no detectable HBV DNA. In the majority of cases, the type of virus, i.e. wild/mutant at preC/C, that was detected during the reactivation was identical to that detected in the pretreatment samples. With respect to the preC promoter region, the two commonest mutations detected were at nt 1762 (A to T) and nt 1764 (G to A). When this region was translated into amino acid sequences, stop codons leading to truncated X protein at carboxyl terminus were found in four patients, three of whom developed HBV reactivation. We conclude that chronic HBV carriers who are HBeAg negative/anti‐HBe positive with nt 1896 mutation (G to A) may be more likely to develop HBV reactivation during cytotoxic chemotherapy than those with the wild type virus. Cytotoxic chemotherapy does not appear to select out mutant HBV, or to be consistently mutagenic in patients who develop HBV reactivation. The occurrence of stop codons in the amino acid sequences of the X protein in three patients who developed HBV reactivation, including one who was detected only at the time of reactivation, is of particular interest, as such mutant viruses remain replication competent.
Generalized classification rules for entity identification

One of the essential tasks in data integration is entity resolution (ER) which will recognize the records that are belonging to the same entity. The entity resolution is referred by many other terms like duplicate detection, pattern matching, etc. Now a days the activities like information integration, information retrieval, crowd sourcing, and pay-as-you-go have involved users to carry out the ER tasks such as to identify whether two entity descriptions are referred to the same entity or not. Previous work of ER involves clustering and comparison approaches which are based on some assumption. The ER gives the poorer quality when such assumptions are not correct. In our approach, we present a new set of entity rules where each rule enumerates all possibilities to identify the correct entity of the records. Additionally, we propose an extended approach (GenR) for efficient and effective rules generation by using a specialized form of term-based entropy measure. We experimentally evaluated the proposed approach using data set with a large no. of records and the data sets with different data characteristics. We report on some promising empirical results which demonstrate performance improvement by using a term-based quality measure.
Sulforaphane as an inducer of glutathione prevents oxidative stress‐induced cell death in a dopaminergic‐like neuroblastoma cell line

The total GSH depletion observed in the substantia nigra (SN) appears to be responsible for subsequent oxidative stress (OS), mitochondrial dysfunction, and dopaminergic cell loss in patients with Parkinson’s disease. A strategy to prevent the OS of dopaminergic cells in the SN may be the use of chemopreventive agents as inducers of endogenous GSH, antioxidant and phase 2 enzymes. In this study, we demonstrated that treatment of the dopaminergic‐like neuroblastoma SH‐SY5Y cell line with sulforaphane (SF), a cruciferous vegetables inducer, resulted in significant increases of total GSH level, NAD(P)H : quinone oxidoreductase‐1, GSH‐transferase and ‐reductase, but not GSH‐peroxidase, catalase and superoxide dismutase activities. Further, the elevation of GSH levels, GSH‐transferase and NAD(P)H:quinone oxidoreductase‐1 activities was correlated to an increase of the resistance of SH‐SY5Y cells to toxicity induced by H2O2 or 6‐hydroxydopamine (6‐OHDA). The pre‐treatment of SH‐SY5Y cells with SF was also shown to prevent various apoptotic events (mitochondrial depolarization, caspase 9 and 3 activation and DNA fragmentation) and necrosis elicited by 6‐OHDA. Further, the impairment of antioxidant capacity and reactive oxygen species formation at intracellular level after exposure to 6‐OHDA was effectively counteracted by pre‐treatment with SF. Last, both the cytoprotective and antioxidant effects of SF were abolished by the addition of buthionine sulfoximine supporting the main role of GSH in the neuroprotective effects displayed by SF. These findings show that SF may play a role in preventing Parkinson’s disease.
Two faces of major lower limb amputations.

OBJECTIVES To review the indications for major lower limb amputations in adults and children in our patient population and to compare our experience in prosthetic rehabilitation with that of other published information. MATERIAL AND METHODS We retrospectively reviewed charts of patients who underwent amputation between 1997 to 2004 at the Orthopaedic Department of B& B Hospital (BBH), Gwarko and Hospital and Rehabilitation center for Disabled Children ( HRDC), Banepa. There were 113 patients at BBH & 89 patients at HRDC. Major amputation was defined as any amputation at or proximal to wrist and ankle. RESULTS Major lower limb amputations constituted 73.58%(39/53) of all major amputations at BBH and 97.77% (44/45) at HRDC. Road traffic accident was found to be number one cause for major lower limb amputations (74.29%) in adult population. In children postburn contracture was the leading cause for amputation (29.54%) followed by Congenital limb conditions (22.72%), Spina bifida with trophic ulcers ( 20.45%), Tumor (13.63%), Chronic Osteomyelitis (6.81%), Trauma (4.54%) and Arthrogryposis (2.27%). Prosthetic fitting and rehabilitation is as yet far from satisfactory in the adult population but all the children who had amputation at HRDC were fitted with prosthesis. CONCLUSION Main causes of major lower limb amputation in both population is largely preventable by instituting safety measures and conducting awareness program. There is a need for an effective prosthetic fitting center for adults.
Reactance domain MUSIC algorithm for electronically steerable parasitic array radiator

Conventional adaptive array antenna processing must observe signals on all of the array antenna elements. However, because the low-cost electronically steerable parasitic array radiator (ESPAR) antenna has only a single-port output, none of the signals on the antenna's parasitic elements can be observed. A direct application of most of the algorithms for the conventional adaptive array antenna is impractical. In this paper, A technique of estimation of direction-of-arrivals (DoAs) is proposed for the ESPAR antenna. This technique is based on the modified MUltiple SIgnal Classification (MUSIC) algorithm. The correlation matrix used in the MUSIC algorithm is estimated from the signal received through the single-port output of the ESPAR antenna as it switches over a set of antenna patterns. Simulation results show that DoAs can be estimated by the reactance domain MUSIC algorithm for ESPAR antennas. Furthermore, the statistical performance on estimation error variance of the reactance domain MUSIC estimator is analyzed and compared with the Crame/spl acute/r-Rao lower bound. Analytic and empirical results show that high-resolution DoAs estimation can be achieved by using the reactance domain MUSIC algorithm for ESPAR antennas.
Effect of endotoxin on permeability of bovine cerebral endothelial cell layers in vitro.

The effect of lipopolysaccharide (LPS) on cultured cerebral endothelial cells was investigated to assess the changes in the trans endothelial electrical resistance (TEER) across the blood-brain barrier that may occur during inflammatory diseases of the central nervous system. Primary cultures of bovine cerebral endothelial cells were cultured to tight monolayers with a TEER of 250 to 300 omega.cm2 on polycarbonate Transwell filters. LPS induced a time- and dose-dependent decline in TEER. Transport of the hydrophilic model compounds sodium fluorescein and fluorescein dextran (MR, 4 kDa) across monolayers of bovine cerebral endothelial cells increased more than 3-fold after treatment of the cells with LPS (50 ng/ml). Treatment of the monolayers with various concentrations of LPS caused a 3-to 4-fold increase in the permeability of bovine cerebral endothelial cells for [125I]bovine serum albumin, which was also preceded by a decrease in TEER. The reduction of TEER by LPS could be inhibited completely by indomethacin (10(-6)M for 30 min), a cyclooxygenase inhibitor, but not by dexamethasone, a glucocorticoid (10(-7) M for 16 hr). In conclusion, LPS administration to blood-brain barrier endothelial cells causes a decrease in TEER which leads to enhanced transport of low and high molecular weight molecules. During this process the production of eicosanoids by the endothelial cells seem to play a key role.
The Pre-attentive L2 Orthographic Perception Mechanism Utilized by Bilinguals with Different Proficiency Levels

Language proficiency is predicted to modulate orthographic-semantic association in second language (L2) vocabulary acquisition, in accordance with the assumptions of the Developmental Bilingual Interactive-Activation model (BIA-d) (Grainger et al., 2010). The current study explored this modulation during pre-attentive L2 orthographic perception. ERPs were recorded from Chinese–English bilinguals with different L2 proficiency during their pre-attentive response to deviant and standard stimuli arranged in the oddball paradigm. Two stimulus types were investigated separately: L2 orthography and L1 orthography. In the L2 orthography condition, a MMN-N400 complex (i.e., deviancy effect) was found in the high L2 proficiency bilinguals, but only a marginally significant reduced negativity in an early time window was found in the low L2 proficiency bilinguals. In the L1 orthography condition, the high and low L2 proficiency bilinguals showed similar deviancy effect in the form of MMN-P3a-LPC complex. The current findings suggest that proficiency modulates pre-attentive L2 orthographic perception, such that the high L2 proficiency bilinguals activate the associated semantic representation instantly upon orthographic decoding, while the orthographic-semantic connection is not activated for the low L2 proficiency bilinguals. This is probably due to their difference in the strength of orthographic-semantic association. These findings contribute to the understanding of orthographic processing by bilinguals at the pre-attentive level and provide supporting evidence for the BIA-d model.
Identification of metastasis-associated genes in colorectal cancer through an integrated genomic and transcriptomic analysis.

OBJECTIVE Identification of colorectal cancer (CRC) metastasis genes is one of the most important issues in CRC research. For the purpose of mining CRC metastasis-associated genes, an integrated analysis of microarray data was presented, by combined with evidence acquired from comparative genomic hybridization (CGH) data. METHODS Gene expression profile data of CRC samples were obtained at Gene Expression Omnibus (GEO) website. The 15 important chromosomal aberration sites detected by using CGH technology were used for integrated genomic and transcriptomic analysis. Significant Analysis of Microarray (SAM) was used to detect significantly differentially expressed genes across the whole genome. The overlapping genes were selected in their corresponding chromosomal aberration regions, and analyzed by using the Database for Annotation, Visualization and Integrated Discovery (DAVID). Finally, SVM-T-RFE gene selection algorithm was applied to identify metastasis-associated genes in CRC. RESULTS A minimum gene set was obtained with the minimum number [14] of genes, and the highest classification accuracy (100%) in both PRI and META datasets. A fraction of selected genes are associated with CRC or its metastasis. CONCLUSIONS Our results demonstrated that integration analysis is an effective strategy for mining cancer-associated genes.
Two-Party Zero-Error Function Computation with Asymmetric Priors

We consider a two party network where each party wishes to compute a function of two correlated sources. Each source is observed by one of the parties. The true joint distribution of the sources is known to one party. The other party, on the other hand, assumes a distribution for which the set of source pairs that have a positive probability is only a subset of those that may appear in the true distribution. In that sense, this party has only partial information about the true distribution from which the sources are generated. We study the impact of this asymmetry on the worst-case message length for zero-error function computation, by identifying the conditions under which reconciling the missing information prior to communication is better than not reconciling it but instead using an interactive protocol that ensures zero-error communication without reconciliation. Accordingly, we provide upper and lower bounds on the minimum worst-case message length for the communication strategies with and without reconciliation. Through specializing the proposed model to certain distribution classes, we show that partially reconciling the true distribution by allowing a certain degree of ambiguity can perform better than the strategies with perfect reconciliation as well as strategies that do not start with an explicit reconciliation step. As such, our results demonstrate a tradeoff between the reconciliation and communication rates, and that the worst-case message length is a result of the interplay between the two factors.
Safety classifications for the fusion DEMO plant of Korea

Regulatory requirements and industrial codes and standards are to be compulsory top-tier prerequisites for the design and construction of a power plant with nuclear technologies. As it will take considerable time and substantial amounts of investment to develop that for the fusion power plants, design studies on a fusion DEMO plant will be carried out in parallel with developing its regulatory requirements and codes and standards. To overcome this dilemma, a tentative set of general design criteria and classification criteria that are to be applicable for the design studies of the fusion DEMO plant of Korea (DEMO Plant) are proposed with the vacuum vessel pressure boundary that corresponds to the Reactor Coolant Pressure Boundary of the nuclear power plant. To determine the tentative set, the radiation release to the environment and consequences of the postulated events in DEMO Plant are analyzed with rough approximation assuming the inherent safety of a fusion DEMO reactor. The classification criteria of the tentative set include safety class, electrical class, quality group and seismic category for the components, structures and systems of DEMO Plant. Use of ASME Section III for the design study of DEMO Plant is also proposed to make the best use of the commonalities between DEMO Plant and existing nuclear power plant.
The Bias Ratio

Many hedge funds invest in illiquid, hard to price securities that offer opportunities for high returns. However, the lack of price transparency makes measuring objective performance of investments in illiquid instruments quite difficult. To calculate monthly returns, managers employ pricing schemes based on the last available traded price, the average of prices received from dealers, or their own best estimate. The consequences of such practices include stale prices, managed prices, and false measures of volatility. A pricing policy applied subjectively can allow the return distribution of a fund to take the shape desired by the manager, rather than one dictated by an unbiased market. The Bias Ratio, presented here, provides a measure of human “bias” used in return calculations. This paper defines a simple return-based formula for the Bias Ratio, which gives a concrete measure of valuation bias for illiquid hedge fund assets. By measuring the shape of return histograms around the critical area surrounding a zero percent return, the Bias Ratio flags funds that might “smooth” returns. 1 Getmansky, Mila; Lo, Andrew; Makarov, Igor; “An Econometric Model of Serial Correlation and Illiquidity In Hedge Fund Returns”, 2003, NBER Working Paper No. w9571Issued in March 2003. 2 Asness, Clifford S. ; Krail, Robert J.; Liew, John M. , “Alternative Investments: Do Hedge Funds Hedge? ”, 2001, Journal of Portfolio Management, Volume 28, Number 1. 3 Weinstein, Eric; Abdulali, Adil, “Hedge fund transparency: quantifying valuation bias for illiquid assets”, June 2002, Risk.
Temporal profile of circadian clock gene expression in a transplanted suprachiasmatic nucleus and peripheral tissues

The mammalian hypothalamic suprachiasmatic nucleus (SCN) is the master oscillator that regulates the circadian rhythms of the peripheral oscillators. Previous studies have demonstrated that the transplantation of embryonic SCN tissues into SCN‐lesioned arrhythmic mice restores the behavioral circadian rhythms of these animals. In our present study, we examined the clock gene expression profiles in a transplanted SCN and peripheral tissues, and also analysed the circadian rhythm of the locomotor activity in SCN‐grafted mice. These experiments were undertaken to elucidate whether the transplanted SCN generates a dynamic circadian oscillation and maintains the phase relationships that can be detected in intact mice. The grafted SCN indeed showed dynamic circadian expression rhythms of clock genes such as mPeriod1 (mPer1) and mPeriod2 (mPer2). Furthermore, the phase differences between the expression rhythms of these genes in the grafted SCN and the locomotor activity rhythms of the transplanted animals were found to be very similar to those in intact animals. Moreover, in the liver, kidney and skeletal muscles of the transplanted animals, the phase angles between the circadian rhythm of the grafted SCN and that of the peripheral tissues were maintained as in intact animals. However, in the SCN‐grafted animals, the amplitudes of the mPer1 and mPer2 rhythms were attenuated in the peripheral tissues. Our current findings therefore indicate that a transplanted SCN has the capacity to generate a dynamic intrinsic circadian oscillation, and can also lock the normal phase angles among the SCN, locomotor activity and peripheral oscillators in a similar manner as in intact control animals.
Emerging clinical principles on the use of bevacizumab for the treatment of malignant gliomas

Despite advances in adjuvant therapy, the prognosis for most patients with high‐grade glioma (HGG) is poor, and almost all HGGs have a likelihood of disease recurrence. HGGs are highly vascularized tumors with elevated expression levels of vascular endothelial growth factor (VEGF), an important mediator of angiogenesis. A compelling biologic rationale, a pressing need for improved therapeutics and positive results from studies of bevacizumab in other tumor types, led to the evaluation of bevacizumab in the treatment of HGG. It was demonstrated previously that bevacizumab, which is a humanized monoclonal antibody that targets VEGF, improved outcomes when combined with chemotherapy (most commonly irinotecan) in patients with recurrent HGG; and, on the basis of an improved objective response rate in 2 prospective phase 2 studies, bevacizumab was granted accelerated approval by the US Food and Drug Administration as a single agent in patients with previously treated glioblastoma (GB). Bevacizumab‐containing therapy has been associated with manageable, class‐specific toxicity; however, severe treatment‐related adverse events are observed in a minority of patients. Preliminary data on bevacizumab‐based therapy in recurrent anaplastic gliomas, in the frontline treatment of GB, and in additional patient populations are also encouraging. With the goal of addressing unanswered questions regarding the optimal use of bevacizumab, the objective of the current review was to provide a summary of the clinical efficacy and safety data on bevacizumab in patients with HGG, the practical issues surrounding the administration of bevacizumab, and ongoing investigations of bevacizumab in additional brain tumor treatment settings. Cancer 2010. © 2010 American Cancer Society.
Variable Nuclear Cytoplasmic Distribution of the 11.5-kDa Zinc-binding Protein (Parathymosin-α) and Identification of a Bipartite Nuclear Localization Signal (*)

The 11.5-kDa zinc-binding protein (ZnBP, parathymosin-α), a potent inactivator of 1-phosphofructokinase, is found only in the cytoplasm of most tissues despite the presence of the putative nuclear localization signal PKRQKT. Recent reports on nuclear uptake of ZnBP could not exclude the participation of unspecific diffusion. We show here that wild-type ZnBP overexpressed in COS cells accumulates exclusively in the nucleus but that ZnBP with a mutated or deleted PKRQKT motif appears both in the nucleus and in the cytoplasm. In contrast, fusion proteins between ZnBP and parts of the endoplasmic reticulum protein calreticulin required the intact PKRQKT motif for nuclear import. The motif RKR, located nine amino acids upstream of the PKRQKT motif, is also involved in the active nuclear import of ZnBP. In contrast to rat hepatocytes and kidney cells in situ, which have ZnBP almost exclusively in the cytosol, we find ZnBP in Reuber H35 hepatoma cells and normal rat kidney cells only in the nuclei. Freshly isolated rat hepatocytes translocate their ZnBP to the nucleus in <24 h during standard cell culture conditions.