Miracle-dz/UniFAR-FTUs huggingface dataset:
Induction of Primary Virus-Cross-Reactive Human Immunodeficiency Virus Type 1-Neutralizing Antibodies in Small Animals by Using an Alphavirus-Derived In Vivo Expression System

ABSTRACT We have studied the induction of neutralizing antibodies by in vivo expression of the human immunodeficiency virus type 1 (HIV-1) envelope by using a Venezuelan equine encephalitis virus (VEE) replicon system with mice and rabbits. The HIV-1 envelope, clone R2, has broad sensitivity to cross-reactive neutralization and was obtained from a donor with broadly cross-reactive, primary virus-neutralizing antibodies (donor of reference serum, HIV-1-neutralizing serum 2 [HNS2]). It was expressed as gp160, as secreted gp140, and as gp160ΔCT with the cytoplasmic tail deleted. gp140 was expressed in vitro at a high level and was predominantly uncleaved oligomer. gp160ΔCT was released by cells in the form of membrane-bound vesicles. gp160ΔCT induced stronger neutralizing responses than the other forms. Use of a helper plasmid for replicon particle packaging, in which the VEE envelope gene comprised a wild-type rather than a host range-adapted sequence, also enhanced immunogenicity. Neutralizing activity fractionated with immunoglobulin G. This activity was cross-reactive among a panel of five nonhomologous primary clade B strains and a Chinese clade C strain and minimally reactive against a Chinese clade E (circulating recombinant form 1) strain. The comparative neutralization of these strains by immune mouse sera was similar to the relative neutralizing effects of HNS2, and responses induced in rabbits were similar to those induced in mice. Together, these results demonstrate that neutralizing antibody responses can be induced in mice within 2 to 3 months that are similar in potency and cross-reactivity to those found in the chronically infected, long-term nonprogressive donor of HNS2. These findings support the expectation that induction of highly cross-reactive HIV-1 primary virus-neutralizing activity by vaccination may be realized.
The Impact of Macroeconomic Condition on The Banks Performance in Indonesia

This paper analyzes the impact of macroeconomic indicator (including the production index, inflation, Bank Indonesia rate, Jakarta stock index, exchange rate and the crude oil price) on the state owned banks’ performance. We apply the Vector Error Correction Model (VECM) on the banking data ranging from 2006-2013, and provide us several findings. First, the impulse response function shows the largest response of the bank overhead cost (BOPO) due to the macroeconomic shock; we argue the volatility of this bank efficiency indicator, reflects the inefficiency of the banks in Indonesian. Second, the amount of loan and the lending to deposit ratio (LDR) provide the weakest response due to the macroeconomic shock. This is in line with the result of variance decomposition, where the macroeconomic variable explains the least of the NPL variation. Third, from all macroeconomic variables we observe, the shock of Bank Indonesia’s rate generally provides the largest response of most of the bank performance indicators; which supports the use of the Bank Indonesia’s rate as effective monetary instrument.
Simplified prognostic model in patients with oxaliplatin-based or irinotecan-based first-line chemotherapy for metastatic colorectal cancer: a GERCOR study.

BACKGROUND The present study was done to establish a prognostic model for patients and trials using an oxaliplatin-based or irinotecan-based first-line chemotherapy in metastatic colorectal cancer. PATIENTS AND METHODS Eight hundred three patients treated with FOLFOX or FOLFIRI in three prospective trials were randomly separated into learning (n = 535) and validation (n = 268) samples. Eleven baseline variables were evaluated in univariate and multivariate analysis as prognostic factors for overall survival, and a prognostic score was developed. RESULTS Independent prognostic factors identified in multivariate analysis for overall survival were performance status (PS) (p < .001), serum lactate dehydrogenase (LDH) (p < .001), and number of metastatic sites (p = .005). A prognostic score based on these three variables was found efficient (Harrell's C index 0.61). This new model was improved by selecting only PS and LDH (Harrell's C index 0.64). Three risk groups for death could be identified: a low-risk group (n = 184; median overall survival [OS] 29.8 months), an intermediate-risk group (n = 223; median OS 19.5 months), and a high-risk group (n = 128; median OS 13.9 months). Median survival for the low-, intermediate-, and high-risk groups were 26.8, 21.1, and 16.5 months, respectively, in the validation sample (Harrell's C index 0.63). CONCLUSIONS Serum LDH level was the main prognostic factor in predicting survival, followed by WHO PS. We identified three risk groups for death depending on these two baseline parameters. This simple prognostic model can be useful for clinician's use and patient stratification in future clinical trials.
Osteopontin expression in a group of lymph node negative breast cancer patients

The aim of this study was to examine the cellular distribution of osteopontin (OPN) protein [by immunohistochemical (IHC) analysis] and mRNA [by in situ hybridization (ISH)] in the primary tumors of lymph node negative (LNN) breast cancer patients and to determine whether the level of immunodetectable OPN may be associated with tumor aggressiveness. We examined OPN levels in tumors from 154 patients with LNN breast cancer who were followed for a median of 7 years (range 1.7–16.3 years). IHC staining for OPN was seen in tumor infiltrating macrophages and lymphocytes in 70% of these tumors, and in the carcinoma cells themselves in 26%. ISH was performed to determine cellular distribution of OPN mRNA expression in sections from selected tumors. OPN mRNA was detected in groups of tumor cells, individual tumor cells and tumor infiltrating macrophages and lymphocytes. Matched sections showed that some tumor cells with IHC staining for OPN protein were also positive for OPN mRNA by ISH, in contrast with previous studies which have shown OPN mRNA expression only in tumor infiltrating inflammatory cells. Our results thus indicate that OPN protein can be produced by breast cancer cells in vivo and suggest that it may also be taken up from the environment (i.e., secreted by inflammatory cells or other tumor cells). Tumor cell IHC staining intensity was then assessed using a semiquantitative scoring system. Univariate analysis showed tumor cell OPN positivity above an optimized cutpoint to be significantly associated with decreased disease‐free survival (DFS) and overall survival (OS). The results of this pilot study thus suggest that the ability of breast cancer cells to either synthesize OPN or to bind and sequester OPN from the microenvironment may be associated with tumor aggressiveness and poor prognosis. Int. J. Cancer (Pred. Oncol.) 79:502–508, 1998. © 1998 Wiley‐Liss, Inc.
Alternate site surge capacity in times of public health disaster maintains trauma center and emergency department integrity: Hurricane Katrina.

BACKGROUND Hospital surge capacity has been advocated to accommodate large increases in demand for healthcare; however, existing urban trauma centers and emergency departments (TC/EDs) face barriers to providing timely care even at baseline patient volumes. The purpose of this study is to describe how alternate-site medical surge capacity absorbed large patient volumes while minimizing impact on routine TC/ED operations immediately after Hurricane Katrina. METHODS From September 1 to 16, 2005, an alternate site for medical care was established. Using an off-site space, the Dallas Convention Center Medical Unit (DCCMU) was established to meet the increased demand for care. Data were collected and compared with TC/ED patient volumes to assess impact on existing facilities. RESULTS During the study period, 23,231 persons displaced by Hurricane Katrina were registered to receive evacuee services in the City of Dallas, Texas. From those displaced, 10,367 visits for emergent or urgent healthcare were seen at the DCCMU. The mean number of daily visits (mean +/- SD) to the DCCMU was 619 +/- 301 visits with a peak on day 3 (n = 1,125). No patients died, 3.2% (n = 257) were observed in the DCCMU, and only 2.9% (n = 236) required transport to a TC/ED. During the same period, the mean number of TC/ED visits at the region's primary provider of indigent care (Hospital 1) was 346 +/- 36 visits. Using historical data from Hospital 1 during the same period of time (341 +/- 41), there was no significant difference in the mean number of TC/ED visits from the previous year (p = 0.26). CONCLUSIONS Alternate-site medical surge capacity provides for safe and effective delivery of care to a large influx of patients seeking urgent and emergent care. This protects the integrity of existing public hospital TC/ED infrastructure and ongoing operations.
Eaf1p Is Required for Recruitment of NuA4 in Targeting TFIID to the Promoters of the Ribosomal Protein Genes for Transcriptional Initiation In Vivo

ABSTRACT NuA4 (nucleosome acetyltransferase of H4) promotes transcriptional initiation of TFIID (a complex of TBP and TBP-associated factors [TAFs])-dependent ribosomal protein genes involved in ribosome biogenesis. However, it is not clearly understood how NuA4 regulates the transcription of ribosomal protein genes. Here, we show that NuA4 is recruited to the promoters of ribosomal protein genes, such as RPS5, RPL2B, and RPS11B, for TFIID recruitment to initiate transcription, and the recruitment of NuA4 to these promoters is impaired in the absence of its Eaf1p component. Intriguingly, impaired NuA4 recruitment in a Δeaf1 strain depletes recruitment of TFIID (a TAF-dependent form of TBP) but not the TAF-independent form of TBP to the promoters of ribosomal protein genes. However, in the absence of NuA4, SAGA (Spt-Ada-Gcn5-acetyltransferase) is involved in targeting the TAF-independent form of TBP to the promoters of ribosomal protein genes for transcriptional initiation. Thus, NuA4 plays an important role in targeting TFIID to the promoters of ribosomal protein genes for transcriptional initiation in vivo. Such a function is mediated via its targeted histone acetyltransferase activity. In the absence of NuA4, ribosomal protein genes lose TFIID dependency and become SAGA dependent for transcriptional initiation. Collectively, these results provide significant insights into the regulation of ribosomal protein gene expression and, hence, ribosome biogenesis and functions.
Diet and feeding behavior of Rhinopithecus bieti at Xiaochangdu, Tibet: adaptations to a marginal environment

The diet and feeding ecology of a wild subpopulation of black‐and‐white snub‐nosed monkeys (Rhinopithecus bieti) were studied at Xiaochangdu in Honglaxueshan Nature Reserve, Tibet. This region is climatologically harsher than any other inhabited by non‐human primates. Black‐and‐white snub‐nosed monkeys fed on 48 parts of 25 plant species, at least three species of lichens and seven species of invertebrates. The number of food items exploited varied markedly among seasons, with dietary diversity being greatest in spring and summer. In winter, black‐and‐white snub‐nosed monkeys had to subsist on fallback foods such as dried grass and bark. Ubiquitous lichens formed a major dietary constituent throughout the year, contributing about 75% of feeding records. Even though lichens act as a staple, our findings signify that the monkeys at Xiaochangdu prefer feeding on foliage, which is higher in protein content than the former. We provide evidence that black‐and‐white snub‐nosed monkeys are able to cope with an array of food items other than lichens and hence can be regarded as feeding generalists. We discuss the results with reference to previous studies on other subpopulations living in habitats that are floristically more diverse and offer more plant food items than the marginal habitat at Xiaochangdu. Am. J. Primatol. 69:1141–1158, 2007. © 2007 Wiley‐Liss, Inc.
Bismuth labeling for the CT assessment of local administration of magnetic nanoparticles

Many therapeutic applications of magnetic nanoparticles involve the local administration of nanometric iron oxide based materials as seeds for magnetothermia or drug carriers. A simple and widespread way of controlling the process using x-ray computed tomography (CT) scanners is desirable. The combination of iron and bismuth in one entity will increase the atenuation of x-rays, offering such a possibility. In order to check this possibility core–shell nanocrystals of iron oxide@bismuth oxide have been synthesized by an aqueous route and stabilized in water by polyethylene glycol (PEG), and we have evaluated their ability to generate contrast by CT and magnetic resonance imaging (MRI) to measure the radiopacity and proton relaxivities using phantoms. High-resolution scanning transmission electron microscopy (STEM) revealed that the material consists of a highly crystalline 8 nm core of maghemite and a 1 nm shell of bismuth atoms either isolated or clustered on the nanocrystal’s surface. The comparison of μCT and MRI images of mice acquired in the presence of the contrast shows that when local accumulations of the magnetic nanoparticles take place, CT images are more superior in the localization of the magnetic nanoparticles than MRI images, which results in magnetic field inhomogeneity artifacts.
Remote Raman Spectra of Benzene Obtained from 217 Meters Using a Single 532 nm Laser Pulse

This report describes a mobile Raman lidar system that has been developed for spectral measurements of samples located remotely at ranges of hundreds of meters. The performance of this system has been quantitatively verified in a lidar calibration experiment using a hard target of standardized reflectance. A new record in detection range was achieved for remote Raman systems using 532 nm laser excitation. Specifically, Raman spectra of liquid benzene were measured with an integration time corresponding to a single 532 nm laser pulse at a distance of 217 meters. The single-shot Raman spectra at 217 meters demonstrated high signal-to-noise ratio and good resolution sufficient for the unambiguous identification of the samples of interest. The transmitter consists of a 20 Hz Nd:YAG laser emitting at 532 nm and 1064 nm and a 178 mm telescope through the use of which allows the system to produce a focused beam at the target location. The receiver consists of a large custom telescope (609 mm aperture) and a Czerny–Turner monochromator equipped with two fast photomultiplier tubes.
Associations between phylogenetic clustering and HLA profile among HIV-infected individuals in San Diego, California.

BACKGROUND Specific sequence changes of human immunodeficiency virus type 1 (HIV-1) in the presence of specific HLA molecules may alter the composition and processing of viral peptides, leading to immune escape. Persistence of these mutations after transmission may leave the genetic fingerprint of the transmitter's HLA profile. Here, we evaluated the associations between HLA profiles and the phylogenetic relationships of HIV sequences sampled from a cohort of recently infected individuals in San Diego, California. METHODS We identified transmission clusters within the study cohort, using phylogenetic analysis of sampled HIV pol genotypes at a genetic distance of <1.5%. We then evaluated the association of specific HLA alleles, HLA homozygosity, HLA concordance, race and ethnicity, and mutational patterns within the clustering and nonclustering groups. RESULTS From 350 cohort participants, we identified 162 clustering individuals and 188 nonclustering individuals. We identified trends for enrichment of particular alleles within individual clusters and evidence of viral escape within those clusters. We also found that discordance of HLA alleles was significantly associated with clustering individuals. CONCLUSIONS Some transmission clusters demonstrate HLA enrichment, and viruses in these HLA-associated clusters often show evidence of escape to enriched alleles. Interestingly, HLA discordance was associated with clustering in our predominantly MSM population.
Carrier-Mediated Norepinephrine Release and Reperfusion Arrhythmias Induced by Protracted Ischemia in Isolated Perfused Guinea Pig Hearts: Effect of Presynaptic Modulation by α2-Adrenoceptor in Mild Hypothermic Ischemia

Yohimbine, an α2-adrenoceptor antagonist, has been reported to protect hypoxic myocardium and inhibit carrier-mediated norepinephrine (NE) release and reperfusion arrhythmias (ventricular fibrillation; VF) in normothermic ischemia. In heart surgery, mild hypothermic (tepid) cardioplegia has been reported to reduce metabolic demand and permit immediate recovery of cardiac function. Therefore, we determined the effect of yohimbine on NE release and reperfusion arrhythmias in isolated perfused guinea pig hearts of tepid temperature (32°C) ischemia model. Stepwise increase of global ischemia period (20, 40, and 60 min) induced a progressive increase of NE release and duration of VF. Neuronal uptake 1 inhibitor desipramine (100 nM) and Na+-H+ exchanger inhibitor 5-N-ethyl-N-isopropyl-amiloride (10 μM) decreased NE and VF in 60-min hypothermic ischemia. This indicated that NE release induced by protracted tepid ischemia was due to carrier-mediated release. Yohimbine (1 μM) markedly reduced NE release and VF (p < 0.01 versus control) and 5-bromo-N-(4,5-dihydro-1H-imidazol-2-yl)-6-quinoxalinamine [UK 14,304 (UK); 10 μM], an α2-adrenoceptor agonist, increased NE release and VF (p < 0.01 versus control). Yohimbine (1 μM) prevented the potentiated effect of UK (10 μM) in hypothermia (p < 0.01 versus UK). Our findings indicate that presynaptic reduction of carrier-mediated NE release seems to be one of the most important factors controlling reperfusion arrhythmias, and α2-adrenoceptor blockade by yohimbine (1 μM) in tepid ischemia may contribute to effective myocardial protection in terms of NE release and reperfusion arrhythmia.
DOT 4 Links Silencing and Cell Growth in Saccharomyces cerevisiae

Transcriptional silencing in Saccharomyces cerevisiae occurs at specific loci and is mediated by a multiprotein complex that includes Rap1p and the Sir proteins. We studied the function of a recently identified gene, DOT4, that disrupts silencing when overexpressed. DOT4 encodes an ubiquitin processing protease (hydrolase) that is primarily located in the nucleus. By two-hybrid analysis, the amino-terminal third of Dot4p interacts with the silencing protein Sir4p. Cells lacking DOT4 exhibited reduced silencing and a corresponding decrease in the level of Sir4p. Together, these findings suggest that Dot4p regulates silencing by acting on Sir4p. In strains with several auxotrophic markers, loss of DOT4 ubiquitin hydrolase activity also results in a slow-growth defect. The defect can be partially suppressed by mutations in a subunit of the 26S proteasome, suggesting that Dot4p has the ability to prevent ubiquitin-mediated degradation. Furthermore, wild-type SIR2, SIR3, and SIR4 are required for full manifestation of the growth defect in a dot4 strain, indicating that the growth defect is caused in part by a silencing-related mechanism. We propose that Dot4p helps to restrict the location of silencing proteins to a limited set of genomic loci.
Effect of severity of arm impairment on response to additional physiotherapy early after stroke

Objective: To investigate effect of initial severity of arm impairment on response to additional physiotherapy for the arm after stroke. Design: In this controlled trial, patients were randomized into one of three groups: routine physiotherapy (RPT) patients received no additional physiotherapy; qualified physiotherapy (QPT) patients received additional treatment from a qualified physiotherapist; assistant physiotherapy (APT) patients received additional treatment from a trained supervised assistant. Comparisons between the whole groups found no significant differences and have been reported elsewhere. In a post hoc analysis, the groups were subdivided according to severity of initial arm impairment. The subgroups were then compared. Setting: A general hospital with acute and rehabilitation facilities for stroke patients. Subjects: Patients (n= 282) between one and five weeks after stroke. Interventions: Ten hours additional physiotherapy were given over a five-week period. The treatment approach reflected current usual British practice. ‘Blind’ outcome assessment was performed after intervention, and at three and six months after stroke. Main outcome measures: Rivermead Motor Assessment Arm Scale, Action Research Arm Test. Results: In more severe patients, no benefits of additional treatment were detected. In less severe patients, significant benefits were found in those who completed treatment with the trained assistant. However, a considerable number of patients did not complete the additional treatment. The content of treatment differed between the QPT and APT groups. Treatment of less severe APT patients emphasized repetitive supervised practice of movements and functional tasks. No significant effects of additional treatment were found in terms of shoulder pain or spasticity. Conclusions: Regardless of whether additional physiotherapy was given or not, patients with severe arm impairment improved very little in arm function. Enabling adaptation to loss of arm function may be an appropriate rehabilitation strategy for some patients. Trends in the data confirm findings of some previous studies that intensive treatment for patients with some motor recovery of the upper limb is effective. Following patient assessment and treatment planning by a qualified physiotherapist, it may be appropriate for guidance of repetitive practice of motor and functional tasks to be delegated to trained and closely supervised assistant staff.
A novel improvement of particle swarm optimization using Dual Factors strategy

The particle swarm optimization, inspired by nature, is widely used for optimizing complex problems and achieves many good stories in practical applications. However, the traditional PSO only focuses on the function value during evolutionary process. It ignores the information of distance between particles and potential regions. A Dual Factors Particle Swarm Optimization (DFPSO) incorporating both of distance and function information is proposed in this paper to help PSO in finding potential global optimal regions. The strategy of the DFPSO increases the diversity of population to yield improved results. The experimental results manifest that the performance, including accuracy and speed, are improved.