Miracle-dz/UniFAR-FTUs huggingface dataset:
Supporting Online Material Recombinant Origin of the Retrovirus Xmrv

Acknowledgments: We thank D. Peterson for the referrals of all the subjects evaluated, J. Weismann for coordinating subject participation, I. Livinti for assistance with data management, E. Delwart and J. Fiddes for comments on the manuscript, and K. Peter for help in preparation of the manuscript. These studies were conducted with support of private funds to the investigators. Patent applications have been filed by Abbott Laboratories relating to detection of XMRV using immunoassays and molecular-based assays. The retrovirus XMRV (xenotropic murine leukemia virus–related virus) has been detected in human prostate tumors and in blood samples from patients with chronic fatigue syndrome, but these findings have not been replicated. We hypothesized that an understanding of when and how XMRV first arose might help explain the discrepant results. We studied human prostate cancer cell lines CWR22Rv1 and CWR-R1, which produce XMRV virtually identical to the viruses recently found in patient samples, as well as their progenitor human prostate tumor xenograft (CWR22) that had been passaged in mice. We detected XMRV infection in the two cell lines and in the later passage xenografts, but not in the early passages. In particular, we found that the host mice contained two proviruses, PreXMRV-1 and PreXMRV-2, which share 99.92% identity with XMRV over >3.2-kilobase stretches of their genomes. We conclude that XMRV was not present in the original CWR22 tumor but was generated by recombination of two proviruses during tumor passaging in mice. The probability that an identical recombinant was generated independently is negligible (~10 −12); our results suggest that the association of XMRV with human disease is due to contamination of human samples with virus originating from this recombination event. M urine leukemia viruses (MLVs) are retroviruses belonging to the genus Gammaretrovirus that cause cancers and other diseases in mice, and they are divided into the ecotropic, amphotropic, polytropic, and xenotropic classes on the basis of their receptor usage. Xenotropic MLVs cannot infect cells from inbred mice but can infect cells from other species , including humans. Xenotropic murine leu-kemia virus–related virus (XMRV) was isolated from a human prostate cancer (PC) in 2006 and has been reported to be present in 6 to 27% of human PCs (1, 2) and in the peripheral blood of 67% of chronic fatigue syndrome (CFS) patients (3). The assertion that XMRV is circulating in the human population has been challenged by several studies that have failed to detect XMRV …
Evaluation of socioeconomic status as a risk factor of pterygium using the Korean National Health and Nutrition Examination Survey 2010 to 2011

Abstract Pterygium is a common conjunctival disorder. The socioeconomic risk factors of pterygium have not been systematically evaluated in Korea. The study investigated risk factors of pterygium considering socioeconomic status. Participants were 9839 adults aged 19 to 74 years, who underwent ophthalmic slit-lamp examinations as part of the Korean National Health and Nutrition Examination Survey 2010 to 2011. Pterygium was diagnosed as a growth of fibrovascular tissue over the cornea. The socioeconomic risk factors were analyzed in association with the presence of pterygium. Multiple logistic regression analysis was used to evaluate the odds ratios for differences in socioeconomic status. The presence of pterygium was associated with diabetes mellitus, hypertension, metabolic syndrome, and sun exposure time (>5 h/d). The blood level of 25-hydroxyvitamin D was higher in the pterygium group than in the control group, but both groups were deficient in 25-hydroxyvitamin D compared with the normal reference level. Pterygium was almost 3 times as frequent among persons who worked outdoors, such as skilled agricultural, forestry, and fishery workers, than among those who worked indoors (odds ratio 3.061, 95% confidence interval 1.946–4.813). Low educational status and longer working hours were also significantly associated with pterygium. This study used a nationwide population-based survey conducted by the Korean Centers for Disease Control and Prevention to reveal that pterygium is associated with low socioeconomic status. Efforts should be made to reduce the risk of pterygium by changing modifiable risk factors, especially among people with low socioeconomic status.
Correlation of magnetic resonance spectroscopic and growth characteristics within Grades II and III gliomas.

OBJECT The accurate diagnosis of World Health Organization Grades II and III gliomas is crucial for the effective treatment of patients with such lesions. Increased cell density and mitotic activity are histological features that distinguish Grade III from Grade II gliomas. Because increased cellular proliferation and density both contribute to the in vivo magnetic resonance (MR) spectroscopic peak corresponding to choline-containing compounds (Cho), the authors hypothesized that multivoxel MR spectroscopy might help identify the tumor regions with the most aggressive growth characteristics, which would be optimal locations for biopsy. They investigated the ability to use one or more MR spectroscopic parameters to predict the MIB-1 cell proliferation index (PI), the terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick-end labeling cell death index (DI), the cell density, and the ratio of proliferation to cell death (PI/DI) within different regions of the same tumor. METHODS Patients with presumed Grades II or III glioma underwent 3D MR spectroscopic imaging prior to surgery, and two or three regions within the tumor were targeted for biopsy retrieval based on their spectroscopic features. Biopsy specimens were extracted from the tumor during image-guided resection, and the PI, DI, and cell density were assessed in the specimens using immunohistochemical methods. CONCLUSIONS The authors found that the relative levels of Cho and N-acetylaspartate (NAA) correlated with the cell density, PI, and PI/DI ratio within different regions of the same tumor and that the association held for the subpopulation of nonenhancing tumors. The association was stronger in tumors with large ranges of Cho/NAA values, irrespective of the presence of contrast enhancement. The findings demonstrate the validity of using MR spectroscopy to identify regions of aggressive growth in presumed Grade II or III gliomas that would be suitable targets for retrieving diagnostic biopsy specimens.
Particle Markov chain Monte Carlo methods

Summary. Markov chain Monte Carlo and sequential Monte Carlo methods have emerged as the two main tools to sample from high dimensional probability distributions. Although asymptotic convergence of Markov chain Monte Carlo algorithms is ensured under weak assumptions, the performance of these algorithms is unreliable when the proposal distributions that are used to explore the space are poorly chosen and/or if highly correlated variables are updated independently. We show here how it is possible to build efficient high dimensional proposal distributions by using sequential Monte Carlo methods. This allows us not only to improve over standard Markov chain Monte Carlo schemes but also to make Bayesian inference feasible for a large class of statistical models where this was not previously so. We demonstrate these algorithms on a non‐linear state space model and a Lévy‐driven stochastic volatility model.
The Darrieus–Landau instability in fast deflagration and laser ablation

The problem of the Darrieus–Landau instability at a discontinuous deflagration front in a compressible flow is solved. Numerous previous attempts to solve this problem suffered from the deficit of boundary conditions. Here, the required additional boundary condition is derived rigorously taking into account the internal structure of the front. The derived condition implies a constant mass flux at the front; it reduces to the classical Darrieus–Landau condition in the limit of an incompressible flow. It is demonstrated that in general the solution to the problem depends on the type of energy source in the flow. In the common case of a strongly localized source, compression effects make the Darrieus–Landau instability considerably weaker. Particularly, the instability growth rate is reduced for laser ablation in comparison to the classical incompressible case. The instability disappears completely in the Chapman–Jouguet regime of ultimately fast deflagration.
Increased cholesterol absorption rather than synthesis is involved in boosted protease inhibitor-associated hypercholesterolaemia

Objective: The aim of this study was to compare the differential effects of first-line efavirenz (EFV)-based vs. boosted lopinavir-based antiretroviral regimens on cholesterol metabolism. Design: Multicentre, open-label, randomized clinical trial. Methods: Forty-nine naive HIV-infected patients were randomized (1 : 1) to receive either ritonavir-boosted lopinavir (LPV/r) or EFV both in combination with tenofovir and emtricitabine (ClinicalTrials.gov: NCT00759070). Lipid profile and serum phytosterols and cholesterol precursors were determined at baseline and after 16 weeks. Results: After 16 weeks of intervention, total and non-HDL cholesterol as well as triglyceride levels significantly increased in the LPV/r-group (+1.0 ± 0.8; +0.8 ± 0.7 and +0.8 ± 1.5 mmol/l, respectively), but not in the EFV-group (+0.4 ± 0.7; +0.4 ± 0.6 and 0.2 ± 0.5 mmol/l, respectively). Markers of cholesterol absorption (campesterol-to-cholesterol and sitosterol-to-cholesterol ratios) significantly increased in the LPV/r-group, but not in the EFV-group, whereas there were no changes in either group of the lathosterol-to-cholesterol ratio, a marker of cholesterol synthesis. Conclusion: Treatment with an LPV/r-based therapy increased total cholesterol relative to EFV-based therapy. Our data suggest that absorption rather than synthesis is the mechanism involved in LPV/r-associated increased total cholesterol.
GENDER DIFFERENCES IN PERSONAL ADVERTISEMENTS IN LITHUANIAN ITV SMS

This study examines a popular Lithuanian iTV SMS program, Telejazz, which broadcasts music and personal ads posted by viewers to the program in the form of text messages. The contents of the televised SMS ads are compared with previous research on personal ads in print media. Despite the novelty and the technical constraints of the convergent iTV SMS medium, content analysis of the personal ads reveals that females and males have contrasting self-presentations and expectations, similar to those found in traditional newspaper ads in English. These findings are interpreted in light of the Lithuanian cultural context, interactional sociolinguistic theories of gender differentiation, and theories of technology adoption/adaption that emphasize ways in which users reinscribe existing social practices in new media.
Influence of Error Rate on Frustration of BCI Users

Brain-Computer Interfaces (BCIs) are still much less reliable than other input devices. The error rates of BCIs range from 5% up to 60%. In this paper, we assess the subjective frustration, motivation, and fatigue of BCI users, when confronted to different levels of error rate. We conducted a BCI experiment in which the error rate was artificially controlled. Our results first show that a prolonged use of BCI significantly increases the perceived fatigue, and induces a drop in motivation. We also found that user frustration increases with the error rate of the system but this increase does not seem critical for small differences of error rate. Thus, for future BCIs, we would advise to favor user comfort over accuracy when the potential gain of accuracy remains small.
Predicting Outcomes in Idiopathic Pulmonary Fibrosis Using Automated Computed Tomographic Analysis

Rationale: Quantitative computed tomographic (CT) measures of baseline disease severity might identify patients with idiopathic pulmonary fibrosis (IPF) with an increased mortality risk. We evaluated whether quantitative CT variables could act as a cohort enrichment tool in future IPF drug trials. Objectives: To determine whether computer‐derived CT measures, specifically measures of pulmonary vessel‐related structures (VRSs), can better predict functional decline and survival in IPF and reduce requisite sample sizes in drug trial populations. Methods: Patients with IPF undergoing volumetric noncontrast CT imaging at the Royal Brompton Hospital, London, and St. Antonius Hospital, Utrecht, were examined to identify pulmonary function measures (including FVC) and visual and computer‐derived (CALIPER [Computer‐Aided Lung Informatics for Pathology Evaluation and Rating] software) CT features predictive of mortality and FVC decline. The discovery cohort comprised 247 consecutive patients, with validation of results conducted in a separate cohort of 284 patients, all fulfilling drug trial entry criteria. Measurements and Main Results: In the discovery and validation cohorts, CALIPER‐derived features, particularly VRS scores, were among the strongest predictors of survival and FVC decline. CALIPER results were accentuated in patients with less extensive disease, outperforming pulmonary function measures. When used as a cohort enrichment tool, a CALIPER VRS score greater than 4.4% of the lung was able to reduce the requisite sample size of an IPF drug trial by 26%. Conclusions: Our study has validated a new quantitative CT measure in patients with IPF fulfilling drug trial entry criteria—the VRS score—that outperformed current gold standard measures of outcome. When used for cohort enrichment in an IPF drug trial setting, VRS threshold scores can reduce a required IPF drug trial population size by 25%, thereby limiting prohibitive trial costs. Importantly, VRS scores identify patients in whom antifibrotic medication prolongs life and reduces FVC decline.
Judgement, myth and hope in life-centred funerals

Funerals led by a celebrant not representing a faith community are rapidly increasing in England. This article argues that these ‘life-centred’ funerals have an implicit theology; like Christian funerals, but in different ways, they invite judgement, myth and hope. How should churches respond to this competition? Imitation is problematic, because the ‘life-centred’ approach is far more than a mere technique to be bolted on to the Christian funeral. The article concludes by sketching some unique resources churches have that cannot be matched by the new breed of celebrants.
MICROWAVE CHAOTIC OSCILLATORS WITH CONTROLLED BANDWIDTH

An approach to design of chaotic oscillators with controlled bandwidth in different frequency bands is proposed. One of possible mathematical models of the oscillator and simulation results are considered. Implementations of microwave chaotic oscillators and experimental results are demonstrated. Index terms – Dynamic chaos, chaotic oscillator, frequency-selective circuit, microstrip line, wideband chaotic oscillations.
Binding of Serotonin to Receptors at Multiple Sites Is Required for Structural Plasticity Accompanying Long-Term Facilitation ofAplysia Sensorimotor Synapses

Long-term changes in the efficacy of Aplysiasensorimotor synapses accompany nonassociative and associative forms of behavioral plasticity. This synapse expresses long-term facilitation either with repeated applications of 5-hydroxytryptamine (5-HT) or with a single pairing of tetanus in the sensory neuron (SN) and bath application of 5-HT. We examined whether structural changes in the SN accompany all forms of long-term synaptic enhancement and the locations at which 5-HT must bind receptors to evoke long-term functional and/or structural changes. Pairing tetanus with one application of 5-HT evoked both functional and structural changes after 24 hr only when 5-HT application was temporally paired with the tetanus and activated receptors on both the SN cell body and terminal region. Repeated application of 5-HT to the terminal region alone failed to evoke any long-term change. Repeated applications of 5-HT to the SN cell body alone evoked a change in synaptic efficacy at 24 hr but failed to increase SN varicosities. Repeated applications of 5-HT to both the SN cell body and the terminal region evoked increases in both synaptic efficacy and the number of SN varicosities at 24 hr. The results indicate that different external stimuli can evoke equivalent forms of long-term synaptic facilitation with or without structural changes in the SNs. Changes in the number of SN varicosities can accompany different forms of long-term facilitation and require the activation of 5-HT receptors at multiple sites.
Deciphering the Molecular Mechanism Underlying the Inhibitory Efficacy of Taiwanese Local Pomegranate Peels against Urinary Bladder Urothelial Carcinoma

Pomegranate (Punica granatum L.) fruit has been demonstrated to have the inhibitory activities to various tumors. In this study, we try to uncover the molecular mechanism underlying the inhibitory capability of Taiwanese local pomegranate fruit to urinary bladder urothelial carcinoma. The results collected from the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay indicated that the ethanol extract of pomegranate peel exhibited better inhibitory activity to human urinary bladder urothelial carcinoma T24 and J82 cells than that of pulp. Furthermore, the ethylacetate layer of peel ethanol extract was observed to have the best inhibitory activity against urinary bladder urothelial carcinoma cells. One of the eight fractions (PEPE2 fraction) collected from the ethylacetate layer with Diaion HP-20 column chromatography demonstrated the highest inhibitory activity in urinary bladder urothelial carcinoma cells. The results of the flow cytometry and apoptotic pathway studies suggested that the inhibitory activity of PEPE2 fraction were attributed to the UBUC cell apoptosis. To confirm the above results, our results of xenograft-induced bladder tumor in nude mice showed that the oral consumption of the ethylacetate layer (2, 5, 10 and 100 mg/kg) could decrease the volume and weight of T24 tumors and caused the apoptosis in the xenografted tumors, which was observed by terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end-labeling assay. This study provided the likelihood that the traditionally non-edible pomegranate peel waste is re-utilized to make an affordable and promising chemopreventive product to prevent UBUC incidence or recurrence.
Chlorambucil Cytotoxicity in Malignant B Lymphocytes Is Synergistically Increased by 2-(Morpholin-4-yl)-benzo[h]chomen-4-one (NU7026)-Mediated Inhibition of DNA Double-Strand Break Repair via Inhibition of DNA-Dependent Protein Kinase

Chlorambucil (CLB) treatment is used in chronic lymphocytic leukemia (CLL) but resistance to CLB develops in association with accelerated repair of CLB-induced DNA damage. Phosphorylated histone H2AX (γH2AX) is located at DNA double-strand break (DSB) sites; furthermore, it recruits and retains damage-responsive proteins. This damage can be repaired by nonhomologous DNA end-joining (NHEJ) and/or homologous recombinational repair (HR) pathways. A key component of NHEJ is the DNA-dependent protein kinase (DNA-PK) complex. Increased DNA-PK activity is associated with resistance to CLB in CLL. We used the specific DNA-PK inhibitor 2-(morpholin-4-yl)-benzo[h]chomen-4-one (NU7026) to sensitize CLL cells to chlorambucil. Our results indicate that in a CLL cell line (I83) and in primary CLL-lymphocytes, chlorambucil plus NU7026 has synergistic cytotoxic activity at nontoxic doses of NU7026. CLB treatment results in G2/M phase arrest, and NU7026 increases this CLB-induced G2/M arrest. Moreover, a kinetic time course demonstrates that CLB-induced DNA-PK activity was inhibited by NU7026, providing direct evidence of the ability of NU7026 to inhibit DNA-PK function. DSBs, visualized as γH2AX, were enhanced 24 to 48 h after CLB and further increased by CLB plus NU7026, suggesting that the synergy of the combination is mediated by NU7026 inhibition of DNA-PK with subsequent inhibition of DSB repair.
News and advice from RSA Laboratories Bulletin

Recent cryptanalytic results on the properties of three popular hash functions have raised questions about their security. This note summarizes these results, gives our assessment of their implications and offers our recommendations for product planners and developers who may be using these algorithms. 1. Introduction A hash function (or more accurately a cryptographic hash function or message-digest algorithm) operates on an input string of arbitrary length and generates an output string of fixed length. This output is commonly called a hash value or a message digest. While much of the motivation for the design of a hash function comes from its usefulness in optimizing the process of digitally signing some document, hash functions can be used for a wide range of purposes.
Investigating Unique Environmental Influences of Parenting Practices on Youth Anxiety

The associations between parenting practices and adolescent anxiety symptoms were examined in both individual and monozygotic (MZ) twin differences levels. Participants were 804 pairs of Chinese MZ adolescent twins aged 10–18 years (M = 13.57, SD = 2.67, 52% females). Twins’ anxiety symptoms were assessed by self- and parent-reports. Twins also reported their perceived parenting practices. On the individual level, parental warmth-reasoning was negatively, whereas harshness-hostility was positively, associated with both self- and parent-reported youth anxiety. On the MZ-twin differences level, the magnitudes of the associations between parenting practices and youth anxiety were decreased. MZ-twin difference in parental warmth-reasoning remained significantly associated with self- and parent-reported youth anxiety; MZ-twin difference in parental harsh-hostility was only significantly associated with self-reported youth anxiety. This study indicated that parental warmth-reasoning and harshness-hostility may be unique environmental experiences that influence youth anxiety, and illustrated the necessity of controlling for gene-environment correlations when examining the true environmental effects of parenting on child behavior.