Miracle-dz/UniFAR-FTUs huggingface dataset:
Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships

Phylogenetic profiles encode patterns of presence or absence of genes across genomes, and these profiles can be used to assign functional relationships to nonhomologous pairs of proteins (Pellegrini et al., Proc Natl Acad Sci USA 1999;96:4284–4288 ). Although it is well known that many proteins were created from combinations of domains, most of the existing implementations of phylogenetic profiles do not consider this fact. Here, we introduce an extension that considers the multidomain nature of proteins and test the method against the known interaction data sets. Whereas earlier implementations associated one entire sequence with one protein phylogenetic profile (Single‐Profile), our method instead breaks the sequence into a set of segments of predetermined size and constructs a separate profile for each segment (Multiple‐Profile). The results show that the Multiple‐Profile method performs as well as the Single‐Profile method. However, the two methods share, surprisingly, a small fraction of their predictions, indicating that the Multiple‐Profile method can detect known interactions missed by the Single‐Profile method. Thus, the Multiple‐Profile method can be used with other methods to determine functional relationships on a genome scale with wider coverage. Proteins 2006. © 2005 Wiley‐Liss, Inc.
THE RELATIONSHIP BETWEEN SAVING AND GROWTH IN SOUTH AFRICA: A TIME SERIES ANALYSIS

This paper uses the Johansen VECM estimation technique to examine the directions of association between saving and growth in South Africa over the period 1946-1992. We examine the aggregate private saving rate and its interaction with investment and growth. The paper finds that the private saving rate has a direct, as well as, an indirect effect on growth. The indirect effect is through the private investment rate. In turn, we find that growth has a positive effect on the private saving rate. The extent of this effect is determined by liquidity constraints. Thus, we have a virtuous cycle, as growth enhances saving, which in turn further enhances growth. Copyright 2005 Economic Society of South Africa.
Outcome of Children with Standard‐Risk T‐Lineage Acute Lymphoblastic Leukemia—Comparison among Different Treatment Strategies

Children with T‐lineage acute lymphoblastic leukemia ALL (T‐ALL) historically have had inferior outcomes compared with the children with precursor‐B ALL (B‐ALL). After 1995, the Children's Cancer Group (CCG) treated patients with B‐ and T‐ALL according to the National Cancer Institute (NCI) risk criteria, basing risk stratification on age and white blood cell (WBC) count regardless of immunophenotype. The Pediatric Oncology Group (POG) treated all the patients with T‐ALL on separate, generally more intensive protocols than those used to treat the patients with B‐ALL.
Intratympanic Sustained-Exposure Dexamethasone Thermosensitive Gel for Symptoms of Ménière's Disease: Randomized Phase 2b Safety and Efficacy Trial

Objective: To evaluate safety and efficacy of a single intratympanic injection of OTO-104, sustained-exposure dexamethasone, in patients with unilateral Ménière's disease. Study Design: Randomized, double-blind, placebo-controlled, Phase 2b study over 5 months. Setting: Fifty-two academic and community otolaryngology centers. Patients: One hundred fifty four patients (77 per group) aged 18 to 85 years inclusive. Intervention: Single intratympanic injection of OTO-104 (12 mg dexamethasone) or placebo. Main Outcome Measures: Efficacy (vertigo) and safety (adverse events, otoscopy, audiometry, tympanometry). Results: Primary endpoint (change from baseline in vertigo rate at Month 3) was not statistically significant (placebo [−43%], OTO-104 [−61%], P = 0.067). Improvements with OTO-104 were observed in prospectively defined secondary endpoints number of days with definitive vertigo, (Month 2 [P = 0.035], Month 3 [P = 0.030]), vertigo severity (Months 2–3, P = 0.046) and daily vertigo counts (Month 2, P = 0.042), and in some Short Form-36 (SF-36) subscales (Month 2 bodily pain P = 0.039, vitality P = 0.045, social functioning P = 0.025). No difference in tinnitus loudness or tinnitus handicap inventory (THI-25) was observed. OTO-104 was well tolerated; no negative impact on safety compared with placebo. Persistent tympanic membrane perforation was observed in two OTO-104 treated patients at study end. Conclusion: OTO-104 was well-tolerated, did not significantly affect change from baseline in vertigo rate, but did reduce number definitive vertigo days, vertigo severity, and average daily vertigo count compared with placebo during Month 3. Results provide insight into analyzing for a vertigo treatment effect and support advancing OTO-104 into Phase 3 clinical trials for the treatment of Ménière's disease symptoms.
Cadmium, mercury, iron, copper, manganese and zinc in the liver and kidney of the Icelandic lamb

The purpose of this study was to evaluate the levels of cadmium, mercury, iron, copper, manganese and zinc in lamb liver and kidney from six areas in Iceland and to compare the results against aerial deposition data for the same elements obtained using moss as an indicator organism. The total number of samples was 96 for each organ. Cadmium was determined by graphite furnace atomic absorption spectrophotometry, mercury by coldvapour atomic absorption, and iron, copper, manganese and zinc by inductively coupled plasma atomic emission spectrophotometry. Analysis of variance determined significance differences among means for areas, and Pearson's correlation coefficients were calculated to study correlation among trace elements in liver and kidney. The mean fresh weight concentrations in lamb liver and kidney respectively were 0.045 and 0.058mg kg -1 for cadmium, 0.009 and 0.012mgkg-1 for mercury, 141 and 52.7mgkg-1 for iron, 28.1 and 2.89mgkg-1 for copper, 4.01 and 1.13mgkg-1 for manganese and 48.7 and 25.2mgkg-1 for zinc. Concentrations of cadmium, mercury and copper in the liver and kidney of the Icelandic lamb were low compared with data from other countries. Iron concentrations in the organs, however, were high. No sample exceeded 46% of the proposed maximum level for cadmium in organs for human consumption in the EC. Cadmium, mercury, iron and copper in the liver and kidney differed significantly between areas. Deposition of cadmium and copper in moss was not a useful indicator in the evaluation of the susceptibility of the Icelandic lamb to accumulation of cadmium and cop per. However, iron levels in Icelandic lamb liver showed the same pattern as results for iron from the moss study. The cadmium and mercury levels of organs from lambs grazing in the vicinity of Mount Hekla a few months after its eruption did not indicate a significant contamination from volcanic activity.
Microbubble contrast agent with focused ultrasound to create brain lesions at low power levels: MR imaging and histologic study in rabbits.

PURPOSE To evaluate magnetic resonance (MR) imaging-based thermometry for predicting the onset and spatial extent of lesions produced by focused ultrasound combined with a microbubble contrast agent (Optison; GE Healthcare, Milwaukee, Wis) and to compare the resulting induced temperature increase and threshold for damage with those in studies performed without the agent. MATERIALS AND METHODS The experiments were approved by the animal care committee. Fifty-three locations in the brains of 15 rabbits were sonicated with various exposure parameters by using a 1.5-MHz focused ultrasound transducer. MR imaging was used to map the temperature rise and, along with light microscopy, to examine the lesions. Diameters of isotherms created from thermometry were compared with the resulting lesions by using Bland-Altman analysis and linear regression. The minimum acoustic power necessary for lesion creation was determined, and the apparent temperature threshold for damage was calculated with probit analysis. These thresholds were compared with prior work performed without the contrast agent. The heating induced with the microbubbles was compared with that in sonications performed without them by using a t test. RESULTS The MR imaging-mapped temperature distributions matched the shape of the lesions. The diameters of isotherms correlated well with diameters measured at contrast material-enhanced MR imaging (mean difference between measurements, 0.0 mm +/- 0.5; R = 0.93). The temperature increase with microbubbles was statistically larger (P < .01) than for sonications performed without microbubbles. In some locations (mostly continuous wave exposures), damage was observed along the ultrasound beam path. The time-averaged acoustic power damage threshold was reduced by 91% for 10-second exposures when compared with earlier studies performed without microbubbles. The probability of producing lesions was 50% at a temperature increase of 5.9 degrees C, 5.5 degrees C lower than was observed earlier without the agent. CONCLUSION MR imaging-based temperature measurements appeared to correlate with focused ultrasound-induced lesions in the brain when microbubbles were present, even though the temperature appeared to be below the threshold for thermal damage.
Measuring efficiency of domestic banks in Taiwan: application of data envelopment analysis and Malmquist index

The purpose of this article is to investigate relative efficiency of management and variation of managerial efficiency among 37 domestic banks in Taiwan. The relative efficiency of management is analysed through Data Envelopment Analysis (DEA) to estimate the competitiveness of each bank and managerial efficiency is to show the efficiency variation of each bank through Malmquist index. This article also links those two types of efficiency by constructing a matrix of relative efficiency and managerial efficiency defining of eight different categories of banks. The empirical results show that all 37 banks possess an average relative efficiency value of 0.591, with a SD of 0.228. And there are 6 banks with an efficiency value of 1. From the results estimated by Malmquist model, it indicates there are 20 banks with an efficiency variation greater than 1. This means that managerial efficiency of those 20 banks has been improving. However, there are 17 banks with an efficiency variation less than 1. This means that managerial efficiency of those 17 banks has been declining.
Risky eating behaviors and beliefs among adolescent girls

This study investigated the prevalence of weight control and binge eating behaviors in a sample of 767 adolescent girls aged 16–20 years, and the differences between adolescents with and without altered eating behaviors regarding anthropometric and body image variables and beliefs associated with eating disorders. Adolescents who engaged in unhealthy strategies were found to be at a higher risk of eating disorders, since these behaviors were accompanied by higher levels of drive for thinness and body dissatisfaction, as well as by beliefs associated with the importance of weight and body shape as a means of personal and social acceptance.
Stock Price Clustering on Option Expiration Dates

This paper presents striking evidence that option trading changes the prices of underlying stocks. In particular, we show that on expiration dates the closing prices of stocks with listed options cluster at option strike prices. On each expiration date, the returns of optionable stocks are altered by an average of at least 16.5 basis points, which translates into aggregate market capitalization shifts on the order of $9 billion. We provide evidence that hedge re-balancing by option market-makers and stock price manipulation by firm proprietary traders contribute to the clustering.
Antioxidant Activity of Guaiazulene and Protection Against Paracetamol Hepatotoxicity in Rats

The effect of guaiazulene, a lipophilic azulene derivative widely found in nature, on radical‐mediated processes is examined. The ability of guaiazulene to inhibit rat hepatic microsomal membrane lipid peroxidation and to scavenge hydroxyl radicals, as well as to interact with 1,1‐diphenyl‐2‐picrylhydrazyl radical (DPPH), was estimated.
Point-of-Decision Signs and Stair Use in a University Worksite Setting: General versus Specific Messages

Purpose. This study tested the effectiveness of two point-of-decision signs to increase stair use and investigated message content by comparing signs with general and specific messages. Design. This study used a quasi-experimental time series design, including a 2-week baseline period: 2 weeks with a general message and 2 weeks with a specific message. Setting. The signs were placed in an eight-story university building. Subjects. The subjects comprised all adults entering the building. During the study, 2997 observations of stair/elevator choice were made. Intervention. A stair-prompt sign with a general message and a sign with a specific message served as the interventions. Measures. Observers measured stair/elevator choice, demographics, and traffic volume. Analysis. Logistic regression analyses were employed, adjusting for covariates. Results. The specific sign intervention showed significantly increased odds of stair use compared to baseline (odds ratio [OR] = 2.04, 95% confidence interval [CI] = 1.46–2.84). The odds of stair use were also significantly greater with the specific sign than the general sign (OR = 1.57, 95% CI = 1.13–2.20). Conclusion. Only the specific sign significantly increased stair use. The results indicate that a specific message may be more effective at promoting stair use.
Glioblastoma multiforme: exploratory radiogenomic analysis by using quantitative image features.

PURPOSE To derive quantitative image features from magnetic resonance (MR) images that characterize the radiographic phenotype of glioblastoma multiforme (GBM) lesions and to create radiogenomic maps associating these features with various molecular data. MATERIALS AND METHODS Clinical, molecular, and MR imaging data for GBMs in 55 patients were obtained from the Cancer Genome Atlas and the Cancer Imaging Archive after local ethics committee and institutional review board approval. Regions of interest (ROIs) corresponding to enhancing necrotic portions of tumor and peritumoral edema were drawn, and quantitative image features were derived from these ROIs. Robust quantitative image features were defined on the basis of an intraclass correlation coefficient of 0.6 for a digital algorithmic modification and a test-retest analysis. The robust features were visualized by using hierarchic clustering and were correlated with survival by using Cox proportional hazards modeling. Next, these robust image features were correlated with manual radiologist annotations from the Visually Accessible Rembrandt Images (VASARI) feature set and GBM molecular subgroups by using nonparametric statistical tests. A bioinformatic algorithm was used to create gene expression modules, defined as a set of coexpressed genes together with a multivariate model of cancer driver genes predictive of the module's expression pattern. Modules were correlated with robust image features by using the Spearman correlation test to create radiogenomic maps and to link robust image features with molecular pathways. RESULTS Eighteen image features passed the robustness analysis and were further analyzed for the three types of ROIs, for a total of 54 image features. Three enhancement features were significantly correlated with survival, 77 significant correlations were found between robust quantitative features and the VASARI feature set, and seven image features were correlated with molecular subgroups (P < .05 for all). A radiogenomics map was created to link image features with gene expression modules and allowed linkage of 56% (30 of 54) of the image features with biologic processes. CONCLUSION Radiogenomic approaches in GBM have the potential to predict clinical and molecular characteristics of tumors noninvasively. Online supplemental material is available for this article.
IFRS and the value relevance of earnings: evidence from the emerging market of Romania

This paper investigates the impact of the mandatory IFRS adoption on the value relevance of earnings on the Bucharest Stock Exchange, at a time when the EU did not have an official position regarding IFRS. Findings suggest that the implementation of IFRS has increased the contemporaneous association between market returns and earnings. Additional analyses reveal that this result is mainly driven by small firms and that the accounting reforms have increased the timeliness of earnings. In the light of the expansion of IFRS worldwide, this paper examines the mandatory IFRS adoption in an institutional setting where accounting reforms were accompanied by economic reforms in preparation for Romania's accession to the EU. Such a single-country case study may help researchers better understand the impact of accounting regulations and institutional factors on the properties of accounting earnings.
TB-infected deer are more closely related than non-infected deer

Identifying mechanisms of pathogen transmission is critical to controlling disease. Social organization should influence contacts among individuals and thus the distribution and spread of disease within a population. Molecular genetic markers can be used to elucidate mechanisms of disease transmission in wildlife populations without undertaking detailed observational studies to determine probable contact rates. Estimates of genealogical relationships within a bovine tuberculosis-infected white-tailed deer (Odocoileus virginianus) population indicated that infected deer were significantly more closely related than non-infected deer suggesting that contact within family groups was a significant mechanism of disease transmission. Results demonstrate that epidemiological models should incorporate aspects of host ecology likely to affect the probability of disease transmission.
On The Robustness of Size and Book‐to‐Market in Cross‐Sectional Regressions

The authors use a robust regression estimator to analyze the risk premia on size and book-to-market. They find that the risk premium on size that was estimated by Eugene F. Fama and Kenneth R. French (1992) completely disappears when the 1 percent most extreme observations are trimmed each month. The authors also show that the negative average of the monthly size coefficients reported by Fama and French can be entirely explained by the sixteen months with the most extreme coefficients. They argue that further investigation of these results could lead to an understanding of the economic forces underlying the size effect, and may also yield important insights into how firms grow. Copyright 1997 by American Finance Association.
A comparison of qualitative and quantitative fecal immunochemical tests in the Korean national colorectal cancer screening program

Abstract Objective. The National Cancer Screening Program (NCSP) has since 2004 provided annual colorectal cancer screening using the fecal immunochemical test (FIT) for individuals aged 50 years or older. The aim of this study was to examine the positivity and detection rates of the FIT and to compare the detection rates of the qualitative and quantitative FITs in participants in the 2009 NCSP. Methods. We analyzed positivity and detection rates according to FIT type (qualitative and quantitative). We used a multinomial logistic regression to analyze the odds ratio of “benign” or “suspicious cancer and cancer” compared to “normal,” adjusted for gender, age, health insurance type, region of residence, hospital type, and FIT type. Results. Of the 1,181,904 participants, 72.8% received a qualitative and 27.2% a quantitative FIT. The positivity rates were 8.1% for the qualitative and 2.5% for the quantitative FIT. The detection rate was 5.2% for the qualitative and 14.4% for the quantitative FIT. The odds ratio of a “suspicious cancer and cancer” versus a “normal” result was 2.73 (95% CI = 2.22–3.35) for the quantitative compared to qualitative FIT, after adjustment. Conclusions. The positivity rate of the qualitative FIT was around three times higher than that of the quantitative FIT. However, the odds ratio for detection of “suspicious cancer and cancer” versus “normal” of the quantitative FIT was about three times higher than that of the qualitative FIT. These findings suggest that quality control may be important, particularly for the qualitative FIT.
Numerical methods for nonlinear equations in option pricing

This thesis explores numerical methods for solving nonlinear partial differential equations (PDEs) that arise in option pricing problems. The goal is to develop or identify robust and efficient techniques that converge to the financially relevant solution for both one and two factor problems. To illustrate the underlying concepts, two nonlinear models are examined in detail: uncertain volatility and passport options. For any nonlinear model, implicit timestepping techniques lead to a set of discrete nonlinear equations which must be solved at each timestep. Several iterative methods for solving these equations are tested. In the cases of uncertain volatility and passport options, it is shown that the frozen coefficient method outperforms two different Newton-type methods. Further, it is proven that the frozen coefficient method is guaranteed to converge for a wide class of one factor problems. A major issue when solving nonlinear PDEs is the possibility of multiple solutions. In a financial context, convergence to the viscosity solution is desired. Conditions under which the one factor uncertain volatility equations are guaranteed to converge to the viscosity solution are derived. Unfortunately, the techniques used do not apply to passport options, primarily because a positive coefficient discretization is shown to not always be achievable. For both uncertain volatility and passport options, much work has already been done for one factor problems. In this thesis, extensions are made for two factor problems. The importance of treating derivative estimates consistently between the discretization and an optimization procedure is discussed. For option pricing problems in general, non-smooth data can cause convergence difficulties for classical timestepping techniques. In particular, quadratic convergence may not be achieved. Techniques for restoring quadratic convergence for linear problems are examined. Via numerical examples, these techniques are also shown to improve the stability of the nonlinear uncertain volatility and passport option problems. Finally, two applications are briefly explored. The first application involves static hedging to reduce the bid-ask spread implied by uncertain volatility pricing. While static hedging has been carried out previously for one factor models, examples for two factor models are provided. The second application uses passport option theory to examine trader compensation strategies. By changing the payoff, it is shown how the expected distribution of trading account balances can be modified to reflect trader or bank preferences.
Managerial Ownership, Information Content of Earnings, and Discretionary Accruals in a Non-Us Setting

This study employs Danish data to examine the empirical relationship between the proportion of managerial ownership and two characteristics of accounting earnings: the information content of earnings and the magnitude of discretionary accruals. In previous research concerning American firms, Warfield et al. (1995) document a positive relationship between managerial ownership and the information content of earnings, and a negative relationship between managerial ownership and discretionary accruals. We question the generality of the Warfield et al. result, as the ownership structure found in most other countries, including Denmark, deviates from the US ownership configuration. In fact, Danish data indicate that the information content of earnings is inversely related to managerial ownership.