Miracle-dz/UniFAR-FTUs huggingface dataset:
A shared Asian origin of the triple-mutant dhfr allele in Plasmodium falciparum from sites across Africa.

BACKGROUND Usefulness of sulfadoxine-pyrimethamine as first-line therapy for uncomplicated Plasmodium falciparum malaria and intermittent preventive treatment in pregnancy throughout sub-Saharan Africa is compromised by the spread of dhfr alleles associated with pyrimethamine resistance. A predominant haplotype associated with the N51I+C59R+S108N triple-mutant dhfr allele has been reported recently in 4 African countries. A more comprehensive picture of the evolution of this mutant allele in Africa is lacking. METHODS Seventy-five P. falciparum isolates carrying the wild-type dhfr allele and 204 carrying the triple-mutant dhfr allele from 11 African countries were selected. The genetic diversity of the chromosomes bearing these alleles was analyzed with 4 microsatellite markers closely linked to the dhfr gene. RESULTS Seventy-three different 4-locus haplotypes carrying the wild-type dhfr allele were found. By contrast, 175 (85%) of 204 isolates carrying the triple-mutant dhfr allele shared a unique haplotype, identical to the one identified in Thailand. For the remaining triple-mutant isolates and one isolate with the quadruple-mutant dhfr allele (N51I+C59R+S108N+I164L), haplotypes were closely related to the predominant haplotype by mutation or recombination. CONCLUSIONS Migration of parasites carrying an ancestral triple-mutant dhfr allele drives the spread of dhfr alleles associated with pyrimethamine resistance throughout West and Central Africa.
Inhibition of Translational Initiation by Let-7 MicroRNA in Human Cells

MicroRNAs (miRNAs) are ∼21-nucleotide-long RNA molecules regulating gene expression in multicellular eukaryotes. In metazoa, miRNAs act by imperfectly base-pairing with the 3′ untranslated region of target messenger RNAs (mRNAs) and repressing protein accumulation by an unknown mechanism. We demonstrate that endogenous let-7 microribonucleoproteins (miRNPs) or the tethering of Argonaute (Ago) proteins to reporter mRNAs in human cells inhibit translation initiation. M7G-cap-independent translation is not subject to repression, suggesting that miRNPs interfere with recognition of the cap. Repressed mRNAs, Ago proteins, and miRNAs were all found to accumulate in processing bodies. We propose that localization of mRNAs to these structures is a consequence of translational repression.
DNA testing in homicide investigations

Objectives With the widespread use of DNA testing, police, death investigators, and attorneys need to be aware of the capabilities of this technology. This review provides an overview of scenarios where DNA evidence has played a major role in homicide investigations in order to highlight important educational issues for police, death investigators, forensic pathologists, and attorneys. Methods This was a nonrandom, observational, retrospective study. Data were obtained from the collective files of the authors from casework during a 15-year period, from 2000 through 2014. Results A series of nine scenarios, encompassing 11 deaths, is presented from the standpoint of the police and death investigation, the forensic pathology autopsy performance, the subsequent DNA testing of evidence, and, ultimately, the final adjudication of cases. Details of each case are presented, along with a discussion that focuses on important aspects of sample collection for potential DNA testing, especially at the crime scene and the autopsy. The presentation highlights the diversity of case and evidence types in which DNA testing played a valuable role in the successful prosecution of the case. Conclusions By highlighting homicides where DNA testing contributed to the successful adjudication of cases, police, death investigators, forensic pathologists, and attorneys will be better informed regarding the types of evidence and situations where such testing is of potential value.
Authorship Attribution: What's Easy and What's Hard?

This paper considers four versions of the authorship attribution problem that are typically encountered in the forensic context and offers algorithmic solutions for each. Part I describes the simple authorship attribution problem described above. Part II considers the long-text verification problem, in which we are asked if two long texts are by the same author. Part III discusses the many-candidates problem, in which we are asked which among thousands of candidate authors is the author of a given text. Finally, Part IV considers the fundamental problem of authorship attribution, in which we are asked if two short texts are by the same author. Although other researchers have considered these problems, here we offer our own solutions to each problem and indicate the degree of accuracy that can be expected in each case under specified conditions.
Lower limb amputee survival

A total of 1710 primary amputees have been studied over a 25 year period and their survival time has been calculated. These were all consecutive primary lower limb amputees admitted to the Dundee Limb Fitting Centre during the period 1965–1989. Overall, the median survival was 4 yr 9 mth for the below-knee amputee (1019 patients) and 4 yr 3 mth for the above-knee amputee (586 patients). The vascular related amputees had an overall median survival of 4 yr. In the two decades 1970–1979 and 1980–1989 there were significant differences between the survival time of the below-knee and above-knee amputee. The survival of the amputee has increased during the two decades from 3 yr 6 mth to 6 yr 6 mth (p>0.001). For the first decade male above-knee and male below-knee amputee median survival was 3 yr 1 mth and 3 yr 11 mth respectively and for the second the survival was 5 yr 9 mth and 6 yr 11 mth for these levels of amputation. For 1970–1979 no significant differences were found between male and female peripheral vascular disease (PVD) and diabetes mellitus related amputee survival. For 1980–1989 significant differences were found between PVD related male above-knee amputees (3 yr 10 mth) and male below-knee amputees (6 yr 7 mth) (p>0.01). Similar results were found for the female patients. Operative mortality was found to be 5% over the period 1975–1989 which compared favourably with previous studies.
PERMANENT GENETIC RESOURCES: Development of microsatellite markers of the Mexican understorey palm Chamaedorea elegans, cross‐species genotyping, and amplification in congeners

With striking morphological diversity and adaptability, Chamaedorea palms constitute an ecologically and economically important understorey component of Neotropical forests. Nine loci developed for Chamaedorea elegans evaluated in three Veracruz populations resulted in a large number of alleles (8–18), and high expected heterozygosity (0.49–0.92), but low observed (0.27–0.65) heterozygosity. Deviations from Hardy–Weinberg and high inbreeding suggest a lack of panmixia. Eight loci optimized for Chamaedorea ernesti‐augustii showed similar patterns of variation. All nine multiplexing loci amplified in other five congeneric species, which will facilitate comparisons within the genus and contribute to the conservation of its genetic resources.
In Vitro Antioxidant Properties of Phloretin—An Important Phytocompound

Reactive oxygen species [ROS] cause oxidative damage to the tissues and protection from such damages is provided by endogenous and exogenous antioxidants. Much research work has been carried out in recent years on the beneficial effect of phenolic compounds which act as natural antioxidants and help to neutralize free radicals. So, this study was aimed to evaluate the in vitro antioxidant capacity of one of the phenolic compounds phloretin. Phloretin was used at four different concentrations like 20, 40, 60 and 80 μg/ml to determine the antioxidant activity by different methods such as total antioxidant capacity, reducing power, DPPH radical scavenging, superoxide anion radical scavenging and metal chelating assays. In addition to that the ascorbic acid was used as reference compound. The results showed that the phloretin displayed potent in vitro antioxidant capacity. It was able to scavenge different in vitro free radicals in all tested concentrations. Among the different concentrations, 80 μg of phloretin has maximum activity when compared to other concentrations in all in vitro antioxidant assays. High antioxidant property and maximum protective effect of phloretin were observed in a concentration dependent manner. The results were expressed as IC50 value. The lowest IC50 value indicates the highest scavenging activity. The reducing power of the phloretin was also found in concentration dependent. According to the results of this study, we concluded that the phloretin possesses antioxidant property. Therefore, phloretin is a powerful antioxidant phytocompound which can protect biological systems against the oxidative stress. From this study, we suggest that the phloretin may be used as a dietary natural antioxidant supplement for preventing free radical related diseases.
Extending the Scalability of Linkage Learning Genetic Algorithms: Theory and Practice

There are two primary objectives of this dissertation. The first goal is to identify certain limits of genetic algorithms that use only fitness for learning genetic linkage. Both an explanatory theory and experimental results to support the theory are provided. The other goal is to propose a better design of the linkage learning genetic algorithm. After understanding the cause of the performance barrier, the design of the linkage learning genetic algorithm is modified accordingly to improve its performance on uniformly scaled problems. This dissertation starts with presenting the background of the linkage learning genetic algorithm. Then, it introduces the use of promoters on the chromosome to improve the performance of the linkage learning genetic algorithm on uniformly scaled problems. The convergence time model is constructed by identifying the sequential behavior, developing the tightness time model, and establishing the connection in between. The use of subchromosome representations is to avoid the limit implied by the convergence time model. The experimental results demonstrate that the use of subchromosome representations may be a promising way to design a better linkage learning genetic algorithm. The study finds that using promoters on the chromosome can improve nucleation potential and promote correct building-block formation. It also observes that the linkage learning genetic algorithm has a consistent, sequential behavior instead of different behaviors on different problems as was previously believed. Moreover, the competition among building blocks of equal salience is the main cause of the exponential growth of convergence time. Finally, adopting subchromosome representations can reduce the competition among building blocks, and therefore, scalable genetic linkage learning for a unimetric approach is possible.
Content Analysis of Social, Environmental Reporting: What is New?

Purpose: The aim of this paper is to review the use of content analysis as a research method in understanding SEA and to examine current contemporary foci of this research tradition. Further, several research method issues relating to the use of content analysis are examined. Methodology: Contemporary focus and research issues are analyzed to provide some future directions for scholars in the field of SEA, by categorizing work in the SEA, social environmental reporting (SER) and intellectual capital reporting (ICR) literature, according to the following: normative literature/theory/commentaries; focus of empirical investigation; quality SER research; combined research methodologies; content analysis method issues. Findings: Literature indicates that few attempts have been made to combine other research methodologies with content analysis although it has proven fruitful with the limited investigation undertaken to examine aspects of SER. Further extending the performance reporting by combining SER with ICR may provide useful information. Research Implications: Increasingly, researchers in the field of social and environmental accounting (SEA) need to be able to justify the specific research methods they use when collecting the empirical data that they examine in order to support and test opinions regarding the merit of different approaches to managing, measuring and reporting of SEA.
A Handwriting Understanding Environment (HUE) for rapid prototyping in handwriting and document analysis research

HUE (the Handwriting Understanding Environment) is a software framework for handwriting and document analysis built around a two-level programming model in which components are implemented in a system programming language (typically C++) and are connected together into prototype systems using the scripting language Tcl Tk. HUE is an extended version of TABS (a previous handwriting analysis framework), and incorporates the authors' experience of using TABS for around 2 years in data-intensive handwriting and document analysis research and evaluation. HUE currently contains 94 C++ components, 7 native data types, 11 custom-built Tcl Tk packages, a novel dynamic user interface, and several demonstration systems implemented as Tcl scripts.
Design and Development of a Command-line Tool for Portable Executable File Analysis and Malware Detection in IoT Devices

Recently, Microsoft unveiled a new operating system called Windows 10. As it is highly expected that Windows 10 will play a significant role in the Internet of Things era, the Portable Executable (PE) format is drawing attention even more widely than before. PE is a standard file format for executables and object code used in MS Windows operating systems. Since a number of various malwares have widely spread by exploiting vulnerabilities of PE structure, the need of automatic tools for PE-malware detection is being magnified. In this paper, we designed and developed a command-line PE file analysis tool using Python language for automatic detection of Windows malware.
Graphene-Based D-Shaped Polymer FBG for Highly Sensitive Erythrocyte Detection

Graphene-based silica fiber-optic sensors, with high sensitivity, fast response, and low cost, have shown great promise for gas sensing applications. In this letter, by covering a monolayer of p-doped graphene on a D-shaped microstructured polymer fiber Bragg grating (FBG), we propose and demonstrate a novel biochemical probe sensor, the graphene-based D-shaped polymer FBG (GDPFBG). Due to the graphene-based surface evanescent field enhancement, this sensor shows high sensitivity to detect surrounding biochemical parameters. By monitoring the Bragg peak locations of the GDPFBG online, human erythrocyte (red blood cell) solutions with different cellular concentrations ranging from 0 to 104 ppm were detected precisely, with the maximum resolution of sub-ppm. Such a sensor is structurally compact, is clinically acceptable, and provides good recoverability, offering a state-of-the-art polymer-fiber-based sensing platform for highly sensitive in situ and in vivo cell detection applications.
Partial Least Square Regression Approach for the Extraction Phosphorus Concentration from Soil VNIR Spectra

The present study used partial least square regression (PLSR) method to establish the relationship between soil reflectance spectra measured under laboratory condition and soil total phosphorus. The spectral range of soil reflectance was divided into two wavelength ranges (320nm~1100nm, and 1000nm~2480nm). Besides original reflectance (R), several spectral parameters were also calculated: derivative reflectance spectra (FDR), inverse-log spectra (Log (1/R)) and Depth. All of the 69 samples were randomly divided into training and test set. Based on the PLSR method, statistical relationships between the four spectral parameters and total phosphorus were established with training set and were validated using the test set. In all models, the prediction values for high phosphorus concentration were lower than the measured values. The precision of models built using near infrared (NIR) range is better than that derived with visible bands except for the depth parameter. Good results indicate that VNIR spectra, especially NIR range, are potentially useful for rapid estimation of phosphorus concentration in soils.
Subrecursive Programming Languages, Part I: efficiency and program structure

The structural complexity of programming languages, and therefore of programs as well, can be measured by the subrecursive class of functions which characterize the language. Using such a measure of structural complexity, we examine the tradeoff relationship between structural and computational complexity. Since measures of structural complexity directly related to high level languages interest us most, we use abstract language models which approximate highly struc+, "-,. , +
Landmark identification based on projective and permutation invariant vectors

We address the issue of environment representation for navigational tasks by using reference scene patterns, the so-called landmarks, to adequately describe the robot's workspace. Mathematical tools from projective geometry are employed for landmark identification. A complete framework is presented for landmark extraction and recognition based on projective and point-permutation invariant vectors.
Pressure response of Aanderaa and Sea-Bird oxygen optodes

We investigated the effect of hydrostatic pressure of up to 6000 dbar on Aanderaa and Sea-Bird oxygen optodes both in the laboratory and in the field. The overall pressure response is a reduction in the O2 reading by 3 – 4 % per 1000 dbar which is closely linear with pressure and increases with temperature. Closer inspection reveals two superimposed processes with opposite effect: an O2-independent pressure response on the luminophore which increases optode O2 readings and an O2-dependent change in luminescence quenching which decreases optode O2 readings. The latter process dominates and is mainly due to a shift in the equilibrium between sensing membrane and sea water under elevated pressures. If only the dominant O2-dependent process is considered, Aanderaa and Sea-Bird optodes differ in their pressure response. Compensation of the O2-independent process, however, yields a uniform O2 dependence for Aanderaa optodes with standard foil and fast-response foil as well as Sea-Bird optodes. A new scheme to calculate optode O2 from raw data is proposed to account for the two processes. The overall uncertainty of the optode pressure correction amounts to 0.3 % per 1000 dbar, mainly due to variability between sensors.
Use of the Free to Play model in games with a purpose: the RoboCorp game case study

Abstract This article presents the RoboCorp game. RoboCorp is a game with a purpose aimed at facilitating the annotation process of a natural language data. What makes this game unique and novel is the use of various mechanisms known from the popular Free to Play model to provide a fun and attractive gameplay. These mechanisms are presented and described in detail in the context of RoboCorp. The obtained annotation results are discussed and compared to other similar annotation tools available.
Estimation of treatment effect under non‐proportional hazards and conditionally independent censoring

In clinical trials with time‐to‐event outcomes, it is common to estimate the marginal hazard ratio from the proportional hazards model, even when the proportional hazards assumption is not valid. This is unavoidable from the perspective that the estimator must be specified a priori if probability statements about treatment effect estimates are desired. Marginal hazard ratio estimates under non‐proportional hazards are still useful, as they can be considered to be average treatment effect estimates over the support of the data. However, as many have shown, under non‐proportional hazard, the ‘usual’ unweighted marginal hazard ratio estimate is a function of the censoring distribution, which is not normally considered to be scientifically relevant when describing the treatment effect. In addition, in many practical settings, the censoring distribution is only conditionally independent (e.g., differing across treatment arms), which further complicates the interpretation. In this paper, we investigate an estimator of the hazard ratio that removes the influence of censoring and propose a consistent robust variance estimator. We compare the coverage probability of the estimator to both the usual Cox model estimator and an estimator proposed by Xu and O'Quigley (2000) when censoring is independent of the covariate. The new estimator should be used for inference that does not depend on the censoring distribution. It is particularly relevant to adaptive clinical trials where, by design, censoring distributions differ across treatment arms. Copyright © 2012 John Wiley & Sons, Ltd.
Innate difference in the endocannabinoid signaling and its modulation by alcohol consumption in alcohol‐preferring sP rats

The present study was undertaken to examine whether genetically predetermined differences in components of the endocannabinoid system were present in the brain of Sardinian alcohol‐preferring (sP) and Sardinian alcohol‐non‐preferring (sNP) rats, a pair of rat lines selectively bred for opposite alcohol preference. The effects of acquisition and maintenance of alcohol drinking, alcohol withdrawal, and alcohol re‐exposure on the endocannabinoid system was also assessed in the striatum of sP rats. The findings revealed significantly higher density of the CB1 receptors and levels of CB1 receptor mRNA, CB1 receptor‐mediated G‐protein coupling, and endocannabinoids in the cerebral cortex, hippocampus and striatum of alcohol‐naive sP rats than sNP rats. A significantly lower expression of mFAAH enzyme was evident in the hippocampus of alcohol‐naive sP rats. Alcohol drinking (during both acquisition and maintenance phases) in sP rats resulted in a significant reduction in striatal CB1 receptor‐mediated G‐protein coupling whereas alcohol withdrawal attenuated this effect. Alcohol consumption was also associated with markedly increased levels of endocannabinoids in the striatum. Co‐administration of the CB1 receptor antagonist, rimonabant (SR141716A) reduced alcohol intake, and reversed alcohol‐induced changes in CB1 receptor‐mediated G‐protein activation. These findings provided a new insight into a potential genetic basis of excessive alcohol consumption, suggesting innate differences in the endocannabinoid system might be associated with higher alcohol preference in sP rats. The data also indicate a modulation of CB1 receptor‐mediated signaling following alcohol consumption, and further strengthen the potential of the endocannabinoid system as a target for the treatment of alcohol related behaviors.
Crystal structure of the hypothetical protein TTHA1013 from Thermus thermophilus HB8

Motoyuki Hattori, Eiichi Mizohata, Miho Manzoku, Yoshitaka Bessho, Kazutaka Murayama, Takaho Terada, Seiki Kuramitsu, Mikako Shirouzu, and Shigeyuki Yokoyama* RIKEN Genomic Sciences Center, Tsurumi, Yokohama, Japan Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan RIKEN Harima Institute at SPring-8, Mikazuki-cho, Sayo, Hyogo, Japan Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan