Miracle-dz/UniFAR-FTUs huggingface dataset:
Group II Intron-Mediated Trans-Splicing in the Gene-Rich Mitochondrial Genome of an Enigmatic Eukaryote, Diphylleia rotans

Although mitochondria have evolved from a single endosymbiotic event, present day mitochondria of diverse eukaryotes display a great range of genome structures, content and features. Group I and group II introns are two features that are distributed broadly but patchily in mitochondrial genomes across branches of the tree of eukaryotes. While group I intron-mediated trans-splicing has been reported from some lineages distantly related to each other, findings of group II intron-mediated trans-splicing has been restricted to members of the Chloroplastida. In this study, we found the mitochondrial genome of the unicellular eukaryote Diphylleia rotans possesses currently the second largest gene repertoire. On the basis of a probable phylogenetic position of Diphylleia, which is located within Amorphea, current mosaic gene distribution in Amorphea must invoke parallel gene losses from mitochondrial genomes during evolution. Most notably, although the cytochrome c oxidase subunit (cox) 1 gene was split into four pieces which located at a distance to each other, we confirmed that a single mature mRNA that covered the entire coding region could be generated by group II intron-mediated trans-splicing. This is the first example of group II intron-mediated trans-splicing outside Chloroplastida. Similar trans-splicing mechanisms likely work for bipartitely split cox2 and nad3 genes to generate single mature mRNAs. We finally discuss origin and evolution of this type of trans-splicing in D. rotans as well as in eukaryotes.
Global Diversification: Developed and Emerging Economies

Within the strait jacket of diversification a la Markowitz and Roy efficient portfolio structures are first enunciated, and then within that generic structure of analytical framework benefits of diversification are studied for developed and emerging economies. The study attempts to examine the level of market segmentation/integration in the emerging markets of South-East Asia. It is found that opportunities for profit making exist for investors by appropriate diversification because the markets are largely segmented in the region. The returns are positively correlated with risk, but not significantly so. Non-market related factors appear more important in deciding the returns, thereby hinting at either a lack of beta's predictive capacity in a global context or operating inefficiencies in the business/economic mechanisms.
List Decoding of Insertions and Deletions

List decoding of insertions and deletions in the Levenshtein metric is considered. The Levenshtein distance between two sequences is the minimum number of insertions and deletions needed to turn one of the sequences into the other. In this paper, a Johnson-like upper bound on the maximum list size when list decoding in the Levenshtein metric is derived. This bound depends only on the length and minimum Levenshtein distance of the code, the length of the received word, and the alphabet size. It shows that polynomial-time list decoding beyond half the Levenshtein distance is possible for many parameters. Further, we also prove a lower bound on list decoding of deletions with the well-known binary Varshamov–Tenengolts codes, which shows that the maximum list size grows exponentially with the number of deletions. Finally, an efficient list decoding algorithm for two insertions/deletions with VT codes is given. This decoder can be modified to a polynomial-time list decoder of any constant number of insertions/deletions.
Reverse Transcriptase-Polymerase Chain Reaction Detection of Cancer Micrometastases in Lymph Nodes by Updated Version

There are few DNA-based studies that detect cancer micrometastases in lymph nodes. We have assayed for the specific detection of carcinoembryonic antigen (CEA)-expressing carcinoma cells in the lymph nodes of patients with gastrointestinal or breast carcinomas. A CEA-specific nested reverse transcriptase (RT)-PCR assay was optimized using limiting dilu tions of a CEA-positive cancer cell line mixed with normal lymphocytes. The expression of CEA mRNA was studied in 100 carcinoma tissues, 75 normal mucosa! tissues, and 15 lymph nodes from patients with choleli thiasis. Each of 117 lymph nodes from 13 patients with carcinoma was divided into two pieces: one was used for histolÃ3gica! examination and the other for RT-PCR, and the results were compared. The sensitivity ratio was one CEA-expressing cancer cell detected in 1 x 10s normal lympho cytes. All carcinoma tissues and normal mucosal tissues expressed CEA mRNA, while no amplification was detected in any control lymph nodes. Thirty of 117 lymph nodes were histologically involved by carcinoma cells, and all of these yielded the expected product by RT-PCR. Of the remain ing 87 histologically negative nodes, CEA mRNA was detected in 47 lymph nodes by RT-PCR. The positive rate increased from 26% by histolÃ3gica! examination to 66% by RT-PCR. The assay by CEA-specific nested RT-PCR is not only sensitive but widely applicable for the detection of cancer micrometastases in lymph nodes. This method may lead to an earlier diagnosis and treatment of patients with subclinical lymph node metastasis.
Constitutively Activated NLRP3 Inflammasome Causes Inflammation and Abnormal Skeletal Development in Mice

The NLRP3 inflammasome complex is responsible for maturation of the pro-inflammatory cytokine, IL-1β. Mutations in NLRP3 are responsible for the cryopyrinopathies, a spectrum of conditions including neonatal-onset multisystem inflammatory disease (NOMID). While excessive production of IL-1β and systemic inflammation are common to all cryopyrinopathy disorders, skeletal abnormalities, prominently in the knees, and low bone mass are unique features of patients with NOMID. To gain insights into the mechanisms underlying skeletal abnormalities in NOMID, we generated knock-in mice globally expressing the D301N NLRP3 mutation (ortholog of D303N in human NLRP3). NOMID mice exhibit neutrophilia in blood and many tissues, including knee joints, and high levels of serum inflammatory mediators. They also exhibit growth retardation and severe postnatal osteopenia stemming at least in part from abnormally accelerated bone resorption, attended by increased osteoclastogenesis. Histologic analysis of knee joints revealed abnormal growth plates, with loss of chondrocytes and growth arrest in the central region of the epiphyses. Most strikingly, a tissue “spike" was observed in the mid-region of the growth plate in the long bones of all NOMID mice that may be the precursor to more severe deformations analogous to those observed in NOMID patients. These findings provide direct evidence linking a NOMID-associated NLRP3-activating mutation to abnormalities of postnatal skeletal growth and bone remodeling.
Long-Term Maintenance of Na+ Channels at Nodes of Ranvier Depends on Glial Contact Mediated by Gliomedin and NrCAM

Clustering of Na+ channels at the nodes of Ranvier is coordinated by myelinating glia. In the peripheral nervous system, axoglial contact at the nodes is mediated by the binding of gliomedin and glial NrCAM to axonal neurofascin 186 (NF186). This interaction is crucial for the initial clustering of Na+ channels at heminodes. As a result, it is not clear whether continued axon-glial contact at nodes of Ranvier is required to maintain these channels at the nodal axolemma. Here, we report that, in contrast to mice that lack either gliomedin or NrCAM, absence of both molecules (and hence the glial clustering signal) resulted in a gradual loss of Na+ channels and other axonal components from the nodes, the formation of binary nodes, and dysregulation of nodal gap length. Therefore, these mice exhibit neurological abnormalities and slower nerve conduction. Disintegration of the nodes occurred in an orderly manner, starting with the disappearance of neurofascin 186, followed by the loss of Na+ channels and ankyrin G, and then βIV spectrin, a sequence that reflects the assembly of nodes during development. Finally, the absence of gliomedin and NrCAM led to the invasion of the outermost layer of the Schwann cell membrane beyond the nodal area and the formation of paranodal-like junctions at the nodal gap. Our results reveal that axon-glial contact mediated by gliomedin, NrCAM, and NF186 not only plays a role in Na+ channel clustering during development, but also contributes to the long-term maintenance of Na+ channels at nodes of Ranvier.
Charges fit to electrostatic potentials. II. Can atomic charges be unambiguously fit to electrostatic potentials?

The present work examines the conditioning of the least‐squares matrix for obtaining potential derived charges and presents a modification of the CHELP method for fitting atomic charges to electrostatic potentials. Results from singular value decompositions (SVDs) of the least‐squares matrices show that, in general, the least‐squares matrix for this fitting problem will be rank deficient. Thus, statistically valid charges cannot be assigned to all the atoms in a given molecule. We find also that, contrary to popular notions, increasing the point density of the fit has little or no influence on the rank of the problem. Improvement in the rank can best be achieved by selecting points closer to the molecular surface. Basis set has, as expected, no effect on the number of charges that can be assigned. Finally, a well‐defined, computationally efficient algorithm (CHELP‐SVD) is presented for determining the rank of the least‐squares matrix in potential‐derived charge fitting schemes, selecting the appropriate subset of atoms to which charges can be assigned based on that rank estimate, and then refitting the selected set of charges. © 1996 by John Wiley & Sons, Inc.
On some weighted Boolean models

An overview is given of some recent work (joint with Adrian Baddeley of Perth and Colette van Lieshout of Warwick) on a new class of random point and set processes, obtained using a rather natural weighting procedure employing quermass integrals. The concept of exact (or perfect) simulation of point processes is then introduced, and a discussion is given of possibilities for perfect simulation of quermass weighted processes.
A generalized iterative scaling algorithm for maximum entropy reasoning in relational probabilistic conditional logic under aggregation semantics

Recently, different semantics for relational probabilistic con- ditionals and corresponding maximum entropy (ME) inference operators have been proposed. In this paper, we study the so-called aggregation semantics that covers both notions of a statistical and subjective view. The computation of its inference operator requires the calculation of the ME-distribution satisfying all probabilistic conditionals. Since each conditional induces a linear constraint on the probability distribution, the optimization problem to solve is the calculation of the probability distribution with maximum entropy under linear constraints. We demon- strate how the well-known Generalized Iterative Scaling (GIS) algorithm technique can be applied to this optimization problem to calculate the maximum entropy distribution in an iterative way. We show how the linear constrains are transformed into normalized feature functions to meet the requirements of GIS and present a practical algorithm which is tailor-made for the computation of the ME-inference operator based on aggregation semantics. We also present a practical implementation of the developed algorithm.
Topological gradient for a fourth order PDE and application to the detection of fine structures in 2D and 3D images

In this paper we describe a new variational approach for the detection of fine structures in an image (like filaments in 2D). This approach is based on the computation of the topological gradient associated to a cost function defined from a regularized version of the data (possibly noisy and / or blurred). We get this approximation by solving a fourth order PDE. The study of the topological sensitivity is made in the case of a crack. We give the numerical algorithm to compute this topological gradient and we illustrate our approach by giving several experimental results in 2D and 3D images.
Intention-to-treat analyses and missing data approaches in pharmacotherapy trials for alcohol use disorders

Objectives Intention to treat (ITT) is an analytic strategy for reducing potential bias in treatment effects arising from missing data in randomised controlled trials (RCTs). Currently, no universally accepted definition of ITT exists, although many researchers consider it to require either no attrition or a strategy to handle missing data. Using the reports of a large pool of RCTs, we examined discrepancies between the types of analyses that alcohol pharmacotherapy researchers stated they used versus those they actually used. We also examined the linkage between analytic strategy (ie, ITT or not) and how missing data on outcomes were handled (if at all), and whether data analytic and missing data strategies have changed over time. Design Descriptive statistics were generated for reported and actual data analytic strategy and for missing data strategy. In addition, generalised linear models determined changes over time in the use of ITT analyses and missing data strategies. Participants 165 RCTs of pharmacotherapy for alcohol use disorders. Results Of the 165 studies, 74 reported using an ITT strategy. However, less than 40% of the studies actually conducted ITT according to the rigorous definition above. Whereas no change in the use of ITT analyses over time was found, censored (last follow-up completed) and imputed missing data strategies have increased over time, while analyses of data only for the sample actually followed have decreased. Conclusions Discrepancies in reporting versus actually conducting ITT analyses were found in this body of RCTs. Lack of clarity regarding the missing data strategy used was common. Consensus on a definition of ITT is important for an adequate understanding of research findings. Clearer reporting standards for analyses and the handling of missing data in pharmacotherapy trials and other intervention studies are needed.
A Hitchhiker's guide to statistical tests for assessing randomized algorithms in software engineering

Randomized algorithms are widely used to address many types of software engineering problems, especially in the area of software verification and validation with a strong emphasis on test automation. However, randomized algorithms are affected by chance and so require the use of appropriate statistical tests to be properly analysed in a sound manner. This paper features a systematic review regarding recent publications in 2009 and 2010 showing that, overall, empirical analyses involving randomized algorithms in software engineering tend to not properly account for the random nature of these algorithms. Many of the novel techniques presented clearly appear promising, but the lack of soundness in their empirical evaluations casts unfortunate doubts on their actual usefulness. In software engineering, although there are guidelines on how to carry out empirical analyses involving human subjects, those guidelines are not directly and fully applicable to randomized algorithms. Furthermore, many of the textbooks on statistical analysis are written from the viewpoints of social and natural sciences, which present different challenges from randomized algorithms. To address the questionable overall quality of the empirical analyses reported in the systematic review, this paper provides guidelines on how to carry out and properly analyse randomized algorithms applied to solve software engineering tasks, with a particular focus on software testing, which is by far the most frequent application area of randomized algorithms within software engineering. Copyright © 2012 John Wiley & Sons, Ltd.
Detection of Histoplasma Antigen by a Quantitative Enzyme Immunoassay

ABSTRACT The second-generation Histoplasma antigen immunoassay is semiquantitative, expressing results as a comparison to a negative control, which requires repeat testing of the prior specimen with the current specimen to accurately determine a change in antigen. Reporting results in this manner often is confusing to the ordering physician and laboratory. Development of a quantitative assay could improve accuracy, reduce interassay variability, and eliminate the need to test the prior sample with the current sample in the same assay. Calibrators with known concentrations of Histoplasma antigen were used to quantitate antigen in specimens from patients with histoplasmosis and from controls. Samples from cases of disseminated histoplasmosis or other mycoses and controls were tested to evaluate the performance characteristics of the quantitative assay. Paired specimens were evaluated to determine if quantitation eliminated the need to test the current and prior specimens in the same assay to assess a change in antigen. The sensitivity in samples from patients with AIDS and disseminated histoplasmosis was 100% in urine and 92.3% in serum. Cross-reactions occurred in 70% of other endemic mycoses, but not in aspergillosis. Specificity was 99% in controls with community-acquired pneumonia, medical conditions in which histoplasmosis was excluded, or healthy subjects. A change in antigen level categorized as an increase, no change, or decrease based on antigen units determined in the same assay agreed closely with the category of change in nanograms/milliliter determined from testing current and prior specimens in different assays. Sensitivity, specificity, and interassay precision are excellent in the new third-generation quantitative Histoplasma antigen immunoassay.
Peformance Comparison Between MIMO and SISO based on Indoor Field Measurements

In this paper, we quantify performance gain achieved if SISO system is replaced with 4x4 MIMO in WLAN setting compatible with IEEE 802.11n standard. We compare throughput and power savings in MIMO by taking field measurements at various indoor locations. Measurements are validated with simulations that include different IEEE TGn channel models. For comparison between MIMO and SISO, we select the Modulation and Coding Scheme (MCS) which yields the highest throughput subject to QoS constraints (PER <10%). We show that throughput gain of 2.5x-3x and power saving of 5-15 dB are achievable in 4x4 MIMO system.
Optimum Zero-forcing Beamforming with Per-antenna Power Constraints

We investigate optimum zero-forcing beamforming in multiple antenna broadcast channels with per-antenna power constraints. We show that standard zero-forcing techniques, such as the Moore-Penrose pseudo-inverse, considered mainly in the context of sum-power constrained systems are suboptimal when there are per-antenna power constraints. We formulate convex optimization problems to find the optimum zero-forcing beamforming vectors. Our results indicate that optimizing the antenna outputs based on the per-antenna constraints may improve the rate considerably when the number of transmit antennas is larger the number of receive antennas. Having more transmit antennas gives rise to additional signal space dimensions that may be exploited effectively to reduce transmit power at particular antennas with limited power budget.
Data language requirements of database machines

The selection of a proper set of operations for a database machine has a great influence on the performance of the overall system. In this paper, we will discuss the data language requirements of database machines. The data language for a proposed relational database machine is presented. Methods for supporting hierarchical and network interfaces using a relational database machine language set are introduced. The relative performance for data access using relational and network interfaces is compared through the evaluation of cost functions. It is shown that the support of a network interface in a relational database machine is feasible, but expensive.
Web-based technical term translation pairs mining for patent document translation

This paper proposes a simple but powerful approach for obtaining technical term translation pairs in patent domain from Web automatically. First, several technical terms are used as seed queries and submitted to search engineering. Secondly, an extraction algorithm is proposed to extract some key word translation pairs from the returned web pages. Finally, a multi-feature based evaluation method is proposed to pick up those translation pairs that are true technical term translation pairs in patent domain. With this method, we obtain about 8,890,000 key word translation pairs which can be used to translate the technical terms in patent documents. And experimental results show that the precision of these translation pairs are more than 99%, and the coverage of these translation pairs for the technical terms in patent documents are more than 84%.
Calcium-Dependent Phosphorylafion of Proteins in Rabbit Ciliary Processes

Calcium-dependent phosphorylation of endogenous substrate proteins in albino rabbit ciliary processes was studied by SDS-polyacrylamide gel electrophoresis and autoradiography. In the soluble fraction, a modest augmentation of phosphorylation was observed by Ca alone and together with the additional activators, calmodulin (CAM) or phorbol myristate acetate (PMA). However, there was a greater enhancement of protein phosphorylation by Ca and activators in the participate fraction. The degree of Ca-CAM-dependent protein phosphorylation was greater than that of Ca-PMA-dependent phosphorylation. Endogenous substrate proteins for Ca-CAM-dependent protein kinases had apparent molecular sizes of 205,170,150,130,77,58,40,32 and 18 kDa. Phosphorylation of the 58 kDa protein band was strongest. This protein was identified as vimentin on the basis of its behavior with Triton-XlOO treatment, and by Western blotting using anti-vimentin antibody. Endogenous substrates of protein kinase C (Ca-PMA-dependent) were located at 87 kDa and possibly in the 56 and 54 kDa protein bands. A 50 kDa protein was found to be phosphorylated in the presence of Ca alone, and was not affected by the presence of other activators (CAM or PMA). A Ca-dependent dephosphorylation of a 43 kDa protein was observed, and some proteins rapidly phosphorylated by Ca-CAM kinase were also relatively quickly dephosphorylated at incubation times greater than 1 min. Invest Ophthalmol Vis Sci 30:723-730,1989
An application of intuitionistic fuzzy sets in text classification

Intuitionistic fuzzy set (IFS) is an extended version of fuzzy set being capable of representing hesitancy degrees. Based on similarity measures for IFSs, a framework for text categorization is presented. Two main challenges are addressed: one is how to represent documents in terms of IFSs; the other is how to learn a pattern of each category from such IFS-based representation. As an exploratory study, the proposed framework is applied to a benchmark data set for text categorization. By using some existing similarity measures for IFSs, the experimental results show that the proposed framework yields satisfactory results.
A rule-based language with functions and sets

A logic based language for manipulating complex objects constructed using set and tuple constructors is introduced. A key feature of the COL language is the use of base and derived data functions. Under some stratification restrictions, the semantics of programs is given by a minimal and justified model that can be computed using a finite sequence of fixpoints. The language is extended using external functions and predicates. An implementation of COL in a functional language is briefly discussed.