Miracle-dz/UniFAR-FTUs huggingface dataset:
A pattern-based nearest neighbor search approach for promoter prediction using DNA structural profiles

MOTIVATION Identification of core promoters is a key clue in understanding gene regulations. However, due to the diverse nature of promoter sequences, the accuracy of existing prediction approaches for non-CpG island (simply CGI)-related promoters is not as high as that for CGI-related promoters. This consequently leads to a low genome-wide promoter prediction accuracy. RESULTS In this article, we first systematically analyze the similarities and differences between the two types of promoters (CGI- and non-CGI-related) from a novel structural perspective, and then devise a unified framework, called PNNP (Pattern-based Nearest Neighbor search for Promoter), to predict both CGI- and non-CGI-related promoters based on their structural features. Our comparative analysis on the structural characteristics of promoters reveals two interesting facts: (i) the structural values of CGI- and non-CGI-related promoters are quite different, but they exhibit nearly similar structural patterns; (ii) the structural patterns of promoters are obviously different from that of non-promoter sequences though the sequences have almost similar structural values. Extensive experiments demonstrate that the proposed PNNP approach is effective in capturing the structural patterns of promoters, and can significantly improve genome-wide performance of promoters prediction, especially non-CGI-related promoters prediction. AVAILABILITY The implementation of the program PNNP is available at http://admis.tongji. edu.cn/Projects/pnnp.aspx.
Hunting for Troll Comments in News Community Forums

There are different definitions of what a troll is. Certainly, a troll can be somebody who teases people to make them angry, or somebody who offends people, or somebody who wants to dominate any single discussion, or somebody who tries to manipulate people’s opinion (sometimes for money), etc. The last definition is the one that dominates the public discourse in Bulgaria and Eastern Europe, and this is our focus in this paper. In our work, we examine two types of opinion manipulation trolls: paid trolls that have been revealed from leaked “reputation management contracts” and “mentioned trolls” that have been called such by several different people. We show that these definitions are sensible: we build two classifiers that can distinguish a post by such a paid troll from one by a non-troll with 81-82% accuracy; the same classifier achieves 81-82% accuracy on so called mentioned troll vs. non-troll posts.
Evidence Levels for Neuroradiology Articles: Low Agreement among Raters

Rating of articles by the original manuscript reviewers and 3 other radiologists at different time points was investigated in 100 AJNR articles. The results show that the levels-of-evidence criteria adopted for use in AJNR did not allow consistent manuscript classification between readers or even by the same reader at 2 time points. BACKGROUND AND PURPOSE: Because evidence-based articles are difficult to recognize among the large volume of publications available, some journals have adopted evidence-based medicine criteria to classify their articles. Our purpose was to determine whether an evidence-based medicine classification used by a subspecialty-imaging journal allowed consistent categorization of levels of evidence among different raters. MATERIALS AND METHODS: One hundred consecutive articles in the American Journal of Neuroradiology were classified as to their level of evidence by the 2 original manuscript reviewers, and their interobserver agreement was calculated. After publication, abstracts and titles were reprinted and independently ranked by 3 different radiologists at 2 different time points. Interobserver and intraobserver agreement was calculated for these radiologists. RESULTS: The interobserver agreement between the original manuscript reviewers was −0.2283 (standard error = 0.0000; 95% CI, −0.2283 to −0.2283); among the 3 postpublication reviewers for the first evaluation, it was 0.1899 (standard error = 0.0383; 95% CI, 0.1149–0.2649); and for the second evaluation, performed 3 months later, it was 0.1145 (standard error = 0.0350; 95% CI, 0.0460–0.1831). The intraobserver agreement was 0.2344 (standard error = 0.0660; 95% CI, 0.1050–0.3639), 0.3826 (standard error = 0.0738; 95% CI, 0.2379–0.5272), and 0.6611 (standard error = 0.0656; 95% CI, 0.5325–0.7898) for the 3 postpublication evaluators, respectively. These results show no-to-fair interreviewer agreement and a tendency to slight intrareviewer agreement. CONCLUSIONS: Inconsistent use of evidence-based criteria by different raters limits their utility when attempting to classify neuroradiology-related articles.
Robust and optimal stabilization of uncertain linear systems using LQR methods

Robust and Optimal stabilization of a class of a Linear Time Invariant (LTI) systems is discussed which exhibit linear time varying (LTV) behavior due to the presence of parametric variations and uncertainties. Linear quadratic methods offer global optimal control solutions for LTI systems. Such methods offer optimal solutions only locally for systems which become LTV due to parametric uncertainties. We propose that such an LTV system can be divided into two or more LTI systems in terms of the operating conditions ranging from nominal to most uncertain. In our proposed approach, two linear quadratic regulators would each be separately designed for nominal operating conditions and the uncertain conditions in a system. It is shown that the switchings between the two regulators depend upon the size of the uncertainty. A machine learning algorithm such as the support vector machine has been used to design a switching surface as a function of only the parametric uncertainties of the system. Extended high gain observers are used to estimate the parametric uncertainties needed for switching between the two regulators. Simulation results are included to demonstrate the performance of the proposed approach.
Estrogen and Cytochrome P450 1B1 Contribute to Both Early- and Late-Stage Head and Neck Carcinogenesis

Squamous cell carcinoma of the head and neck (HNSCC) is the sixth most common type of cancer in the United States. The goal of this study was to evaluate the contribution of estrogens to the development of HNSCCs. Various cell lines derived from early- and late-stage head and neck lesions were used to characterize the expression of estrogen synthesis and metabolism genes, including cytochrome P450 (CYP) 1B1, examine the effect of estrogen on gene expression, and evaluate the role of CYP1B1 and/or estrogen in cell motility, proliferation, and apoptosis. Estrogen metabolism genes (CYP1B1, CYP1A1, catechol-o-methyltransferase, UDP-glucuronosyltransferase 1A1, and glutathione-S-transferase P1) and estrogen receptor (ER) β were expressed in cell lines derived from both premalignant (MSK-Leuk1) and malignant (HNSCC) lesions. Exposure to estrogen induced CYP1B1 2.3- to 3.6-fold relative to vehicle-treated controls (P = 0.0004) in MSK-Leuk1 cells but not in HNSCC cells. CYP1B1 knockdown by shRNA reduced the migration and proliferation of MSK-Leuk1 cells by 57% and 45%, respectively. Exposure of MSK-Leuk1 cells to estrogen inhibited apoptosis by 26%, whereas supplementation with the antiestrogen fulvestrant restored estrogen-dependent apoptosis. Representation of the estrogen pathway in human head and neck tissues from 128 patients was examined using tissue microarrays. The majority of the samples exhibited immunohistochemical staining for ERβ (91.9%), CYP1B1 (99.4%), and 17β-estradiol (88.4%). CYP1B1 and ERβ were elevated in HNSCCs relative to normal epithelium (P = 0.024 and 0.008, respectively). These data provide novel insight into the mechanisms underlying head and neck carcinogenesis and facilitate the identification of new targets for chemopreventive intervention. Cancer Prev Res; 4(1); 107–15. ©2011 AACR.
Complicated grief and related bereavement issues for DSM‐5

Bereavement is a severe stressor that typically incites painful and debilitating symptoms of acute grief that commonly progresses to restoration of a satisfactory, if changed, life. Normally, grief does not need clinical intervention. However, sometimes acute grief can gain a foothold and become a chronic debilitating condition called complicated grief. Moreover, the stress caused by bereavement, like other stressors, can increase the likelihood of onset or worsening of other physical or mental disorders. Hence, some bereaved people need to be diagnosed and treated. A clinician evaluating a bereaved person is at risk for both over‐and under‐diagnosis, either pathologizing a normal condition or neglecting to treat an impairing disorder. The authors of DSM IV focused primarily on the problem of over‐diagnosis, and omitted complicated grief because of insufficient evidence. We revisit bereavement considerations in light of new research findings. This article focuses primarily on a discussion of possible inclusion of a new diagnosis and dimensional assessment of complicated grief. We also discuss modifications in the bereavement V code and refinement of bereavement exclusions in major depression and other disorders. Depression and Anxiety, 2011. © 2011 Wiley‐Liss, Inc.
Developing an Instrument to Evaluate Habitual Physical Activity Level of Elementary School-aged Children in Large Populations : A Preliminary Study

Objectives: This study is an explorative study for developing an instrument to measure habitual physical activity level of school-aged children. Methods: HPAQ-S consists of 41 items and a self-reported 5-day recall instrument designed to assess habitual physical activity level for school-aged children. For the validity and reliability test, a sample consisted of 28 children, aged 10-11 years old. Results: 41 question items showed an acceptable internal consistency (cronbach's alpha=.89). A significant positive correlation with the pedometer results (r=.69, p＜.001) and with Borg’s questionnaire (r=.76, p＜.001) support the validity of HPAQ-S. Conclusion: HPAQ-S may be more useful for measuring habitual physical activity level of elementary school-aged children in large populations.
I know it is important but is it my responsibility? Embedding literacy strategies across the middle school curriculum

This article reports a study on the responses of a group of 49 Western Australian middle school teachers to a year-long professional learning experience, entitled the Making the Links Project. This project was established to help teachers of various learning areas adapt their practices to significant changes in the educational context. In accordance with imminent changes in the curriculum (the Australian Curriculum) and as a response to a national literacy testing agenda (National Assessment Program – Literacy and Numeracy [NAPLAN]), the teachers concerned have been under new pressure to teach literacy across the curriculum. Furthermore, they are now expected to teach Year 7, taught historically in primary school settings. This article presents a discussion of teachers’ perceptions of their responsibilities in terms of teaching literacy within their learning areas and how these perceptions changed over the course of the professional learning experience. It also discusses teachers’ responses to ‘trying out’ some literacy pedagogies more traditionally used in primary school settings.
Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding

DNA barcoding should provide rapid, accurate and automatable species identifications by using a standardized DNA region as a tag. Based on sequences available in GenBank and sequences produced for this study, we evaluated the resolution power of the whole chloroplast trnL (UAA) intron (254–767 bp) and of a shorter fragment of this intron (the P6 loop, 10–143 bp) amplified with highly conserved primers. The main limitation of the whole trnL intron for DNA barcoding remains its relatively low resolution (67.3% of the species from GenBank unambiguously identified). The resolution of the P6 loop is lower (19.5% identified) but remains higher than those of existing alternative systems. The resolution is much higher in specific contexts such as species originating from a single ecosystem, or commonly eaten plants. Despite the relatively low resolution, the whole trnL intron and its P6 loop have many advantages: the primers are highly conserved, and the amplification system is very robust. The P6 loop can even be amplified when using highly degraded DNA from processed food or from permafrost samples, and has the potential to be extensively used in food industry, in forensic science, in diet analyses based on feces and in ancient DNA studies.
Fool me twice: Exploring and exploiting error tolerance in physics-based animation

The error tolerance of human perception offers a range of opportunities to trade numerical accuracy for performance in physics-based simulation. However, most prior work on perceptual error tolerance either focus exclusively on understanding the tolerance of the human visual system or burden the application developer with case-specific implementations such as Level-of-Detail (LOD) techniques. In this article, based on a detailed set of perceptual metrics, we propose a methodology to identify the maximum error tolerance of physics simulation. Then, we apply this methodology in the evaluation of four case studies. First, we utilize the methodology in the tuning of the simulation timestep. The second study deals with tuning the iteration count for the LCP solver. Then, we evaluate the perceptual quality of Fast Estimation with Error Control (FEEC) [Yeh et al. 2006]. Finally, we explore the hardware optimization technique of precision reduction.
Continuation methods for adapting simulated skills

Modeling the large space of possible human motions requires scalable techniques. Generalizing from example motions or example controllers is one way to provide the required scalability. We present techniques for generalizing a controller for physics-based walking to significantly different tasks, such as climbing a large step up, or pushing a heavy object. Continuation methods solve such problems using a progressive sequence of problems that trace a path from an existing solved problem to the final desired-but-unsolved problem. Each step in the continuation sequence makes progress towards the target problem while further adapting the solution. We describe and evaluate a number of choices in applying continuation methods to adapting walking gaits for tasks involving interaction with the environment. The methods have been successfully applied to automatically adapt a regular cyclic walk to climbing a 65cm step, stepping over a 55cm sill, pushing heavy furniture, walking up steep inclines, and walking on ice. The continuation path further provides parameterized solutions to these problems.
Uncertainties assessment in global sensitivity indices estimation from metamodels

Global sensitivity analysis is often impracticable for complex and resource intensive numerical models, as it requires a large number of runs. The metamodel approach replaces the original model by an approximated code that is much faster to run. This paper deals with the information loss in the estimation of sensitivity indices due to the metamodel approximation. A method for providing a robust error assessment is presented, hence enabling significant time savings without sacrificing on precision and rigor. The methodology is illustrated on two different types of metamodels: one based on reduced basis, the other one on RKHS interpolation.
Comparative Evaluation of the Gut Microbiota Associated with the Below- and Above-Ground Life Stages (Larvae and Beetles) of the Forest Cockchafer, Melolontha hippocastani

A comparison of the diversity of bacterial communities in the larval midgut and adult gut of the European forest cockchafer (Melolontha hippocastani) was carried out using approaches that were both dependent on and independent of cultivation. Clone libraries of the 16S rRNA gene revealed 150 operational taxonomic units (OTUs) that belong to 11 taxonomical classes and two other groups that could be classified only to the phylum level. The most abundant classes were β, δ and γ-proteobacteria, Clostridia, Bacilli, Erysipelotrichi and Sphingobacteria. Although the insect’s gut is emptied in the prepupal stage and the beetle undergoes a long diapause period, a subset of eight taxonomic classes from the aforementioned eleven were found to be common in the guts of diapausing adults and the larval midguts (L2, L3). Moreover, several bacterial phylotypes belonging to these common bacterial classes were found to be shared by the larval midgut and the adult gut. Despite this, the adult gut bacterial community represented a subset of that found in the larvae midgut. Consequently, the midgut of the larval instars contains a more diverse bacterial community compared to the adult gut. On the other hand, after the bacteria present in the larvae were cultivated, eight bacterial species were isolated. Moreover, we found evidence of the active role of some of the bacterial species isolated in food digestion, namely, the presence of amylase and xylanolytic properties. Finally, fluorescence in situ hybridization allowed us to confirm the presence of selected species in the insect gut and through this, their ecological niche as well as the metagenomic results. The results presented here elucidated the heterogeneity of aerobic and facultative bacteria in the gut of a holometabolous insect species having two different feeding habits.
Clinicopathologic Analysis of Early-stage Sporadic Ovarian Carcinoma

The reported experience with early-stage (FIGO stage I/II) ovarian carcinoma (OC) is limited given that the majority of women with OC are diagnosed at an advanced stage. There has not been an extensive review of these tumors, and since the pathologic criteria differentiating invasive and borderline tumors have evolved over time, the issue of whether a proportion of these tumors should be reclassified has not been addressed. We identified patients with stage I/II invasive OC who underwent primary surgical management at Memorial Sloan-Kettering Cancer Center from 1980 to 2000. Patients known to have a BRCA mutation or a family history of breast/ovarian cancer were excluded. Hematoxylin and eosin slide review, blinded to clinical outcomes, using current diagnostic criteria for ovarian carcinomas and borderline ovarian tumors, was performed. Progression-free survival (PFS) and disease-specific survival (DSS) were estimated and compared. Hematoxylin and eosin slides were reviewed for 140 of the 145 patients identified. The diagnosis was changed to borderline (low malignant potential) in 41 cases (29.3%). Twenty-nine (70.7%) of 41 changes in diagnosis involved endometrioid and mucinous tumors. This was attributable to the application of recently revised criteria for distinguishing borderline tumors from carcinomas. None of the originally diagnosed clear cell carcinomas was reclassified as borderline. The distribution of histologic subtypes among the 94 carcinomas included 26 serous (27.7%), 25 clear cell (26.6%), 22 endometrioid (23.4%), 10 mixed (10.6%), 6 mucinous (6.4%), 2 malignant Brenner (2.1%), and 3 adenocarcinomas, not otherwise specified (3.2%). Adjuvant therapy was given to 84 (89.4%) of the 94 patients with carcinomas. The 5-year PFS and DSS were significantly greater for the group of cases that was reclassified as borderline (4.5% vs. 26.2% progressed [P = 0.006]; 4.5% vs. 25.6% died [P = 0.003]). The 5-year PFS and DSS were significantly worse for carcinomas with a TP53 mutation (22.6% vs. 41.2% progressed [P = 0.04]; 21.7% vs. 24.7% died [P = 0.04]). There were no statistically significant differences in outcome between stages I versus II, tumor grades, clear cell histology versus other, and stage IC preoperative versus intraoperative rupture. We concluded that a large number of cases originally diagnosed as early-stage sporadic OC were borderline tumors. Clear cell histology does not confer a worse prognosis compared with other histologies. The presence of a TP53 mutation was an adverse prognostic indicator.
Model for macroevolutionary dynamics

Significance Genera are often viewed as artificial constructs of taxonomic practice. Here, we show that a stochastic model that includes three events with constant rates—species formation, extinction of species, and origination of new genera—can describe well the species-within-genus distributions for large taxa. Predictions from the model, including origination times of large taxa and origination rates of genera, match values obtained by other methods. Likewise, estimated extinction rates are close to speciation rates, which is consistent with the paleontological record. The model’s success emphasizes that, although taxonomic groupings are manmade, they nonetheless reflect natural evolutionary processes. The highly skewed distribution of species among genera, although challenging to macroevolutionists, provides an opportunity to understand the dynamics of diversification, including species formation, extinction, and morphological evolution. Early models were based on either the work by Yule [Yule GU (1925) Philos Trans R Soc Lond B Biol Sci 213:21–87], which neglects extinction, or a simple birth–death (speciation–extinction) process. Here, we extend the more recent development of a generic, neutral speciation–extinction (of species)–origination (of genera; SEO) model for macroevolutionary dynamics of taxon diversification. Simulations show that deviations from the homogeneity assumptions in the model can be detected in species-per-genus distributions. The SEO model fits observed species-per-genus distributions well for class-to-kingdom–sized taxonomic groups. The model’s predictions for the appearance times (the time of the first existing species) of the taxonomic groups also approximately match estimates based on molecular inference and fossil records. Unlike estimates based on analyses of phylogenetic reconstruction, fitted extinction rates for large clades are close to speciation rates, consistent with high rates of species turnover and the relatively slow change in diversity observed in the fossil record. Finally, the SEO model generally supports the consistency of generic boundaries based on morphological differences between species and provides a comparator for rates of lineage splitting and morphological evolution.
Distribution and Respiratory Activity of Mycobacteria in Household Water System of Healthy Volunteers in Japan

The primary infectious source of nontuberculous mycobacteria (NTM), which are known as opportunistic pathogens, appears to be environmental exposure, and it is important to reduce the frequency of exposure from environmental sources for preventing NTM infections. In order to achieve this, the distribution and respiratory activity of NTM in the environments must be clarified. In this study, we determined the abundance of mycobacteria and respiratory active mycobacteria in the household water system of healthy volunteers using quantitative PCR and a fluorescent staining method, because household water has been considered as one of the possible infectious sources. We chose healthy volunteer households in order to lessen the effect of possible residential contamination from an infected patient. We evaluated whether each sampling site (bathroom drain, kitchen drain, bath heater pipe and showerhead) have the potential to be the sources of NTM infections. Our results indicated that drains in the bathroom and kitchen sink are the niche for Mycobacterium spp. and M. avium cells were only detected in the bathtub inlet. Both physicochemical and biologic selective pressures may affect the preferred habitat of Mycobacterium spp. Regional differences also appear to exist as demonstrated by the presence (US) or absence (Japan) of Mycobacterium spp. on showerheads. Understanding of the country specific human activities and water usage will help to elucidate the infectious source and route of nontuberculous mycobacterial disease.