Miracle-dz/UniFAR-FTUs huggingface dataset:
In Vitro Interaction of the Housekeeping SecA1 with the Accessory SecA2 Protein of Mycobacterium tuberculosis

The majority of proteins that are secreted across the bacterial cytoplasmic membrane leave the cell via the Sec pathway, which in its minimal form consists of the dimeric ATP-driven motor protein SecA that associates with the protein-conducting membrane pore SecYEG. Some Gram-positive bacteria contain two homologues of SecA, termed SecA1 and SecA2. SecA1 is the essential housekeeping protein, whereas SecA2 is not essential but is involved in the translocation of a subset of proteins, including various virulence factors. Some SecA2 containing bacteria also harbor a homologous SecY2 protein that may form a separate translocase. Interestingly, mycobacteria contain only one SecY protein and thus both SecA1 and SecA2 are required to interact with SecYEG, either individually or together as a heterodimer. In order to address whether SecA1 and SecA2 cooperate during secretion of SecA2 dependent proteins, we examined the oligomeric state of SecA1 and SecA2 of Mycobacterium tuberculosis and their interactions with SecA2 and the cognate SecA1, respectively. We conclude that both SecA1 and SecA2 individually form homodimers in solution but when both proteins are present simultaneously, they form dissociable heterodimers.
Inter-word eye behaviour during reading is not invariant to character size: Evidence against systematic saccadic range error in reading

The present study re-investigated the effect of character size on eye behaviour during reading, in order to test McConkie, Kerr, Reddix, and Zola's (1988) Saccadic Range Error (SRE) hypothesis. This assumes that saccades are biased to move the eyes a constant, optimal distance in the task (i.e., range error), while aiming at the centre of peripherally selected target words. Results showed in contradiction with this hypothesis, (1) that the linear relationship between the eye launch site and the mean landing sites in words is not invariant to character size, and (2) that the optimal launch-site distance to the centre of words varies depending on the spatial extent of the words, and differs from the mean length of saccades in the task. We propose an alternative, Center-of-Gravity hypothesis, which a priori accounts for the launch-site effect and its variations with character size, and suggests that research in reading may benefit from reconsidering the role of character size.
Established Risk Factors Account for Most of the Racial Differences in Cardiovascular Disease Mortality

Background Cardiovascular disease (CVD) mortality varies across racial and ethnic groups in the U.S., and the extent that known risk factors can explain the differences has not been extensively explored. Methods We examined the risk of dying from acute myocardial infarction (AMI) and other heart disease (OHD) among 139,406 African-American (AA), Native Hawaiian (NH), Japanese-American (JA), Latino and White men and women initially free from cardiovascular disease followed prospectively between 1993–1996 and 2003 in the Multiethnic Cohort Study (MEC). During this period, 946 deaths from AMI and 2,323 deaths from OHD were observed. Relative risks of AMI and OHD mortality were calculated accounting for established CVD risk factors: body mass index (BMI), hypertension, diabetes, smoking, alcohol consumption, amount of vigorous physical activity, educational level, diet and, for women, type and age at menopause and hormone replacement therapy (HRT) use. Results Established CVD risk factors explained much of the observed racial and ethnic differences in risk of AMI and OHD mortality. After adjustment, NH men and women had greater risks of OHD than Whites (69% excess, P<0.001 and 62% excess, P = 0.003, respectively), and AA women had greater risks of AMI (48% excess, P = 0.01) and OHD (35% excess, P = 0.007). JA men had lower risks of AMI (51% deficit, P<0.001) and OHD (27% deficit, P = 0.001), as did JA women (AMI, 37% deficit, P = 0.03; OHD, 40% deficit, P = 0.001). Latinos had underlying lower risk of AMI death (26% deficit in men and 35% in women, P = 0.03). Conclusion Known risk factors explain the majority of racial and ethnic differences in mortality due to AMI and OHD. The unexplained excess in NH and AA and the deficits in JA suggest the presence of unmeasured determinants for cardiovascular mortality that are distributed unequally across these populations.
Impact of Previous ART and of ART Initiation on Outcome of HIV-Associated Tuberculosis

Background. Combination antiretroviral therapy (cART) has progressively decreased mortality of HIV-associated tuberculosis . To date, however, limited data on tuberculosis treatment outcomes among coinfected patients who are not ART-naive at the time of tuberculosis diagnosis are available. Methods. A multicenter, observational study enrolled 246 HIV-infected patients diagnosed with tuberculosis, in 96 Italian infectious diseases hospital units, who started tuberculosis treatment. A polytomous logistic regression model was used to identify baseline factors associated with the outcome. A Poisson regression model was used to explain the effect of ART during tuberculosis treatment on mortality, as a time-varying covariate, adjusting for baseline characteristics. Results. Outcomes of tuberculosis treatment were as follows: 130 (52.8%) were successfully treated, 36 (14.6%) patients died in a median time of 2 months (range: 0–16), and 80 (32.6%) had an unsuccessful outcome. Being foreign born or injecting drug users was associated with unsuccessful outcomes. In multivariable Poisson regression, cART during tuberculosis treatment decreased the risk of death, while this risk increased for those who were not ART-naive at tuberculosis diagnosis. Conclusions. ART during tuberculosis treatment is associated with a substantial reduction of death rate among HIV-infected patients. However, patients who are not ART-naive when they develop tuberculosis remain at elevated risk of death.
Blood pressure and calcium intake are related tobone density in adult males

Based on the premise that elevated blood pressure and low bone mass have both been associated with poor Ca nutriture and disturbances in Ca metabolism, a cross-sectional study was employed to determine if blood pressure and dietary Ca intake were significantly related to bone mass. Forty-seven men between 24–77 years of age with blood pressure values ranging from normal to mildly elevated comprised the study group. Blood pressure was measured with a random-zero sphygmomanometer. Bone mineral content (BMC) and density (BMD) of the hip, spine and total body were measured with dual-photon absorptiometry. Dietary intake and physical activity were also assessed. Multiple linear regression analysis was used for statistical analysis. After adjusting for known confounding variables (age, BMI, Ca intake, and others) diastolic blood pressure was negatively related to BMC (P ≤ 0·05) and BMD (P ≤ 0·01) of the total body, trochanteric region (P < 0·01) and Ward's triangle (P < 0·05), and to BMC of the femoral neck (P < 0·05) and lumbar spine, although the latter was just shy of statistical significance (P = 0·058). Systolic blood pressure was negatively related to trochanteric BMD (P = 0·04) and BMC (P = 0·06). Ca intake was positively related to total body BMD (P = 0·005), and BMC of the lumbar spine (P = 0·05). In this population of men, Ca intake was a positive predictor, and blood pressure was a negative predictor of regional measures of bone mass. These findings support the concept that independent of age, BMI and Ca intake, elevated blood pressure varies indirectly with bone mass and density, known predictors of osteoporotic fractures. Future studies are needed to determine whether elevated blood pressure is causally related to the development of low bone mass, and what role dietary Ca plays in that pathway.
Using argumentation to control lexical choice: a functional unification implementation

This thesis presents new surface generation techniques that improve on both aspects of surface generation: (1) lexical choice, which consists of choosing words and their associated syntactic structures and (2) syntactic realization, which consists of combining these partial structures into grammatical sentences. The thesis investigates the impact of the pragmatic situation on surface generation. Because surface generation depends directly on many aspects of the situation, these new techniques allow a purely conceptual input to be expressed by a greater variety of linguistic forms and with more sensitivity to pragmatic factors than was previously possible. Specifically, this research focuses on the impact on lexical choice of one part of the pragmatic situation: the speaker's argumentative intent, i.e., the goal of the speaker to convince the hearer of a certain conclusion. The argumentative intent can be realized by a variety of evaluative expressions appearing at various ranks in the syntactic structure. This thesis describes the selection of four classes of evaluative expressions: judgment determiners (i.e., many), scalar adjectives (i.e., difficult), connotative verbs (i.e., require, enjoy) and argumentative connectives (i.e., but, so). These four classes were not addressed in previous generators. The scFUF formalism is introduced in this thesis to address the issue of complex constraint interaction arising when performing lexical choice under pragmatic constraints. scFUF is derived from Functional Unification Grammars (scFUGs), a formalism previously used for syntactic realization only. scFUF extends scFUGs by providing new mechanisms for control, for expressing hierarchical relations and for using modular knowledge sources. These extensions make scFUF capable of handling lexical choice. In addition, this thesis describes the use of scFUF to develop scSURGE, one of the largest and most widely used syntactic realization grammar available. Finally these new generation techniques are applied to the implementation of scADVISOR II, a question-answering system helping students to choose classes for a semester. In particular, scADVISOR II uses the increased expressive flexibility provided by these techniques to convince a student to choose different classes by presenting the same objective data, retrieved from an underlying knowledge base, in different linguistic forms using evaluative expressions.
Gliding Resistance of Extrasynovial and Intrasynovial Tendons through the A2 Pulley*

The gliding ability of the flexor digitorum profundus tendon and of the palmaris longus tendon through the A2 pulley was compared, in terms of gliding resistance, with use of a system that we developed. Fourteen digits and the ipsilateral palmaris longus tendons from fourteen cadavera were used. The average gliding resistance at the interface between the palmaris longus tendon and the A2 pulley was found to be greater than that between the flexor digitorum profundus tendon and the A2 pulley under similar loading conditions. We concluded that the gliding ability of the palmaris longus tendon was inferior to that of the flexor digitorum profundus tendon in vitro. CLINICAL RELEVANCE: The findings of the present study are consistent with those of in vivo experiments in which extrasynovial tendon grafts have been associated with substantial formation of adhesions. The adhesions may be explained by the poor gliding ability of the palmaris longus tendon. The palmaris longus tendon may have limitations, because of gliding resistance, when it is used as a graft to reconstruct flexor tendons in the digits.
Towards active object tracking via a binocular vision system

The problem of active object tracking system is discussed. A binocular vision system having the ability of actively tracking moving objects, especially human object is designed and implemented. Management software is also developed for further study. The key technologies on active tracking of one moving object by such a binocular system have been studied. The general architecture is firstly analyzed, and then the realization of target detection and tracking algorithm is given. Finally, a complete corresponding mechanism in the tracking process for the two cameras in case that they track different targets is proposed and discussed.
Adaptationism and molecular biology: An example based on ADHD

Rather than starting with traits and speculating whether selective forces drove evolution in past environments, we propose starting with a candidate gene associated with a trait and testing first for patterns of selection at the DNA level. This can provide limitations on the number of traits to be evaluated subsequently by adaptationism as described by Andrews et al.
Microfluidic delivery of small molecules into mammalian cells based on hydrodynamic focusing

Microfluidics‐based cell assays offer high levels of automation and integration, and allow multiple assays to be run in parallel, based on reduced sample volumes. These characteristics make them attractive for studies associated with drug discovery. Controlled delivery of drug molecules or other exogenous materials into cells is a critical issue that needs to be addressed before microfluidics can serve as a viable platform for drug screening and studies. In this study, we report the application of hydrodynamic focusing for controlled delivery of small molecules into cells immobilized on the substrate of a microfluidic device. We delivered calcein AM which was permeant to the cell membrane into cells, and monitored its enzymatic conversion into fluorescent calcein during and after the delivery. Different ratios of the sample flow to the side flow were tested to determine how the conditions of hydrodynamic focusing affected the delivery. A 3D numerical model was developed to help understand the fluid flow, molecular diffusion due to hydrodynamic focusing in the microfluidic channel. The results from the simulation indicated that the calcein AM concentration on the outer surface of a cell was determined by the conditions of hydrodynamic focusing. By comparing the results from the simulation with those from the experiment, we found that the calcein AM concentration on the cell outer surface correlated very well with the amount of the molecules delivered into the cell. This suggests that hydrodynamic focusing provides an effective way for potentially quantitative delivery of exogenous molecules into cells at the single cell or subcellular level. We expect that our technique will pave the way to high‐throughput drug screening and delivery on a microfluidic platform. Biotechnol. Bioeng. 2008;100: 150–158. © 2007 Wiley Periodicals, Inc.
Development of a memetic algorithm for Dynamic Multi-Objective Optimization and its applications for online neural network modeling of UAVs

Dynamic multi-objective optimization (DMO) is one of the most challenging class of optimization problems where the objective functions change over time and the optimization algorithm is required to identify the corresponding Pareto optimal solutions with minimal time lag. DMO has received very little attention in the past and none of the existing multi-objective algorithms perform satisfactorily on test problems and a handful of such applications have been reported. In this paper, we introduce a memetic algorithm (MA) and illustrate its performance for online neural network (NN) identification of the multi-input multi-output unmanned aerial vehicle (UAV) system. As a typical case, the longitudinal model of the UAV is considered and the performance of a NN trained with the memetic algorithm is compared to another trained with Levenberg-Marquardt training algorithm using mini-batches. The memetic algorithm employs an orthogonal epsilon-constrained formulation to deal with multiple objectives and a sequential quadratic programming (SQP) solver is embedded as its local search mechanism to improve the rate of convergence. The performance of the memetic algorithm is presented for two benchmarks Fisherpsilas Discriminant Analysis (FDA), FDA1 and modified FDA2 before highlighting its benefits for online NN model identification for UAVs. Observations from our recent work indicated that Mean Square Error (MSE) alone may not always be a good measure for training the networks. Hence the MSE and maximum absolute value of the instantaneous error is considered as objectives to be minimized which requires a Dynamic MO algorithm. The proposed memetic algorithm is aimed to solve such identification problems and the same can be extended to control problems.
A Probabilistic Approach to Aggregating Anomalies for Unsupervised Anomaly Detection with Industrial Applications

This paper presents a novel, unsupervised approach to detecting anomalies at the collective level. The method probabilistically aggregates the contribution of the individual anomalies in order to detect significantly anomalous groups of cases. The approach is unsupervised in that as only input, it uses a list of cases ranked according to its individual anomaly score. Thus, any anomaly detection algorithm can be used for scoring individual anomalies, both supervised and unsupervised approaches. The applicability of the proposed approach is shown by applying it to an artificial data set and to two industrial data sets — detecting anomalously moving cranes (model-based detection) and anomalous fuel consumption (neighbour-based detection).
VIDEOS AND ANIMATIONS FOR VOCABULARY LEARNING: A STUDY ON DIFFICULT WORDS

Studies on using still images and dynamic videos in multimedia annotations produced inconclusive results. A further examination, however, showed that the principle of using videos to explain complex concepts was not observed in the previous studies. This study was intended to investigate whether videos, compared with pictures, better assist English learners to learn difficult words. It adopted a three-group immediate posttest and delayed posttest quasi-experimental design. Ten target words were selected and embedded in a reading text, each of which was annotated by three annotation types: text-only, text and picture, and text and video. Three intact classes, a total of 88 students, were recruited in a junior high school in northern Taiwan, each of which was randomly assigned to one of the three groups. All participants took the pretest two weeks before the experiment, the immediate posttest after reading the text, and the delayed posttest two weeks after the experiment. The result revealed significant differences between the three groups, in which the video group outperformed the other two groups. Pedagogical implications and suggestions for future research are also given.
Barriers to Intimate Sexuality: Concerns and Meaning-Based Therapy Approaches.

Despite the voracious need for intimate connection, Western society does not promote intimacy, particularly with regard to partner sexuality. Obstacles to sexual intimacy that are discussed include: Media portrayals of sexual and gender role stereotypes, performance-oriented sexual standards, the invisibility of the elderly as sexual beings, and the glamorization of nonrelational sexuality and clandestine affairs. Unfortunately, the sex therapy literature, too, tends to focus on depersonalized and goal-oriented models of sexuality. Paradigms which can overcome barriers and promote intimate sexual connections are required. This article calls for humanistically based changes, in the media and in sex therapy, to satisfy the need for sexual intimacy.
Difference in Incidence of Spontaneous Mutations between Herpes Simplex Virus Types 1 and 2

ABSTRACT Spontaneous mutations within the herpes simplex virus (HSV) genome are introduced by errors during DNA replication. Indicative of the inherent mutation rate of HSV DNA replication, heterogeneous HSV populations containing both acyclovir (ACV)-resistant and ACV-sensitive viruses occur naturally in both clinical isolates and laboratory stocks. Wild-type, laboratory-adapted HSV type 1 (HSV-1) strains KOS and Cl101 reportedly accumulate spontaneous ACV-resistant mutations at a frequency of approximately six to eight mutants per 104plaque-forming viruses (U. B. Dasgupta and W. C. Summers, Proc. Natl. Acad. Sci. USA 75:2378–2381, 1978; J. D. Hall, D. M. Coen, B. L. Fisher, M. Weisslitz, S. Randall, R. E. Almy, P. T. Gelep, and P. A. Schaffer, Virology 132:26–37, 1984). Typically, these resistance mutations map to the thymidine kinase (TK) gene and render the virus TK deficient. To examine this process more closely, a plating efficiency assay was used to determine whether the frequencies of naturally occurring mutations in populations of the laboratory strains HSV-1 SC16, HSV-2 SB5, and HSV-2 333 grown in MRC-5 cells were similar when scored for resistance to penciclovir (PCV) and ACV. Our results indicate that (i) HSV mutants resistant to PCV and those resistant to ACV accumulate at approximately equal frequencies during replication in cell culture, (ii) the spontaneous mutation frequency for the HSV-1 strain SC16 is similar to that previously reported for HSV-1 laboratory strains KOS and Cl101, and (iii) spontaneous mutations in the laboratory HSV-2 strains examined were 9- to 16-fold more frequent than those in the HSV-1 strain SC16. These observations were confirmed and extended for a group of eight clinical isolates in which the HSV-2 mutation frequency was approximately 30 times higher than that for HSV-1 isolates. In conclusion, our results indicate that the frequencies of naturally occurring, or spontaneous, HSV mutants resistant to PCV and those resistant to ACV are similar. However, HSV-2 strains may have a greater propensity to generate drug-resistant mutants than do HSV-1 strains.
Data-driven semantic concept analysis for automatic actionable ontology design

The paper objectives are twofold: to discuss the essence and challenges of automatic ontology design as applied to the Big data semantic modeling and to present Semantic Concept Analysis (SCA), a framework specifically developed for automatic actionable ontology design in Big data scenario. This framework integrates the data-driven DBpedia-based technology for semi-automatic design of the ontology concept hierarchy and Formal Concept Analysis (FCA), which formal concept specialization structure is built as dual one with regard to the ontology concept hierarchy. The SCA model of big data is built iteratively through interleaving use of data-driven ontology generalization step and subsequent formal concept specialization step. In this procedure, each of the pair of steps controls the other one. Indeed, ontology generalization step determines the dual formal concepts of the next specialization level, whereas the extent cardinality of each generated formal concept is used as attribute of the stopping criterion for the iterative ontology generalization design process. The proposed SCA framework technology is validated experimentally through its software prototyping and subsequent computer experimentation.