Miracle-dz/UniFAR-FTUs huggingface dataset:
Budgeted Batch Bayesian Optimization With Unknown Batch Sizes

Parameter settings profoundly impact the performance of machine learning algorithms and laboratory experiments. The classical grid search or trial-error methods are exponentially expensive in large parameter spaces, and Bayesian optimization (BO) offers an elegant alternative for global optimization of black box functions. In situations where the black box function can be evaluated at multiple points simultaneously, batch Bayesian optimization is used. Current batch BO approaches are restrictive in that they fix the number of evaluations per batch, and this can be wasteful when the number of specified evaluations is larger than the number of real maxima in the underlying acquisition function. We present the Budgeted Batch Bayesian Optimization (B3O) for hyper-parameter tuning and experimental design - we identify the appropriate batch size for each iteration in an elegant way. To set the batch size flexible, we use the infinite Gaussian mixture model (IGMM) for automatically identifying the number of peaks in the underlying acquisition functions. We solve the intractability of estimating the IGMM directly from the acquisition function by formulating the batch generalized slice sampling to efficiently draw samples from the acquisition function. We perform extensive experiments for both synthetic functions and two real world applications - machine learning hyper-parameter tuning and experimental design for alloy hardening. We show empirically that the proposed B3O outperforms the existing fixed batch BO approaches in finding the optimum whilst requiring a fewer number of evaluations, thus saving cost and time.
Expression Levels of TLRs Involved in Viral Recognition in PBMCs from HIV-1-Infected Patients Failing Antiretroviral Therapy

Objective: The aim of this study was to evaluate whether gene expression of Toll-like receptor (TLR)-3, TLR4, TLR7 and TLR9 was impaired in patients with chronic HIV-1 infection who were failing to respond to antiretroviral therapy. Methods: Transcripts encoding TLRs were assayed by quantitative real time RT-PCR on peripheral blood mononuclear cells derived from patients with HIV-1 infection who were responding or not responding to antiretroviral therapy and healthy control subjects. Results: Chronic HIV-1-infected patients who failed to respond to therapy showed reduced expression of TLRs 3, 4 and 9, together with increased expression of TLR7, as compared to healthy subjects. Moreover, a trend towards a higher expression of TLR3 and TLR9 was observed in responder patients compared with non-responders. In addition, we found lower levels of TRLs 3, 7 and 9 in patients with high levels of HIV-1 RNA compared to those with lower levels of viremia. Conclusions: These findings demonstrate that in chronic HIV-1-positive patients who were failing to respond to the therapy, there were substantial changes in TLRs expression. This is likely to be an important determinant of the clinical course of HIV-1 infection.
Synergism of the malononitrilamides 279 and 715 with cyclosporine A in the induction of long‐term cardiac allograft survival

Abstract We tested here the effects of malononitrilamide (MNA) 279 and MNA 715 (derivatives of A771726, the active metabolite of leflunomide) in monotherapy and in combination with cyclosporine A (CSA) on heterotopically transplanted rat cardiac allografts (BN) [Brown Norway Lewis]. Both MNAs (5–20 mg/kg) displayed a dose‐dependent increase of efficacy. The combination of CSA (5 mg/kg) with the MNAs (5 and 10 mg/kg) showed a synergistic effect in the prolongation of allograft survival and in the induction of long‐term allograft survival. To investigate the immunological mechanism responsible for long‐term allograft survival, we transplanted second set (BN) and third party (Dark Agouti) skin allografts on the tail of long‐term surviving rats. The cause for long‐term allograft survival turned out to be a donor‐specific tolerance. We formulate a hypothesis for the mechanism of the synergism of the combination MNA + CSA in the induction of tolerance.
HPLC–MS/MS Analysis of a Traditional Chinese Medical Formulation of Bu-Yang-Huan-Wu-Tang and Its Pharmacokinetics after Oral Administration to Rats

Bu-yang-huan-wu-tang (BYHWT) is one of the most popular formulated traditional Chinese medicine prescriptions, and is widely for prevention of ischemic cardio-cerebral vascular diseases and stroke-induced disability. A specific high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) has been developed and validated for simultaneous quantification of the nine main bioactive components, i.e., astragaloside I, astragaloside II, astragaloside IV, formononetin, ononin, calycosin, calycosin-7-O-β-d-glucoside, ligustilide and paeoniflorin in rat plasma after oral administration of BYHWT extract. This method was applied to investigate the pharmacokinetics in conscious and freely moving rats. No significant matrix effects were observed. The overall analytical procedure was rapid and reproducible, which makes it suitable for quantitative analysis of a large number of samples. Among them, three astragalosides and four isoflavones in A. membranaceus, ligustilide in Radix Angelicae Sinensis and Rhizoma Ligustici Chuanxiong and paeoniflorin in Radix Paeoniae Rubra were identified. This developed method was then successfully applied to pharmacokinetic studies of the nine bioactive constituents after oral administration of BYHWT extracts in rats. The pharmacokinetic data demonstrated that astragaloside I, astragaloside II, astragaloside IV and ligustilide presented the phenomenon of double peaks. The other herbal ingredients of formononetin, ononin, calycosin, calycosin-7-O-β-d-glucoside and paeoniflorin appeared together in a single and plateau absorption phase. These phenomenona suggest that these components may have multiple absorption sites, regulation of enterohepatic circulation or the gastric emptying rate, or there is ingredient-ingredient interaction. These pharmacokinetic results provide a constructive contribution to better understand the absorption mechanism of BYHWT and to support additional clinical evaluation.
No Association of Type 2 Diabetes Risk Variants and Prostate Cancer Risk: the Multiethnic Cohort and PAGE

Background: Epidemiologic studies have found evidence of an inverse association between diabetes status and prostate cancer risk. We explored the hypothesis that common genetic variation may explain, in part, the inverse association between diabetes and prostate cancer. Methods: We tested 17 diabetes risk variants for association with prostate cancer risk in a prostate cancer case–control study of 2,746 cases and 3,317 controls from five racial/ethnic groups in the Multiethnic Cohort (MEC) study. Results: After adjustment for multiple testing, none of the alleles were statistically significantly associated with prostate cancer risk. Aggregate scores that sum the risk alleles were also not significantly associated with risk. Conclusions: We did not find evidence of association of this set of diabetes risk alleles with prostate cancer. Impact: Resequencing and fine-mapping of the loci for diabetes and prostate cancer that were identified by genome-wide association studies are necessary to understand any genetic contribution for the inverse association between these common diseases. Cancer Epidemiol Biomarkers Prev; 20(9); 1979–81. ©2011 AACR.
Disturbance and Delay Robustness Guarantees of Gradient Systems Based on Static Noncooperative Games With an Application to Feedback Control for PEV Charging Load Allocation

This paper investigates robustness of gradient-type dynamical systems derived from static noncooperative games with a large number of players. The control objective is to drive state variables to the vicinities of Nash equilibria in the presence of disturbance and time-delay. The framework of integral input-to-state stability for large-scale systems is employed for verifying such global robustness. Several robustness criteria are presented, and Lyapunov-Krasovskii functionals are constructed. The developed theory is applied to the plug-in electric vehicle charging problem of allocating the charging load to the overnight demand valley to reduce the impact on the electric grid. Securing robustness of the dynamic load allocation is important, since eliminating uncertainties in demand predictions would become harder due to energy storage integration coupled with various energy-aware technologies. Introducing feedback, this paper guarantees stability and achieves robustness of the allocation dynamics subject to communication delay when demand predictions are not accurate. The usefulness of the proposed decentralized scheme is illustrated by numerical simulations.
An optimal decomposition algorithm for tree edit distance

The <i>edit distance</i> between two ordered rooted trees with vertex labels is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling existing nodes, as well as inserting new nodes. In this article, we present a worst-case <i>O</i>(<i>n</i><sup>3</sup>)-time algorithm for the problem when the two trees have size <i>n</i>, improving the previous best <i>O</i>(<i>n</i><sup>3</sup> log <i>n</i>)-time algorithm. Our result requires a novel adaptive strategy for deciding how a dynamic program divides into subproblems, together with a deeper understanding of the previous algorithms for the problem. We prove the optimality of our algorithm among the family of <i>decomposition strategy</i> algorithms—which also includes the previous fastest algorithms—by tightening the known lower bound of Ω(<i>n</i><sup>2</sup> log<sup>2</sup> <i>n</i>) to Ω(<i>n</i><sup>3</sup>), matching our algorithm's running time. Furthermore, we obtain matching upper and lower bounds for decomposition strategy algorithms of Θ(<i>nm</i><sup>2</sup> (1 + log <i>n</i>/<i>m</i>)) when the two trees have sizes <i>m</i> and <i>n</i> and <i>m</i> < <i>n</i>.
Isobias and alloiobias functions in animal psycophysics.

An analogue of the human yes-no detection task was used to train six pigeons to discriminate luminance differences under two different reinforcer-scheduling procedures. When a controlled reinforce-ratio procedure was used, relative stimulus frequency was constant at . 5, and relative reinforcer frequency for correct detections was held constant at three different values for each of five luminance differences. When an uncontrolled reinforcer-ratio procedure (the typical detection paradigm) was used, relative reinforcer frequency for correct detections was allowed to covary with changes in relative stimulus frequency for each of five luminance differences. Two measures of bias, response bias (Davison & Tustin, 1978) and the detection-theory likelihood-ratio measure (beta obt), were compared. The controlled reinforcer-ratio procedure generated equal- or iso-response-bias functions, and the uncontrolled reinforcer-ratio procedure gave changing or alloio-response-bias functions. The Davison-Tustin model accounted for 88% and 93% of the data variance in the controlled and uncontrolled reinforcer-ratio procedures, respectively. The best-fitting equal-beta functions accounted for an average of 53% and 69%, respectively, in the two procedures. In addition, neither procedure gave constant measures of beta obt for constant bias manipulations across different discriminability measures.
Key Odorants Regulate Food Attraction in Drosophila melanogaster

In insects, the search for food is highly dependent on olfactory sensory input. Here, we investigated whether a single key odorant within an odor blend or the complexity of the odor blend influences the attraction of Drosophila melanogaster to a food source. A key odorant is defined as an odorant that elicits a difference in the behavioral response when two similar complex odor blends are offered. To validate that the observed behavioral responses were elicited by olfactory stimuli, we used olfactory co-receptor Orco mutants. We show that within a food odor blend, ethanol functions as a key odorant. In addition to ethanol other odorants might serve as key odorants at specific concentrations. However, not all odorants are key odorants. The intensity of the odor background influences the attractiveness of the key odorants. Increased complexity is only more attractive in a concentration-dependent range for single compounds in a blend. Orco is necessary to discriminate between two similarly attractive odorants when offered as single odorants and in food odor blends, supporting the importance of single odorant recognition in odor blends. These data strongly indicate that flies use more than one strategy to navigate to a food odor source, depending on the availability of key odorants in the odor blend and the alternative odor offered.
Determinants of Maternal Sex Steroids During the First Half of Pregnancy

OBJECTIVE: To examine the associations of maternal and child characteristics with early pregnancy maternal concentrations of testosterone, androstenedione, progesterone, 17-hydroxyprogesterone, and estradiol (E2). METHODS: We analyzed these hormones among 1,343 women with singleton pregnancies who donated serum samples to the Finnish Maternity Cohort from 1986 to 2006 during the first half of pregnancy (median 11 weeks). The associations of maternal and child characteristics with hormone concentrations were investigated by correlation and multivariable regression. RESULTS: Women older than age 30 years had lower androgen and E2 but higher progesterone concentrations than women younger than that age. Multiparous women had 14% lower testosterone, 11% lower androstenedione and 17-hydroxyprogesterone, 9% lower progesterone, and 16% lower E2 concentrations compared with nulliparous women (all P<.05). Smoking mothers had 11%, 18%, and 8% higher testosterone, androstenedione, and 17-hydroxyprogesterone levels, respectively, but 10% lower progesterone compared with nonsmoking women (all P<.05). E2 concentrations were 9% higher (P<.05) among women with a female fetus compared with those with a male fetus. CONCLUSION: Parity, smoking, and, to a lesser extent, maternal age and child sex are associated with sex steroid levels during the first half of a singleton pregnancy. The effects of smoking on the maternal hormonal environment and the possible long-term deleterious consequences on the fetus deserve further evaluation. LEVEL OF EVIDENCE: II
Short-range FMCW monopulse radar for hand-gesture sensing

Intelligent driver assistance systems have become important in the automotive industry. One key element of such systems is a smart user interface that tracks and recognizes drivers' hand gestures. Hand gesture sensing using traditional computer vision techniques is challenging because of wide variations in lighting conditions, e.g. inside a car. A short-range radar device can provide additional information, including the location and instantaneous radial velocity of moving objects. We describe a novel end-to-end (hardware, interface, and software) short-range FMCW radar-based system designed to effectively sense dynamic hand gestures. We provide an effective method for selecting the parameters of the FMCW waveform and for jointly calibrating the radar system with a depth sensor. Finally, we demonstrate that our system guarantees reliable and robust performance.
Comparison of hyperalgesia induced by capsaicin injection and controlled heat injury: effect on temporal summation

The relationship between induction of central sensitization and facilitation of temporal summation to repetitive stimulation is still unclear. The aim of this study was to investigate temporal summation before and after the induction of secondary hyperalgesia by two different experimental methods: capsaicin injection and controlled heat injury. The effect of each injury model was assessed on a separate day with an interval of at least 5 days. Twelve healthy volunteers participated. Each experiment was performed using electrical, radiant heat, mechanical impact, and punctuate stimuli consecutively. The pain threshold (PT) to a single stimulus and the summation threshold to five repetitive stimuli for electrical (2 Hz) and radiant heat (0.83 Hz) were assessed within the secondary hyperalgesic area. The degree of temporal summation for stimulus intensities of 0.8, 1.0, and 1.2 times the baseline pain thresholds were evaluated by the increase in visual analogue scale (VAS) scores from the first to the fifth stimulus of the train. Further, the degrees of temporal summation were assessed for mechanical impact and punctuate stimuli within the primary and secondary hyperalgesic areas. The contra-lateral forearm served as control (no injury). The pain threshold and the summation threshold to electrical and heat stimuli decreased significantly within the secondary hyperalgesic area after the injury induced by both heat injury or capsaicin injection. However, there was no temporal summation for heat and electrical stimuli in either model. In contrast, for the mechanical impact and punctuate mechanical stimuli the degree of temporal summation was significantly facilitated in the secondary hyperalgesic areas compared with the baseline and the control arm in both models. In the primary hyperalgesic area, the degree of temporal summation was facilitated to mechanical impact and punctuate stimuli but only following the capsaicin injection. In conclusion, the temporal summation mechanism for mechanical stimuli was facilitated in the secondary hyperalgesic area.
An exploration of young people’s experiences of posttraumatic growth and their understanding of what helps in this process following bereavement

Bereavement during adolescence is not a minority experience. Despite this, bereavement research has tended to neglect this cohort of individuals (Ribbens McCarthy, 2007). Psychological conceptualisations of trauma and grief have tended to focus on the negative impact of such events, potentially limiting our understanding of post-trauma reactions (Kilmer, 2006). Posttraumatic growth (PTG) is a construct that aims to encapsulate the experience of those who endure horror and trauma and yet still experience positive growth, which is transformative and goes beyond ‘coping’ (Kilmer, 2006). This is a relatively new construct and research exploring PTG in young people directly is in its infancy. This study sets out to explore young people’s experiences following bereavement, in particular whether young people experience any personal or systemic growth and if so, what they feel helps in this process. This study recruited 7 young people who had experienced bereavement at least one year previously. Participants were interviewed about their experience of growth and change following bereavement. Data was analysed using Interpretative Phenomenological Analysis. Three super-ordinate themes were identified following the analysis of data, these were: being ‘in-relation’ with the deceased, the coping process and growth in self. The findings from this study suggest that young people do experience growth and change following bereavement, both personally and within their surrounding systems. This growth appears to be a result of a coping process in which the young people took an active role. The findings also demonstrate the importance of an ongoing relationship with the deceased that is evolving and continuous rather than static. Clinical implications and recommendations for future research are discussed.
EMG signal based control of an intelligent wheelchair

This paper presents a novel artificial neural network approach to control an intelligent wheelchair using myoelectric signals. The work is divided into six stages out of which feature extraction and classification are the main stages for this research. The type of classification technique used is Multi-Layer Perceptron. The EMG data is collected by placing the electrodes on the forearm muscles. This data is segmented for every 200 milliseconds after which the feature extraction is performed using mean absolute value. The signals are fed to the artificial neural networks and processed to attain parameters that are related to the muscles temporal hand activities. The resulting commands are sent to drive the wheelchair according to the user's intention. The software was tested on the intelligent wheelchair in real-time, which confirm that the system is robust for different gender and environments.
Cost-effectiveness of neck-specific exercise with or without a behavioral approach versus physical activity prescription in the treatment of chronic whiplash-associated disorders

Background: Fifty percent of people injured by whiplash still report neck pain after 1 year and costs associated with whiplash associated disorders (WAD) are mostly attributed to health service and sick-leave costs in chronic conditions. With increasing health care expenditures the economic impact of interventions needs to be considered. Objective: To analyze the cost-effectiveness of physiotherapist-led neck-specific exercise without (NSE) or with a behavioral approach (NSEB), or prescription of physical activity (PPA) in chronic WAD, grade 2 to 3. Methods: This is a secondary cost-effectiveness analysis of a multicenter randomized clinical trial of 216 participants with chronic WAD grade 2 to 3. The interventions were physiotherapist-led neck-specific exercise without or with a behavioral approach, or prescription of physical activity for 12 weeks. Incremental cost-effectiveness ratios (ICERs) were determined after 1 year and bootstrapped cost-effectiveness planes and sensitivity analyses of physiotherapy visits were performed. Health care and production loss costs were included and quality-adjusted life years (QALYs) were estimated, using the Euroqol-5D questionnaire. Comparisons with the Short Form-6D, and neck disability index (NDI) were also made. Results: The 1-year follow-up was completed by 170 participants (79%). Both physiotherapist-led groups improved in health related quality of life. The intervention cost alone, per quality-adjusted life year (QALY) gain in the NSE group was US$ 12,067. A trend for higher QALY gains were observed in the NSEB group but the costs were also higher. The ICERs varied depending on questionnaire used, but the addition of a behavioral approach to neck-specific exercise alone was not cost-effective from a societal perspective (ICER primary outcome $127,800 [95% confidence interval [CI], 37,816–711,302]). The sensitivity analyses confirmed the results. The prescription of physical activity did not result in any QALY gain and the societal costs were not lower. Conclusion: Neck-specific exercise was cost-effective from a societal perspective in the treatment of chronic WAD compared with the other exercise interventions. ICERS varied depending on health-related quality of life questionnaires used, but the addition of a behavioral approach was not cost-effective from a societal perspective. The prescription of physical activity did not result in any QALY gain and was thus not considered a relevant option.