LLukas22/scidocs huggingface dataset:
Robust and efficient parameter estimation in dynamic models of biological systems

Dynamic modelling provides a systematic framework to understand function in biological systems. Parameter estimation in nonlinear dynamic models remains a very challenging inverse problem due to its nonconvexity and ill-conditioning. Associated issues like overfitting and local solutions are usually not properly addressed in the systems biology literature despite their importance. Here we present a method for robust and efficient parameter estimation which uses two main strategies to surmount the aforementioned difficulties: (i) efficient global optimization to deal with nonconvexity, and (ii) proper regularization methods to handle ill-conditioning. In the case of regularization, we present a detailed critical comparison of methods and guidelines for properly tuning them. Further, we show how regularized estimations ensure the best trade-offs between bias and variance, reducing overfitting, and allowing the incorporation of prior knowledge in a systematic way. We illustrate the performance of the presented method with seven case studies of different nature and increasing complexity, considering several scenarios of data availability, measurement noise and prior knowledge. We show how our method ensures improved estimations with faster and more stable convergence. We also show how the calibrated models are more generalizable. Finally, we give a set of simple guidelines to apply this strategy to a wide variety of calibration problems. Here we provide a parameter estimation strategy which combines efficient global optimization with a regularization scheme. This method is able to calibrate dynamic models in an efficient and robust way, effectively fighting overfitting and allowing the incorporation of prior information.
Comparative study of the antimicrobial efficacy of chlorhexidine gel, chlorhexidine solution and sodium hypochlorite as endodontic irrigants.

The purpose of this study was to assess the in vitro the antimicrobial efficacy of chlorhexidine gluconate gel as an endodontic auxiliary chemical substance compared to sodium hypochlorite (NaOCl) and chlorhexidine gluconate solution. The antimicrobial efficacy of the tested substances was evaluated using the agar diffusion test. The growth inhibition zones produced by 0.2%, 1% and 2% chlorhexidine gel were evaluated against 5 facultative anaerobic bacteria and 4 pigmented Gram-negative anaerobes, and compared to the results obtained by NaOCl and chlorhexidine solution. The largest growth inhibition zones were produced when the test bacteria were in contact with 2% chlorhexidine gluconate gel (11.79 mm), being significantly different (p<0.05) from the growth inhibition zones produced by all NaOCl concentrations, including 5.25% (9.54 mm). However, there was no statistically significant difference (p>0.05) between the growth inhibition zones obtained with equal concentrations of chlorhexidine solution and gel. The results of this study indicate that, as far as its antimicrobial properties are concerned, chlorhexidine gel has a great potential to be used as an endodontic auxiliary chemical substance.
Pigeon-inspired optimization: a new swarm intelligence optimizer for air robot path planning

Purpose – The purpose of this paper is to present a novel swarm intelligence optimizer — pigeoninspired optimization (PIO) — and describe how this algorithm was applied to solve air robot path planning problems. Design/methodology/approach – The formulation of threat resources and objective function in air robot path planning is given. The mathematical model and detailed implementation process of PIO is presented. Comparative experiments with standard differential evolution (DE) algorithm are also conducted. Findings – The feasibility, effectiveness and robustness of the proposed PIO algorithm are shown by a series of comparative experiments with standard DE algorithm. The computational results also show that the proposed PIO algorithm can effectively improve the convergence speed, and the superiority of global search is also verified in various cases. Originality/value – In this paper, the authors first presented a PIO algorithm. In this newly presented algorithm, map and compass operator model is presented based on magnetic field and sun, while landmark operator model is designed based on landmarks. The authors also applied this newly proposed PIO algorithm for solving air robot path planning problems.
Information dissemination via electronic word-of-mouth: Good news travels fast, bad news travels faster!

The purpose of this research is to investigate negativity bias in secondary electronic word-of-mouth (eWOM). Two experiments, one laboratory and one field, were conducted to study actual dissemination behavior. The results demonstrate a strong tendency toward the negative in the dissemination of secondary commercial information. In line with Dynamic Social Impact Theory, our findings show that consumers disseminate online negative content to more recipients, for a longer period of time and in more elaborated and assimilated manner than they do positive information. The research is important from both a theoretical and managerial perspective. In the former, it enriches existing literature on eWOM by providing insight into theoretical dimensions of the negativity theory not examined before (duration, role of valence, elaboration, and assimilation). Findings provide managerial insights into designing more effective WOM and publicity campaigns. 2014 Elsevier Ltd. All rights reserved.
WHEN AUTOENCODERS MEET RECOMMENDER SYSTEMS : COFILS APPROACH

of Dissertation presented to COPPE/UFRJ as a partial fulfillment of the requirements for the degree of Master of Science (M.Sc.) WHEN AUTOENCODERS MEET RECOMMENDER SYSTEMS: COFILS APPROACH Julio César Barbieri Gonzalez de Almeida
Growth and some properties of Cr11Ge19

Abstract Cr 11 Ge 19 belongs to a large family of materials known as the Nowotny chimney-ladder compounds, some of which were recently proposed as advanced thermoelectric materials, particularly because of their low thermal conductivity related to their relatively complex crystal structure. In order to assess the potential of the compound Cr 11 Ge 19 for thermoelectric applications, we grew large single crystals of this peritectic compound by a vertical gradient freeze technique and measured the thermoelectric properties of the crystals. Cr 11 Ge 19 forms peritectically at 1201 K and crystals were grown from Ge-rich solutions. The conditions and the results of the crystal growth experiments are presented. The crystals were characterized by X-ray diffractometry, Laue technique, and electron probe microanalysis. The results of the thermoelectric property measurements suggest that Cr 11 Ge 19 has a metallic behavior and therefore presents little interest for thermoelectric applications.
Chaplaincy and Mental Health Care in Aotearoa New Zealand: An Exploratory Study

This paper summarizes an initial exploratory study undertaken to consider the ministry of New Zealand chaplaincy personnel working within the mental health care context. This qualitative research (a first among New Zealand mental health care chaplains) was not concerned with specific health care institutions per se, but solely about the perspectives of chaplains concerning their professional contribution and issues they experienced when trying to provide pastoral care to patients, families, and clinical staff involved in mental health care. Data from a single focus group indicated that chaplains were fulfilling various WHO-ICD-10AM pastoral interventions as a part of a multidisciplinary and holistic approach to mental health care; however, given a number of frustrations identified by participants, which either impeded or thwarted their professional role as chaplains, a number of improvements were subsequently identified in order to develop the efficiency and effectiveness of chaplaincy and thus maximize the benefits of pastoral care to patients, families, and clinical staff. Some implications of this exploratory study relating to mental health care chaplaincy, ecclesiastical organizations, health care institutions, and government responsibilities and the need for further research are noted.
Power , effect and sample size using GPower : practical issues for researchers and members of research ethics committees

Introduction Since the introduction of a new UK Ethics Committee Authority (UKECA) in 2004 and the setting up of the Central Office for Research Ethics Committees (COREC), research proposals have come under greater scrutiny than ever before. The era of self-regulation in UK research ethics has ended (Kerrison and Pollock, 2005). The UKECA recognise various committees throughout the UK that can approve proposals for research in NHS facilities (National Patient Safety Agency, 2007), and the scope of research for which approval must be sought is defined by the National Research Ethics Service, which has superceded COREC. Guidance on sample size (Central Office for Research Ethics Committees, 2007: 23) requires that 'the number should be sufficient to achieve worthwhile results, but should not be so high as to involve unnecessary recruitment and burdens for participants'. It also suggests that formal sample estimation size should be based on the primary outcome, and that if there is more than one outcome then the largest sample size should be chosen. Sample size is a function of three factors – the alpha level, beta level and magnitude of the difference (effect size) hypothesised. Referring to the expected size of effect, COREC (2007: 23) guidance states that 'it is important that the difference is not unrealistically high, as this could lead to an underestimate of the required sample size'. In this paper, issues of alpha, beta and effect size will be considered from a practical perspective. A freely-available statistical software package called GPower (Buchner et al, 1997) will be used to illustrate concepts and provide practical assistance to novitiate researchers and members of research ethics committees. There are a wide range of freely available statistical software packages, such as PS (Dupont and Plummer, 1997) and STPLAN (Brown et al, 2000). Each has features worth exploring, but GPower was chosen because of its ease of use and the wide range of study designs for which it caters. Using GPower, sample size and power can be estimated or checked by those with relatively little technical knowledge of statistics. Alpha and beta errors and power Researchers begin with a research hypothesis – a 'hunch' about the way that the world might be. For example, that treatment A is better than treatment B. There are logical reasons why this can never be demonstrated as absolutely true, but evidence that it may or may not be true can be obtained by …
Smoothing Parameter and Model Selection for General Smooth Models

This paper discusses a general framework for smoothing para meter estimation for models with regular likelihoods constructed in terms of unknown smooth functio ns f covariates. Gaussian random effects and parametric terms may also be present. By construction the me thod is numerically stable and convergent, and enables smoothing parameter uncertainty to be quantified. T he latter enables us to fix a well known problem with AIC for such models, thereby improving the range of m del selection tools available. The smooth functions are represented by reduced rank spline like smoot hers, with associated quadratic penalties measuring function smoothness. Model estimation is by penalized l ikelihood maximization, where the smoothing parameters controlling the extent of penalization are esti mated by Laplace approximate marginal likelihood. The methods cover, for example, generalized additive model s for non-exponential family responses (for example beta, ordered categorical, scaled t distribution, negative binomial and Tweedie distributions), generalized additive models for location scale and shape (for e xample two stage zero inflation models, and Gaussian location-scale models), Cox proportional hazard s models and multivariate additive models. The framework reduces the implementation of new model classes t o the coding of some standard derivatives of the log likelihood.
Anti-stigma training for medical students: the Education Not Discrimination project.

BACKGROUND
Education Not Discrimination (END) is the component of the Time to Change programme intended to reduce mental health stigma among professionals and professional trainees.


AIMS
To investigate the impact of the END anti-stigma programme on medical students immediately and after 6 months with regard to knowledge, attitudes, behaviour and empathy.


METHOD
A total of 1452 medical students participated in the study (intervention group n = 1066, control group n = 386). Participants completed questionnaires at baseline, and at immediate and 6-month follow-up. Groups were compared for changes in stigma outcomes.


RESULTS
All measures improved in both groups, particularly among students with less knowledge and more stigmatising attitudes and intended behaviour at baseline. At immediate follow-up the intervention group demonstrated significantly greater improvements in stigma-related knowledge and reductions in stigma-related attitudes and intended behaviour, relative to the control group. At 6 months' follow-up, however, only one attitude item remained significantly better.


CONCLUSIONS
Although the intervention produced short-term advantage there was little evidence for its persistent effect, suggesting a need for greater integration of ongoing measures to reduce stigma into the medical curriculum.
Dose-dependent augmentation of cardiac systolic function with the selective cardiac myosin activator, omecamtiv mecarbil: a first-in-man study

BACKGROUND
Decreased systolic function is central to the pathogenesis of heart failure in millions of patients worldwide, but mechanism-related adverse effects restrict existing inotropic treatments. This study tested the hypothesis that omecamtiv mecarbil, a selective cardiac myosin activator, will augment cardiac function in human beings.


METHODS
In this dose-escalating, crossover study, 34 healthy men received a 6-h double-blind intravenous infusion of omecamtiv mecarbil or placebo once a week for 4 weeks. Each sequence consisted of three ascending omecamtiv mecarbil doses (ranging from 0·005 to 1·0 mg/kg per h) with a placebo infusion randomised into the sequence. Vital signs, blood samples, electrocardiographs (ECGs), and echocardiograms were obtained before, during, and after each infusion. The primary aim was to establish maximum tolerated dose (the highest infusion rate tolerated by at least eight participants) and plasma concentrations of omecamtiv mecarbil; secondary aims were evaluation of pharmacodynamic and pharmacokinetic characteristics, safety, and tolerability. This study is registered at ClinicalTrials.gov, number NCT01380223.


FINDINGS
The maximum tolerated dose of omecamtiv mecarbil was 0·5 mg/kg per h. Omecamtiv mecarbil infusion resulted in dose-related and concentration-related increases in systolic ejection time (mean increase from baseline at maximum tolerated dose, 85 [SD 5] ms), the most sensitive indicator of drug effect (r(2)=0·99 by dose), associated with increases in stroke volume (15 [2] mL), fractional shortening (8% [1]), and ejection fraction (7% [1]; all p<0·0001). Omecamtiv mecarbil increased atrial contractile function, and there were no clinically relevant changes in diastolic function. There were no clinically significant dose-related adverse effects on vital signs, serum chemistries, ECGs, or adverse events up to a dose of 0·625 mg/kg per h. The dose-limiting toxic effect was myocardial ischaemia due to excessive prolongation of systolic ejection time.


INTERPRETATION
These first-in-man data show highly dose-dependent augmentation of left ventricular systolic function in response to omecamtiv mecarbil and support potential clinical use of the drug in patients with heart failure.


FUNDING
Cytokinetics Inc.
Traveling Magnetic Field for Homogeneous Wireless Power Transmission

A novel concept for wireless power transmission using inductive coupling is proposed to transmit power homogeneously over a large working area. This concept includes a specially designed winding group on the transmitting side to generate a traveling magnetic field, which causes an alternating magnetic flux through a receiving coil that is located in this field and, therefore, induces a voltage in the coil. The prototype system provides an effective working area of 180 times 220 mm for one or more power receivers that is 4.0 mm thick and 11.5 mm in diameter. Each receiver receives a constant power of about 330 mW at 3.1 plusmn 0.4 V dc operating voltage throughout the working area. A possible application of this concept is the powering of untethered microrobots
Reversible physiological transdifferentiation in the adipose organ.

All mammals are provided with two distinct adipose cells, white and brown adipocytes. White adipocytes store lipids to provide fuel to the organism, allowing intervals between meals. Brown adipocytes use lipids to produce heat. Previous descriptions have implied their localization in distinct sites of the body; however, it has been demonstrated that they are present together in many depots, which has led to the new concept of the adipose organ. In order to explain their coexistence the hypothesis of reversible physiological transdifferentiation has been developed, i.e. they are contained together because they are able to convert, one into the other. In effect, if needed the brown component of the organ could increase at the expense of the white component and vice versa. This plasticity is important because the brown phenotype of the organ is associated with resistance to obesity and its related disorders. A new example of reversible physiological transdifferentiation of adipocytes is offered by the mammary gland during pregnancy, lactation and post-lactation stages. The gravidic hormonal stimulus seems to trigger a transdifferentiation of adipocytes into milk-producing and secreting epithelial glands. In the post-lactation period some of the epithelial cells of the mammary gland seem to transdifferentiate into adipocytes. Recent unpublished results suggest that explanted adipose tissue, as well as explanted isolated mature adipocytes, is able to transdifferentiate into glands with epithelial markers of milk-secreting mammary glands. These findings, if confirmed, seem to suggest new windows into the cell biology frontiers of adipocytes.
Clinicopathological features and prognosis of mucin-producing bile duct tumor and mucinous cystic tumor of the liver: a multi-institutional study by the Japan Biliary Association.

BACKGROUND
The aim of this study was to determine the clinicopathological features and surgical outcomes of mucinous cystic neoplasm of the liver (MCN) and mucin-producing intraductal papillary neoplasm of the intrahepatic bile duct (M-IPNB).


METHODS
We performed a multi-institutional, retrospective study of patients with MCN or M-IPNB pathologically defined by the presence or absence of an ovarian-like stroma.


RESULTS
The M-IPNB and MCN were diagnosed in 119 and nine patients, respectively. MCN was observed in female patients, while M-IPNB produced symptoms of cholangitis. M-IPNBs were classed as low or intermediate grade in 53 cases, high grade in 23 and invasive carcinoma in 43. Fifty-one of the M-IPNBs were the pancreatobiliary type (PT), 33 were the intestinal type (IT), 23 were the oncocytic type (OT), and 12 were the gastric type (GT). The 1-, 5- and 10-year survival rates for the 105 patients with M-IPNB were 96%, 84% and 81%, respectively, while the 5-year survival rate for patients with MCN was 100%. OT and GT M-IPNB had better 10-year survival rates than PT and IT M-IPNB.


CONCLUSIONS
Although MCN has different features from M-IPNB, both diseases have a good prognosis after resection. The cellular type of M-IPNB appears to predict outcome.
Quantitative Fluorescence Determination of Long-Fragment DNA in Stool as a Marker for the Early Detection of Colorectal Cancer

BACKGROUND
A variety of molecular markers have been evaluated for the development of a non-invasive approach to the diagnosis of colorectal cancer. We aimed to validate the diagnostic accuracy, using the same threshold as in the previous pilot study, of fluorescent long DNA test as a relatively simple and inexpensive tool for colorectal cancer detection.


METHODS
A case-control study was conducted on 100 healthy subjects and 100 patients at first diagnosis of colorectal cancer. Human long-fragment DNA in stool was quantified by fluorescence primers and a standard curve and expressed in DNA nanograms.


RESULTS
We validated the 25-ng value, which emerged as the most accurate cut-off in the pilot study, obtaining 79% (95% CI, 71-87%) sensitivity and 89% (95% CI, 83-95%) specificity. Specificity was very high for all cut-off values (15-40 ng) analyzed, ranging from 78 to 96%. Sensitivity was only slightly lower, reaching 84% at the lowest cut-off and maintaining a good level at the higher values. Diagnostic potential was independent of gender, age and tumor site.


CONCLUSION
Fecal DNA analysis is a non-invasive and fairly simple test showing high diagnostic potential. These characteristics, together with the small amount of stool required, make it potentially suitable to be used alongside or as an alternative to current non-invasive screening approaches. Our next step will be to validate these results in a large-scale cohort study of a screening population, which is needed prior to implementation into clinical practice.
BPS: a learning algorithm for capturing the dynamic nature of speech

A novel backpropagation learning algorithm for a particular class of dynamic neural networks in which some units have a local feedback is proposed. Hence these networks can be trained to respond to sequences of input patterns. This algorithm has the same order of space and time requirements as backpropagation applied to feedforward networks. The authors present experimental results and comparisons with a speech recognition problem.<<ETX>>
Distributed Finite Element Analysis Implementation in .NET

The paper describe a detailed study into the object-oriented implementation of distributed finite element analysis on desktop computers using the .NET framework. Numerical tests where carried out and reasonable speed-up was achieved, particularly for direct solution methods. It is concluded that .NET provides a viable framework for implementing distributed computing on networks of personal computers.
A Modeling Study of the TPC-C Benchmark

The TPC-C benchmark is a new benchmark approved by the TPC council intended for comparing database platforms running a medium complexity transaction processing workload. Some key aspects in which this new benchmark differs from the TPC-A benchmark are in having several transaction types, some of which are more complex than that in TPC-A, and in having data access skew. In this paper we present results from a modelling study of the TPC-C benchmark for both single node and distributed database management systems. We simulate the TPC-C workload to determine expected buffer miss rates assuming an LRU buffer management policy. These miss rates are then used as inputs to a throughput model. From these models we show the following: (i) We quantify the data access skew as specified in the benchmark and show what fraction of the accesses go to what fraction of the data. (ii) We quantify the resulting buffer hit ratios for each relation as a function of buffer size. (iii) We show that close to linear scale-up (about 3% from the ideal) can be achieved in a distributed system, assuming replication of a read-only table. (iv) We examine the effect of packing hot tuples into pages and show that significant price/performance benefit can be thus achieved. (v) Finally, by coupling the buffer simulations with the throughput model, we examine typical disk/memory configurations that maximize the overall price/performance.