Miracle-dz/UniFAR-FTUs huggingface dataset:
Chaste: using agile programming techniques to develop computational biology software

Cardiac modelling is the area of physiome modelling where the available simulation software is perhaps most mature, and it therefore provides an excellent starting point for considering the software requirements for the wider physiome community. In this paper, we will begin by introducing some of the most advanced existing software packages for simulating cardiac electrical activity. We consider the software development methods used in producing codes of this type, and discuss their use of numerical algorithms, relative computational efficiency, usability, robustness and extensibility. We then go on to describe a class of software development methodologies known as test-driven agile methods and argue that such methods are more suitable for scientific software development than the traditional academic approaches. A case study is a project of our own, Cancer, Heart and Soft Tissue Environment, which is a library of computational biology software that began as an experiment in the use of agile programming methods. We present our experiences with a review of our progress thus far, focusing on the advantages and disadvantages of this new approach compared with the development methods used in some existing packages. We conclude by considering whether the likely wider needs of the cardiac modelling community are currently being met and suggest that, in order to respond effectively to changing requirements, it is essential that these codes should be more malleable. Such codes will allow for reliable extensions to include both detailed mathematical models—of the heart and other organs—and more efficient numerical techniques that are currently being developed by many research groups worldwide.
The development of emotional values among students of Polytechnic of Varaždin

Au tor za ko res pon den ci ju/Corresponding aut hor: Marijana Neuberg, Msc. , lecturer, University of the North, the University Centre Varazdin, Department of Nursing, Jurja Križanića 33, 42000 Varaždin, Croatia • Tel: +385-98-493 371 • E-mail:marijana.neuberg@unin.hr Received September 17th 2014; Accepted January 30th 2015; Razvoj emocionalnih vrijednosti studenata stručnih studija Veleučilišta u Varaždinu
Sensitivity of phage lambda upon variations of the Gibbs free energy

We investigate the sensitivity of production rates (activities) of the regulatory proteins CI (repressor) and Cro at the right operator (OR) of bacteriophage lambda. The DNA binding energies of CI, Cro, and RNA polymeraseare perturbed to check the uncertainty of the activity, due to the experimental error, by means of a computational scattering method according to which the binding energies are simultaneously chosen at random around the literature values, with a width corresponding to the experimental error. In a grand canonical ensemble, with the randomly drawn protein-DNA binding energies as input, we calculate the corresponding activities of the promoters P R M and P R . By repeating this procedure we obtain a mean value of the activity that roughly corresponds to wild-type (unperturbed) activity. The standard deviation emerging from this scheme, a measure of the sensitivity due to experimental error, is significant (typically >20% relative to wild-type activity), but still the promoter activities are sufficiently separated to make the switch feasible. We also suggest a new, compact way of presenting repressor and Cro data.
Recombination Patterns in Aphthoviruses Mirror Those Found in Other Picornaviruses

ABSTRACT Foot-and-mouth disease virus (FMDV) is thought to evolve largely through genetic drift driven by the inherently error-prone nature of its RNA polymerase. There is, however, increasing evidence that recombination is an important mechanism in the evolution of these and other related picornoviruses. Here, we use an extensive set of recombination detection methods to identify 86 unique potential recombination events among 125 publicly available FMDV complete genome sequences. The large number of events detected between members of different serotypes suggests that horizontal flow of sequences among the serotypes is relatively common and does not incur severe fitness costs. Interestingly, the distribution of recombination breakpoints was found to be largely nonrandom. Whereas there are clear breakpoint cold spots within the structural genes, two statistically significant hot spots precisely separate these from the nonstructural genes. Very similar breakpoint distributions were found for other picornovirus species in the genera Enterovirus and Teschovirus. Our results suggest that genome regions encoding the structural proteins of both FMDV and other picornaviruses are functionally interchangeable modules, supporting recent proposals that the structural and nonstructural coding regions of the picornaviruses are evolving largely independently of one another.
ORIGINAL ARTICLES: Morphology and Location of Restenosis Following Bare Metal Coronary Stenting

Restenosis following bare metal coronary stenting is common. The location and characteristics of restenotic lesions in patients who have undergone coronary stent implantation is not well described. The purpose of this study was to determine the location, type and temporal distribution of stent-related restenosis. We reviewed the clinical and angiographic characteristics of 203 consecutive patients with stentrelated restenosis undergoing a repeat clinically-indicated coronary angiogram, 30 days to 1 year after the index procedure. All lesions within 10 mm of the proximal and distal margins of the stent were included in the analysis. An angiographic classification was developed based on lesion location. Class I lesions were those occurring within the stent, and Class II comprised those lesions occurring within 10 mm of the proximal and distal stent edge. We classified a total of 234 stent-related restenosis lesions. Class I lesions were found in 52% of patients, and Class II in 48%. Three-fifths of the patients who developed new lesions at a stent edge presented 1–3 months following the initial procedure, which was significantly earlier than other lesion types (p < 0.001). A substantial number of patients undergoing repeat angiography after stent placement have lesions proximate, but peripheral, to the stent. This may limit the effectiveness of stent-based efforts to reduce restenosis. The time interval between coronary stenting and symptom recurrence appears to vary according to lesion location.
WISH-PC 2 : A Unique Xenograft Model of Human Prostatic Small Cell Carcinoma 1

Prostatic small cell carcinoma is an aggressive subtype of prostate cancer that usually appears as a progression of the original adenocarcinoma. We describe here the WISH-PC2, a novel neuroendocrine xenograft of small cell carcinoma of the prostate. This xenograft was established from a poorly differentiated prostate adenocarcinoma and is serially transplanted in immune-compromised mice where it grows within the prostate, liver, and bone, inducing osteolytic lesions with foci of osteoblastic activity. It secretes to the mouse Chromogranin A and expresses prostate plasma carcinoma tumor antigen-1, six-transmembrane epithelial antigen of the prostate, and members of theErb-B receptor family. It does not express prostate-specific antigen, prostate stem cell antigen, prostate-specific membrane antigen, and androgen receptor, and it grows independently of androgen. Altogether, WISH-PC2 provides an unlimited source in which to study the involvement of neuroendocrine cells in the progression of prostatic adenocarcinoma and can serve as a novel model for the testing of new therapeutic strategies for prostatic small cell carcinoma.
Investigation of covalent aflatoxin B1-DNA adducts formed in vivo in rainbow trout (Salmo gairdneri) embryos and liver.

The formation of covalent aflatoxin-DNA adducts has been studied in embryo and yearling stages of the rainbow trout (Salmo gairdneri). A linear relationship was found between the amount of aflatoxin B1 (AFB1) absorbed into 21-day-old eggs and the level of covalent modification of embryo DNA after exposure to 0.25 to 0.5 p.p.m. aqueous solutions of AFB1 for 1 h; higher concentrations resulted in absorption of a greater proportion of AFB1. The principal covalent product, identified after acid and enzymatic hydrolysis of isolated embryo DNA, was chromatographically identical to 2,3-dihydro-2-(N7-guanyl)-3-hydroxy aflatoxin B1. Additional AFB1 derivatives which were present are believed to be formed by chemical transformation of this product in DNA producing an aflatoxin-formamidopyrimidine adduct and the metabolic activation of other aflatoxin metabolites, such as aflatoxin M1 and aflatoxin P1. Although the eggs were exposed to AFB1 for a short time, covalent modification of DNA was evident over an extended period. The highest level of covalent products was present at approximately 24 h after exposure to 0.5 p.p.m. AFB1. Ninety-six hours later, this level had decreased slightly; however, the distribution of covalent adducts had changed: formamidopyrimidine adducts now represented up to 50% of the hydrolyzed aflatoxin derivatives. A similar pattern of covalent aflatoxin derivatives was found in the liver DNA of yearling trout 10 h after the administration of 0.3 mg/kg AFB1.
Four and two wheel transformable dynamic mobile platform

In this paper, we developed a novel dynamic mobile platform capable of transforming between four wheel rapid driving mode with ZMP stabilization and two wheel balancing mode. Usually, the four wheel mobile platforms have low acceleration due to the high center of mass. Using the feed-forward ZMP stabilization method, we achieved high acceleration performance with maintaining stable ZMP. We use a LQR controller for two wheel balancing mode. In the two wheel balancing mode, there are two different driving modes, self-balancing mode, human-riding mode. The transformation between four wheel and two wheel mode is made possible by swing up and swing down control method. We prove the dynamic performance of mobile platform by experimental results.
Information Replication Strategy in Unstructured Peer-to-Peer Networks Using Thematic Agents

We present in this article a method to wisely replicate information in an unstructured peer-to-peer network. We make no assumption on the network topology. Thematic agents move randomly on the network and estimate the level of redundancy of the specific information they are dealing with. They can delete or create replicas if this estimated redundancy is too high or too low. Experiments show that we can achieve an homogeneous distribution of information in a distributed environment while achieving a high level of fault tolerance.
Distributed Beamforming for Relay Networks Based on Second-Order Statistics of the Channel State Information

In this paper, the problem of distributed beamforming is considered for a wireless network which consists of a transmitter, a receiver, and relay nodes. For such a network, assuming that the second-order statistics of the channel coefficients are available, we study two different beamforming design approaches. As the first approach, we design the beamformer through minimization of the total transmit power subject to the receiver quality of service constraint. We show that this approach yields a closed-form solution. In the second approach, the beamforming weights are obtained through maximizing the receiver signal-to-noise ratio (SNR) subject to two different types of power constraints, namely the total transmit power constraint and individual relay power constraints. We show that the total power constraint leads to a closed-form solution while the individual relay power constraints result in a quadratic programming optimization problem. The later optimization problem does not have a closed-form solution. However, it is shown that using semidefinite relaxation, this problem can be turned into a convex feasibility semidefinite programming (SDP), and therefore, can be efficiently solved using interior point methods. Furthermore, we develop a simplified, thus suboptimal, technique which is computationally more efficient than the SDP approach. In fact, the simplified algorithm provides the beamforming weight vector in a closed form. Our numerical examples show that as the uncertainty in the channel state information is increased, satisfying the quality of service constraint becomes harder, i.e., it takes more power to satisfy these constraints. Also our simulation results show that when compared to the SDP-based method, our simplified technique suffers a 2-dB loss in SNR for low to moderate values of transmit power.
The Efficacy of Dexmedetomidine Versus Morphine for Postoperative Analgesia After Major Inpatient Surgery

Thirty-four patients scheduled for elective inpatient surgery were randomized equally to receive either dexmedetomidine (initial loading dose of 1-&mgr;g/kg over 10 min followed by 0.4 &mgr;g · kg−1 · h−1 for 4 h) or morphine sulfate (0.08 mg/kg) 30 min before the end of surgery. We determined heart rate (HR), mean arterial blood pressure (MAP), respiratory rate (RR), sedation and analgesia (visual analog scale), and use of additional morphine in the postanesthesia care unit (PACU) and up to 24 h after surgery. Groups were similar for patient demographics, ASA physical status, surgical procedure, baseline hemodynamics, and intraoperative use of drugs and fluids. Dexmedetomidine-treated patients had slower HR in the PACU (by an average of 16 bpm), whereas MAP, RR, and level of sedation were similar between groups. During Phase I recovery, dexmedetomidine-treated patients required significantly less morphine to achieve equivalent analgesia (PACU dexmedetomidine group, 4.5 ± 6.8 mg; morphine group, 9.2 ± 5.2 mg). Sixty minutes into recovery only 6 of 17 dexmedetomidine patients required morphine in contrast to 15 of 17 in the morphine group. The administration of dexmedetomidine before the completion of major inpatient surgical procedures significantly reduced, by 66%, the early postoperative need for morphine and was associated with a slower HR in the PACU.
Role of Protease Activated Receptor 1 and 2 Signaling in Hypoxia-Induced Angiogenesis

Objective—Tissue factor (TF) initiates coagulation and indirectly triggers thrombin-dependent protease activated receptor (PAR) signaling. The TF–VIIa complex also directly cleaves PAR2 and promotes angiogenesis in vitro in TF cytoplasmic domain-deleted (TF&dgr;CT) mice. Here we address the effect of PAR1 and PAR2 deficiency on angiogenesis in vivo. Methods and Results—In hypoxia-driven angiogenesis of oxygen induced retinopathy (OIR), wild-type, PAR1−/−, PAR2−/−, and TF&dgr;CT mice showed a comparable regression of the superficial vascular plexus during the initial exposure of mice to hyperoxia. However, TF&dgr;CT mice revascularized areas of central vaso-obliteration significantly faster than wild-type animals. Pharmacological inhibition of the TF–VIIa complex, but not of Xa, and blockade of tyrosine kinase receptor pathways with Gleevec reversed accelerated angiogenesis of TF&dgr;CT mice to revascularization rates observed in wild-type mice. Genetic deletion of PAR2, but not of PAR1, abolished enhanced revascularization of TF&dgr;CT mice. PAR1 knock-out animals were indistinguishable from wild-type mice in the model of retinal neoangiogenesis and angiogenesis-dependent subcutaneous tumor growth was unaltered in PAR1- and PAR2-deficient animals. Conclusion—Loss of the TF cytoplasmic domain results in accelerated hypoxia-induced angiogenesis mediated by TF–VIIa signaling. PAR2 signaling is sufficient for this proangiogenic effect without apparent contributions of mouse host cell PAR1.
Growth and differentiation.

The convergent trend in biological sciences already apparent in the past few years recently became more pronounced. Fields which used to be the privileged property of a restricted group are now claimed by students of different disciplines. As a consequence, in 1961, the embryo no longer belongs to the embryologist nor the microbe to the microbiologist. Barely had the fences between different biological sciences been removed when new concepts developed and old concepts appeared in a new light. Possibly no concepts profited more from this invasive trend than the old concepts of growth and differentiation. Only a few decades ago, these words conveyed mainly the idea of the developing embryo and of the laborious and intricate processes which mold it into a complete and self-supporting organism. Today, many of the biologists preoccupied with these concepts are not familiar with the embryo and, for that matter, would not be able to identify one if they were confronted with it. At present the words “growth and d.
Potential Benefits and Harms of Intermittent Energy Restriction and Intermittent Fasting Amongst Obese, Overweight and Normal Weight Subjects—A Narrative Review of Human and Animal Evidence

Intermittent energy restriction (IER) has become popular as a means of weight control amongst people who are overweight and obese, and is also undertaken by normal weight people hoping spells of marked energy restriction will optimise their health. This review summarises randomised comparisons of intermittent and isoenergetic continuous energy restriction for weight loss to manage overweight and obesity. It also summarises the potential beneficial or adverse effects of IER on body composition, adipose stores and metabolic effects from human studies, including studies amongst normal weight subjects and relevant animal experimentation. Six small short term (<6 month) studies amongst overweight or obese individuals indicate that intermittent energy restriction is equal to continuous restriction for weight loss, with one study reporting greater reductions in body fat, and two studies reporting greater reductions in HOMA insulin resistance in response to IER, with no obvious evidence of harm. Studies amongst normal weight subjects and different animal models highlight the potential beneficial and adverse effects of intermittent compared to continuous energy restriction on ectopic and visceral fat stores, adipocyte size, insulin resistance, and metabolic flexibility. The longer term benefits or harms of IER amongst people who are overweight or obese, and particularly amongst normal weight subjects, is not known and is a priority for further investigation.
Age-Specificity of Clinical Dengue during Primary and Secondary Infections

Background This study aims to estimate the age-specific risks of clinical dengue attack (i.e., the risk of symptomatic dengue among the total number of dengue virus (DENV) infections) during primary and secondary infections. Methods We analyzed two pieces of epidemiological information in Binh Thuan province, southern Vietnam, i.e., age-specific seroprevalence and a community-wide longitudinal study of clinical dengue attack. The latter data set stratified febrile patients with DENV infection by age as well as infection parity. A simple modeling approach was employed to estimate the age-specific risks of clinical dengue attack during primary and secondary infections. Results Using the seroprevalence data, the force of infection was estimated to be 11.7% (95% confidence intervals (CI): 10.8–12.7) per year. Median age (and the 25–75 percentiles) of dengue fever patients during primary and secondary infections were 12 (9–20) and 20 (14–31) years, respectively. The estimated age-specific risk of clinical dengue increases as a function of age for both primary and secondary infections; the estimated proportion of symptomatic patients among the total number of infected individuals was estimated to be <7% for those aged <10 years for both primary and secondary infections, but increased as patients become older, reaching to 8–11% by the age of 20 years. Conclusions/Significance For both primary and secondary infections, higher age at DENV infection was shown to result in higher risk of clinical attack. Age as an important modulator of clinical dengue explains recent increase in dengue notifications in ageing countries in Southeast Asia, and moreover, poses a paradoxical problem of an increase in adult patients resulting from a decline in the force of infection, which may be caused by various factors including time-dependent variations in epidemiological, ecological and demographic dynamics.
A Method for Chronically Implanting Stimulating Electrodes into the Brains of Locusts, and some Results of Stimulation

1. Methods are described for implanting permanent stainless-steel electrodes into the brains of locusts, for stimulating the brain under near-normal conditions, and for localizing the electrode subsequently. 2. Threshold currents measured under these conditions are lower than those required in acute preparations, or if the animal is restrained. 3. The results of stimulation are described for four common aspects of behaviour. These are antennal movement, locomotion, feeding and sexual behaviour. 4. The effect of stimulation on antennal and locomotory movements largely confirms previous work on crickets. 5. Feeding and foraging behaviour, which is a very common result, is shown to be almost completely determined by peripheral stimuli at the time of brain stimulation. The role of the latter is permissive or disinhibitory rather than causal or excitatory. 6. Integrated sexual behaviour is occasionally inhibited, but never elicited, by stimulation. This contrasts with observations on crickets, and its implications are discussed.
The Bartonella vinsonii subsp. arupensis Immunodominant Surface Antigen BrpA Gene, Encoding a 382-Kilodalton Protein Composed of Repetitive Sequences, Is a Member of a Multigene Family Conserved among Bartonella Species

ABSTRACT Bartonella proteins that elicit an antibody response during an infection are poorly defined; therefore, to characterize antigens recognized by the host, a Bartonella genomic expression library was screened with serum from an infected mouse. This process led to the discovery of a Bartonella vinsonii subsp. arupensis gene encoding a 382-kDa protein, part of a gene family encoding large proteins, each containing multiple regions of repetitive segments. The genes were termed brpA to -C (bartonella repeat protein) and bore significant similarity to genes encoding the BadA adhesin protein and members of the variably expressed outer membrane protein family of proteins from Bartonella henselae and Bartonella quintana, respectively.
Towards an evaluation standard for speech control concepts in real-world scenarios

Speech control is still mainly evaluated through statistical performance measures (recognition rate, insertion rate, etc.) considering the performance of a speech recognizer under laboratory or artificial noise conditions. All these measures give no idea about the practical usability of a speech interface, since practical aspects concern more than operational aspects of the speech recognizer inside a product. Since it was felt, that no evaluation standard so far fulfills the practical requirements for speech controlled products, this paper aims in the establishment of an open design-and evaluation standard for speech control concepts in real-world scenarios. First, the behaviour of the users and the normal environmental conditions (typical noises) were evaluated in usability experiments. Data recordings were conducted, trying to capture these typical usage requirements in a special corpus (Apollo-corpus). Finally, a set of standard desktop, as well as embedded speech recognizers were tested for their performance under these real world conditions.