Miracle-dz/UniFAR-FTUs huggingface dataset:
Phase transition in the economically modeled growth of a cellular nervous system

Spatially embedded complex networks, such as nervous systems, the Internet, and transportation networks, generally have nontrivial topological patterns of connections combined with nearly minimal wiring costs. However, the growth rules shaping these economical tradeoffs between cost and topology are not well understood. Here, we study the cellular nervous system of the nematode worm Caenorhabditis elegans, together with information on the birth times of neurons and on their spatial locations. We find that the growth of this network undergoes a transition from an accelerated to a constant increase in the number of links (synaptic connections) as a function of the number of nodes (neurons). The time of this phase transition coincides closely with the observed moment of hatching, when development switches metamorphically from oval to larval stages. We use graph analysis and generative modeling to show that the transition between different growth regimes, as well as its coincidence with the moment of hatching, may be explained by a dynamic economical model that incorporates a tradeoff between topology and cost that is continuously negotiated and renegotiated over developmental time. As the body of the animal progressively elongates, the cost of longer-distance connections is increasingly penalized. This growth process regenerates many aspects of the adult nervous system’s organization, including the neuronal membership of anatomically predefined ganglia. We expect that similar economical principles may be found in the development of other biological or manmade spatially embedded complex systems.
Intense training: the key to optimal performance before and during the taper

The training load is markedly reduced during the taper so that athletes recover from intense training and feel energized before major events. Load reduction can be achieved by reducing the intensity, volume and/or frequency of training, but with reduced training load there may be a risk of detraining. Training at high intensities before the taper plays a key role in inducing maximal physiological and performance adaptations in both moderately trained subjects and highly trained athletes. High‐intensity training can also maintain or further enhance training‐induced adaptations while athletes reduce their training before a major competition. On the other hand, training volume can be markedly reduced without a negative impact on athletes' performance. Therefore, the training load should not be reduced at the expense of intensity during the taper. Intense exercise is often a performance‐determining factor during match play in team sports, and high‐intensity training can also elicit major fitness gains in team sport athletes. A tapering and peaking program before the start of a league format championship or a major tournament should be characterized by high‐intensity activities.
Neutron Stars with a Stable, Light Supersymmetric Baryon

If a light gluino exists, the lightest gluino-containing baryon, S0, is a possible candidate for self-interacting dark matter. In this scenario, the simplest explanation for the observed ratio ΩDM/Ωb ≈ 6-10 is that m ~ 900 MeV c-2; at present, this is not excluded by particle physics. Such an S0 could be present in neutron stars, with the hyperon formation serving as an intermediate stage. We calculate equilibrium compositions and the equation of state for high-density matter with S0, and we find that for a wide range of parameters, the properties of neutron stars with S0 are consistent with observations. In particular, the maximum mass of a nonrotating star is 1.7-1.8 M☉, and the presence of S0 is helpful in reconciling observed cooling rates with hyperon formation.
What Underlies the Assessment of Conditionals ?

According to some theorists, the strength of a conditional statement is determined solely by the extent to which the conditional’s antecedent is sufficient for its consequent. On this view, the strength of conditionals is independent of the degree to which the antecedent is necessary for the consequent. Data from four experiments reported here demonstrate that when people evaluate conditionals, they are also sensitive to whether the antecedent is necessary for the consequent. Conditionals are perceived as stronger the more necessary the antecedent is for the consequent. We discuss the implications of these results for theories of the meaning of conditional statements.
The Clinical Features and Expression of bcl-2, Cyclin D1, p53, and Proliferating Cell Nuclear Antigen in Syndromic and Nonsyndromic Keratocystic Odontogenic Tumor

AbstractThe aim of this study was to describe the clinical features and expression of bcl-2, cyclin D1, p53, and proliferating cell nuclear antigen (PCNA) antibodies in syndromic (nevoid basal cell carcinoma syndrome [NBCCS]) and nonsyndromic patients diagnosed with keratocystic odontogenic tumor (KCOT). Methods: This descriptive study comprised 5 patients of KCOT associated with NBCCS and 8 patients of nonsyndromic type treated in the Department of Oral Maxillofacial Surgery, Universiti Kebangsaan Malaysia Medical Centre between years 1998 and 2011. The clinical features (site, size, treatment, and recurrence), demographic characteristics, and immunohistochemistry results using antibodies of bcl-2, cyclin D1, p53, and PCNA were examined. The association of the antibody expression and the type of KCOT was analyzed using Fisher exact test.Results: Altogether there were 13 patients, 5 with syndromic KCOT (1 patient met 3 major criteria of NBCCS) and 8 with sporadic KCOT. The age range for syndromic KCT was 11 to 21 years (mean 16.00 years, SD 4.36) and 10 to 54 years (median 24.50 years, interquartile range 19.00) for the nonsyndromic KCOT. Tumor recurrence occurred in 3 patients (7.7%); 1 patient from the syndromic and 2 patients from the nonsyndromic. The most positive expression was observed in PCNA for both the syndromic and nonsyndromic samples and the least positive expression involved the p53.Conclusion: PCNA, bcl-2 protein, and cyclin D1 expressions could be useful in evaluating the proliferative activity of the tumor and the aggressiveness of the clinical presentation; however, the authors would propose for larger sample size research for more definitive results.
Ultrastructural changes during asexual multiple reproduction in Trichomonas vaginalis

Trichomonas vaginalis, a flagellated protozoan parasite, is commonly found in the genitourinary tract of humans. Its mode of reproduction has always been reported to be binary fission. The high parasite numbers seen in a relatively short period in in vitro cultures led us to believe that there must be other modes of reproduction. The present study for the first time provides transformational evidence at the ultrastructural level seen in tropohozoites of T. vaginalis undergoing a multiple asexual mode of reproduction. The findings show that the single cell with a nucleus is capable of dividing to as many as eight nuclei within the cytoplasmic body. Before the commencement of division, the nucleus remained round or ovoid in shape with condensed chromatin masses and only a few endoplasmic reticula surrounding the nucleus. During the division, the nucleus started to elongate and become irregular in shape with visible chromatin masses condensing with the accumulation of numerous endoplasmic reticula. Nuclear division gave rise to as many as eight nuclei within a cell, which could be seen to be connected by numerous endoplasmic reticula. In addition, a high number of hydrogenosomes and vacuoles can be seen in multinucleated T. vaginalis compared with single nucleated T. vaginalis. This study confirms that multiple modes of nuclear division do exist in T. vaginalis and are a precursor to progeny formation. Introduction Trichomoniasis occurs worldwide, and it has been estimated that more than 200 million people are infected with Trichomonas vaginalis per year (WHO 1995). Men with symptoms mainly complain of mild dysuria (Rein and Queiroz 2001) and may be associated with urethritis (Krieger and Alderate 1999) or an irritating persistent or chronic urethritis (Gelbart et al. 1990). Common complaints include scanty, clear to mucopurelent discharge, mild pruritus, or burning sensation immediately after sexual intercourse (Petrin et al. 1998). Trichomoniasis may be responsible in cervical neoplasia growth, postoperative infections, infertility, adverse pregnancy effect, and atypical pelvic inflammatory disease among women (Soper 2004). The infection, once established, persists for long and short periods in females and males, respectively (Petrin et al. 1998). The mode of reproduction has always been binary fission, but the high numbers of parasites in a relatively short period seen in in vitro cultures led us to believe that there could be other modes of reproduction. In the present study, we provide evidence at the ultrastructural level for the existence of this mode of reproduction and show sequential transformational events leading to multiple nuclei formation within the organism. Materials and methods Sample collection of T. vaginalis Vaginal swab samples were collected from cervical neoplasia as well as symptomatic female patients of the Obstetrics Y. A :K. S (*) Department of Parasitology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia e-mail: suresh@um.edu. my Parasitol Res DOI 10.1007/s00436-011-2705-9
Author's Personal Copy the Journal of Systems and Software Agile Requirements Prioritization in Large-scale Outsourced System Projects: an Empirical Study

In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: Keywords: Agile requirements engineering Requirements prioritization Outsourced software development Requirements dependencies Large projects Distributed project management Qualitative research Case study a b s t r a c t The application of agile practices for requirements prioritization in distributed and outsourced projects is a relatively recent trend. Hence, not all of its facets are well-understood. This exploratory study sets out to uncover the concepts that practitioners in a large software organization use in the prioritization process and the practices that they deem good. We seek to provide a rich analysis and a deep understanding of three cases in an exploratory study that was carried out in a large and mature company, widely recognized for its excellence and its engagement in outsourced software development. We used in-depth interviews for data collection and grounded theory techniques for data analysis. Our exploration efforts yielded the following findings: (i) understanding requirements dependencies is of paramount importance for the successful deployment of agile approaches in large outsourced projects. (ii) Next to business value, the most important prioritization criterion in the setting of outsourced large agile projects is risk. (iii) The software organization has developed a new artefact that seems to be a worthwhile contribution to agile software development in the large: 'delivery stories', which complement user stories with technical implications, effort estimation and associated risk. The delivery stories play a pivotal role in requirements prioritization. (iv) The vendor's domain knowledge is a key asset for setting up successful client-developer collaboration. (v) The use of agile prioritization practices depends on the type of project outsourcing arrangement. Our findings contribute to the empirical software engineering literature by bringing a rich analysis of cases in agile and distributed contexts, from a vendor's perspective. We also discuss the possible implications of the results for research and in practice.
The subjective equivalence of sinusoidal and random whole-body vibration in the sitting position (an experimental study using the "floating reference vibration" method).

An experimental technique known as the ‘floating reference’ method was developed to compare the subjective response of seated subjects to sinusoidal vibrations in the range l-10Hz with those produced by narrow-band random vibration (Gaussian distribution) centred on the same frequencies. Male and female subjects were asked to adjust the r.m.s. amplitude of each test vibraiion until it produced an overall sensation equivalent to that caused by a reference vibration. The frequency content and r.m.s. values of the random stimuli measured on the seat attachment plate are representative of vibration environments associated with earth-moving machines and tractors for agricultural and forestry use. The results have a small dispersion and show that subjects generally appear to be slightly more sensitive to random excitation than to sinusoidal (approximately I dBwhen averaged over the range 1-10 Hz). This difference of sensitivity decreases at higher frequencies, but was observed in all three translational directi.
Madagascar's Mangroves: Quantifying Nation-Wide and Ecosystem Specific Dynamics, and Detailed Contemporary Mapping of Distinct Ecosystems

Mangrove ecosystems help mitigate climate change, are highly biodiverse, and provide critical goods and services to coastal communities. Despite their importance, anthropogenic activities are rapidly degrading and deforesting mangroves world-wide. Madagascar contains 2% of the world’s mangroves, many of which have undergone or are starting to exhibit signs of widespread degradation and deforestation. Remotely sensed data can be used to quantify mangrove loss and characterize remaining distributions, providing detailed, accurate, timely and updateable information. We use USGS maps produced from Landsat data to calculate nation-wide dynamics for Madagascar’s mangroves from 1990 to 2010, and examine change more closely by partitioning the national distribution in to primary (i.e., >1000 ha) ecosystems; with focus on four Areas of Interest (AOIs): Ambaro-Ambanja Bays (AAB), Mahajamba Bay (MHJ), Tsiribihina Manombolo Delta (TMD) and Bay des Assassins (BdA). Results indicate a nation–wide net-loss of 21% (i.e., 57,359 ha) from 1990 to 2010, with dynamics varying considerably among primary mangrove ecosystems. Given the limitations of national-level maps for certain localized applications (e.g., carbon stock inventories), building on two previous studies for AAB and MHJ, we employ Landsat data to produce detailed, contemporary mangrove maps for TMD and BdA. These contemporary, AOI-specific maps provide improved detail and accuracy over the USGS national-level maps, and are being applied to conservation and restoration initiatives through the Blue Ventures’ Blue Forests programme and WWF Madagascar West Indian Ocean Programme Office’s work in the region.
Risk Factors for Inadequate TB Case Finding in Rural Western Kenya: A Comparison of Actively and Passively Identified TB Patients

Background The findings of a prevalence survey conducted in western Kenya, in a population with 14.9% HIV prevalence suggested inadequate case finding. We found a high burden of infectious and largely undiagnosed pulmonary tuberculosis (PTB), that a quarter of the prevalent cases had not yet sought care, and a low case detection rate. Objective and methods We aimed to identify factors associated with inadequate case finding among adults with PTB in this population by comparing characteristics of 194 PTB patients diagnosed in a health facility after self-report, i.e., through passive case detection, with 88 patients identified through active case detection during the prevalence survey. We examined associations between method of case detection and patient characteristics, including HIV-status, socio-demographic variables and disease severity in univariable and multivariable logistic regression analyses. Findings HIV-infection was associated with faster passive case detection in univariable analysis (crude OR 3.5, 95% confidence interval (CI) 2.0–5.9), but in multivariable logistic regression this was largely explained by the presence of cough, illness and clinically diagnosed smear-negative TB (adjusted OR (aOR) HIV 1.8, 95% CI 0.85–3.7). Among the HIV-uninfected passive case detection was less successful in older patients aOR 0.76, 95%CI 0.60–0.97 per 10 years increase), and women (aOR 0.27, 95%CI 0.10–0.73). Reported current or past alcohol use reduced passive case detection in both groups (0.42, 95% CI 0.23–0.79). Among smear-positive patients median durations of cough were 4.0 and 6.9 months in HIV-infected and uninfected patients, respectively. Conclusion HIV-uninfected patients with infectious TB who were older, female, relatively less ill, or had a cough of a shorter duration were less likely found through passive case detection. In addition to intensified case finding in HIV-infected persons, increasing the suspicion of TB among HIV-uninfected women and the elderly are needed to improve TB case detection in Kenya.
Diagnosis and treatment of community‐acquired pneumonia in children

INTRODUCTION Community-acquired pneumonia (CAP) is the leading killer of children aged <5 years in developing countries and a cause of substantial disease burden in developed countries (1). Therefore, effective management of paediatric CAP is an important public health goal with substantial social and economic implications throughout the world. However, the solution evidently should be different in developing and developed countries.
Generation of an Attenuated Tiantan Vaccinia Virus Strain by Deletion of Multiple Genes

An attenuated vaccinia virus-MVTTEAB-was constructed by deletion of non-essential gene segments related to the immunomodulatory and virulence functions of the vaccinia virus Tiantan strain (VVTT). The shuttle plasmids pTC-EGFP, pTE-EGFP, pTA35-EGFP, pTB-EGFP, and pTA66-EGFP were constructed and combined with the early and late strong promoter pE/L and EGFP as an exogenous selectable marker. Then, through the homologous recombination technology and Cre/loxP system, the following gene fragments were gradually knocked out one by one: TC7L-TK2L, TE3L, TA35R, TB13R, and TA66R. Ultimately, the five-segment-deleted attenuated strain MVTTEAB was obtained. Knockout of these segments and genetic stability of MVTTEAB were confirmed, and it was also shown that knockout of these segments did not affect the replication ability of the virus. Further, a series of in vivo and in vitro experiments demonstrated that the virulence of MVTTEAB was attenuated significantly, but at same time, high immunogenicity was maintained. These results indicate that MVTTEAB has potential for clinical use as a safe viral vector or vaccine with good attenuation and immunogenicity.
Comparison of respiratory-induced variations in photoplethysmographic signals

Photoplethysmography (PPG) is an optical method for detecting blood volume changes in tissue. Respiratory-induced intensity, frequency and amplitude variations are contained in the PPG signal; thus, an understanding of the relationships between all of these variations and respiration is essential to advancing respiration monitoring based on PPG. This study investigated correlations between respiratory-induced variations extracted from PPG and simultaneous respiratory signals. PPG signals were recorded from 28 healthy subjects under eight different conditions. Six respiratory-induced variations, i.e. the period of the systole, diastole and pulse, the amplitude of the systole and diastole, and the intensity variation, were determined from the PPG signal. The results indicate that, compared with the period of the pulse, the period of the systole and diastole correlates weakly with respiration; the amplitude of the diastole has a stronger correlation with respiration than the amplitude of the systole. For men, when the respiratory rate is less than 10 breaths min−1, the period of the pulse has the strongest correlation with respiration, whereas up to or above 15 breaths min−1, the intensity variation becomes strongest in the sitting posture, while the amplitude of the diastole is strongest in the supine posture. For women, compared with the other variations, the period of the pulse has nearly the strongest correlation with respiration, independent of respiratory rate or posture.
Identification of Fibroblast Growth Factor Receptor 3 (FGFR3) as a Protein Receptor for Botulinum Neurotoxin Serotype A (BoNT/A)

Botulinum neurotoxin serotype A (BoNT/A) causes transient muscle paralysis by entering motor nerve terminals (MNTs) where it cleaves the SNARE protein Synaptosomal-associated protein 25 (SNAP25206) to yield SNAP25197. Cleavage of SNAP25 results in blockage of synaptic vesicle fusion and inhibition of the release of acetylcholine. The specific uptake of BoNT/A into pre-synaptic nerve terminals is a tightly controlled multistep process, involving a combination of high and low affinity receptors. Interestingly, the C-terminal binding domain region of BoNT/A, HC/A, is homologous to fibroblast growth factors (FGFs), making it a possible ligand for Fibroblast Growth Factor Receptors (FGFRs). Here we present data supporting the identification of Fibroblast Growth Factor Receptor 3 (FGFR3) as a high affinity receptor for BoNT/A in neuronal cells. HC/A binds with high affinity to the two extra-cellular loops of FGFR3 and acts similar to an agonist ligand for FGFR3, resulting in phosphorylation of the receptor. Native ligands for FGFR3; FGF1, FGF2, and FGF9 compete for binding to FGFR3 and block BoNT/A cellular uptake. These findings show that FGFR3 plays a pivotal role in the specific uptake of BoNT/A across the cell membrane being part of a larger receptor complex involving ganglioside- and protein-protein interactions.
Classification of Defoliated Trees Using Tree-Level Airborne Laser Scanning Data Combined with Aerial Images

Climate change and rising temperatures have been observed to be related to the increase of forest insect damage in the boreal zone. The common pine sawfly (Diprion pini L.) (Hymenoptera, Diprionidae) is regarded as a significant threat to boreal pine forests. Defoliation by D. pini can cause severe growth loss and tree mortality in Scots pine (Pinus sylvestris L.) (Pinaceae). In this study, logistic LASSO regression, Random Forest (RF) and Most Similar Neighbor method (MSN) were investigated for predicting the defoliation level of individual Scots pines using the features derived from airborne laser scanning (ALS) data and aerial images. Classification accuracies from 83.7% (kappa 0.67) to 88.1% (kappa 0.76) were obtained depending on the method. The most accurate result was produced using RF with a combination of data from the two sensors, while the accuracies when using ALS and image features separately were 80.7% and 87.4%, respectively. Evidently, the combination of ALS and aerial images in detecting needle losses is capable of providing satisfactory estimates for individual trees.