Miracle-dz/UniFAR-FTUs huggingface dataset:
The developmental emergence of coupled activity as cooperative aggregation in rat pups

Rat pups (Rattus norvegicus) are born blind and deaf yet manage to wriggle about in a huddle, dynamically adjusting their positions and thereby displaying thermoregulation and energy conservation at the level of the group. As pups develop, their activity and mobility outpace the development of their visual and auditory systems making it increasingly difficult to aggregate and maintain aggregation while still blind and deaf. The developmental emergence of coupled activity may be one mechanism that facilitates aggregation. Our previous research has shown that the activity of a seven–day–old pup is independent of the activity of the litter mates it contacts. However, we hypothesized that, by day 10, more active and mobile pups will exhibit coupled activity, becoming increasingly quiescent when in contact with other behaviourally quiescent pups. In order to test this hypothesis, we used individual–based modelling. Because the structure of the model was complex, we used a Darwinian algorithm for evolving a model that behaved like ten–day–old pups aggregating in an arena. Sensitivity to quiescent individuals was manifested in some litters by the transitory spreading of quiescence across aggregates of both real and virtual pups (a contagion effect). As pups develop, individual behaviour becomes increasingly contingent on the behaviour of others revealing what may be a basic component in the development of cooperative behaviour.
A comparison of absorption inhibition and absorption elution methods for estimation of ABO blood groups in saliva

Background: ABO blood groups are the primary, most common, conspicuous, and easily detectable groups. These blood group specific antigens are not the exclusive domain of the erythrocyte, but abundantly present in many other bodily secretions such as sweat, semen and even saliva. Absorption inhibition and absorption elution are the main methods to detect salivary blood group antigens. The aim of this study is to detect the secretor status of 100 samples of saliva and to compare the diagnostic efficacy of absorption elution method and absorption inhibition methods in detecting the ABO (H) blood group antigens in secretors. Materials and Methods: Totally 100 un-stimulated whole saliva samples were analyzed for the presence of ABO (H) blood group specific antigens by absorption inhibition and absorption elution methods. Initially, secretor status was ascertained by detecting the H antigen in saliva, and both methods were used to detect the blood groups from saliva and the results were compared with that of blood which were statistically analyzed. Results: Of the 100 samples, 77 secretors and 23 non-secretors. Using absorption inhibition method 62 out of 77 samples gave results that matched with blood. Using absorption elution 70 out of 77 samples gave matching results. Absorption elution depicted better sensitivity, more true positive matches with blood as well as a higher Kappa coefficient. Conclusion: Absorption elution gave better results than absorption inhibition.
Routine use of ultrasound guided tandem placement in intracavitary brachytherapy for the treatment of cervical cancer – a South Indian institutional experience

Purpose Intracavitary brachytherapy necessitates the insertion of a tandem applicator through the cervical os into the uterine cavity. Blind insertion of the tandem may result in suboptimal tandem placement. This decreases the control of the tumor locally and may result in uterine perforation. Although routine real time ultrasound guided tandem placement has shown better results, it is seldom practised. The aim of this work is to evaluate the role of routine real-time intraoperative trans-abdominal ultrasound guided tandem placement in intracavitary brachytherapy for the treatment of cervical cancer. Material and methods This is a prospective single institutional study conducted from April 2013 to May 2015. A total of 96 patients of locally advanced cervical cancer were treated with routine ultrasound guided brachytherapy amounting to a total of 282 intracavitary applications. Results In 78 of the study patients, the cervical os could be easily identified visually, which was then confirmed with ultrasound guidance. In another 12 patients, though the os could be identified visually, uterine sounding was only possible under ultrasound guidance. In another 4 patients, the cervical os could not be identified visually as the cervix was flushed with vagina and ultrasound guidance was necessary for accurate os identification. In 2 of the study patients, intraoperative ultrasound helped in identifying the patients suitable for interstitial brachytherapy rather than intracavitary brachytherapy. Out of the 96 study patients, the length of the uterine canal changed in 15 patients during the subsequent brachytherapy application. Conclusions This procedure is strongly advocated for proper placement of the tandem applicator and to avoid perforations. It is an accurate, fast, easily available, and cost-effective method. Hence, it can be incorporated in intracavitary applications for cervical cancers even in the developing countries where cost, accessibility, and time are important issues.
Rietveld refinement of the crystallographic structure of human dental enamel apatites

Abstract Rietveld refinements using 12 sets of X-ray diffraction powder data from milligram samples of human dental enamel provide detailed information about the structure and composition of enamel apatite. The principal difference in atomic parameters between enamel apatite and Holly Springs hydroxylapatite is in O2, which is reflected in a reduction in the P-O2 bond length of 0.085 Å and PO4 volume by 3.6%. Modeling the hexad axis scattering with a single OH⁻ ion gives a 0.089 Å shift of the ion further away from the mirror plane at z = 1⁄4. The known distributed electron density along the hexad axis in enamel has been confirmed by direct comparison with synthetic hydroxylapatite. Although the CO32- ion position could not be determined directly, evidence for partial replacement of PO43- by CO32- ions came from an 8% diminution of the P site occupancy compared with that in stoichiometric hydroxylapatite. The observed reduction in the P-O2 bond length and PO4 volume in enamel is also consistent with this substitution. The loss of negative charge caused by CO32- replacing PO43- ions and loss of OH⁻ ions is compensated by loss of Ca2+ ions from Ca2 sites. The calculated density from the X-ray results is 3.021 g/cm3, in agreement with deductions from previous chemical analyses.
Complexity Properties of Critical Sets of Arguments

In an abstract argumentation framework, there are often multiple plausible ways to evaluate (or label) the status of each argument as accepted, rejected, or undecided. But often there exists a critical set of arguments whose status is sufficient to determine uniquely the status of every other argument. Once an agent has decided its position on a critical set of arguments, then essentially the entire framework has been evaluated. Likewise, once a group, e.g. a jury, agrees on the status of a critical set of arguments, all of their different views over all other arguments are resolved. Thus, critical sets of arguments are important both for efficient evaluation by individual agents and for collective agreement by groups of such. To exploit this idea in practice, however, a number of computational questions must be considered. In particular, how much computational effort is needed to verify that a set is, indeed, a critical set or a minimal critical set. In this paper we determine exact bounds on the computational complexity of these and related questions. In addition we provide similar analyses of issues: a concept closely related to critical set and derived in terms of (equivalence) classes of arguments related through “common” labelling behaviours.
Free-energy landscape of simple liquids near the glass transition

Properties of the free-energy landscape in phase space of a dense hard-sphere system characterized by a discretized free-energy functional of the Ramakrishnan-Yussouff form are investigated numerically. A considerable number of glassy local minima of the free energy are located and the distribution of an appropriately defined `overlap' between minima is calculated. The process of transition from the basin of attraction of a minimum to that of another one is studied using a new `microcanonical' Monte Carlo procedure, leading to a determination of the effective height of free-energy barriers that separate different glassy minima. The general appearance of the free-energy landscape resembles that of a putting green: deep minima separated by a fairly flat structure. The growth of the effective free-energy barriers with increasing density is consistent with the Vogel-Fulcher law, and this growth is primarily driven by an entropic mechanism.
The Ability of Diagnostic Spinal Injections to Predict Surgical Outcomes

BACKGROUND:Since their first description more than 80 yr ago, the use of diagnostic spinal injections to predict surgical outcomes has been the subject of intense controversy. Because there are no standardized guidelines or substantive reviews on this topic, their use has remained inconsistent. METHODS:Diagnostic procedures included in this review were lumbar and cervical discography, lumbar facet blocks, lumbar and cervical selective nerve root blocks, and sacroiliac (SI) joint injections. We garnered materials via MEDLINE and OVID search engines, books and book chapters, bibliographic references, and conference proceedings. RESULTS:The lack of randomized, comparative studies for all blocks limited the conclusions that could be drawn. For the data that do exist, there is limited evidence that lumbar discography improves fusion outcomes, and no evidence that it influences disk replacement results. Although limited in scope, the current literature supports the notion that cervical discography improves surgical outcomes. There is strong evidence that lumbar selective nerve root blocks improve the identification of a symptomatic nerve root(s), and moderate evidence that both lumbar and cervical nerve root blocks improve surgical outcomes. The data supporting surgery for facet arthropathy are weak, and the use of screening blocks does not appear to improve outcomes. The data supporting SI joint fusion for degenerative, nontraumatic injuries are similarly weak. Because the most reliable method to diagnose a painful SI joint is with low volume, diagnostic injections, one might reasonably conclude that screening blocks improve surgical outcomes. However, this conclusion is not supported by indirect evidence. CONCLUSIONS:The ability to evaluate the effect of diagnostic blocks on surgical outcomes is limited by a lack of randomized studies, methodological flaws, and wide-ranging discrepancies with regard to injection variables, surgical technique, and outcome measures. More research is needed to optimize injection techniques and determine which, if any, diagnostic screening blocks can improve surgical outcomes.
Turning a Shove into a Nudge? A "Labeled Cash Transfer" for Education †

Conditional Cash Transfers (CCTs) have been shown to increase human capital investments, but their standard features make them expensive. We use a large randomized experiment in Morocco to estimate an alternative government-run program, a “labeled cash transfer” (LCT): a small cash transfer made to fathers of school-aged children in poor rural communities, not conditional on school attendance but explicitly labeled as an education support program. We document large gains in school participation. Adding conditionality and targeting mothers made almost no difference in our context. The program increased parents’ belief that education was a worthwhile investment, a likely pathway for the results. (JEL H23, I24, 128, I38, J24, O15, O18) This paper evaluates the impact of a “labeled cash transfer” (LCT). The program we evaluate features small transfers, targeted to poor communities (with all households eligible in those communities), and paid out to fathers. The program is unconditional but retains an implicit endorsement of education through its school-based enrollment procedure. This program was designed and implemented on a (randomized) pilot basis by Morocco’s Ministry of Education. Within the same experiment, conducted over 600 communities, we compared it to three variants: (i) making the transfer explicitly conditional on regular attendance, (ii) making payments to mothers instead of fathers, and (iii) doing both at the same time.
Parallel De Bruijn Graph Construction and Traversal for De Novo Genome Assembly

De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous fragments called reads. We study optimized parallelization of the most time-consuming phases of Meraculous, a state of-the-art production assembler. First, we present a new parallel algorithm for k-mer analysis, characterized by intensive communication and I/O requirements, and reduce the memory requirements by 6.93×. Second, we efficiently parallelize de Bruijn graph construction and traversal, which necessitates a distributed hash table and is a key component of most de novo assemblers. We provide a novel algorithm that leverages one-sided communication capabilities of the Unified Parallel C (UPC) to facilitate the requisite fine-grained parallelism and avoidance of data hazards, while analytically proving its scalability properties. Overall results show unprecedented performance and efficient scaling on up to 15,360 cores of a Cray XC30, on human genome as well as the challenging wheat genome, with performance improvement from days to seconds.
Bradykinin-12-lipoxygenase-VR1 signaling pathway for inflammatory hyperalgesia

The capsaicin-sensitive vanilloid receptor (VR1) was recently shown to play an important role in inflammatory pain (hyperalgesia), but the underlying mechanism is unknown. We hypothesized that pain-producing inflammatory mediators activate capsaicin receptors by inducing the production of fatty acid agonists of VR1. This study demonstrates that bradykinin, acting at B2 bradykinin receptors, excites sensory nerve endings by activating capsaicin receptors via production of 12-lipoxygenase metabolites of arachidonic acid. This finding identifies a mechanism that might be targeted in the development of new therapeutic strategies for the treatment of inflammatory pain.
A Careful Look at Modern Case Selection Methods

Case studies appear prominently in political science, sociology, and other social science fields. A scholar employing a case study research design in an effort to estimate causal effects must confront the question, how should cases be selected for analysis? This question is important because the results derived from a case study research program ultimately and unavoidably rely on the criteria used to select the cases. While the matter of case selection is at the forefront of research on case study design, an analytical framework that can address it in a comprehensive way has yet to be produced. We develop such a framework and use it to evaluate nine common case selection methods. Our simulation-based results show that the methods of simple random sampling, influential case selection, and diverse case selection generally outperform other common methods. And, when a research design mandates that only a very small number of cases, say one or two, be selected in the course of a research program, the very simple method of sampling from the largest cell of a 2 × 2 table is competitive with other, more complicated, case selection methods. We show as well that a number of common case selection strategies work well only in idiosyncratic situations, and we argue that these methods should be abandoned in favor of the more powerful and robust case selection methods that our analytical framework identifies.
Occlusal Disharmonies Modulate Central Catecholaminergic Activity in the Rat

Occlusal disharmonies have classically been thought to be involved in the etiopathogenesis of bruxism, as have, more recently, alterations in central neurotransmission, particularly dopaminergic neurotransmission. However, the connection between these two factors has still not been established. In this study, we assessed the effects of diverse occlusal disharmonies, maintained for either 1 day or 14 days, on neurochemical indices of dopaminergic and noradrenergic activity in the striatum, frontal cortex, and hypothalamus of the rat. The in vivo activity of tyrosine hydroxylase, determined as the accumulation of 3,4-dihydroxyphenylalanine (DOPA), 30 min after the administration of 3-hydroxybenzylhydrazine, a DOPA decarboxylase inhibitor, and dopamine and noradrenaline contents were quantified by high-performance liquid chromatography with electrochemical detection. The wearing of an acrylic cap on both lower incisors for 1 day induced a significant increase in DOPA accumulation in the regions analyzed, with parallel increases in dopamine levels in the hypothalamus and dopamine and noradrenaline in the frontal cortex. After the cap was maintained for 14 days, DOPA accumulation tended to return to control values, except in the left striatum, thereby causing an imbalance between hemispheres. In contrast, 1 or 14 days after the lower left and the upper right incisors were cut, less pronounced changes in catecholaminergic neurotransmission were found in the brain areas studied. Moreover, the cutting of one lower incisor did not modify either DOPA accumulation or dopamine and noradrenaline contents in the striatum or hypothalamus. These results provide experimental evidence of a modulation of central catecholaminergic neurotransmission by occlusal disharmonies, being dependent on the nature of the incisal alteration and on the time during which it was maintained.
Direct simulation Monte Carlo schemes for Coulomb interactions in plasmas

We consider the development of Monte Carlo schemes for molecules with Coulomb interactions. We generalize the classic algorithms of Bird and Nanbu-Babovsky for rarefied gas dynamics to the Coulomb case thanks to the approximation introduced by Bobylev and Nanbu (Theory of collision algorithms for gases and plasmas based on the Boltzmann equation and the Landau-Fokker-Planck equation, Physical Review E, Vol. 61, 2000). Thus, instead of considering the original Boltzmann collision operator, the schemes are constructed through the use of an approximated Boltzmann operator. With the above choice larger time steps are possible in simulations; moreover the expensive acceptance-rejection procedure for collisions is avoided and every particle collides. Error analysis and comparisons with the original Bobylev-Nanbu (BN) scheme are performed. The numerical results show agreement with the theoretical convergence rate of the approximated Boltzmann operator and the better performance of Bird-type schemes with respect to the original scheme.
Prediction of response to sibutramine therapy in obese non‐diabetic and diabetic patients

Background: Early weight loss is generally considered to predict long‐term weight outcome in obese patients, and this is reflected in prescribing guidelines for antiobesity drugs. For example, the current prescribing guidelines for the antiobesity drug, sibutramine, indicate that if patients have not lost 2 kg (or 4 lb) in the first 4 weeks of treatment with sibutramine 10 mg, the physician should re‐evaluate the therapy, which may result in increasing the dose to 15 mg or discontinuation. This regimen may deny treatment to a large group of patients who might otherwise benefit, particularly patients with type 2 diabetes who often find it more difficult to lose weight than non‐diabetic obese individuals.
Assessing the Effectiveness of Monitoring Control and Surveillance of Illegal Fishing: The Case of West Africa

This paper assesses illegal fishing in West Africa, one of the regions most affected by Illegal, Unreported and Unregulated fishing (IUU) in the world. The catch, the economic loss and the amount recovered through Monitoring, Control and Surveillance (MCS) are calculated based on a reconstruction method, and the information made available through national MCS units, between 2010 and 2016 in an effort to assess the effectiveness of surveillance efforts in the region. Results show considerable loss of revenues for Mauritania, Senegal, The Gambia, Guinea Bissau, Guinea and Sierra Leone, estimated at 2.3 billion USD annually, while a minimal amount of 13 million USD is recovered through MCS. In addition, this paper finds that countries touched by the Ebola crisis (Guinea and Sierra Leone) drive a tremendous increase in the loss generated by illegal fishing. However, further analysis shows that the overall severity of illegal fishing, as defined by a range of types investigated here, declines as the fines against the most severe forms of IUU fishing increase. Finally this study finds that Sierra Leone and The Gambia have the highest scoring MCS systems, and were the countries where the most offenders are caught and charged with the highest fines, while Senegal’s new legislations which improved MCS during 2015 does not appear to show on the scoring results. This study finds that illegal fishing amounts the equivalent of 65% of the legal reported catch from West Africa and poses serious concern for food security, and the economy in the region.
Elucidating the decline of North American Atlantic salmon with a time-dependent matrix model

vii List of Abbreviations Used . viii Acknowledgements . ix Chapter
Attentional disorders in patients with complex partial epilepsy.

UNLABELLED A study of concentrated attention patterns in epileptic patients was conducted with the objectives: characterization of the patients' epileptic condition; assessment of the concentrated attention levels in epileptic and nonepileptic individuals; comparison of the attention levels of the two groups. An evaluation was performed of 50 adult outpatients with complex partial seizures and 20 non-epileptic individuals (comparative group) at the Neuroepilepsy Ambulatory Unit, State University of Campinas SP, Brazil. METHOD characterization of seizure types, frequency and duration; concentrated attention assessment (Concentrated Attention Test - Toulouse-Pi ron); comparison of the epileptic with non-epileptic individuals. RESULTS A statistically significant difference was observed between the groups with regard to Correct Response, Wrong Response and No Response. A difference was observed in relation to Time, but it was statistically insignificant. The epileptic patients presented inferior cognitive performance in relation to concentrated attention when compared with the non-epileptic individuals, findings compatible with the clinical complaints.