Miracle-dz/UniFAR-FTUs huggingface dataset:
Twin studies as a model for exploring the aetiology of autoimmune thyroid disease

Twins are an important resource for evaluating the relative contribution of genetic and environmental factors in determining a phenotype. During the last decades, a number of twin studies have investigated the aetiology of several phenotypes related to thyroid autoimmunity. Taken together, these studies have provided valid and unbiased information regarding the influence of genetic and environmental factors in the aetiology of autoimmune thyroid disease (AITD). The comparison of concordance rates between monozygotic (MZ) and dizygotic twins provides irrefutable evidence of a genetic component, and biometric twin modelling shows that approximately 75% of the total phenotypic variance in AITD is because of genetic effects. On the other hand, the lack of complete concordance in MZ twin pairs is proof of environmental and/or epigenetic factors also playing an important role. The impact of environmental triggers such as cigarette smoking, birth characteristics, infection with Yersinia enterocolitica, microchimerism and degree of X chromosome inactivation (XCI) has been evaluated by investigating AITD discordant twin pairs. These studies indicate that smoking, Y. enterocolitica infection and skewed XCI may be causally associated with clinically overt AITD, but not with the presence of thyroid autoantibodies in euthyroid subjects. Microchimerism, but not birth weight, might play a role in AITD. Twin studies offer several features that uniquely enhance our ability to localize genes and understand their function. Future twin studies should incorporate information on genetic, epigenetic and environmental variation thereby enhancing our ability to quantify the precise effect of specific risk factors.
Analytical Model for Predicting Shear Strengths of Interior Reinforced Concrete Beam-Column Joints for Seismic Resistance

A softened strut-and-tie model was previously developed for determining the shear strengths of exterior beam-column joints for seismic resistance. This existing model originates from the strut-and-tie concept and satisfies equilibrium, compatibility, and the constitutive laws of cracked reinforced concrete. This paper examines the applicability of the previously proposed model to interior beam-column joints. The calculated shear capacities of 56 interior joints were compared with the experimental results, and good agreement was obtained.
Using insurance to increase internet security

Managing security risks in the Internet has so far mostly involved methods to reduce the risks and the severity of the damages. Those methods reduce but do not eliminate risk, and the question remains on how to handle the residual risk. Current schemes applied by Internet Service Providers (ISPs) penalize the users, who suffer from the consequences. In this paper, we take a new approach to the problem of Internet security and advocate managing the residual risk by buying insurance against it and consequently re-arranging the incentive chain. We first analyze the current state of the Internet and investigate if it is possible to alleviate the existing problems by introducing insurance schemes. By performing detailed analysis we define an insurance policy that can survive in a competitive market. Following that, we analyze the impact of insurance-based ISPs on the rest of the network and attempt to answer whether using insurance can increase the overall security of the system and provide incentive to other ISPs to implement such policies.
Developmental Changes in Medial Auditory Thalamic Contributions to Associative Motor Learning

Eyeblink conditioning (EBC) was used in the current study to examine the mechanisms underlying the ontogeny of associative motor learning in rats. Eyeblink conditioning emerges ontogenetically between postnatal day 17 (P17) and P24 in rats. Previous studies used electrical stimulation to show that the ontogeny of EBC is influenced by developmental changes in input from the medial auditory thalamus to the pontine nuclei, which in turn affects input to the cerebellum. The current study used tetrode recordings to examine the ontogeny of medial auditory thalamic sensory responses to the conditioned stimulus (CS) and learning-related activity during EBC. Rat pups were implanted with multiple tetrodes in the medial nucleus of the medial geniculate (MGm) and suprageniculate (SG) and trained on delay EBC on P17–P19, P24–P26, or P31–P33 while recording spike activity. Developmental changes in MGm and SG sensory-related activity were found during a pretraining session with unpaired presentations of the auditory CS and periorbital stimulation unconditioned stimulus (US). Substantial developmental changes were observed in learning-related activity in the MGm and SG during CS–US paired training. The ontogenetic changes in learning-related activity may be related to developmental changes in input to the medial auditory thalamus from the amygdala and cerebellum. The findings suggest that the ontogeny of associative motor learning involves developmental changes in sensory input to the thalamus, amygdala input to the thalamus, thalamic input to the pontine nuclei, and cerebellar feedback to the thalamus.
A missing link in blending

fig. 1 Droplet elongation rate d(L, c, σ, ηd , ηc, R0) By integrating d (figure 1), the droplet deformation L in any time-dependent flow can be predicted, relating morphology with flow history. Results Step in elongation rate c In figure 2, model predictions are compared with experimental results by Janssen [2]. The numbers denote the ratio between the imposed and the critical capillary number Cac (Cac: breakup in steady flow). Experimental results Model prediction
Positivity of the English Language

Over the last million years, human language has emerged and evolved as a fundamental instrument of social communication and semiotic representation. People use language in part to convey emotional information, leading to the central and contingent questions: (1) What is the emotional spectrum of natural language? and (2) Are natural languages neutrally, positively, or negatively biased? Here, we report that the human-perceived positivity of over 10,000 of the most frequently used English words exhibits a clear positive bias. More deeply, we characterize and quantify distributions of word positivity for four large and distinct corpora, demonstrating that their form is broadly invariant with respect to frequency of word use.
Seizures and other neurologic sequelae of bacterial meningitis in children.

BACKGROUND Although the mortality rate among children with bacterial meningitis has decreased dramatically in recent decades, some patients are left with neurologic sequelae. It has not been clearly established which features of the acute illness predict the chronic neurologic sequelae, including late seizures or epilepsy. METHODS We followed 185 infants and children prospectively during and after acute bacterial meningitis. The mean duration of follow-up was 8.9 years (range, 0.1 to 15.5). During the first six years standard neurologic examinations were performed; telephone interviews were conducted thereafter. RESULTS One month after meningitis, 69 children (37 percent) had neurologic abnormalities. Many of these signs resolved within a year, leaving only 26 children (14 percent) with persistent deficits: 18 (10 percent) had only sensorineural hearing loss, and 8 (4 percent) had multiple neurologic deficits. Thirteen children (7 percent) had one or more late seizures not associated with fever. The presence of persistent neurologic deficits indicative of cerebral injury was the only independent predictor of late afebrile seizures (P less than 0.001). CONCLUSIONS After bacterial meningitis only children with permanent neurologic deficits are at high risk for epilepsy. Those with normal examinations after the acute illness have an excellent change of escaping serious neurologic sequelae, including epilepsy.
Mechanism of asymmetric ovarian development in chick embryos

In most animals, the gonads develop symmetrically, but most birds develop only a left ovary. A possible role for estrogen in this asymmetric ovarian development has been proposed in the chick, but the mechanism underlying this process is largely unknown. Here, we identify the molecular mechanism responsible for this ovarian asymmetry. Asymmetric PITX2 expression in the left presumptive gonad leads to the asymmetric expression of the retinoic-acid (RA)-synthesizing enzyme, RALDH2, in the right presumptive gonad. Subsequently, RA suppresses expression of the nuclear receptors Ad4BP/SF-1 and estrogen receptor α in the right ovarian primordium. Ad4BP/SF-1 expressed in the left ovarian primordium asymmetrically upregulates cyclin D1 to stimulate cell proliferation. These data suggest that early asymmetric expression of PITX2 leads to asymmetric ovarian development through up- or downregulation of RALDH2, Ad4BP/SF-1, estrogen receptor α and cyclin D1.
Surface texture measurement for additive manufacturing

The surface texture of additively manufactured metallic surfaces made by powder bed methods is affected by a number of factors, including the powder’s particle size distribution, the effect of the heat source, the thickness of the printed layers, the angle of the surface relative to the horizontal build bed and the effect of any post processing/finishing. The aim of the research reported here is to understand the way these surfaces should be measured in order to characterise them. In published research to date, the surface texture is generally reported as an Ra value, measured across the lay. The appropriateness of this method for such surfaces is investigated here. A preliminary investigation was carried out on two additive manufacturing processes—selective laser melting (SLM) and electron beam melting (EBM)—focusing on the effect of build angle and post processing. The surfaces were measured using both tactile and optical methods and a range of profile and areal parameters were reported. Test coupons were manufactured at four angles relative to the horizontal plane of the powder bed using both SLM and EBM. The effect of lay—caused by the layered nature of the manufacturing process—was investigated, as was the required sample area for optical measurements. The surfaces were also measured before and after grit blasting.
Mitogen- and Stress-Activated Protein Kinase 1 Mediates cAMP Response Element-Binding Protein Phosphorylation and Activation by Neurotrophins

Activation of the transcription factor cAMP response element-binding protein (CREB) by neurotrophins is believed to regulate the survival, differentiation, and maturation of neurons in the CNS and PNS. Although phosphorylation of Ser133 is critical for the expression of CREB-regulated genes, the identity of neurotrophin-regulated Ser133 kinases has remained controversial. We show here that neurotrophin-induced CREB phosphorylation in CNS neurons depends exclusively on the extracellular signal-regulated kinase 1/2-activated kinase mitogen- and stress-activated protein kinase 1 (MSK1). Small interfering RNA directed against ribosomal S6 kinase 1 (RSK1) and RSK2 reduced phosphorylation of a RSK substrate but did not effect CREB-dependent transcription. However, expression of a selective inhibitory MSK1 mutant markedly attenuated BDNF-stimulated CREB phosphorylation and CREB-mediated transcription. Moreover, the ability of neurotrophins to stimulate CREB phosphorylation was abolished in CNS neurons from MSK1 knock-out mice. Consistent with a role for MSK1 in Ser133 phosphorylation, neurotrophin-induced expression of CREB-regulated genes was attenuated in MSK-deficient neurons. These results indicate that MSK1 is the major neurotrophin-activated Ser133 kinase in CNS neurons.
When Will Information Retrieval Be "Good Enough"? User Effectiveness As a Function of Retrieval Accuracy

We describe a user study that examined the relationship between the quality of an Information Retrieval system and the eectiveness of its users in performing a task. The task involves nding answer facets of questions pertaining to a collection of newswire documents over a six month period. We articially created sets of ranked lists at increasing levels of quality by blending the output of a state-of-the-art retrieval system with truth data created by annotators. Subjects performed the task by using these ranked lists to guide their labeling of answer passages in the retrieved articles. We found that as system accuracy improves, subject time on task and error rate decrease, and the rate of nding new correct answers increases. There is a large intermediary region in which the utility dierence is not signicant; our results suggest that there is some threshold of accuracy for this task beyond which user utility improves rapidly, but more experiments are needed to examine the area around that threshold closely.
Broad iron line in the fast spinning neutron-star system 4U 1636-53

We analysed the X-ray spectra of six observations, simultaneously taken with XMM-Newton and Rossi X-ray Timing Explorer (RXTE), of the neutron-star low-mass X-ray binary 4U 1636-53. The observations cover several states of the source, and therefore a large range of inferred mass accretion rate. These six observations show a broad emission line in the spectrum at around 6.5 keV, likely due to iron. We fitted this line with a set of phenomenological models of a relativistically broadened line, plus a model that accounts for relativistically smeared and ionized reflection from the accretion disc. The latter model includes the incident emission from both the neutron-star surface or boundary layer and the corona that is responsible for the high-energy emission in these systems. From the fits with the reflection model we found that in four out of the six observations the main contribution to the reflected spectrum comes from the neutron-star surface or boundary layer, whereas in the other two observations the main contribution to the reflected spectrum comes from the corona. We found that the relative contribution of these two components is not correlated to the state of the source. From the phenomenological models, we found that the iron line profile is better described by a symmetric, albeit broad, profile. The width of the line cannot be explained only by Compton broadening, and we therefore explored the case of relativistic broadening. We further found that the direct emission from the disc, boundary layer and corona generally evolved in a manner consistent with the standard accretion disc model, with the disc and boundary layer becoming hotter and the disc moving inwards as the source changed from the hard to the soft state. The iron line, however, did not appear to follow the same trend.
Dynamical features of the MAPK cascade

The MAP kinase cascade is an important signal transduction system in molecular biology for which a lot of mathematical modelling has been done. This paper surveys what has been proved mathematically about the qualitative properties of solutions of the ordinary differential equations arising as models for this biological system. It focusses, in particular, on the issues of multistability and the existence of sustained oscillations. It also gives a concise introduction to the mathematical techniques used in this context, bifurcation theory and geometric singular perturbation theory, as they relate to these specific examples. In addition further directions are presented in which the applications of these techniques could be extended in the future.
Metabolism of DDT analogues by a Pseudomonas sp

A Pseudomonas sp. rapidly metabolized several nonchlorinated analogues of DDT, with the exception of 2,2-diphenylethanol, as the sole carbon source. Several of the mono-p-chloro-substituted diphenyl analogues were also metabolized as the sole carbon source by the bacterium. The resulting chlorinated aromatic acid metabolites were not further metabolized. The isolate was unable to metabolize p,p'-dichlorodiphenyl analogues as the sole carbon source.
Mortality among Canadian military personnel exposed to low-dose radiation.

We carried out a cohort study of mortality among 954 Canadian military personnel exposed to low-dose ionizing radiation during nuclear reactor clean-up operations at Chalk River Nuclear Laboratories, Chalk River, Ont. , and during observation of atomic test blasts in the United States and Australia in the 1950s. Two controls matched for age, service, rank and trade were selected for each exposed subject. Mortality among the exposed and control groups was ascertained by means of record linkage with the Canadian Mortality Data Base. Survival analysis with life-table techniques did not reveal any difference in overall mortality between the exposed and control groups. Analysis of cause-specific mortality showed similar mortality patterns in the two groups; there was no elevation in the exposed group in the frequency of death from leukemia or thyroid cancer, the causes of death most often associated with radiation exposure. Analysis of survival by recorded gamma radiation dose also did not show any effect of radiation dose on mortality. The findings are in agreement with the current scientific literature on the risk of death from exposure to low-dose radiation.
Maternal morphine alters parvalbumin immunoreactivity patterns in neonatal mouse brain

The influence of chronic maternal morphine on the parvalbumin immunoreactive patterns in developing mouse brain was studied. Female Swiss mice were administered daily saline or morphine (30 or 60 mg/kg) for a period of 7 days before mating, gestation, and 21 days postpartum. Their pups were sacrificed on postnatal day 18 and the brains were examined histologically and immunohistochemically for parvalbumin‐positive neurons. Histological observations revealed no significant changes in the cell number of the morphine‐exposed neonatal forebrain, whereas the number of parvalbumin‐positive neurons increased in layers II–IV of the parietal cortex I. Moreover, the number of parvalbumin‐positive dendrites increased remarkably in the cingulate and parietal I cortices of the morphine‐exposed neonates, indicating the region‐specific increase in the PV immunoreactive profiles. These results are consistent with the key roles played by the above brain regions in the altered behavioral patterns of the maternally addicted neonates, such as impaired somatosensory and cognitive performances. The mechanism of morphine action on parvalbumin expression in neonatal mouse brain is not evident, but alterations in the expression patterns of parvalbumin in specific regions of the developing brain might be one of the cellular mechanisms by which addictive drugs modify the functional aspects of the developing CNS. Synapse 35:265–271, 2000. © 2000 Wiley‐Liss, Inc.
Scaling of Metabolic Scaling within Physical Limits

Both the slope and elevation of scaling relationships between log metabolic rate and log body size vary taxonomically and in relation to physiological or developmental state, ecological lifestyle and environmental conditions. Here I discuss how the recently proposed metabolic-level boundaries hypothesis (MLBH) provides a useful conceptual framework for explaining and predicting much, but not all of this variation. This hypothesis is based on three major assumptions: (1) various processes related to body volume and surface area exert state-dependent effects on the scaling slope for metabolic rate in relation to body mass; (2) the elevation and slope of metabolic scaling relationships are linked; and (3) both intrinsic (anatomical, biochemical and physiological) and extrinsic (ecological) factors can affect metabolic scaling. According to the MLBH, the diversity of metabolic scaling relationships occurs within physical boundary limits related to body volume and surface area. Within these limits, specific metabolic scaling slopes can be predicted from the metabolic level (or scaling elevation) of a species or group of species. In essence, metabolic scaling itself scales with metabolic level, which is in turn contingent on various intrinsic and extrinsic conditions operating in physiological or evolutionary time. The MLBH represents a “meta-mechanism” or collection of multiple, specific mechanisms that have contingent, state-dependent effects. As such, the MLBH is Darwinian in approach (the theory of natural selection is also meta-mechanistic), in contrast to currently influential metabolic scaling theory that is Newtonian in approach (i.e., based on unitary deterministic laws). Furthermore, the MLBH can be viewed as part of a more general theory that includes other mechanisms that may also affect metabolic scaling.
An IPSec Accelerator Design for a 10Gbps In-Line Security Network Processor

The IP security protocol (IPSec) is an important and widely used security protocol in the IP layer. But the implementation of the IPSec is a computing intensive work which greatly limits the performance of the high speed network. In this paper, a high performance IPSec accelerator used in a 10Gbps in-line network security processor (NSP) is presented. The design integrates the protocol processing and the cryptographic processing; the transport/tunnel mode of the AH, ESP security protocols and the AES, HMAC-SHA-1 cryptographic algorithms are realized by hardware. An efficient partial crossbar data transfer skeleton with iSLIP scheduling algorithm is adopted to realize the maximum utilization of the computation resources in the accelerator. The number of AH, ESP, AES, HMAC-SHA-1 cores in the design can be configured to meet the different applications. By simulation, with 8 protocol IP-cores and 24 crypto IP-cores connected to the crossbar in the IPSec accelerator, the design gives a peak throughput for the AH protocol transport mode of 11.28Gbps at the average of 512 bytes packet length under a clock rate of 300MHz. The hardware verification is implemented on a Virtex-5 XC5VSX95T based FPGA board. Low power design methods are also used in the design to reduce the power dissipation.
Correction: Comparative Genomics of the Anopheline Glutathione S-Transferase Epsilon Cluster

The middle initials were omitted from the first, fourth, fifth, and sixth authors' names. The correct names are: Constância FJ Ayres, Craig S Wilding, Daniel J Rigden and Martin J Donnelly. The correct citation is: Ayres CFJ, Muller P, Dyer N, Wilding CS, Rigden DJ, et al. (2011) Comparative Genomics of the Anopheline Glutathione S-Transferase Epsilon Cluster. PLoS ONE 6(12): e29237. doi:10.1371/journal.pone. 0029237
Predator detection enables juvenile Lymnaea to form long-term memory

SUMMARY Learning and memory provide the flexibility an organism requires to respond to changing social and ecological conditions. Juvenile Lymnaea have previously been shown to have a diminished capacity to form long-term memory (LTM) following operant conditioning of aerial respiratory behavior. Juvenile Lymnaea, however, can form LTM following classical conditioning of appetitive behaviors. Here, we demonstrate that laboratory-reared juvenile Lymnaea have the ability to detect the presence of a sympatric predator (i.e. crayfish) and respond to the predator by altering their aerial respiratory behavior. In addition to increasing their total breathing time, predator detection confers on juvenile Lymnaea an enhanced capability to form LTM following operant conditioning of aerial respiratory behavior. That is, these juveniles now have the ability to form long-lasting memory. These data support the hypothesis that biologically relevant levels of stress associated with predator detection induce behavioral phenotypic alterations (i.e. enhanced LTM formation) in juveniles, which may increase their fitness. These data also support the notion that learning and memory formation in conjunction with predator detection is a form of inducible defense.