Miracle-dz/UniFAR-FTUs huggingface dataset:
Colonization rates and distances of a host butterfly and two specific parasitoids in a fragmented landscape

Summary 1 We describe the pattern of colonization of suitable, but currently empty, habitat by a host butterfly and two specialist parasitoids living in a highly fragmented landscape. 2 Using survey data collected over 8 years, field sampling and small-scale experiments we show that the ability of the Glanville fritillary butterfly ( Melitaea cinxia ) to colonize new habitat is intermediate between that of its two larval primary parasitoids. 3 The butterfly forms a classic metapopulation, which the parasitoid Hyposoter horticola experiences as a single patchily distributed host population because of its high rate of dispersal and long colonization distances. In contrast, most of the local butterfly populations are presently inaccessible to the parasitoid Cotesia melitaearum, which has a limited dispersal range and therefore persists only in tightly clustered networks of host populations. 4 At the regional scale, the butterfly may escape C. melitaearum by colonizing empty habitat, but host dispersal does not limit parasitism by H. horticola, which consequently must be limited by local interaction. 5 The parasitoid H. horticola mostly avoids direct competition with C. melitaearum because the majority of H. horticola populations are outside the range of dispersal by current C. melitaearum populations. In contrast, all C. melitaearum populations experience competition with H. horticola .
Relationship between fatty acid delivery and fatty acid oxidation during strenuous exercise.

To evaluate the extent to which decreased plasma free fatty acid (FFA) concentration contributes to the relatively low rates of fat oxidation during high-intensity exercise, we studied FFA metabolism in six endurance-trained cyclists during 20-30 min of exercise [85% of maximal O2 uptake (VO2max)]. They were studied on two occasions: once during a control trial when plasma FFA concentration is normally low and again when plasma FFA concentration was maintained between 1 and 2 mM by intravenous infusion of lipid (Intralipid) and heparin. During the 20-30 min of exercise, fat and carbohydrate oxidation were measured by indirect calorimetry, and the rates of appearance (Ra) of plasma FFA and glucose were determined by the constant infusion of [6,6-2H2]glucose and [2H2]palmitate. Lipid-heparin infusion did not influence the Ra or rate of disappearance of glucose. During exercise in the control trial, Ra FFA failed to increase above resting levels (11.0 +/- 1.2 and 12.4 +/- 1.7 mumol.kg-1.min-1 for rest and exercise, respectively) and plasma FFA concentration dropped from a resting value of 0.53 +/- 0.08 to 0.29 +/- 0.02 mM. The restoration of plasma FFA concentration resulted in a 27% increase in total fat oxidation (26.7 +/- 2.6 vs. 34.0 +/- 4.4 mumol.kg-1.min-1, P < 0.05) with a concomitant reduction in carbohydrate oxidation, apparently due to a 15% (P < 0.05) reduction in muscle glycogen utilization. However, the elevation of plasma FFA concentration during exercise at 85% VO2max only partially restored fat oxidation compared with the levels observed during exercise at 65% VO2max. These findings indicate that fat oxidation is normally impaired during exercise at 85% VO2max because of the failure of FFA mobilization to increase above resting levels, but this explains only part of the decline in fat oxidation when exercise intensity is increased from 65 to 85% VO2max.
A Tighter Erdős‐Pósa Function for Long Cycles

We prove that there exists a bivariate function f with f(k,ℓ)=O(ℓ·klogk) such that for every natural k and ℓ, every graph G has at least k vertex‐disjoint cycles of length at least ℓ or a set of at most f(k,ℓ) vertices that meets all cycles of length at least ℓ. This improves a result by Birmelé et al. (Combinatorica, 27 (2007), 135–145), who proved the same result with f(k,ℓ)=Θ(ℓ·k2) .
On the Effectiveness of Distributed Worm Monitoring

Distributed monitoring of unused portions of the IP address space holds the promise of providing early and accurate detection of high-profile security events, especially Internet worms. While this observation has been accepted for some time now, a systematic analysis of the requirements for building an effective distributed monitoring infrastructure is still missing. In this paper, we attempt to quantify the benefits of distributed monitoring and evaluate the practicality of this approach. To do so we developed a new worm propagation model that relaxes earlier assumptions regarding the uniformity of the underlying vulnerable population. This model allows us to evaluate how the size of the monitored address space, as well the number and locations of monitors, impact worm detection time. We empirically evaluate the effect of these parameters using traffic traces from over 1.5 billion suspicious connection attempts observed by more than 1600 intrusion detection systems dispersed across the Internet. Our results show that distributed monitors with half the allocated space of a centralized monitor can detect non-uniform scanning worms in half the time. Moreover, a distributed monitor of the same size as a centralized monitor can detect the worm four times faster. Furthermore, we show that even partial knowledge of the vulnerable population density can be used to improve monitor placement. Exploiting information about the location of the vulnerable population leads, in some cases, to detection time that is seven times as fast compared to random monitor deployment.
Kernels for Generalized Multiple-Instance Learning

The multiple-instance learning (MIL) model has been successful in numerous application areas. Recently, a generalization of this model and an algorithm for it were introduced, showing significant advantages over the conventional MIL model on certain application areas. Unfortunately, that algorithm is not scalable to high dimensions. We adapt that algorithm to one using a support vector machine with our new kernel k\wedge. This reduces the time complexity from exponential in the dimension to polynomial. Computing our new kernel is equivalent to counting the number of boxes in a discrete, bounded space that contain at least one point from each of two multisets. We show that this problem is #P-complete, but then give a fully polynomial randomized approximation scheme (FPRAS) for it. We then extend k by enriching its representation into a new kernel kmin, and also consider a normalized version of k\wedge that we call k (which may or may not not be a kernel, but whose approximation yielded positive semidefinite Gram matrices in practice). We then empirically evaluate all three measures on data from content-based image retrieval, biological sequence analysis, and the musk data sets. We found that our kernels performed well on all data sets relative to algorithms in the conventional MIL model.
Therapy for Specific Problems Therapy for Specific Problems : Youth Tobacco Cessation

Neuropsychological studies show that cognitive deficits associated with Alzheimer’s disease (AD) are distinct from age-associated cognitive decline. Quantitative and qualitative differences are apparent across many cognitive domains, but are especially obvious in episodic memory (particularly delayed recall), semantic knowledge, and some aspects of executive functions. The qualitatively distinct pattern of deficits is less salient in very old AD patients than in younger AD patients. Although decline in episodic memory is usually the earliest cognitive change that occurs prior to the development of the AD dementia syndrome, asymmetry in cognitive abilities may also occur in this “preclinical” phase of the disease and predict imminent dementia. Discrete patterns of cognitive deficits occur in AD and several neuropathologically distinct ageassociated neurodegenerative disorders. Knowledge of these differences helps to clinically distinguish among various causes of dementia and provides useful models for understanding brain-behavior relationships that mediate cognitive abilities affected in various neurodegenerative diseases. 257 A nn u. R ev . P sy ch ol . 2 00 9. 60 :2 57 -2 82 . D ow nl oa de d fr om a rj ou rn al s. an nu al re vi ew s. or g by H eb re w U ni ve rs ity o f Je ru sa le m o n 05 /0 6/ 09 . F or p er so na l u se o nl y. ANRV364-PS60-10 ARI 27 October 2008 16:15 Dementia: syndrome of acquired intellectual impairment of sufficient severity to interfere with social or occupational functioning caused by brain dysfunction
Complexity of Human Antibody Response to Dengue Virus: Implication for Vaccine Development

The four serotypes of dengue virus (DENV) are the leading cause of arboviral diseases in humans. Decades of efforts have made remarkable progress in dengue vaccine development. Despite the first dengue vaccine (dengvaxia from Sanofi Pasteur), a live-attenuated tetravalent chimeric yellow fever-dengue vaccine, has been licensed by several countries since 2016, its overall moderate efficacy (56.5–60.8%) in the presence of neutralizing antibodies during the Phase 2b and 3 trials, lower efficacy among dengue naïve compared with dengue experienced individuals, and increased risk of hospitalization among young children during the follow-up highlight the need for a better understanding of humoral responses after natural DENV infection. Recent studies of more than 300 human monoclonal antibodies (mAbs) against DENV have led to the discovery of several novel epitopes on the envelope protein recognized by potent neutralizing mAbs. This information together with in-depth studies on polyclonal sera and B-cells following natural DENV infection has tremendous implications for better immunogen design for a safe and effective dengue vaccine. This review outlines the progress in our understanding of mouse mAbs, human mAbs, and polyclonal sera against DENV envelope and precursor membrane proteins, two surface proteins involved in vaccine development, following natural infection; analyses of these discoveries have provided valuable insight into new strategies involving molecular technology to induce more potent neutralizing antibodies and less enhancing antibodies for next-generation dengue vaccine development.
Mutations in the M-Gene Segment Can Substantially Increase Replication Efficiency of NS1 Deletion Influenza A Virus in MDCK Cells

ABSTRACT Influenza viruses unable to express NS1 protein (delNS1) replicate poorly and induce large amounts of interferon (IFN). They are therefore considered candidate viruses for live-attenuated influenza vaccines. Their attenuated replication is generally assumed to result from the inability to counter the antiviral host response, as delNS1 viruses replicate efficiently in Vero cells, which lack IFN expression. In this study, delNS1 virus was parallel passaged on IFN-competent MDCK cells, which resulted in two strains that were able to replicate to high virus titers in MDCK cells due to adaptive mutations especially in the M-gene segment but also in the NP and NS gene segments. Most notable were clustered U-to-C mutations in the M segment of both strains and clustered A-to-G mutations in the NS segment of one strain, which presumably resulted from host cell-mediated RNA editing. The M segment mutations in both strains changed the ratio of M1 to M2 expression, probably by affecting splicing efficiency. In one virus, 2 amino acid substitutions in M1 additionally enhanced virus replication, possibly through changes in the M1 distribution between the nucleus and the cytoplasm. Both adapted viruses induced levels of IFN equal to that of the original delNS1 virus. These results show that the increased replication of the adapted viruses is not primarily due to altered IFN induction but rather is related to changes in M1 expression or localization. The mutations identified in this paper may be used to enhance delNS1 virus replication for vaccine production.
Two Signatures of Implicit Intergroup Attitudes

Long traditions in the social sciences have emphasized the gradual internalization of intergroup attitudes and the putatively more basic tendency to prefer the groups to which one belongs. In four experiments (N = 883) spanning two cultures and two status groups within one of those cultures, we obtained new evidence that implicit intergroup attitudes emerge in young children in a form indistinguishable from adult attitudes. Strikingly, this invariance from childhood to adulthood holds for members of socially dominant majorities, who consistently favor their in-group, as well as for members of a disadvantaged minority, who, from the early moments of race-based categorization, do not show a preference for their in-group. Far from requiring a protracted period of internalization, implicit intergroup attitudes are characterized by early enculturation and developmental invariance.
Expression of epidermal growth factor receptor: risk factor in uveal melanoma.

PURPOSE To investigate the prognostic significance of the expression of epidermal growth factor receptor (EGFR) in uveal melanoma. EGFR is a transmembrane glycoprotein, and its expression has been correlated with the development of metastases in various malignancies. METHODS Frozen sections from 22 primary uveal melanomas were examined for EGFR expression by a three-step immunoperoxidase staining, using a mouse anti-human EGFR IgG2b monoclonal antibody. The results were compared with patient survival and clinical and histopathologic parameters. RESULTS EGFR expression could not be determined on one tumor due to excessive pigmentation. Two patients died of causes unrelated to melanoma, and two patients were lost to follow-up. Out of 21 tumors, six tumors showed immunoreactivity for EGFR. Five of these six patients (83%) died due to metastases, compared with 2 (17%) of 12 patients with no EGFR expression (Kaplan-Meier analysis P = 0.0004). EGFR-positive tumors tended to have a greater tumor prominence and a higher mitotic rate. CONCLUSIONS The expression of EGFR was significantly correlated with death due to metastatic disease and therefore can be regarded as an important prognostic factor in human uveal melanoma.
The neural signal for the intensity of a tactile stimulus

The effect of indenting the skin at different rates on the perceived intensity of the stimulus was studied by indenting the skin of the fingertip with two triangular waveforms, given as a pair. The subjects were asked to judge which member of the pair was more intense. Perceived intensity was found to increase both with the depth and the speed of the indentation. In contrast, changes in the rate of skin indentation had little influence on perceived skin indentation depth. This suggests that intensity and depth are different attributes of tactile sensibility. Since the skin is viscous, a rapid indentation is more forceful than a slow indentation of the same depth, raising the possibility that perceived intensity is related to stimulus force. Even though intensity judgments were more closely correlated with the force of a stimulus than with the indentation it produced, a rapidly increasing force was felt as more intense than one that increased more slowly but attained the same final magnitude. When mechanoreceptors in the palmar aspect of the monkey's hand were excited with triangular stimuli like those used in the psychophysical studies, their discharge frequency increased with the rate of skin indentation. However, the receptors were distinctly more rate sensitive than the human judgments of stimulus intensity, suggesting that impulse summation in the central nervous system summates (integrates in the mathematical sense) the receptor input so as to enhance, relatively, the perceived intensity of the slower stimuli. (ABSTRACT TRUNCATED AT 250 WORDS)
A Conserved Functional Domain of Drosophila Coracle Is Required for Localization at the Septate Junction and Has Membrane-organizing Activity

The protein 4.1 superfamily is comprised of a diverse group of cytoplasmic proteins, many of which have been shown to associate with the plasma membrane via binding to specific transmembrane proteins. Coracle, a Drosophila protein 4.1 homologue, is required during embryogenesis and is localized to the cytoplasmic face of the septate junction in epithelial cells. Using in vitro mutagenesis, we demonstrate that the amino-terminal 383 amino acids of Coracle define a functional domain that is both necessary and sufficient for proper septate junction localization in transgenic embryos. Genetic mutations within this domain disrupt the subcellular localization of Coracle and severely affect its genetic function, indicating that correct subcellular localization is essential for Coracle function. Furthermore, the localization of Coracle and the transmembrane protein Neurexin to the septate junction display an interdependent relationship, suggesting that Coracle and Neurexin interact with one another at the cytoplasmic face of the septate junction. Consistent with this notion, immunoprecipitation and in vitro binding studies demonstrate that the amino-terminal 383 amino acids of Coracle and cytoplasmic domain of Neurexin interact directly. Together these results indicate that Coracle provides essential membrane-organizing functions at the septate junction, and that these functions are carried out by an amino-terminal domain that is conserved in all protein 4.1 superfamily members.
Glutamine kinetics and protein turnover in end-stage renal disease.

Alanine and glutamine constitute the two most important nitrogen carriers released from the muscle. We studied the intracellular amino acid transport kinetics and protein turnover in nine end-stage renal disease (ESRD) patients and eight controls by use of stable isotopes of phenylalanine, alanine, and glutamine. The amino acid transport kinetics and protein turnover were calculated with a three-pool model from the amino acid concentrations and enrichment in the artery, vein, and muscle compartments. Muscle protein breakdown was more than synthesis (nmol.min(-1). 100 ml leg(-1)) during hemodialysis (HD) (169.8 +/- 20.0 vs. 125.9 +/- 21.8, P < 0.05) and in controls (126.9 +/- 6.9 vs. 98.4 +/- 7.5, P < 0.05), but synthesis and catabolism were comparable pre-HD (100.7 +/- 15.7 vs. 103.4 +/- 14.8). Whole body protein catabolism decreased by 15% during HD. The intracellular appearance of alanine (399.0 +/- 47.1 vs. 243.0 +/- 34.689) and glutamine (369.7 +/- 40.6 vs. 235.6 +/- 27.5) from muscle protein breakdown increased during dialysis (nmol.min(-1). 100 ml leg(-1), P < 0.01). However, the de novo synthesis of alanine (3,468.9 +/- 572.2 vs. 3,140.5 +/- 467.7) and glutamine (1,751.4 +/- 82.6 vs. 1,782.2 +/- 86.4) did not change significantly intradialysis (nmol.min(-1). 100 ml leg(-1)). Branched-chain amino acid catabolism (191.8 +/- 63.4 vs. -59.1 +/- 42.9) and nonprotein glutamate disposal (347.0 +/- 46.3 vs. 222.3 +/- 43.6) increased intradialysis compared with pre-HD (nmol.min(-1). 100 ml leg(-1), P < 0.01). The mRNA levels of glutamine synthase (1.45 +/- 0.14 vs. 0.33 +/- 0.08, P < 0.001) and branched-chain keto acid dehydrogenase-E2 (3.86 +/- 0.48 vs. 2.14 +/- 0.27, P < 0.05) in the muscle increased during HD. Thus intracellular concentrations of alanine and glutamine are maintained during HD by augmented release of the amino acids from muscle protein catabolism. Although muscle protein breakdown increased intradialysis, the whole body protein catabolism decreased, suggesting central utilization of amino acids released from skeletal muscle.
Risky prey behavior evolves in risky habitats

Longstanding theory in behavioral ecology predicts that prey should evolve decreased foraging rates under high predation threat. However, an alternative perspective suggests that growth into a size refuge from gape-limited predation and the future benefits of large size can outweigh the initial survival costs of intense foraging. Here, I evaluate the relative contributions of selection from a gape-limited predator (Ambystoma opacum) and spatial location to explanations of variation in foraging, growth, and survival in 10 populations of salamander larvae (Ambystoma maculatum). Salamander larvae from populations naturally exposed to intense A. opacum predation risk foraged more actively under common garden conditions. Higher foraging rates were associated with low survival in populations exposed to free-ranging A. opacum larvae. Results demonstrate that risky foraging activity can evolve in high predation-risk habitats when the dominant predators are gape-limited. This finding invites the further exploration of diverse patterns of prey foraging behavior that depends on natural variation in predator size-selectivity. In particular, prey should adopt riskier behaviors under predation threat than expected under existing risk allocation models if foraging effort directly reduces the duration of risk by growth into a size refuge. Moreover, evidence from this study suggests that foraging has evolved over microgeographic scales despite substantial modification by regional gene flow. This interaction between local selection and spatial location suggests a joint role for adaptation and maladaptation in shaping species interactions across natural landscapes, which is a finding with implications for dynamics at the population, community, and metacommunity levels.
Polyunsaturated Fatty Acid Levels in Maternal Erythrocytes of Japanese Women during Pregnancy and after Childbirth

Background: The transport of polyunsaturated fatty acids (PUFAs), such as arachidonic acid (ARA, 20:4n-6) and docosahexaenoic acid (DHA, 22:6n-3), to the fetus from maternal stores increases depending on the fetal requirements for PUFA during the last trimester of pregnancy. Therefore, maternal blood PUFA changes physiologically with gestational age. However, the changes in PUFA levels in maternal blood erythrocytes during pregnancy and after childbirth have not been fully investigated in a fish-eating population. Objective: To examine the changes of ARA and DHA levels in maternal erythrocytes with the progress of pregnancy and the relationship between maternal and umbilical cord erythrocyte PUFA levels in pregnant Japanese women who habitually eat fish and shellfish. Design: This study was performed as a part of the adjunct study of the Japan Environment and Children’s Study (JECS). The participants were 74 pregnant women. The maternal blood samples were collected at 27, 30, and 36 weeks of pregnancy, and 2 days and 1 month after delivery, and umbilical cord blood was collected at delivery. The fatty acid levels of erythrocytes in these blood samples were determined. Results: ARA and DHA levels in maternal erythrocytes tended to decrease with the progress of pregnancy. While the DHA level decreased further after delivery, the ARA level returned to the value at 27 weeks of pregnancy within 1 month after delivery. The n-3 and n-6 PUFA levels in maternal erythrocytes at 27, 30, and 36 weeks of pregnancy were significantly positively correlated with the corresponding fatty acid levels in umbilical cord erythrocytes. Conclusion: The present findings showed a significant change in erythrocyte PUFA levels during pregnancy and after childbirth in a fish-eating population. The PUFA levels of maternal blood after the second trimester may be a reliable marker for predicting PUFA levels in infants’ circulating blood.