Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence divergence and copy number of the middle- and long-wave photopigment genes in old world monkeys

We have studied the sequence and organization of the genes for the middle-wave (MW) and long-wave (LW) cone photopigment genes in six species of Old World monkeys. Previous studies have shown that the MW and LW pigments of all six species exhibit peak sensitivities near 535 nm and 565 nm, respectively, and thus resemble the equivalent human pigments. In the case of man, the protein components of the MW and LW photopigments differ by 15 amino acids, although only seven of these differences involve non-homologous substitutions and are therefore candidates for a role in spectral tuning. Regions corresponding to exons 4 and 5 of these genes, and including five such candidate sites, were sequenced in the Old World monkeys. In contrast to the equivalent human genes, substitutions were found at two of these sites, position 233 and 309 of the MW gene in all six species. The role of amino acid substitutions in the spectral tuning of these photopigments is discussed. A comparision of the nucleotide sequences of the MW and LW genes provides evidence for sequence homogenization within species; the role of gene conversion in the evolution of these genes is discussed. The close juxtaposition and homology of the MW and LW genes on the X chromosome is thought to underlie the high frequency of colour vision defects in man and the presence in many individuals of extra copies of the MW gene. A study of a group of talapoin (Ceropithecus talapoin) monkeys has revealed a similar numerical polymorphism for this gene to that present in man. In contrast to the situation in man, where the MW and LW genes may contain a shortened first intron, restriction digests of genomic DNA showed that the size of this intron does not differ across the six species of Old World monkeys examined.
An opposition-based hybrid Artificial Bee Colony with differential evolution

This paper presents an opposition-based hybrid Artificial Bee Colony (ABC) with Differential Evolution (DE) algorithm for solving continuous problems. The proposed algorithm, called OABCDE, employs an efficient mutation operation of DE and a crossover-like mechanism to enhance the convergence of ABC without adding parameters. The opposition-based learning routine is periodically executed to prevent being trapped in local optima. The numerical experimentation uses 16 widely-accepted nonlinear benchmark functions of different characteristics and tests at 30, 60 and 100 dimensions. The results demonstrate that OABCDE achieves a superior performance compared to the advance qABC [9] (a recent hybrid ABC and DE) and Opposition-based DE [15].
Mutual Knowledge of Rationality in the Electronic Mail Game

This paper reexamines the paradoxical aspect of the electronic mail game (Rubinstein, 1989). The electronic mail game is a coordination game with payoff uncertainty. At a Bayesian Nash equilibrium of the game, players cannot achieve the desired coordination of actions even when a high order of mutual knowledge of payoff functions obtains. We want to make explicit the role of knowledge about rationality of players, not only that of payoff functions. For this purpose, we use an extended version of the belief system model developed by Aumann and Brandenburger (1995). We propose a certain way of embedding the electronic mail game in an belief system. And we show that for rational players to coordinate their actions, for any embedding belief systems, it is necessary that the upper bound order of mutual knowledge of payoff functions exceeds the upper bound order of mutual knowledge of rationality. This result implies that under common knowledge of rationality, the coordination never occurs, which is similar to Rubinstein's result. We point out, however, that there exists a class embedding belief systems for which the above condition is also sufficient for the desired coordination.
The Role of Lhca Complexes in the Supramolecular Organization of Higher Plant Photosystem I*

In this work, Photosystem I supercomplexes have been purified from Lhca-deficient lines of Arabidopsis thaliana using a mild detergent treatment that does not induce loss of outer antennas. The complexes have been studied by integrating biochemical analysis with electron microscopy. This allows the direct correlation of changes in protein content with changes in supramolecular structure of Photosystem I to get information about the position of the individual Lhca subunits, the association of the antenna to the core, and the influence of the individual subunits on the stability of the system. Photosystem I complexes with only two or three antenna complexes were purified, showing that the binding of Lhca1/4 and Lhca2/3 dimers to the core is not interdependent, although weak binding of Lhca2/3 to the core is stabilized by the presence of Lhca4. Moreover, Lhca2 and Lhca4 can be associated with the core in the absence of their “dimeric partners. ” The structure of Photosystem I is very rigid, and the absence of one antenna complex leaves a “hole” in the structure that cannot be filled by other Lhcas, clearly indicating that the docking sites for the individual subunits are highly specific. There is, however, an exception to the rule: Lhca5 can substitute for Lhca4, yielding highly stable PSI supercomplexes with a supramolecular organization identical to the WT.
Pathological Basis for Deficient Excitatory Drive to Cortical Parvalbumin Interneurons in Schizophrenia.

OBJECTIVE Deficient excitatory drive to parvalbumin-containing cortical interneurons is proposed as a key neural substrate for altered gamma oscillations and cognitive dysfunction in schizophrenia. However, a pathological entity producing such a deficit has not been identified. The authors tested the hypothesis that cortical parvalbumin interneurons receive fewer excitatory synaptic inputs in individuals with schizophrenia. METHOD Fluorescent immunohistochemistry, confocal microscopy, and post-image processing techniques were used to quantify the number of putative excitatory synapses (i.e., the overlap of vesicular glutamate transporter 1-positive [VGlut1+] puncta and postsynaptic density protein 95-positive [PSD95+] puncta) per surface area of parvalbumin-positive (PV+) or calretinin-positive (CR+) neurons in the dorsolateral prefrontal cortex from schizophrenia subjects and matched unaffected comparison subjects. RESULTS Mean density of VGlut1+/PSD95+ puncta on PV+ neurons was 18% lower in schizophrenia, a significant difference. This deficit was not influenced by methodological confounds or schizophrenia-associated comorbid factors, not present in monkeys chronically exposed to antipsychotic medications, and not present in CR+ neurons. Mean density of VGlut1+/PSD95+ puncta on PV+ neurons predicted the activity-dependent expression levels of parvalbumin and glutamic acid decarboxylase 67 (GAD67) in schizophrenia subjects but not comparison subjects. CONCLUSIONS To the authors' knowledge, this is the first demonstration that excitatory synapse density is lower selectively on parvalbumin interneurons in schizophrenia and predicts the activity-dependent down-regulation of parvalbumin and GAD67. Because the activity of parvalbumin interneurons is required for generation of cortical gamma oscillations and working memory function, these findings reveal a novel pathological substrate for cortical dysfunction and cognitive deficits in schizophrenia.
Hepatoprotective, DNA Damage Prevention and Antioxidant Potential of Spirulina platensis on CCl4- Induced Hepatotoxicity in Mice

In the present study, we have evaluated the hepatoprotective and antioxidant effects of Spirulina platensis against CCl4-induced hepatotoxicity in mice. Activities of liver marker enzymes; Alanine transaminase and Aspartate transaminasewere estimated, as well as lipid peroxidation and antioxidant status (glutathione peroxidase) were determined in liver homogenate. DNA damage in liver was also evaluated by means of Comet assay. CCl4 induction (1 mg/kg b.wt) significantly increases the levels of liver marker enzymesand lipid peroxidation, and caused the depletion of antioxidant status. Treatment of Spirulinaplatensis (800mg/kg/b.wt) to CCl4 challenged mice resulted in decreased liver marker enzymes activity, DNA damage and lipid peroxidation levels with increase in antioxidant status. Our study clearly demonstrates that Spirulina platensis shows hepatoprotective effect through its antioxidant activity on CCl4-induced hepatotoxicity in mice.
The effect of casein genotypes selection on the genetic structure of Romanian Spotted , Holstein Friesian and Montbéliarde cattle populations and the genetic variability of kappa-casein and beta-lactoglobulin in Romanian Grey Steppe

This scientific paper aims to provide a theoretical selection model in Romanian Spotted, Holstein Friesian and Montbéliarde cattle populations reared in the Romanian farms, considering the results from the scientific reports regarding the main casein alleles and their genotypes influence on cheese production. Furthermore, the genotype and allele frequencies at κ-CN and β-LG loci in Romanian Grey Steppe, one of the oldest Romanian cattle breed, were calculated. The alleles frequencies changing rate due to the selection applied (Δp, Δq, Δr) was established as a result of the difference between the allele frequencies after the selection and before that: Δp=p’A-pA; Δq= q’B-qB and Δr=r’C-rC. As a result of assumed selection, it occurred in Romanian Spotted investigated population a β-CN A, B and C alleles increased frequencies by 8.88%, 2.36% and 0.36% respectively and a κ-CN B allele increased frequency by 8.36%. In Holstein Friesian investigated population, the expected results on β-CN locus were achieved, the Aallele frequency decreased by 11.19% and the A and B allele frequencies compensatory increased by 8.22% and 2.96%, respectively. As a result of the total selection applied for the κ-CN AE, BE and EE genotypes, the E allele was completely removed from the investigated Holstein Friesian population, the B favourable for cheese production allele frequency increased by 9.97% and that for A allele decreased by 2.87%. A new selection model for Montbéliarde investigated population was unnecessary, the genetic structure of these individuals being obviously directed towards obtaining milk for cheese production. Considering the κ-CN and β-LG genotypes found in Romanian Grey Steppe investigated population, the frequencies for the A and B identified alleles were: 0.464 and 0.536 respectively for κ-CN and 0.409 and 0.591 for β-LG. The AB genotype was the most prevalent both for κ-CN and β-LG proteins (0.491 and 0.564 respectively) whereas the AA genotype was with the least frequencies (0.218 and 0.127 respectively) for the same proteins.
Pedestrians, Autonomous Vehicles, and Cities

Autonomous vehicles, popularly known as self-driving cars, have the potential to transform travel behavior. However, existing analyses have ignored strategic interactions with other road users. In this article, I use game theory to analyze the interactions between pedestrians and autonomous vehicles, with a focus on yielding at crosswalks. Because autonomous vehicles will be risk-averse, the model suggests that pedestrians will be able to behave with impunity, and autonomous vehicles may facilitate a shift toward pedestrian-oriented urban neighborhoods. At the same time, autonomous vehicle adoption may be hampered by their strategic disadvantage that slows them down in urban traffic.
The conserved ninth C-terminal heptad in thyroid hormone and retinoic acid receptors mediates diverse responses by affecting heterodimer but not homodimer formation

The receptors for thyroid hormone (T3R), all-trans-retinoic acid (RAR), and 9-cis-retinoic acid (RXR) bind DNA response elements as homo- and heterodimers. The ligand-binding domains of these receptors contain nine conserved heptads proposed to play a role in dimerization. Mutant receptors with changes in the first or last hydrophobic amino acids in the highly conserved ninth heptad of chick T3R alpha [cT3R alpha(L365R) and cT3R(L372R)] and human RAR alpha (hRAR alpha) [hRAR(M377R) and hRAR(L384R)] reveal that this heptad is essential for certain heterodimeric interactions and for diverse functional activities. Without ligands, wild-type receptors form both homodimers and heterodimers, while these mutants form only homodimers. Surprisingly, the cognate ligand for each mutant enables heterodimer formation between cT3R(L365R) and RAR or RXR and between hRAR(M377R) and T3R or RXR. Both cT3R(L365R) and hRAR(M377R) mediate ligand-dependent transcriptional regulation. However, unlike the wild-type receptor, non-ligand-associated cT3R(L365R) does not suppress the basal activity of certain promoters containing thyroid hormone response elements, suggesting that this silencing effect of T3R is mediated by unliganded heterodimers of T3R and endogenous RXR or related factors. Heterodimerization is also necessary for the strong ligand-independent inhibition between T3R and RAR on a common response element, since the ninth-heptad mutants function as poor inhibitors. However, with a T3R-specific response element, hRAR(M377R) acts as a retinoic acid-dependent inhibitor of cT3R, indicating the importance of heterodimerization for this inhibition. Our studies also suggest that the ninth heptad is necessary for the dominant inhibition of wild-type T3Rs by mutant T3Rs, as has been found for the thyroid hormone-resistant syndrome in humans. Thus, the ninth heptad repeat is required for heterodimerization, suppression of basal promoter activity, and dominant negative effects of T3R and RAR. Lastly, the finding that cT3R(L365R) and hRAR(M377R) require ligands for heterodimer formation also raises the possibility that heterodimeric interactions are mediated by the ninth heptad without ligands but by a second region of these receptors with ligands.
The N-terminal Moiety of CDC25Mm, a GDP/GTP Exchange Factor of Ras Proteins, Controls the Activity of the Catalytic Domain

This work describes the in vitro properties of full-length CDC25Mm (1262 amino acid residues), a GDP/GTP exchange factor (GEF) of H-ras p21. CDC25Mm, isolated as a recombinant protein in Escherichia coli and purified by various chromatographic methods, could stimulate the H-ras p21·GDP dissociation rate; however, its specific activity was 25 times lower than that of the isolated catalytic domain comprising the last C-terminal 285 residues (C-CDC25Mm285) and 5 times lower than the activity of the C-terminal half-molecule (631 residues). This reveals a negative regulation of the catalytic domain by other domains of the molecule. Accordingly, the GEF activity of CDC25Mm was increased severalfold by the Ca2+-dependent protease calpain that cleaves around a PEST-like region (residues 798-853), producing C-terminal fragments of 43-56 kDa. In agreement with the presence of an IQ motif on CDC25Mm (residues 202-229), calmodulin interacted functionally with the exchange factor. Depending on the calmodulin concentration an inhibition up to 50% of the CDC25Mm-induced nucleotide exchange activity on H-ras p21 was observed, an effect requiring Ca2+ ions. Calmodulin also inhibited C-CDC25Mm285 but with a ∼100 times higher IC50 than in the case of CDC25Mm (∼10 μM versus 0.1 μM, respectively). Together, these results emphasize the role of the other domains of CDC25Mm in controlling the activity of the catalytic domain and support the involvement of calmodulin and calpain in the in vivo regulation of the CDC25Mm activity.
Sugarcane Cultivar Response to High Summer Water Tables in the Everglades

Sugarcane (interspecific hybrids of Saccharum spp.) in the Everglades Agricultural Area (EAA) in Florida is frequently subjected to periods of higher-than-desired water levels. This study was conducted to evaluate yields of nine sugarcane cultivars subjected to two higher-than-conventional water tables in the EAA during the summer rainy season from the plant cane through the second-ratoon annual crop cydes. Field experiments were planted in February 1997 and January 1998. During the summers from 1997 through 1999, we sought to maintain water <15 cm below the soil surface (BSS) in the wetter field and from 15 to 38 cm BSS in the drier field. Water tables for sugarcane in the EAA fluctuate from 40 to 95 cm BSS. Targeted water levels were achieved for 40 d in 1997, 104 d in 1998, and 96 d in 1999 in the wetter field and for 35 d in 1997, 96 d in 1998, and 82 d in 1999 in the drier field. The mean sugar per hectare in the wetter field was 91.7% that of the drier field. Yields of Canal Point (CP) 72-2086' and CP 82-1172' were not affected by water table. Cultivar CP 85-1308 had higher yields in the wetter field in two of five harvests. Sugar per hectare of CP 80-1743' was reduced by 25.1% in the wetter field. The variability among commercial cultivars to maintain yields at high water tables suggests that routine screening of promising sugarcane genotypes under high water tables would help identify more cultivars that maintain high yields in wetter conditions in the EAA.
Neuroticism, Extraversion, and Mortality in the UK Health and Lifestyle Survey: A 21-Year Prospective Cohort Study

Objective: To examine the influence of neuroticism and extraversion on all-cause and cause-specific mortality over 21 years after controlling for risk factors. Methods: Participants were members of the Health and Lifestyle Survey, a British nationwide sample survey of 9003 adults. At baseline (1984 to 1985), individuals completed a sociodemographic and health questionnaire, underwent physical health examination, and completed the Eysenck Personality Inventory. Mortality was assessed for 21 years after baseline. A total of 5424 individuals had complete data. Results: After controlling for age and gender, 1-standard deviation (SD) increase in neuroticism was related to 9% (hazard ratio (HR) = 1.09; 95% Confidence Interval (CI) = 1.03–1.16) increased risk of mortality from all causes. The association was nonsignificant (HR = 1.05; 95% CI = 0.99–1.11) after additionally controlling for occupational social class, education, smoking, alcohol consumption, physical activity, and health. There was 12% (HR = 1.12; 95% CI = 1.03–1.21) increased risk of death from cardiovascular disease associated with 1-SD increase in neuroticism. This was still significant after adjustment. When the sample was divided into 40- to 59-year-olds and those ≥60 years, neuroticism remained a significant risk for all-cause mortality and cardiovascular disease mortality; associations were nonsignificant after controlling for all covariates. Neuroticism was not associated with deaths from stroke, respiratory disease, lung cancer, or other cancers. Extraversion was protective of death from respiratory disease (HR = 0.84; 95% CI = 0.70– 1.00). Conclusions: After controlling for several risk factors, high neuroticism was significantly related to risk of death from cardiovascular disease. The effects of neuroticism on death from cardiovascular disease may be mediated by sociodemographic, health behavior, and physiological factors. EPI = Eysenck Personality Inventory; HR = hazard ratio; CI = Confidence Interval; HALS = Health and Lifestyle Survey; CVD = cardiovascular disease; CHD = coronary heart disease; BMI = body mass index; BP = blood pressure; FEV = forced expiratory volume.
Chemotherapeutic Activity in a Mouse Model of Cryptococcosis with Cutaneous and Nasal Involvement

Summary: A rhinotropic, dermatotropic isolate of Cryptococcus neoformans was used to produce generalized systemic infection in mice. Cutaneous involvement with gross nasal enlargement was reproducible and was used in conjugation with mortality to measure the progress of infection in chemotherapy studies. Nasal enlargement and death were scored over a period of 50 days after infection and used to calculate an index of infection. The index of infection in untreated animals followed a similar and reproducible course in four independent experiments. The first signs of infection (nasal enlargement) were seen 15 days after i.v. injection of 104 cells of Cr. neoformans per mouse. The effects of antifungal chemotherapy depended on the start of treatment, with more favorable effects resulting from earlier treatment initiation. Ketoconazole, itraconazole, fluconazole, ICI 195°739, terbinafine, amorolfine, 5‐fluorocytosine, and amphotericin B were tested. The best activity was seen with ICI 195°739 (highly active) and fluconazole, followed by itraconazole and ketoconazole. Only high doses of amphotericin B were active. 5‐Fluorocytosine was only active when given early in the course of the infection. Terbinafine and amorolfine were inactive. This model provides a way to examine directly the antifungal effects in disseminated cutaneous cryptococcosis.
BRAIN BIOMECHANICS : STEADY-STATE CONSOLIDATION THEORY OF HYDROCEPHALUS

In this paper we apply Biot's classical theory of consolidation to the brain in simplified geometry, in order to find explicit formulas for its response to internally applied loads. We show that the observed brain compliance can be understood in terms of Biot's concept of jacketed compressibility, with the result that the Poisson ratio is considerably less than the value 112 used in early numerical simulations of hydrocephalus. Using existing data, we also derive approximate values for both the shear modulus and the Poisson ratio of the brain.
Immunohistological localization of melatonin in the pineal gland and retina of the rat

Abstract: An incubation procedure for the demonstration of melatonin is described using freeze‐dried, unfixed material embedded in vacuum directly in glycolmethacrylate. The results indicate the binding of melatonin in the nucleus of pineal parenchymal cells and in the outer nuclear layer of the retina of rats; binding is greater at night than during the day.
Temperature-Sensitive Mutations in the Putative Herpes Simplex Virus Type 1 Terminase Subunits pUL15 and pUL33 Preclude Viral DNA Cleavage/Packaging and Interaction with pUL28 at the Nonpermissive Temperature

ABSTRACT Terminases comprise essential components of molecular motors required to package viral DNA into capsids in a variety of DNA virus systems. Previous studies indicated that the herpes simplex virus type 1 UL15 protein (pUL15) interacts with the pUL28 moiety of a pUL28-pUL33 complex to form the likely viral terminase. In the current study, a novel temperature-sensitive mutant virus was shown to contain a mutation in UL33 codon 61 predicted to change threonine to proline. At the nonpermissive temperature, this virus, designated ts8-22, replicated viral DNA and produced capsids that became enveloped at the inner nuclear membrane but failed to form plaques or to cleave or package viral DNA. Incubation at the nonpermissive temperature also precluded coimmunoprecipitation of UL33 protein with its normal interaction partners encoded by UL28 and UL15 in ts8-22-infected cells and with pUL28 in transient-expression assays. Moreover, a temperature-sensitive mutation in UL15 precluded coimmunoprecipitation of pUL15 with the UL28 and UL33 proteins at the nonpermissive temperature. We conclude that interactions between putative terminase components are tightly linked to successful viral DNA cleavage and packaging.