Miracle-dz/UniFAR-FTUs huggingface dataset:
Superoptimal Perceptual Integration Suggests a Place-Based Representation of Pitch at High Frequencies

Pitch, the perceptual correlate of sound repetition rate or frequency, plays an important role in speech perception, music perception, and listening in complex acoustic environments. Despite the perceptual importance of pitch, the neural mechanisms that underlie it remain poorly understood. Although cortical regions responsive to pitch have been identified, little is known about how pitch information is extracted from the inner ear itself. The two primary theories of peripheral pitch coding involve stimulus-driven spike timing, or phase locking, in the auditory nerve (time code), and the spatial distribution of responses along the length of the cochlear partition (place code). To rule out the use of timing information, we tested pitch discrimination of very high-frequency tones (>8 kHz), well beyond the putative limit of phase locking. We found that high-frequency pure-tone discrimination was poor, but when the tones were combined into a harmonic complex, a dramatic improvement in discrimination ability was observed that exceeded performance predicted by the optimal integration of peripheral information from each of the component frequencies. The results are consistent with the existence of pitch-sensitive neurons that rely only on place-based information from multiple harmonically related components. The results also provide evidence against the common assumption that poor high-frequency pure-tone pitch perception is the result of peripheral neural-coding constraints. The finding that place-based spectral coding is sufficient to elicit complex pitch at high frequencies has important implications for the design of future neural prostheses to restore hearing to deaf individuals. SIGNIFICANCE STATEMENT The question of how pitch is represented in the ear has been debated for over a century. Two competing theories involve timing information from neural spikes in the auditory nerve (time code) and the spatial distribution of neural activity along the length of the cochlear partition (place code). By using very high-frequency tones unlikely to be coded via time information, we discovered that information from the individual harmonics is combined so efficiently that performance exceeds theoretical predictions based on the optimal integration of information from each harmonic. The findings have important implications for the design of auditory prostheses because they suggest that enhanced spatial resolution alone may be sufficient to restore pitch via such implants.
Semiparametric Estimation of a Sample Selection Model in the Presence of Endogeneity

In this paper, we derive a semiparametric estimation procedure for the sample selection model when some covariates are endogenous. Our approach is to augment the main equation of interest with a control function which accounts for sample selectivity as well as endogeneity of covariates. In contrast to existing methods proposed in the literature, our approach allows that the same endogenous covariates may enter the main and the selection equation. We show that our proposed estimator is \sqrtn-consistent and derive its asymptotic distribution. We provide Monte Carlo evidence on the small sample behavior of our estimator and present an empirical application. Finally, we brie y consider an extension of our model to quantile regression settings and provide guidelines for estimation.
The Roles of Different Sources of Social Support on Emotional Well-Being among Chinese Elderly

Background Social support has been widely known as a protective factor for the emotional well-being (EWB) of older adults, but less studies have investigated the roles of different sources of social support (i.e., family and friend support) on different facets of EWB (i.e., positive affect and negative affect) simultaneously. Methodology and Findings In this study, the associations between family/friend support and positive/negative affect were investigated in a sample of 700 Chinese elderly. The EWB and social support were measured with a 12-item affective wordlist (Kahneman et al., 2004) and a self-prepared questionnaire. The results showed that (1) the order of contact frequency and mutual support followed a hierarchical order from spouse, children, to friends; (2) zero-order correlations of both family support and friend support were associated with more positive affect and less negative affect; and when compared with the relative role of family and friend support, (3) spouse (children if spouse is not available) support had greater contribution on decreasing negative affect, while friend support had greater influence on increasing positive affect, even after controlling the demographic, self-rated health and life events variables. Conclusion Family and friend support play different roles on the two facets of EWB of the elderly. These results were better explained in light of the task specificity model rather than the hierarchical compensatory model. Moreover, positive affect may be enhanced by friend support (based on personal interests and selectable) rather than family support (bonded by kinship and not selectable), which added evidences to the socioemotional selectivity theory.
Blended Rotor-Spun Yarns with a High Proportion of Flax

We present the results of tests on rotor-spun blended yarns, made with a high proportion of flax, and rotor-spun all-cotton yarns. Of special concern was the method of preparing the fibres and sliver. The flax/cotton sliver was made up of medium-long cotton, and the flax fibre was shortened and reduced in diameter by mechanical cottonising. The basic composition of the flax/cotton sliver was 30% cotton and 70% mechanically cottonised flax. The optimum linear density of the yarns was 40 tex. The experiments enabled the optimum values of twist and linear density to be found, at which the quality parameters of the yarns produced were acceptable. In addition, a comparative analysis of the produced cotton yarn and flax/cotton yarn was made. The flax/cotton yarn with a high proportion of flax is suitable for both weaving and knitting.
Altered Metabolic Signature in Pre-Diabetic NOD Mice

Altered metabolism proceeding seroconversion in children progressing to Type 1 diabetes has previously been demonstrated. We tested the hypothesis that non-obese diabetic (NOD) mice show a similarly altered metabolic profile compared to C57BL/6 mice. Blood samples from NOD and C57BL/6 female mice was collected at 0, 1, 2, 3, 4, 5, 6, 7, 9, 11, 13 and 15 weeks and the metabolite content was analyzed using GC-MS. Based on the data of 89 identified metabolites OPLS-DA analysis was employed to determine the most discriminative metabolites. In silico analysis of potential involved metabolic enzymes was performed using the dbSNP data base. Already at 0 weeks NOD mice displayed a unique metabolic signature compared to C57BL/6. A shift in the metabolism was observed for both strains the first weeks of life, a pattern that stabilized after 5 weeks of age. Multivariate analysis revealed the most discriminative metabolites, which included inosine and glutamic acid. In silico analysis of the genes in the involved metabolic pathways revealed several SNPs in either regulatory or coding regions, some in previously defined insulin dependent diabetes (Idd) regions. Our result shows that NOD mice display an altered metabolic profile that is partly resembling the previously observation made in children progressing to Type 1 diabetes. The level of glutamic acid was one of the most discriminative metabolites in addition to several metabolites in the TCA cycle and nucleic acid components. The in silico analysis indicated that the genes responsible for this reside within previously defined Idd regions.
Host Genetic Control of the Microbiota Mediates the Drosophila Nutritional Phenotype

ABSTRACT A wealth of studies has demonstrated that resident microorganisms (microbiota) influence the pattern of nutrient allocation to animal protein and energy stores, but it is unclear how the effects of the microbiota interact with other determinants of animal nutrition, including animal genetic factors and diet. Here, we demonstrate that members of the gut microbiota in Drosophila melanogaster mediate the effect of certain animal genetic determinants on an important nutritional trait, triglyceride (lipid) content. Parallel analysis of the taxonomic composition of the associated bacterial community and host nutritional indices (glucose, glycogen, triglyceride, and protein contents) in multiple Drosophila genotypes revealed significant associations between the abundance of certain microbial taxa, especially Acetobacteraceae and Xanthamonadaceae, and host nutritional phenotype. By a genome-wide association study of Drosophila lines colonized with a defined microbiota, multiple host genes were statistically associated with the abundance of one bacterium, Acetobacter tropicalis. Experiments using mutant Drosophila validated the genetic association evidence and reveal that host genetic control of microbiota abundance affects the nutritional status of the flies. These data indicate that the abundance of the resident microbiota is influenced by host genotype, with consequent effects on nutrient allocation patterns, demonstrating that host genetic control of the microbiome contributes to the genotype-phenotype relationship of the animal host.
In vivo optical imaging of amblyopia: Digital subtraction autofluorescence and split‐spectrum amplitude‐decorrelation angiography

Amblyopia is a visual impairment that is attributed to either abnormal binocular interactions or visual deprivation. The retina and choroids have been shown to be involved in the development of amblyopia. The purpose of this study was to investigate the retinal and choroidal microstructural abnormalities of amblyopia using digital subtraction autofluorescence and split‐spectrum amplitude‐decorrelation angiography (SSADA) approaches.
Biapenem Inactivation by B2 Metallo β-Lactamases: Energy Landscape of the Post-Hydrolysis Reactions

Background The first line of defense by bacteria against β-lactam antibiotics is the expression of β-lactamases, which cleave the amide bond of the β-lactam ring. In the reaction of biapenem inactivation by B2 metallo β-lactamases (MβLs), after the β-lactam ring is opened, the carboxyl group generated by the hydrolytic process and the hydroxyethyl group (common to all carbapenems) rotate around the C5–C6 bond, assuming a new position that allows a proton transfer from the hydroxyethyl group to C2, and a nucleophilic attack on C3 by the oxygen atom of the same side-chain. This process leads to the formation of a bicyclic compound, as originally observed in the X-ray structure of the metallo β-lactamase CphA in complex with product. Methodology/Principal Findings QM/MM and metadynamics simulations of the post-hydrolysis steps in solution and in the enzyme reveal that while the rotation of the hydroxyethyl group can occur in solution or in the enzyme active site, formation of the bicyclic compound occurs primarily in solution, after which the final product binds back to the enzyme. The calculations also suggest that the rotation and cyclization steps can occur at a rate comparable to that observed experimentally for the enzymatic inactivation of biapenem only if the hydrolysis reaction leaves the N4 nitrogen of the β-lactam ring unprotonated. Conclusions/Significance The calculations support the existence of a common mechanism (in which ionized N4 is the leaving group) for carbapenems hydrolysis in all MβLs, and suggest a possible revision of mechanisms for B2 MβLs in which the cleavage of the β-lactam ring is associated with or immediately followed by protonation of N4. The study also indicates that the bicyclic derivative of biapenem has significant affinity for B2 MβLs, and that it may be possible to obtain clinically effective inhibitors of these enzymes by modification of this lead compound.
Seasonal Patterns of Body Temperature Daily Rhythms in Group-Living Cape Ground Squirrels Xerus inauris

Organisms respond to cyclical environmental conditions by entraining their endogenous biological rhythms. Such physiological responses are expected to be substantial for species inhabiting arid environments which incur large variations in daily and seasonal ambient temperature (Ta). We measured core body temperature (Tb) daily rhythms of Cape ground squirrels Xerus inauris inhabiting an area of Kalahari grassland for six months from the Austral winter through to the summer. Squirrels inhabited two different areas: an exposed flood plain and a nearby wooded, shady area, and occurred in different social group sizes, defined by the number of individuals that shared a sleeping burrow. Of a suite of environmental variables measured, maximal daily Ta provided the greatest explanatory power for mean Tb whereas sunrise had greatest power for Tb acrophase. There were significant changes in mean Tb and Tb acrophase over time with mean Tb increasing and Tb acrophase becoming earlier as the season progressed. Squirrels also emerged from their burrows earlier and returned to them later over the measurement period. Greater increases in Tb, sometimes in excess of 5°C, were noted during the first hour post emergence, after which Tb remained relatively constant. This is consistent with observations that squirrels entered their burrows during the day to ‘offload’ heat. In addition, greater Tb amplitude values were noted in individuals inhabiting the flood plain compared with the woodland suggesting that squirrels dealt with increased environmental variability by attempting to reduce their Ta-Tb gradient. Finally, there were significant effects of age and group size on Tb with a lower and less variable Tb in younger individuals and those from larger group sizes. These data indicate that Cape ground squirrels have a labile Tb which is sensitive to a number of abiotic and biotic factors and which enables them to be active in a harsh and variable environment.
What’s in a Smile? Cultural Differences in the Effects of Smiling on Judgments of Trustworthiness

How do people detect trustworthiness in others? Some researchers have shown that research participants trust smiling faces more than non-smiling faces. We examined cultural differences in this “smile effect. ” We investigated whether three elements of a smile (smile intensity at the eyes, smile intensity at the mouth, and facial symmetry) would differently influence American and Japanese participants’ judgments of trustworthiness. In our experiment, images of 54 American and 69 Japanese male faces were initially rated for intensity of expression in the eyes and mouth, and for symmetry of the smile, by Japanese participants. The images were then presented to 142 American and 80 Japanese participants, who were asked to rate each face’s trustworthiness. The results showed that Japanese participants rated as more trustworthy faces with greater upper-half intensity and greater smile symmetry, but rated as less trustworthy faces with greater lower-half intensity. In contrast, American participants rated as more trustworthy faces with greater lower-half intensity, but there was no influence of upper-half smile intensity, nor of smile symmetry.
Biased Gene Conversion in Rhizobium etli Is Caused by Preferential Double-Strand Breaks on One of the Recombining Homologs

ABSTRACT Gene conversion, the nonreciprocal transfer of information during homologous recombination, is the main process that maintains identity between members of multigene families. Gene conversion in the nitrogenase (nifH) multigene family of Rhizobium etli was analyzed by using a two-plasmid system, where each plasmid carried a copy of nifH. One of the nifH copies was modified, creating restriction fragment length polymorphisms (RFLPs) spaced along the gene. Once the modified plasmid was introduced into R. etli, selection was done for cointegration with a resident plasmid lacking the RFLPs. Most of the cointegrate molecules harbor gene conversion events, biased toward a gain of RFLPs. This bias may be explained under the double-strand break repair model by proposing that the nifH gene lacking the RFLPs suffers a DNA double-strand break, so the incoming plasmid functions as a template for repairing the homolog on the resident plasmid. To support this proposal, we cloned an SceI site into the nifH homolog that had the RFLPs used for scoring gene conversion. In vivo expression of the meganuclease I-SceI allowed the generation of a double-strand break on this homolog. Upon introduction of this modified plasmid into an R. etli strain lacking I-SceI, biased gene conversion still favored the retention of markers on the incoming plasmid. In contrast, when the recipient strain ectopically expressed I-SceI, a dramatic reversal in gene conversion bias was seen, favoring the preservation of resident sequences. These results show that biased gene conversion is caused by preferential double-strand breaks on one of the recombining homologs. IMPORTANCE In this work, we analyzed gene conversion by using a system that entails horizontal gene transfer followed by homologous recombination in the recipient cell. Most gene conversion events are biased toward the acquisition of the incoming sequences, ranging in size from 120 bp to 800 bp. This bias is due to preferential cutting of resident DNA and can be reversed upon introduction of a double-strand break on the incoming sequence. Since conditions used in this work are similar to those in horizontal gene transfer, it provides evidence that, upon transfer, the resident DNA preferentially acquires gene variants.
The miR-106b-25 polycistron, activated by genomic amplification, functions as an oncogene by suppressing p21 and Bim.

BACKGROUND & AIMS Barrett's esophagus (BE) is a highly premalignant disease that predisposes to the development of esophageal adenocarcinoma (EAC); however, the involvement of microRNAs (miRs) in BE-EAC carcinogenic progression is not known. METHODS Esophageal cultured cells (HEEpiC, QhTRT, ChTRT, GihTRT, and OE-33) and esophageal tissues (22 normal epithelia, 24 BE, and 22 EAC) were studied. MiR microarrays and quantitative reverse-transcription polymerase chain reaction (RT-PCR) were employed to explore and verify differentially expressed miRs. Quantitative genomic PCR was performed to study copy number variation at the miR-106b-25 polycistron and MCM7 gene locus on chromosome 7q22.1. In vitro cell proliferation, cell cycle, and apoptosis assays and in vivo tumorigenesis experiments were performed to elucidate biologic effects of the miR-106b-25 polycistron. Western blotting and luciferase assays were performed to confirm direct messenger RNA (mRNA) targeting by the miR-106b-25 polycistron. RESULTS The miR-106b-25 polycistron exerted potential proliferative, antiapoptotic, cell cycle-promoting effects in vitro and tumorigenic activity in vivo. MiRs-93 and -106b targeted and inhibited p21, whereas miR-25 targeted and inhibited Bim. This polycistron was upregulated progressively at successive stages of neoplasia, in association with genomic amplification and overexpression of MCM7. In addition, miRs-93 and -106b decreased p21 mRNA, whereas miR-25 did not alter Bim mRNA, suggesting the following discrete miR effector mechanisms: (1) for p21, mRNA degradation; (2) for Bim, translational inhibition. CONCLUSIONS The miR-106b-25 polycistron is activated by genomic amplification and is potentially involved in esophageal neoplastic progression and proliferation via suppression of 2 target genes: p21 and Bim.
Secondary expansion of the transient subplate zone in the developing cerebrum of human and nonhuman primates

Significance The subplate zone, a transient cellular compartment of the embryonic cerebrum, has expanded in size and complexity during primate evolution, culminating in humans. Here, the application of multiple methods, including labeling time and place of neuronal origin and subsequent changes in their positions in macaque monkey embryos, and the use of histo- and immunochemistry in human fetal cerebral tissue of comparable prenatal ages reveals extraordinary cellular dynamics and unexpected secondary displacement of neurons. These findings may have significance for understanding cortical development and evolution and may provide insight into the pathogenesis of cortical disorders, as well as hypoxic-ischemic lesions in preterm infants. The subplate (SP) was the last cellular compartment added to the Boulder Committee’s list of transient embryonic zones [Bystron I, Blakemore C, Rakic P (2008) Nature Rev Neurosci 9(2):110–122]. It is highly developed in human and nonhuman primates, but its origin, mode, and dynamics of development, resolution, and eventual extinction are not well understood because human postmortem tissue offers only static descriptive data, and mice cannot serve as an adequate experimental model for the distinct regional differences in primates. Here, we take advantage of the large and slowly developing SP in macaque monkey to examine the origin, settling pattern, and subsequent dispersion of the SP neurons in primates. Monkey embryos exposed to the radioactive DNA replication marker tritiated thymidine ([3H]dT, or TdR) at early embryonic ages were killed at different intervals postinjection to follow postmitotic cells' positional changes. As expected in primates, most SP neurons generated in the ventricular zone initially migrate radially, together with prospective layer 6 neurons. Surprisingly, mostly during midgestation, SP cells become secondarily displaced and widespread into the expanding SP zone, which becomes particularly wide subjacent to the association cortical areas and underneath the summit of its folia. We found that invasion of monoamine, basal forebrain, thalamocortical, and corticocortical axons is mainly responsible for this region-dependent passive dispersion of the SP cells. Histologic and immunohistochemical comparison with the human SP at corresponding fetal ages indicates that the same developmental events occur in both primate species.
Convergence analysis of general neural networks under almost periodic stimuli

In this paper, we investigate the convergence dynamics of 2N almost periodic encoded patterns of general neural networks subjected to external almost periodic stimuli, including almost periodic delays. Invariant regions are established for the existence of 2N almost periodic encoded patterns under two classes of activation functions. By employing the property of ℳ︁‐cone and inequality technique, attracting basins are estimated and some criteria are derived for the networks to converge exponentially toward 2N almost periodic encoded patterns. The results obtained are new; they extend and generalize the corresponding results existing in the previous literature. Copyright © 2008 John Wiley & Sons, Ltd.
Scientific Reporting

This article is based on a presentation that was made at the 2014 annual meeting of the editorial board of Health Education & Behavior. The article addresses critical issues related to standards of scientific reporting in journals, including concerns about external and internal validity and reporting bias. It reviews current reporting guidelines, effects of adopting guidelines, and offers suggestions for improving reporting. The evidence about the effects of guideline adoption and implementation is briefly reviewed. Recommendations for adoption and implementation of appropriate guidelines, including considerations for journals, are provided.