Miracle-dz/UniFAR-FTUs huggingface dataset:
Stimuli Reduce the Dimensionality of Cortical Activity

The activity of ensembles of simultaneously recorded neurons can be represented as a set of points in the space of firing rates. Even though the dimension of this space is equal to the ensemble size, neural activity can be effectively localized on smaller subspaces. The dimensionality of the neural space is an important determinant of the computational tasks supported by the neural activity. Here, we investigate the dimensionality of neural ensembles from the sensory cortex of alert rats during periods of ongoing (intertrial) and stimulus-evoked activity. We find that dimensionality grows linearly with ensemble size, and grows significantly faster during ongoing activity compared to evoked activity. We explain these results using a spiking network model based on a clustered architecture. The model captures the difference in growth rate between ongoing and evoked activity and predicts a characteristic scaling with ensemble size that could be tested in high-density multi-electrode recordings. Moreover, we present a simple theory that predicts the existence of an upper bound on dimensionality. This upper bound is inversely proportional to the amount of pair-wise correlations and, compared to a homogeneous network without clusters, it is larger by a factor equal to the number of clusters. The empirical estimation of such bounds depends on the number and duration of trials and is well predicted by the theory. Together, these results provide a framework to analyze neural dimensionality in alert animals, its behavior under stimulus presentation, and its theoretical dependence on ensemble size, number of clusters, and correlations in spiking network models.
Functional Performance Testing in Athletes with Functional Ankle Instability

Purpose To determine if functional performance deficits are present in athletes with functional ankle instability (FAI) compared to healthy athletes using various functional performance tests. Methods Sixty two athletes (mean age-21.7±1.8years; height-168.2±9.1cm; weight-63.8±11.0kg) participated in this case control study. Athletes were divided into two groups: athletes with FAI (FAI group, n=31) and healthy athletes (Non-FAI group, n=31). The FAI group was further divided into two subgroups: FAI with giving way (FAI-GW), FAI with no giving way (FAI-NGW). Functional performance was assessed with the single-limb hopping test, figure-of-8 hop test, side-hop test, single-limb hurdle test, square hop test and single hop test. Results Significant differences (P<0.05) were observed for all the functional performance tests (FPTs) except the single hop test between FAI and Non-FAI groups; between FAI-GW, FAI-NGW and Non-FAI groups. Additionally, the involved limb performed significantly worse (P<0.05) than the contra-lateral uninvolved limb of the FAI-GW group for the above-mentioned FPTs. Conclusion Significant functional performance deficits were observed in the FAI group in all tests except single hop test with greater deficits observed in the FAI-GW group. Hence, these tests can be used to determine the presence of FAI. However no deficits were identified for the test involving sagittal plane functional activities suggesting that this test can not be used as a criterion to discriminate individuals with FAI. It was further ascertained that functional performance was not affected by limb dominance.
Posttranslational Amelogenin Processing and Changes in Matrix Assembly during Enamel Development

The extracellular tooth enamel matrix is a unique, protein-rich environment that provides the structural basis for the growth of long and parallel oriented enamel crystals. Here we have conducted a series of in vivo and in vitro studies to characterize the changes in matrix shape and organization that take place during the transition from ameloblast intravesicular matrices to extracellular subunit compartments and pericrystalline sheath proteins, and correlated these changes with stages of amelogenin matrix protein posttranslational processing. Our transmission electron microscopic studies revealed a 2.5-fold difference in matrix subunit compartment dimensions between secretory vesicle and extracellular enamel protein matrix as well as conformational changes in matrix structure between vesicles, stippled materials, and pericrystalline matrix. Enamel crystal growth in organ culture demonstrated granular mineral deposits associated with the enamel matrix framework, dot-like mineral deposits along elongating initial enamel crystallites, and dramatic changes in enamel matrix configuration following the onset of enamel crystal formation. Atomic force micrographs provided evidence for the presence of both linear and hexagonal/ring-shaped full-length recombinant amelogenin protein assemblies on mica surfaces, while nickel-staining of the N-terminal amelogenin N92 His-tag revealed 20 nm diameter oval and globular amelogenin assemblies in N92 amelogenin matrices. Western blot analysis comparing loosely bound and mineral-associated protein fractions of developing porcine enamel organs, superficial and deep enamel layers demonstrated (i) a single, full-length amelogenin band in the enamel organ followed by 3 kDa cleavage upon entry into the enamel layer, (ii) a close association of 8–16 kDa C-terminal amelogenin cleavage products with the growing enamel apatite crystal surface, and (iii) a remaining pool of N-terminal amelogenin fragments loosely retained between the crystalline phases of the deep enamel layer. Together, our data establish a temporo-spatial correlation between amelogenin protein processing and the changes in enamel matrix configuration that take place during the transition from intracellular vesicle compartments to extracellular matrix assemblies and the formation of protein coats along elongating apatite crystal surfaces. In conclusion, our study suggests that enzymatic cleavage of the amelogenin enamel matrix protein plays a key role in the patterning of the organic matrix framework as it affects enamel apatite crystal growth and habit.
Immune-system activation depletes retinal carotenoids in house finches (Carpodacus mexicanus)

SUMMARY The costs of developing, maintaining, and activating the immune system have been cited as an important force shaping life-history evolution in animals. Immunological defenses require energy, nutrients and time that might otherwise be devoted to other life-history traits like sexual displays or reproduction. Carotenoid pigments in animals provide a unique opportunity to track the costs of immune activation, because they are diet-derived, modulate the immune system, and are used to develop colorful signals of quality. Carotenoids also accumulate in the retinas of birds, where they tune spectral sensitivity and provide photoprotection. If carotenoid accumulation in the retina follows the patterns of other tissues, then immune activation may deplete retinal carotenoid levels and impact visual health and function. To test this hypothesis, we challenged molting wild-caught captive house finches (Carpodacus mexicanus) with weekly injections of lipopolysaccharide (LPS) and phytohaemagglutinin (PHA) over the course of 8 weeks. Immunostimulated adult males and females produced significant antibody responses and molted more slowly than uninjected control birds. After 8 weeks, immune-challenged birds had significantly lower levels of specific retinal carotenoid types (galloxanthin and zeaxanthin), but there were no significant differences in the plasma, liver or feather carotenoid levels between the treatment groups. These results indicate that immune-system activation can specifically deplete retinal carotenoids, which may compromise visual health and performance and represent an additional somatic and behavioral cost of immunity.
Systematic analysis of neuronal wiring of the rodent deep cerebellar nuclei reveals differences reflecting adaptations at the neuronal circuit and internuclear levels

A common view of the architecture of different brain regions is that, despite their heterogeneity, they have optimized their wiring schemes to make maximal use of space. Based on experimental findings, computational models have delineated how about two‐thirds of the neuropil is filled out with dendrites and axons optimizing cable costs and conduction time while keeping the connectivity at the highest level. However, whether this assumption can be generalized to all brain regions has not yet been tested. Here we quantified and charted the components of the neuropil in the four deep cerebellar nuclei (DCN) of the rat's brain. We segmented and traced the neuropil stained with one of two antibodies, one antibody against dendritic microtubule‐associated proteins (MAP2a,b) and the second against the Purkinje cell axons (PCP2). We compared fiber length density, average fiber diameter, and volume fraction within different components of the DCN in a random, systematic fashion. We observed differences in dendritic and axonal fiber length density, average fiber diameters, and volume fraction within the four different nuclei that make up the DCN. We observe a relative increase in the length density of dendrites and Purkinje cell axons in two of the DCN, namely, the posterior interposed nucleus and the lateral nucleus. Furthermore, the DCN have a surprisingly low volume fraction of their dendritic length density, which we propose is related to their special circuitry. In summary, our results show previously unappreciated functional adaptations among these nuclei. J. Comp. Neurol. 522:2481–2497, 2014. © 2014 Wiley Periodicals, Inc.
Fibroadenoma versus phyllodes tumor: distinguishing factors in patients diagnosed with fibroepithelial lesions after a core needle biopsy.

PURPOSE We aimed to identify factors that might help differentiate phyllodes tumors from fibroadenomas among cases in which a fibroepithelial breast lesion was diagnosed from core needle biopsy (CNB) under imaging guidance. MATERIALS AND METHODS A retrospective review was performed on 213 lesions in 200 patients who had undergone both CNB and excisional biopsy during a four-year period between 2008 and 2011. The final pathology revealed 173 fibroadenomas and 40 phyllodes tumors. The data, including patient characteristics, clinical presentation, and mammography, ultrasonography (US), and pathology findings were analyzed. RESULTS Upon univariable analysis, the factors that significantly helped to identify phyllodes tumors consisted of the presenting symptoms (palpable mass or breast pain), increased size on clinical examination, hyperdense mass on mammogram, and the following three US features: heterogeneous echo, presence of round cysts within the mass, and presence of clefts within the mass. The pathologist's suggestion of a phyllodes tumor was also helpful. The factors that remained statistically significant upon multivariable analysis consisted of symptoms of breast pain, the presence of clefts on US, the presence of round cysts on US and the pathologist's favoring of phyllodes tumors from a CNB specimen. CONCLUSION A multidisciplinary approach was needed to distinguish phyllodes tumors from fibroadenomas in patients who had undergone CNB. US findings (clefts and round cysts), suggestive pathological diagnoses, and clinical symptoms were all useful for the decision to surgically remove the fibroepithelial lesions diagnosed from CNB.
Lies and Cognition: How do we tell lies and can we detect them?

The present thesis focuses on two main areas of deception research. The first of these examines the cognitive processes involved in telling a lie and the second examines human ability to detect deception. Since deception research has historically lacked a solid theoretical basis, this work extends previous research by providing a greater theoretical understanding of both the processes involved in telling lies, and also those involved in successfully discriminating truthful messages from deceptive ones. In the first section, a simple response time paradigm is used to examine how cognitive processes differ when individuals lie compared to when they tell the truth. This paradigm is manipulated to examine the effect of a variety of different factors on potential processing differences, such as the number of lie response options available and the order of lie and truth responses. Overall, the contention that telling a lie is more cognitively demanding than telling the truth was supported. This additional cognitive load should aid in the discrimination of false and truthful messages by human observers. The second section of the thesis therefore examines individual differences in human ability to detect deception. A number of individual difference variables were examined, including extraversion and autism spectrum characteristics, allowing for the exploration of the potential relationship of these measures with both deception detection accuracy and degree of truth bias when judging the messages of individuals from different cultural backgrounds. Overall, reliable individual differences in ability levels were not found. A positive relationship between extraversion and degree of truth bias, however, was demonstrated when participants judged individuals from the same cultural background as themselves compared to a different cultural background.
Amino Acid Intakes Are Inversely Associated with Arterial Stiffness and Central Blood Pressure in Women12

Background: Although data suggest that intakes of total protein and specific amino acids (AAs) reduce blood pressure, data on other cardiovascular disease risk factors are limited. Objective: We examined associations between intakes of AAs with known mechanistic links to cardiovascular health and direct measures of arterial stiffness, central blood pressure, and atherosclerosis. Methods: In a cross-sectional study of 1898 female twins aged 18–75 y from the TwinsUK registry, intakes of 7 cardioprotective AAs (arginine, cysteine, glutamic acid, glycine, histidine, leucine, and tyrosine) were calculated from food-frequency questionnaires. Direct measures of arterial stiffness and atherosclerosis included central systolic blood pressure (cSBP), mean arterial pressure (MAP), augmentation index (AI), pulse wave velocity (PWV), and intima–media thickness (IMT). ANCOVA was used to assess the associations between endpoints of arterial stiffness and intake (per quintile), adjusting for potential confounders. Results: In multivariable analyses, higher intakes of total protein and 7 potentially cardioprotective AAs were associated with lower cSBP, MAP, and PWV. Higher intakes of glutamic acid, leucine, and tyrosine were most strongly associated with PWV, with respective differences of −0.4 ± 0.2 m/s (P-trend = 0.02), −0.4 ± 0.2 m/s (P-trend = 0.03), and −0.4 ± 0.2 m/s (P-trend = 0.03), comparing extreme quintiles. There was a significant interaction between AA intakes and protein source, and higher intakes of AAs from vegetable sources were associated with lower central blood pressure and AI. Higher intakes of glutamic acid, leucine, and tyrosine from animal sources were associated with lower PWV. Conclusions: These data provide evidence to suggest that intakes of several AAs are associated with cardiovascular benefits beyond blood pressure reduction in healthy women. The magnitude of the observed associations was similar to those previously reported for other lifestyle factors. Increasing intakes of these AAs could be an important and readily achievable way to reduce cardiovascular disease risk.
A Vaccine against Nicotine for Smoking Cessation: A Randomized Controlled Trial

Background Tobacco dependence is the leading cause of preventable death and disabilities worldwide and nicotine is the main substance responsible for the addiction to tobacco. A vaccine against nicotine was tested in a 6-month randomized, double blind phase II smoking cessation study in 341 smokers with a subsequent 6-month follow-up period. Methodology/Principal Findings 229 subjects were randomized to receive five intramuscular injections of the nicotine vaccine and 112 to receive placebo at monthly intervals. All subjects received individual behavioral smoking cessation counseling. The vaccine was safe, generally well tolerated and highly immunogenic, inducing a 100% antibody responder rate after the first injection. Point prevalence of abstinence at month 2 showed a statistically significant difference between subjects treated with Nicotine-Qβ (47.2%) and placebo (35.1%) (P = 0.036), but continuous abstinence between months 2 and 6 was not significantly different. However, in subgroup analysis of the per-protocol population, the third of subjects with highest antibody levels showed higher continuous abstinence from month 2 until month 6 (56.6%) than placebo treated participants (31.3%) (OR 2.9; P = 0.004) while medium and low antibody levels did not increase abstinence rates. After 12 month, the difference in continuous abstinence rate between subjects on placebo and those with high antibody response was maintained (difference 20.2%, P = 0.012). Conclusions Whereas Nicotine-Qβ did not significantly increase continuous abstinence rates in the intention-to-treat population, subgroup analyses of the per-protocol population suggest that such a vaccination against nicotine can significantly increase continuous abstinence rates in smokers when sufficiently high antibody levels are achieved. Immunotherapy might open a new avenue to the treatment of nicotine addiction. Trial Registration Swiss Medical Registry 2003DR2327; ClinicalTrials.gov NCT00369616
Protective effects of agonists of growth hormone-releasing hormone (GHRH) in early experimental diabetic retinopathy

Significance The studies described here are relevant to the cure of diabetic retinopathy, a leading cause of blindness with currently limited therapeutic options. Here we provided evidence showing that agonists of growth hormone-releasing hormone (GHRH) can significantly diminish retinal neurovascular injury characterizing the early stages of diabetic retinopathy through antioxidant and anti-inflammatory effects. The results of the presented studies provide information on the potential therapeutic effects of GHRH agonists and shed light on the role of hypothalamic hormones in retinal physiology and their effect on visual disorders. In addition, our findings suggest protective effects of GHRH analogs in other disease conditions affecting retinal neuronal cells and, possibly, other nonretinal neurons. The potential therapeutic effects of agonistic analogs of growth hormone-releasing hormone (GHRH) and their mechanism of action were investigated in diabetic retinopathy (DR). Streptozotocin-induced diabetic rats (STZ-rats) were treated with 15 μg/kg GHRH agonist, MR-409, or GHRH antagonist, MIA-602. At the end of treatment, morphological and biochemical analyses assessed the effects of these compounds on retinal neurovascular injury induced by hyperglycemia. The expression levels of GHRH and its receptor (GHRH-R) measured by qPCR and Western blotting were significantly down-regulated in retinas of STZ-rats and in human diabetic retinas (postmortem) compared with their respective controls. Treatment of STZ-rats with the GHRH agonist, MR-409, prevented retinal morphological alteration induced by hyperglycemia, particularly preserving survival of retinal ganglion cells. The reverse, using the GHRH antagonist, MIA-602, resulted in worsening of retinal morphology and a significant alteration of the outer retinal layer. Explaining these results, we have found that MR-409 exerted antioxidant and anti-inflammatory effects in retinas of the treated rats, as shown by up-regulation of NRF-2-dependent gene expression and down-regulation of proinflammatory cytokines and adhesion molecules. MR-409 also significantly down-regulated the expression of vascular endothelial growth factor while increasing that of pigment epithelium-derived factor in diabetic retinas. These effects correlated with decreased vascular permeability. In summary, our findings suggest a neurovascular protective effect of GHRH analogs during the early stage of diabetic retinopathy through their antioxidant and anti-inflammatory properties.
Pregnancy loss in dairy cows: the contributing factors, the effects on reproductive performance and the economic impact

This study investigated the effects of the herd, cow parity, the insemination protocol and season on the incidence of pregnancy loss (PL) in dairy herds. Furthermore, we determined the downstream effects of PL on reproductive performance and its economic impact. The overall incidence rate of PL was 6.9% in 1,001 pregnant cows and its incidence peaked (p < 0.01) during the second trimester of gestation. GLIMMIX analysis revealed that cow parity was the important risk factor for the PL. The odds ratio showed that the likelihood of PL in cows with parities of 1 or 2 was decreased by 0.6 or 0.5 fold compared to the cows with a parity of 3 or higher. Following PL, the mean rate of endometritis was 23.2% and endometritis was more common (p < 0.05) when PL occurred during the third trimester than during the first and second trimesters. The mean culling rate was 46.4% and this did not differ with the period of PL. The overall mean intervals from PL to the first service and conception were 63.4 and 101.8 days, respectively. The mean interval from PL to first service was longer (p < 0.01) for cows with PL during the third trimester than for the cows with PL during the first and second trimesters. The economic loss resulting from each PL was estimated at approximately $2,333, and this was largely due to an extended calving interval and increased culling. These results suggest that cow parity affects the incidence of PL, which extends calving interval and causes severe economic loss of dairy herds.
Influences of Endplate Removal and Bone Mineral Density on the Biomechanical Properties of Lumbar Spine

Purpose To investigate (1) effects of endplate removal and bone mineral density (BMD) on biomechanical properties of lumbar vertebrae (2) whether the distributions of mechanical strength and stiffness of endplate are affected by BMD. Methods A total of thirty-one lumbar spines (L1-L5) collected from fresh cadavers were used in this study. Bone density was measured using lateral DEXA scans and parts of samples were performed with partial or entire endplate removal. All the specimens were divided into three BMD groups. According to endplate integrity of the lumbar vertebrae, each BMD group was then divided into three subgroups: subgroup A: intact endplate; subgroup B: central region of endplate removal; subgroup C: entire endplate removal. The axial compression test was conducted with material testing system at a speed of 2mm/min. The experimental results were statistically analyzed using SPSS 17.0. Results (1) Significant differences of biomechanical properties occurred among normal BMD, osteoporotic and serious osteoporotic group (P<0.05). (2) Spearman analysis showed that BMD was positively correlated with the failure load and stiffness of lumbar vertebrae. (3) For each BMD group, significant differences of biomechanical properties were found between subgroup A and C, and between subgroup B and C (P<0.05). (4) For each BMD group, there was no statistical difference of biomechanical properties between subgroup A and B (P>0.05). Conclusions Entire endplate removal can significantly decrease the structural properties of lumbar vertebrae with little change in biomechanical properties by preservation of peripheral region of the endplate. BMD is positively correlated to the structural properties of the lumbar vertebrae.