julilili42/papers huggingface dataset:
Dynamic sex-specific responses to synthetic songs in a duetting suboscine passerine
2018-08-29

Many bird species produce temporally coordinated duets and choruses, requiring the rapid integration of auditory perception and motor production. While males and females of some species are known to participate in these displays for sex-specific purposes, few studies have identified perceptual features that trigger sex-specific contributions of coordinated song. Especially little is known about perception and production in duetting suboscine passerines, which are thought to have innate songs and largely static, rather than dynamic, vocal behavior. Here, we used synthetic stimuli in a playback experiment on chestnut-backed antbirds (Myrmeciza exsul) to (1) test whether differences in song frequency (Hz) can trigger sex-specific vocal behavior in a suboscine passerine (2) test for the functions of duetting in males and females of this species, and (3) determine whether these suboscines can dynamically adjust the temporal and spectral features of their songs. We found sex-specific responses to synthetic playback manipulated in song frequency (Hz), providing evidence that in this context males sing in duets for general territory defense and females join in for mate guarding purposes. In addition, we found that the birds altered the frequency, duration, and timing of their songs depending on the frequency of the playback songs. Thus, we show that these birds integrate spectral and temporal information about conspecific songs and actively modulate their responses in sex-specific ways.
NFIX-Mediated Inhibition of Neuroblast Branching Regulates Migration Within the Adult Mouse Ventricular–Subventricular Zone
2018-08-29

Abstract Understanding the migration of newborn neurons within the brain presents a major challenge in contemporary biology. Neuronal migration is widespread within the developing brain but is also important within the adult brain. For instance, stem cells within the ventricular–subventricular zone (V-SVZ) and the subgranular zone of dentate gyrus of the adult rodent brain produce neuroblasts that migrate to the olfactory bulb and granule cell layer of the dentate gyrus, respectively, where they regulate key brain functions including innate olfactory responses, learning, and memory. Critically, our understanding of the factors mediating neuroblast migration remains limited. The transcription factor nuclear factor I X (NFIX) has previously been implicated in embryonic cortical development. Here, we employed conditional ablation of Nfix from the adult mouse brain and demonstrated that the removal of this gene from either neural stem and progenitor cells, or neuroblasts, within the V-SVZ culminated in neuroblast migration defects. Mechanistically, we identified aberrant neuroblast branching, due in part to increased expression of the guanylyl cyclase natriuretic peptide receptor 2 (Npr2), as a factor contributing to abnormal migration in Nfix-deficient adult mice. Collectively, these data provide new insights into how neuroblast migration is regulated at a transcriptional level within the adult brain.
An Algebraic Decision Procedure for Two-Variable Logic with a Between Relation
2018-08-29

In earlier work (LICS 2016), the authors introduced two-variable first-order logic supplemented by a binary relation that allows one to say that a letter appears between two positions. We found an effective algebraic criterion that is a necessary condition for definability in this logic, and conjectured that the criterion is also sufficient, although we proved this only in the case of two-letter alphabets. Here we prove the general conjecture. The proof is quite different from the arguments in the earlier work, and required the development of novel techniques concerning factorizations of words. We extend the results to binary relations specifying that a factor appears between two positions.
On Intrinsic Quadrics
2018-08-29

Abstract An intrinsic quadric is a normal projective variety with a Cox ring defined by a single quadratic relation. We provide explicit descriptions of these varieties in the smooth case for small Picard numbers. As applications, we figure out in this setting the Fano examples and (affirmatively) test Fujita’s freeness conjecture.
A Novel Fluorescence-Labeled Curcumin Conjugate: Synthesis, Evaluation and Imaging on Human Cell Lines
2018-08-29

Curcumin, as the main ingredient of the curcuma spice, has increasingly become the target of scientific research. The turmeric root where the spice is obtained from has been widely used in the traditional medicine. Moreover, scientific studies have found that curcumin has anti-inflammatory, anti-cancer, anti-angiogenic effects as well as antibacterial properties. Recently, curcumin has gathered interest as a potential therapeutic agent in the research on Alzheimer’s disease. A consistent problem in the investigative and therapeutic applications of curcumin is its poor solubility in aqueous solutions. In the present study, we synthesized a conjugate of curcumin, the amino acid lysine and the fluorescent dye fluorescein. This conjugate was soluble in cell culture medium and facilitated the examination of curcumin with fluorescence imaging methods. We studied the cell growth impact of unmodified curcumin on seven different human cell lines and then analyzed the uptake and cellular localization of our curcumin conjugate with confocal laser scanning imaging and flow cytometry on the seven cell lines. We found that unbound curcumin inhibited cell growth in vitro and was not taken up into the cells. The curcumin conjugate was internalized into the cell cytoplasm in a dot-like pattern and cellular uptake correlated with the cell membrane damage which was measured using propidium iodide. The CAL-72 osteosarcoma cell exhibited 3-4fold increased conjugate uptake and a strong uniform fluorescein staining in addition to the dot-like pattern observed in all cell lines. In conclusion, we successfully synthesized a novel water-soluble fluorescent curcumin conjugate which showed a strong preference for CAL-72 osteosarcoma cells in vitro.
The rod signaling pathway in marsupial retinae
2018-08-29

The retinal rod pathway, featuring dedicated rod bipolar cells (RBCs) and AII amacrine cells, has been intensely studied in placental mammals. Here, we analyzed the rod pathway in a nocturnal marsupial, the South American opossum Monodelphis domestica to elucidate whether marsupials have a similar rod pathway. The retina was dominated by rods with densities of 338,000-413,000/mm2. Immunohistochemistry for the RBC-specific marker protein kinase Cα (PKCα) and the AII cell marker calretinin revealed the presence of both cell types with their typical morphology. This is the first demonstration of RBCs in a marsupial and of the integration of RBCs and AII cells in the rod signaling pathway. Electron microscopy showed invaginating synaptic contacts of the PKCα-immunoreactive bipolar cells with rods; light microscopic co-immunolabeling for the synaptic ribbon marker CtBP2 confirmed dominant rod contacts. The RBC axon terminals were mostly located in the innermost stratum S5 of the inner plexiform layer (IPL), but had additional side branches and synaptic varicosities in strata S3 and S4, with S3-S5 belonging to the presumed functional ON sublayer of the IPL, as shown by immunolabeling for the ON bipolar cell marker Gγ13. Triple-immunolabeling for PKCα, calretinin and CtBP2 demonstrated RBC synapses onto AII cells. These features conform to the pattern seen in placental mammals, indicating a basically similar rod pathway in M. domestica. The density range of RBCs was 9,900-16,600/mm2, that of AII cells was 1,500-3,260/mm2. The numerical convergence (density ratio) of 146-156 rods to 4.7-6.0 RBCs to 1 AII cell is within the broad range found among placental mammals. For comparison, we collected data for the Australian nocturnal dunnart Sminthopsis crassicaudata, and found it to be similar to M. domestica, with rod-contacting PKCα-immunoreactive bipolar cells that had axon terminals also stratifying in IPL strata S3-S5.
A freeze-and-thaw induced-fragment of the microtubule-associated protein Tau in rat brain extracts: implications for the biochemical assessment of neurotoxicity
2018-08-29

ABSTRACT Tau is a microtubule-associated protein responsible for controlling the stabilization of microtubules in neurons. Tau function is regulated by phosphorylation. However, in some neurological diseases Tau becomes aberrantly hyperphosphorylated, which contributes to the pathogenesis of neurological diseases, known as tauopathies. Western blotting (WB) has been widely employed to determine Tau levels in neurological disease models. However, Tau quantification by WB should be interpreted with care, as this approach has been recognized as prone to produce artifactual results if not properly performed. In this study, our goal was to evaluate the influence of a freeze-and-thaw cycle, a common procedure preceding WB, to the integrity of Tau in brain homogenates from rats, 3xTg-AD mice and human samples. Homogenates were prepared in ice-cold RIPA buffer supplemented with protease/phosphatase inhibitors. Immediately after centrifugation, an aliquot of the extracts was analyzed via WB to quantify total and phosphorylated Tau levels. The remaining aliquots were stored for at least 2 weeks at either −20°C or −80°C and then subjected to WB. Extracts from rodent brains submitted to freeze-and-thaw presented a ~25 kDa fragment immunoreactive to anti-Tau antibodies. An in-gel digestion followed by mass spectrometry analysis in excised bands revealed this ~25 kDa species corresponds to a Tau fragment. Freeze-and-thaw-induced Tau proteolysis was detected even when extracts were stored at −80°C. This phenomenon was not observed in human samples at any storage condition tested. Based on these findings, we strongly recommend the use of fresh extracts of brain samples in molecular analysis of Tau levels in rodents.
Systemic control of legume susceptibility to rhizobial infection by a mobile microRNA
2018-08-30

Keeping the doors open for symbiosis Nitrogen fixation by legumes results from a symbiotic partnership between plant and microbes. These together elaborate nodules on the plant roots that house the bacteria. Tsikou et al. identified a microRNA made in the aboveground shoots of Lotus japonicus that translocates to the plant's roots. In the roots, the microRNA posttranscriptionally regulates a key suppressor of symbiosis, thus keeping the uninfected root susceptible to productive infection by symbiotic bacteria. Science , this issue p. 233
Using herbaria to study global environmental change
2018-08-30

Summary During the last centuries, humans have transformed global ecosystems. With their temporal dimension, herbaria provide the otherwise scarce long‐term data crucial for tracking ecological and evolutionary changes over this period of intense global change. The sheer size of herbaria, together with their increasing digitization and the possibility of sequencing DNA from the preserved plant material, makes them invaluable resources for understanding ecological and evolutionary species’ responses to global environmental change. Following the chronology of global change, we highlight how herbaria can inform about long‐term effects on plants of at least four of the main drivers of global change: pollution, habitat change, climate change and invasive species. We summarize how herbarium specimens so far have been used in global change research, discuss future opportunities and challenges posed by the nature of these data, and advocate for an intensified use of these ‘windows into the past’ for global change research and beyond.
Comparative Genomics Reveal a Flagellar System, a Type VI Secretion System and Plant Growth-Promoting Gene Clusters Unique to the Endophytic Bacterium Kosakonia radicincitans
2018-08-30

The recent worldwide discovery of plant growth-promoting (PGP) <i>Kosakonia radicincitans</i> in a large variety of crop plants suggests that this species confers significant influence on plants, both in terms of yield increase and product quality improvement. We provide a comparative genome analysis which helps to unravel the genetic basis for <i>K. radicincitans'</i> motility, competitiveness and plant growth-promoting capacities. We discovered that <i>K. radicincitans</i> carries multiple copies of complex gene clusters, among them two flagellar systems and three type VI secretion systems (T6SSs). We speculate that host invasion may be facilitated by different flagella, and bacterial competitor suppression by effector proteins ejected via T6SSs. We found a large plasmid in <i>K. radicincitans</i> DSM 16656<sup>T</sup>, the species type strain, that confers the potential to exploit plant-derived carbon sources. We propose that multiple copies of complex gene clusters in <i>K. radicincitans</i> are metabolically expensive but provide competitive advantage over other bacterial strains in nutrient-rich environments. The comparison of the DSM 16656<sup>T</sup> genome to genomes of other genera of enteric plant growth-promoting bacteria (PGPB) exhibits traits unique to DSM 16656<sup>T</sup> and <i>K. radicincitans</i>, respectively, and traits shared between genera. We used the output of the <i>in silico</i> analysis for predicting the purpose of genomic features unique to <i>K. radicincitans</i> and performed microarray, PhyloChip, and microscopical analyses to gain deeper insight into the interaction of DSM 16656<sup>T</sup>, plants and associated microbiota. The comparative genome analysis will facilitate the future search for promising candidates of PGPB for sustainable crop production.
The reciprocal relation between sleep and memory in infancy: Memory‐dependent adjustment of sleep spindles and spindle‐dependent improvement of memories
2018-08-30

Abstract Sleep spindle activity in infants supports their formation of generalized memories during sleep, indicating that specific sleep processes affect the consolidation of memories early in life. Characteristics of sleep spindles depend on the infant's developmental state and are known to be associated with trait‐like factors such as intelligence. It is, however, largely unknown which state‐like factors affect sleep spindles in infancy. By varying infants’ wake experience in a within‐subject design, here we provide evidence for a learning‐ and memory‐dependent modulation of infant spindle activity. In a lexical‐semantic learning session before a nap, 14‐ to 16‐month‐old infants were exposed to unknown words as labels for exemplars of unknown object categories. In a memory test on the next day, generalization to novel category exemplars was tested. In a nonlearning control session preceding a nap on another day, the same infants heard known words as labels for exemplars of already known categories. Central–parietal fast sleep spindles increased after the encoding of unknown object–word pairings compared to known pairings, evidencing that an infant's spindle activity varies depending on its prior knowledge for newly encoded information. Correlations suggest that enhanced spindle activity was particularly triggered, when similar unknown pairings were not generalized immediately during encoding. The spindle increase triggered by previously not generalized object–word pairings, moreover, boosted the formation of generalized memories for these pairings. Overall, the results provide first evidence for a fine‐tuned regulation of infant sleep quality according to current consolidation requirements, which improves the infant long‐term memory for new experiences.
Earliest evidence of caries lesion in hominids reveal sugar-rich diet for a Middle Miocene dryopithecine from Europe
2018-08-30

The formation of dental caries is mainly caused by dietary habits and therefore, may contain information for dietary reconstructions of fossil hominids. This study investigates the caries lesion in the 12.5 Ma old type specimen of Dryopithecus carinthiacus Mottl 1957 (Primates, Hominidae) from St. Stefan (Austria). Potential food sources are identified on associated palynological data, which allow conclusions about food quality, sugar availability and the hominid metabolism during the Middle Miocene. Using micro computed tomography (μCT) and scanning electron microscopy (SEM) we provide a detailed analysis and characterization of the individuals' caries type. Its lesion is compared with a dataset of 311 wild chimpanzees, indicating morphological and etiological differences in caries formation between both species. The affected molar of D. carinthiacus reveals features known from severe dental caries in humans: (1) Cavitation with steep walls and smooth surface; (2) Reparative dentine at the roof of the pulp chamber; (3) Sclerotic dentine below the cavitation; (4) Association with dental calculus and (5) Unilateral usage of the healthy right tooth row. Its advanced primary caries, initiating on the intact enamel surface, indicates a frequent intake of highly cariogenic sugar-rich fruits, which likely exceeds the frugivory of extant chimpanzees. This finding corresponds with the associated palynological record, which infers a habitat with nearly year-round supply (9-10 months/year) of high quality foods (>carbohydrates; < fibers). Our conclusions challenge the model of a step-wise increase in dietary quality during hominid evolution and support the uricase hypothesis, which discusses the hominid autapomorphy of a fructose-based fat accumulation for periods of starvation. This model receives further validation by the identification of soft-tissue preservation, interpreted as fossilized white adipose cells, in the articulated hominid skeleton of Oreopithecus bamboli from Italy.
Distinguishing black holes and naked singularities with iron line spectroscopy
2018-08-30

It is commonly thought that the final product of gravitational collapse is a black hole. Nevertheless, theoretical studies have not yet provided a final answer to the question whether black holes are the only possible outcome or whether naked singularities are also allowed. Observational tests may thus represent a complementary approach. In the present paper, we consider the Janis-Newman-Winicour metric, which describes a rotating source with a surface-like naked singularity. We calculate iron line shapes in the reflection spectrum of a putative disk around a Janis-Newman-Winicour singularity and we compare our results with the iron line shapes expected in the spectrum of a Kerr black hole. While it is difficult to distinguish the two spacetimes from the iron line shape in general, it seems that Janis-Newman-Winicour singularities cannot mimic fast-rotating Kerr black holes observed at a low or moderate inclination angle. Our analysis thus suggests that available observations of specific sources can already constrain the possible existence of Janis-Newman-Winicour singularities in the Universe.
Basics of Colour Research
2018-08-30

Colour vision is one of the fundamentals of visual perception. Contrary to popular belief, colour is not a property of objects, but rather a construction of our brain. While we have a relatively good understanding of basic processes of colour vision in the early visual pathway, there is still a considerable need for research regarding the involvement of higher brain functions as well as the diverse cultural, social and communicative functions of colours. In relation to colour perception and cultural colour preferences, it is important to study the cortical networks which are involved in memory formation, evaluation and decision-making processes from a psychophysical point of view. The latter are subject to diverse cultural influences, the complexity of which will be outlined at the end of this article using the example of the significance of colours in India and Japan. This is done to illustrate the fact that colour research should include a historico-cultural component, which can be provided by teams of researchers from different disciplines. The goal of the article is to offer the reader a short introduction into the perception of colours and to bridge the gap between the neurobiological perspective and the possible dimensions of an intercultural research approach on the symbolic context and history of colours.
A Five-MicroRNA Signature Predicts Survival and Disease Control of Patients with Head and Neck Cancer Negative for HPV Infection
2018-08-31

Abstract Purpose: Human papillomavirus (HPV)–negative head and neck squamous cell carcinoma (HNSCC) is associated with unfavorable prognosis, while independent prognostic markers remain to be defined. Experimental Design: We retrospectively performed miRNA expression profiling. Patients were operated for locally advanced HPV-negative HNSCC and had received radiochemotherapy in eight different hospitals (DKTK-ROG; n = 85). Selection fulfilled comparable demographic, treatment, and follow-up characteristics. Findings were validated in an independent single-center patient sample (LMU-KKG; n = 77). A prognostic miRNA signature was developed for freedom from recurrence and tested for other endpoints. Recursive-partitioning analysis was performed on the miRNA signature, tumor and nodal stage, and extracapsular nodal spread. Technical validation used qRT-PCR. An miRNA–mRNA target network was generated and analyzed. Results: For DKTK-ROG and LMU-KKG patients, the median follow-up was 5.1 and 5.3 years, and the 5-year freedom from recurrence rate was 63.5% and 75.3%, respectively. A five-miRNA signature (hsa-let-7g-3p, hsa-miR-6508-5p, hsa-miR-210-5p, hsa-miR-4306, and hsa-miR-7161-3p) predicted freedom from recurrence in DKTK-ROG [hazard ratio (HR) 4.42; 95% confidence interval (CI), 1.98−9.88, P &amp;lt; 0.001], which was confirmed in LMU-KKG (HR 4.24; 95% CI, 1.40−12.81, P = 0.005). The signature also predicted overall survival (HR 3.03; 95% CI, 1.50−6.12, P = 0.001), recurrence-free survival (HR 3.16; 95% CI, 1.65−6.04, P &amp;lt; 0.001), and disease-specific survival (HR 5.12; 95% CI, 1.88−13.92, P &amp;lt; 0.001), all confirmed in LMU-KKG data. Adjustment for relevant covariates maintained the miRNA signature predicting all endpoints. Recursive-partitioning analysis of both samples combined classified patients into low (n = 17), low-intermediate (n = 80), high-intermediate (n = 48), or high risk (n = 17) for recurrence (P &amp;lt; 0.001). Conclusions: The five-miRNA signature is a strong and independent prognostic factor for disease recurrence and survival of patients with HPV-negative HNSCC. See related commentary by Clump et al., p. 1441
A nuclear ribosomal DNA phylogeny of Acer inferred with maximum likelihood, splits graphs, and motif analysis of 606 sequences
2018-08-31

The multi-copy internal transcribed spacer (ITS) region of nuclear ribosomal DNA is widely used to infer phylogenetic relationships among closely related taxa. Here we use maximum likelihood (ML) and splits graph analyses to extract phylogenetic information from approximately 600 mostly cloned ITS sequences, representing 81 species and subspecies of Acer, and both species of its sister Dipteronia. Additional analyses compared sequence motifs in Acer and several hundred Anacardiaceae, Burseraceae, Meliaceae, Rutaceae, and Sapindaceae ITS sequences in GenBank. We also assessed the effects of using smaller data sets of consensus sequences with ambiguity coding (accounting for within-species variation) instead of the full (partly redundant) original sequences. Neighbor-nets and bipartition networks were used to visualize conflict among character state patterns. Species clusters observed in the trees and networks largely agree with morphology-based classifications; of de Jong's (1994) 16 sections, nine are supported in neighbor-net and bipartition networks, and ten by sequence motifs and the ML tree; of his 19 series, 14 are supported in networks, motifs, and the ML tree. Most nodes had higher bootstrap support with matrices of 105 or 40 consensus sequences than with the original matrix. Within-taxon ITS divergence did not differ between diploid and polyploid Acer, and there was little evidence of differentiated parental ITS haplotypes, suggesting that concerted evolution in Acer acts rapidly.