Miracle-dz/UniFAR-FTUs huggingface dataset:
Zooplankton provide early warnings of a regime shift in a whole lake manipulation

Regime shifts are massive changes among alternate ecosystem states. Predicting regime shifts is difficult, but statistical indicators such as increasing variance or autocorrelation may provide early warnings of their impending onset. We conducted a 4 yr lake manipulation to test for early warnings prior to a food‐web transition by adding largemouth bass (Micropterus salmoides) to a lake dominated by small fishes, and thereby drive a trophic cascade that altered zooplankton biomass, community composition, and body size. Declining catches of small fishes were associated with shifts to larger bodied species of Daphnia. We measured zooplankton biomass daily in a reference and manipulated lake and calculated variance and autocorrelation of the zooplankton time series using 28 d rolling windows. We asked whether the variance in the manipulated lake (relative to the reference lake) increased and whether autocorrelation approached unity (a value suggested by theory) prior to the food‐web regime shift. The variance and autocorrelation of zooplankton biomass were similar between the two lakes in the first 2 yr of the manipulation. During the third year, variance was much higher and autocorrelation approached unity for sustained periods in the manipulated but not in the reference lake. Variance and autocorrelation were similar between the two lakes during the fourth year as the food‐web transition moved to completion. The joint response of variance and autocorrelation in year 3 provided an early warning of the food‐web transition consistent with theoretical expectation.
P instability factor: An active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases

Miniature inverted-repeat transposable elements (MITEs) are widespread and abundant in both plant and animal genomes. Despite the discovery and characterization of many MITE families, their origin and transposition mechanism are still poorly understood, largely because MITEs are nonautonomous elements with no coding capacity. The starting point for this study was P instability factor (PIF), an active DNA transposable element family from maize that was first identified following multiple mutagenic insertions into exactly the same site in intron 2 of the maize anthocyanin regulatory gene R. In this study we report the isolation of a maize Tourist-like MITE family called miniature PIF (mPIF) that shares several features with PIF elements, including identical terminal inverted repeats, similar subterminal sequences, and an unusual but striking preference for an extended 9-bp target site. These shared features indicate that mPIF and PIF elements were amplified by the same or a closely related transposase. This transposase was identified through the isolation of several PIF elements and the identification of one element (called PIFa) that cosegregated with PIF activity. PIFa encodes a putative protein with homologs in Arabidopsis, rice, sorghum, nematodes, and a fungus. Our data suggest that PIFa and these PIF-like elements belong to a new eukaryotic DNA transposon superfamily that is distantly related to the bacterial IS5 group and are responsible for the origin and spread of Tourist-like MITEs.
Comparison of the expression of 5 heat shock proteins in benign and malignant salivary gland tumor tissues

The objective of this study was to analyze the significance and potential value of heat shock proteins (HSPs) in salivary gland tumors. We found that expression of HSP60, HSP70, HSP86 and HSP84 were all upregulated in both salivary gland benign tumors and malignant tumors, and that the expression of HSP70, HSP86 and HSP84 was more greatly overexpressed in the malignant tumors (each P<0.01). For HSP27, expression was upregulated both in malignant and benign tumors, with less expression observed in malignant tumors (P<0.01). In malignant tumors, expression of HSP27 was negatively correlated with the age of the patients, size of the tumor tissue, occurrence of neural invasion and metastasis (each P<0.05). Additionally, in malignant tumors, HSP70 and HSP86 were both positively correlated with occurrence site, neural invasion and metastasis (each P<0.05), while HSP60 was only negatively correlated with the age of the patients (P<0.05). HSP86 was also positively correlated with malignant degree (P<0.01). In malignant tumors, the proliferation index (PI), which was marked by proliferating cell nuclear antigen (PCNA; PCNA-PI) was 49.95±14.569, which was significantly higher compared with that in benign tumors (P<0.001), which was in accordance with the upregulation of HSP70, HSP86 or HSP84; however, an adverse correlation was found between HSP27 expression and PCNA (each P<0.05). In conclusion, these results suggest that HSPs are involved in the occurrence and development of salivary gland tumors. HSP70, HSP86 and HSP84 retained the higher multiplication capability of the malignant tumor cells, however, HSP27 did not. Thus, the upregulation of HSP70, HSP86 and HSP84 and the downregulation of HSP27 may all be used as biomarkers of the occurrence and development of malignant salivary gland tumors. Moreover, the extremely high expression of HSP86 and HSP84 in benign tumors indicates the malignant transformation potential.
Temporal Contrast Adaptation in the Input and Output Signals of Salamander Retinal Ganglion Cells

We investigated how the light-evoked input and output signals of salamander retinal ganglion cells adapt to changes in temporal contrast, i.e., changes in the depth of the temporal fluctuations in the light intensity about the mean. Increasing the temporal contrast sped the kinetics and reduced the sensitivity of both the light-evoked input currents measured at the ganglion cell soma and the output spike trains of the cell. The decline in sensitivity of the input currents after an increase in contrast had two distinct kinetic components with fast (<2 sec) and slow (>10 sec) time constants. The recovery of sensitivity after a decrease in contrast was dominated by a single component with an intermediate (4–18 sec) time constant. Contrast adaptation differed for on and offcells, with both the kinetics and amplitude of the light-evoked currents of off cells adapting more strongly than those ofon cells. Contrast adaptation in the input currents of a ganglion cell, however, was unable to account for the extent of adaptation in the output spike trains of the cell, indicating that mechanisms intrinsic to the ganglion cell contributed. Indeed, when fluctuating currents were injected into a ganglion cell, the sensitivity of spike generation decreased with increased current variance. Pharmacological experiments indicated that adaptation of spike generation to the current variance was attributable to properties of tetrodotoxin-sensitive Na+ channels.
Effect of Analysis Window Duration on Speech Intelligibility

In this letter, we investigate the effect of the analysis window duration on speech intelligibility in a systematic way. In speech processing, the short-time magnitude spectrum is believed to contain the majority of the intelligible information. Consequently, in our experiments, we construct speech stimuli based purely on the short-time magnitude spectrum. We conduct subjective listening tests in the form of a consonant recognition task to assess intelligibility as a function of analysis window duration. In our investigations, we also employ three objective speech intelligibility measures based on the speech transmission index (STI). The experimental results show that the analysis window duration of 15-35 ms is the optimum choice when speech is reconstructed from the short-time magnitude spectrum.
Frontiers in Cellular Neuroscience Cellular Neuroscience Review Article

respectively. [Note that K K o + K i + exp(/) − = FE RT ]. At room temperature RT/F = 25 mV. Throughout the remainder of this review RT/F is replaced by 25. The value of P K derived from the results in Figure 1 is 1.25 × 10 −2 cm s −1 as compared to 1.2 × 10 −3 cm s −1 for frog node of Ranvier, the preparation in which the GHK result was fi rst demonstrated (Frankenhauser, 1962). This comparison suggests that K + is 10 times more permeable in squid giant axons relative to frog nerve (see Summary). One question which arises from these results is what is the GHK equivalent at the single channel level? K ions are believed to pass through K + selective channels in a single fi le manner along a row of three K + binding sites (Hodgkin and Keynes, 1955; Zhou et al., 2001). This result is schematically illustrated in the top left inset of Figure 2. Two sites are shown to be occupied by a K ion which is consistent with the that a K + channel contains at most a single " vacancy " and that movement of K + through the channel can be viewed as movement of the " vacancy " through the channel. The prediction of the model is (Clay, 1991) 1 2 2 25 3 25 2 25 (2) where a is the frequency of collisions of K ions with the channel, N K is the K + channel density (typically 100 µ −2 for nerve membrane, Conti et al., 1975), q is the unit electronic charge, d 1 = 0.07, and d 2 = 0.18. The parameter a is given by 9.
The origin of life: look up and look down.

Consideration of the origin of life on Earth allows us to frame some of the most profound and interesting questions in science and philosophy and tests our deepest understanding of geological, chemical, and biological principles. The origin of life challenges our ability to integrate and dissect relationships between planetary evolution, geology and conditions of early Earth, and biochemistry and biological complexity (Wills and Bada, 2001). The origin of life attracts people to science, as indicated by a large number of popular books (Davies, 2000; Smith and Szathmary, 2000; Zubay, 2000; Duve, 2002; Fenchel, 2002; Schopf, 2002; Hazen, 2005; Luisi, 2006; Yockey, 2006; Meinesz, 2008; Rauchfuss, 2008; Attenborough, 2010; Deamer, 2011) and highly visible personalities that frequent the popular press. As a scientific endeavor, the origin of life is a retracing of the transition from prebiotic to biotic, which can be accomplished in both directions, from the bottom up or from the top down (Fig. 1).
Distributional learning of vowel categories in infants and adults

Distributional learning is learning from simple exposure to the environment, without receiving explicit instruction or feedback. This thesis examines to what extent this basic form of learning contributes to learning the vowels of a language, both in infancy, when the mother tongue must be acquired, and in adulthood, when new languages can be learned. The results are based on neurophysiological (i.e., ERP or event-related potential) and behavioural experiments, and on an extensive literature review of possible neural correlates. The dissertation provides a number of insights: (1) 2-to-3-month old infants already learn from a distributional training. This means that distributional learning can contribute to the development of language-specific speech perception, which infants start showing from 6 months of life onwards; (2) Adults can also learn from a distributional training. They probably learn to use increasingly subtle cues to identify the vowels of the new language. However, the capacity for distributional learning is smaller than in infants; (3) The observed distributional training effects (both those in this dissertation and those obtained in other studies) may not be due to the number of peaks in the training distributions. Future research should determine whether a prominent other candidate factor, namely the dispersion of the distributions, is responsible for the effects instead.
Performance Measurement and Modeling to Evaluate Various Effects on a Shared Memory Multiprocessor

Shared-memory multiprocessor performance is strongly affected by factors such as sequential code, barriers, cache coherence, virtual memory paging, and the multiprocessor system itself with resource scheduling and multiprogramming. Several timing models and analysis for these effects are presented. A modified Ware model based on these timing models is given to evaluate comprehensive performance of a shared-memory multiprocessor. Performance measurement has been done on the Encore Multimax, a shared-memory multiprocessor. The evaluation models are the analyses based on a general shared-memory multiprocessor system and architecture and can be applied to other types of shared-memory multiprocessors. Analytical and experimental results give a clear understanding of the various effects and a correct measure of the performance, which are important for the effective use of a shared-memory multiprocessor. >
Schulische Suchtprävention nach dem Lebenskompetenzkonzept Ergebnisse einer vierjährigen Interventionsstudie

Ziel: Mittels einer langsschnittlichen Interventionsstudie mit 4 Messzeitpunkten, an der 675 Schuler teilnahmen, wird die suchtpraventive Wirkung des Lebenskompetenzprogramms (LKP) ALF untersucht. Methodik: »ALF  Allgemeine Lebenskompetenzen und Fertigkeiten« ist ein Manual mit dem Lehrkrafte in der 5. bis 7. Klasse in 24 Einheiten allgemeine und spezifische Fertigkeiten trainieren (z. B. Problemlosen, Standfestigkeit gegenuber Substanzangeboten) und Wissen uber Alkohol, Tabak und Drogen vermitteln. 26 Klassen wurden zufallig der Experimental- oder Kontrollbedingung zugewiesen. Die Schuler wurden per Fragebogen zu Substanzkonsum, Lehrkrafte und Schuler zu Implementation und Akzeptanz des Programms befragt. Ergebnisse: Die Programminhalte konnten fast vollstandig umgesetzt werden. Die Akzeptanz war auf Lehrer- und Schulerseite hoch. Nach der 5. Klasse war der Anteil aktueller Raucher, nach der 6. Klasse der Anteil Trunkenheitserfahrener in den ALF-Klassen signifikant niedriger als in den K.
MicroRNA involvement in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the third cause of cancer‐related death worldwide. Curative options for HCC are limited and exclusively available for patients carrying an early stage HCC. In advanced stages, traditional chemotherapy proved to be only marginally effective or even toxic. Thus, the identification of new treatment options is needed. New targets for non‐conventional treatment will necessarily take advantage of progresses on the molecular pathogenesis of HCC. MicroRNAs (miRNAs) are a group of tiny RNAs with a fundamental role in the regulation of gene expression. Aberrant expression of several miRNAs was found to be involved in human hepatocarcinogenesis. miRNA expression signatures were correlated with bio‐pathological and clinical features of HCC. In some cases, aberrantly expressed miRNAs could be linked to cancer‐associated pathways, indicating a direct role in liver tumourigenesis. For example, up‐regulation of mir‐221 and mir‐21 could promote cell cycle progression, reduce cell death and favour angiogenesis and invasion. These findings suggest that miRNAs could become novel molecular targets for HCC treatment. The demonstration of in vivo efficacy and safety of anti‐miRNA compounds has opened the way to their use in clinical trials.
Rapid, low-technology, field- and laboratory-applicable immunodiagnosis of Schistosoma mansoni

The nitrocelluloseor polystyrene-based enzyme-linked immunosorbent assays described by Rossi et al. (3), which employ the purified microsomal antigens (MA) of Schistosoma mansoni to detect S. mansoni antibodies, appear very promising. Their rapidity and simplicity and their colorimetric endpoint are indeed valuable assets. The S. mansoni MA-coated polystyrene surfaces are reported to be stable at room temperature for 6 months, while the antigen-sensitized sticks are stable for 3 weeks at 45°C. Nevertheless, further investigations to predict the field stability of various kit components in developing countries are desirable. In such areas, high ambient temperatures exceeding 40°C, marked diurnal variation in sunlight and humidity, and drought are a rule rather than an exception. Environmental rigors have been incriminated in the continuing failures of vaccines (1). Similar failures with immunodiagnostic tests for S. mansoni (3) could be prevented by deliberately exposing kit components to rough and careless handling to mimic field conditions. Only maintenance of the excellent sensitivities and specificities of such kits during rigorous treatment could be expected to prevent unpredictable disasters during their field use in areas in developing countries endemic for S. mansoni. The suitability of nitrocelluloseand polystyrene-based assays for detection of S. mansoni antibodies in blood samples collected earlier on filter paper strips should also be determined by applying dried, blood-impregnated filter papers directly to S. mansoni MA-coated strips. With the use of a mucosal transudate rather than the whole saliva, the technique might be feasible as an S. mansoni antibody screen. Liposome immunoassays, which employ antibodies conjugated to liposomes (artificial phospholipids) containing a dye (rhodamine sulfate), are available for detection of antigens in clinical specimens. They do not require a solid phase for generation of a signal by the antibody-enzyme conjugate since the signal is generated by release of rhodamine sulfate dye upon the antigen-antibody reaction (2). The S. mansoni MA-coated liposomes might prove to be more valuable than enzyme-linked immunosorbent assay reactions on nitrocellulose or polystyrene (3) for screening for S. mansoni antibodies. Liposome or enzyme-linked immunosorbent assay kits could be expected for antibody screening for S. hematobium or S. japonicum in the near future.
The RON1/FRY1/SAL1 Gene Is Required for Leaf Morphogenesis and Venation Patterning in Arabidopsis1[W][OA]

To identify genes involved in vascular patterning in Arabidopsis (Arabidopsis thaliana), we screened for abnormal venation patterns in a large collection of leaf shape mutants isolated in our laboratory. The rotunda1-1 (ron1-1) mutant, initially isolated because of its rounded leaves, exhibited an open venation pattern, which resulted from an increased number of free-ending veins. We positionally cloned the RON1 gene and found it to be identical to FRY1/SAL1, which encodes an enzyme with inositol polyphosphate 1-phosphatase and 3′ (2′),5′-bisphosphate nucleotidase activities and has not, to our knowledge, previously been related to venation patterning. The ron1-1 mutant and mutants affected in auxin homeostasis share perturbations in venation patterning, lateral root formation, root hair length, shoot branching, and apical dominance. These similarities prompted us to monitor the auxin response using a DR5-GUS auxin-responsive reporter transgene, the expression levels of which were increased in roots and reduced in leaves in the ron1-1 background. To gain insight into the function of RON1/FRY1/SAL1 during vascular development, we generated double mutants for genes involved in vein patterning and found that ron1 synergistically interacts with auxin resistant1 and hemivenata-1 but not with cotyledon vascular pattern1 (cvp1) and cvp2. These results suggest a role for inositol metabolism in the regulation of auxin responses. Microarray analysis of gene expression revealed that several hundred genes are misexpressed in ron1-1, which may explain the pleiotropic phenotype of this mutant. Metabolomic profiling of the ron1-1 mutant revealed changes in the levels of 38 metabolites, including myoinositol and indole-3-acetonitrile, a precursor of auxin.
The Hard Problem of Consciousness Studies

The question addressed by the hard problem of philosophy (3), how cognitive representation is acquired from the physical properties of self and the external, is examined from a perspective originating with Boethius(14) that knowledge is dependant on the nature of the perceiver and discussed with respect to the philosophy of George Berkeley (1,2,7) concerning the existence of matter with respect to perception. An account of the trails of history, scientific method, with respect to the naming and delineation of the hard problem suggest that its topic of address is a factor of plural elements-perceived as singular, a monism, only an aspect of its universality is perceived. A surface aspect is what seduces scientifically and, as a result, a confusion involving excessive abstraction and perceptually absent empirical fact, is postulated to accompany a false morality-an inclination to conquer it from scientific method is attributed to a seduction by naturally existing perplexity that is intermingled with unknown physical elements, themselves rooted from the same singular perplexity such that an ensuing interrogation targeted at the physical world and unavoidingly overlapping with the strictly philosophical has taken place. An invisible paper thin but sharp and self denigrating third facet to the commonly known philosophical walls, within the perplexing and the logical incongruence's, an artifact of perception and modeling of nature, results in a combined scientific (physical) and philosophical (reflective) assailing of natural paradox in a pursuit to summit human sufferings that are suggested to be, at least in part, of an unnatural and physical origin. Included as a conceptual tool is a section that discusses all possible human behavior as intuitively contained by the set of all the possible paths of nature emerged up to present and continued to emerge.
MDM2 polymorphism increases susceptibility to childhood acute myeloid leukemia: A report from the Children's Oncology Group

The variant polymorphism in the gene MDM2, SNP309, leads to increased level of mdm2 protein and subsequent downregulation of p53 tumor suppressor pathway. Presence of this single nucleotide polymorphism (SNP) has been associated with earlier tumorigenesis in patients with Li–Fraumeni syndrome, as well as decreased survival in patients with CLL. In addition, cells homozygous (G/G) for SNP 309 were found to have 10‐fold increase resistance to topoisomerase II inhibitors in vitro.
Population genetic structure in migratory sandhill cranes and the role of Pleistocene glaciations

Previous studies of migratory sandhill cranes (Grus canadensis) have made significant progress explaining evolution of this group at the species scale, but have been unsuccessful in explaining the geographically partitioned variation in morphology seen on the population scale. The objectives of this study were to assess the population structure and gene flow patterns among migratory sandhill cranes using microsatellite DNA genotypes and mitochondrial DNA haplotypes of a large sample of individuals across three populations. In particular, we were interested in evaluating the roles of Pleistocene glaciation events and postglaciation gene flow in shaping the present‐day population structure. Our results indicate substantial gene flow across regions of the Midcontinental population that are geographically adjacent, suggesting that gene flow for most of the region follows an isolation‐by‐distance model. Male‐mediated gene flow and strong female philopatry may explain the differing patterns of nuclear and mitochondrial variation. Taken in context with precise geographical information on breeding locations, the morphologic and microsatellite DNA variation shows a gradation from the Arctic‐nesting subspecies G. c. canadensis to the nonArctic subspecies G. c. tabida. Analogous to other Arctic‐nesting birds, it is probable that the population structure seen in Midcontinental sandhill cranes reflects the result of postglacial secondary contact. Our data suggest that subspecies of migratory sandhills experience significant gene flow and therefore do not represent distinct and independent genetic entities.