Nominalization and alternations in biomedical language

Background

This paper presents data on alternations in the argument structure of common domain-specific verbs and their associated verbal nominalizations in the PennBioIE corpus. Alternation is the term in theoretical linguistics for variations in the surface syntactic form of verbs, e.g. the different forms of stimulate in FSH stimulates follicular development and follicular development is stimulated by FSH. The data is used to assess the implications of alternations for biomedical text mining systems and to test the fit of the sublanguage model to biomedical texts.

Methodology/Principal Findings

We examined 1,872 tokens of the ten most common domain-specific verbs or their zero-related nouns in the PennBioIE corpus and labelled them for the presence or absence of three alternations. We then annotated the arguments of 746 tokens of the nominalizations related to these verbs and counted alternations related to the presence or absence of arguments and to the syntactic position of non-absent arguments. We found that alternations are quite common both for verbs and for nominalizations. We also found a previously undescribed alternation involving an adjectival present participle.

Conclusions/Significance

We found that even in this semantically restricted domain, alternations are quite common, and alternations involving nominalizations are exceptionally diverse. Nonetheless, the sublanguage model applies to biomedical language. We also report on a previously undescribed alternation involving an adjectival present participle.     

Spontaneous Sleep-Like Brain State Alternations and Breathing Characteristics in Urethane Anesthetized Mice

Brain state alternations resembling those of sleep spontaneously occur in rats under urethane anesthesia and they are closely linked with sleep-like respiratory changes. Although rats are a common model for both sleep and respiratory physiology, we sought to determine if similar brain state and respiratory changes occur in mice under urethane. We made local field potential recordings from the hippocampus and measured respiratory activity by means of EMG recordings in intercostal, genioglossus, and abdominal muscles. Similar to results in adult rats, urethane anesthetized mice displayed quasi-periodic spontaneous forebrain state alternations between deactivated patterns resembling slow wave sleep (SWS) and activated patterns resembling rapid eye movement (REM) sleep. These alternations were associated with an increase in breathing rate, respiratory variability, a depression of inspiratory related activity in genioglossus muscle and an increase in expiratory-related abdominal muscle activity when comparing deactivated (SWS-like) to activated (REM-like) states. These results demonstrate that urethane anesthesia consistently induces sleep-like brain state alternations and correlated changes in respiratory activity across different rodent species. They open up the powerful possibility of utilizing transgenic mouse technology for the advancement and translation of knowledge regarding sleep cycle alternations and their impact on respiration.     

Balance between noise and adaptation in competition models of perceptual bistability

Perceptual bistability occurs when a physical stimulus gives rise to two distinct interpretations that alternate irregularly. Noise and adaptation processes are two possible mechanisms for switching in neuronal competition models that describe the alternating behaviors. Either of these processes, if strong enough, could alone cause the alternations in dominance. We examined their relative role in producing alternations by studying models where by smoothly varying the parameters, one can change the rhythmogenesis mechanism from being adaptation-driven to noise-driven. In consideration of the experimental constraints on the statistics of the alternations (mean and shape of the dominance duration distribution and correlations between successive durations) we ask whether we can rule out one of the mechanisms. We conclude that in order to comply with the observed mean of the dominance durations and their coefficient of variation, the models must operate within a balance between the noise and adaptation strength—both mechanisms are involved in producing alternations, in such a way that the system operates near the boundary between being adaptation-driven and noise-driven.     

Modeling Consonant-Vowel Coarticulation for Articulatory Speech Synthesis

A central challenge for articulatory speech synthesis is the simulation of realistic articulatory movements, which is critical for the generation of highly natural and intelligible speech. This includes modeling coarticulation, i.e., the context-dependent variation of the articulatory and acoustic realization of phonemes, especially of consonants. Here we propose a method to simulate the context-sensitive articulation of consonants in consonant-vowel syllables. To achieve this, the vocal tract target shape of a consonant in the context of a given vowel is derived as the weighted average of three measured and acoustically-optimized reference vocal tract shapes for that consonant in the context of the corner vowels /a/, /i/, and /u/. The weights are determined by mapping the target shape of the given context vowel into the vowel subspace spanned by the corner vowels. The model was applied for the synthesis of consonant-vowel syllables with the consonants /b/, /d/, /g/, /l/, /r/, /m/, /n/ in all combinations with the eight long German vowels. In a perception test, the mean recognition rate for the consonants in the isolated syllables was 82.4%. This demonstrates the potential of the approach for highly intelligible articulatory speech synthesis.     

Unusual alternations of floral organs in Paeonia: structure and possible mechanism of formation

Morphological analysis of flowers was carried out in Paeonia cultivars. Some unusual alternations of floral organs were described: sepal-(petal-stamen) x N-carpel, where 2 < or = n < or = 4 (appearance of an additional zone of petal and stamen formation in the medial flower part). The identity of floral organs was not affected in the flowers with this unusual alternation. It was shown on the basis of mathematical simulation of the genes responsible for flower development that these alternations may be determined by increased pool of stem cells, which may lead to delayed termination of flower development.     

The biopolymer metabolism of the connective tissue in the aorta under intraventricular injections of neuropeptides]

The metabolism of connective tissue biopolymers in the blood serum and in the aorta under repeated intraventricular injections of P-substance, L-enkephalin and B-endorphine was studied in chronic experiments on rabbits. The alternations of the central neurochemical processes, caused by prolonged intraventricular injections of neuropeptides were proved to lead to intensification of metabolic processes in the connective tissue characterized by the accumulation of its biopolymers in the aorta wall. The injection of P-substance, in contrast to opioid peptides, is accompanied by more marked alternations.     

Cyclic and sleep-like spontaneous alternations of brain state under urethane anaesthesia

Background

Although the induction of behavioural unconsciousness during sleep and general anaesthesia has been shown to involve overlapping brain mechanisms, sleep involves cyclic fluctuations between different brain states known as active (paradoxical or rapid eye movement: REM) and quiet (slow-wave or non-REM: nREM) stages whereas commonly used general anaesthetics induce a unitary slow-wave brain state.

Methodology/Principal Findings

Long-duration, multi-site forebrain field recordings were performed in urethane-anaesthetized rats. A spontaneous and rhythmic alternation of brain state between activated and deactivated electroencephalographic (EEG) patterns was observed. Individual states and their transitions resembled the REM/nREM cycle of natural sleep in their EEG components, evolution, and time frame (∼11 minute period). Other physiological variables such as muscular tone, respiration rate, and cardiac frequency also covaried with forebrain state in a manner identical to sleep. The brain mechanisms of state alternations under urethane also closely overlapped those of natural sleep in their sensitivity to cholinergic pharmacological agents and dependence upon activity in the basal forebrain nuclei that are the major source of forebrain acetylcholine. Lastly, stimulation of brainstem regions thought to pace state alternations in sleep transiently disrupted state alternations under urethane.

Conclusions/Significance

Our results suggest that urethane promotes a condition of behavioural unconsciousness that closely mimics the full spectrum of natural sleep. The use of urethane anaesthesia as a model system will facilitate mechanistic studies into sleep-like brain states and their alternations. In addition, it could also be exploited as a tool for the discovery of new molecular targets that are designed to promote sleep without compromising state alternations.     

Induction of oscillatory ventilation pattern using dynamic modulation of heart rate through a pacemaker

For disease states characterized by oscillatory ventilation, an ideal dynamic therapy would apply a counteracting oscillation in ventilation. Modulating respiratory gas transport through the circulation might allow this. We explore the ability of repetitive alternations in heart rate, using a cardiac pacemaker, to elicit oscillations in respiratory variables and discuss the potential for therapeutic exploitation. By incorporating acute cardiac output manipulations into an integrated mathematical model, we observed that a rise in cardiac output should yield a gradual rise in end-tidal CO2 and, subsequently, ventilation. An alternating pattern of cardiac output might, therefore, create oscillations in CO2 and ventilation. We studied the effect of repeated alternations in heart rate of 30 beats/min with periodicity of 60 s, on cardiac output, respiratory gases, and ventilation in 22 subjects with implanted cardiac pacemakers and stable breathing patterns. End-tidal CO2 and ventilation developed consistent oscillations with a period of 60 s during the heart rate alternations, with mean peak-to-trough relative excursions of 8.4 +/- 5.0% (P < 0.0001) and 24.4 +/- 18.8% (P < 0.0001), respectively. Furthermore, we verified the mathematical prediction that the amplitude of these oscillations would depend on those in cardiac output (r = 0.59, P = 0.001). Repetitive alternations in heart rate can elicit reproducible oscillations in end-tidal CO2 and ventilation. The size of this effect depends on the magnitude of the cardiac output response. Harnessed and timed appropriately, this cardiorespiratory mechanism might be exploited to create an active dynamic responsive pacing algorithm to counteract spontaneous respiratory oscillations, such as those causing apneic breathing disorders.     

The formation of micritic limestones and the development of limestone-marl alternations in the Silurian of Gotland,Sweden

Summary Micritic limestone-marl alternations make up the major part of the Silurian strata on Gotland (Sweden). Their position on the stable Baltic Shield protected them from deep burial and tectonic stress and allowed the preservation of early stages of burial diagenesis, including lithification. In the micritic limestones certain characteristics have been preserved (e.g., pitted microspar crystals, sharp boundaries between microspar and components, lack of deformation phenomena) that offer insights into their formation. We suppose the formation of these micritic limestones and limestone-marl alternations to be based on a rhythmic diagenesis within an aragonite solution zone (ASZ) close below the sediment surface. The micritic limestones are the product of a poikilotopic cementation of carbonate muds which consisted of varying portions of aragonitic, calcitic and terrigenous matter. Their microspar crystals show the primary size and shape of the cements lithifying the original carbonate mud. Dissolution of aragonite in the marls provided the carbonate for the lithification of the limestones. By cementation, the limestone beds evaded further compaction. The marls, which already underwent a volume decrease by aragonite depletion, lacked cement and became more and more compacted due to increasing sedimentary overburden. Although field observations show that primary differences in material influence the development of limestone-marl alternations they are not required for their formation.     

Graphemic alternations in English as a reflex of morphological structure

Graphemic alternations such as <y>-replacement (e.g. <lady–ladies>) are obligatory in inflectional processes, but they do not occur in compounding (cf. <ladybug, *ladibug>). In derivational processes, the obligatoriness varies depending on the suffix (cf. <happiness, puppydom>). This variation in graphemic alternations is used to determine the juncture strength of derivational products. On the basis of the 450 million word Corpus of Contemporary American English (CoCA), 46 suffixes are investigated. The resulting scale is found to correlate closely with the type parsing ratio from Hay and Baayen (in Yearbook of Morphology 2001, pp. 203–235, 2002), a purely morphological measure. As the graphemic alternations investigated are not mirrored in phonology, the results are taken to be an argument for a partly autonomous writing system that can in turn be used to argue for or against morphological structure, quite like phonological sandhi or liaison phenomena.     

Binaral Rivalry in the Presence of Visual Perceptual and Semantic Influences

When two different odorants are presented simultaneously to the two nostrils, we experience alternations in olfactory percepts, a phenomenon called binaral rivalry. Little is known about the nature of such alternations. Here we investigate this issue by subjecting unstable and stable olfactory percepts to the influences of visual perceptual or semantic cues as participants engage in simultaneous samplings of either two different odorants (binaral) or a single odorant and water (mononaral), one to each nostril. We show that alternations of olfactory percepts in the binaral setting persist in the presence of visual perceptual and semantic modulations. We also show that perceptual cues have a stronger effect than semantic cues in the binaral case, whereas their effects are comparable in the mononaral setting. Our findings provide evidence that an inherent, stimulus-driven process underlies binaral rivalry despite its general susceptibility to top-down influences.     

Ca2+-activated chloride channel activity during Ca2+ alternans in ventricular myocytes

Cardiac alternans, defined beat-to-beat alternations in contraction, action potential (AP) morphology or cytosolic Ca transient (CaT) amplitude, is a high risk indicator for cardiac arrhythmias. We investigated mechanisms of cardiac alternans in single rabbit ventricular myocytes. CaTs were monitored simultaneously with membrane currents or APs recorded with the patch clamp technique. A strong correlation between beat-to-beat alternations of AP morphology and CaT alternans was observed. During CaT alternans application of voltage clamp protocols in form of pre-recorded APs revealed a prominent Ca²⁺-dependent membrane current consisting of a large outward component coinciding with AP phases 1 and 2, followed by an inward current during AP repolarization. Approximately 85% of the initial outward current was blocked by Cl^? channel blocker DIDS or lowering external Cl^? concentration identifying it as a Ca²⁺-activated Cl^? current (I_CaCC). The data suggest that I_CaCC plays a critical role in shaping beat-to-beat alternations in AP morphology during alternans.     

Interhemispheric switching mediates perceptual rivalry

BACKGROUND: Binocular rivalry refers to the alternating perceptual states that occur when the images seen by the two eyes are too different to be fused into a single percept. Logothetis and colleagues have challenged suggestions that this phenomenon occurs early in the visual pathway. They have shown that, in alert monkeys, neurons in the primary visual cortex continue to respond to their preferred stimulus despite the monkey reporting its absence. Moreover, they found that neural activity higher in the visual pathway is highly correlated with the monkey's reported percept. These and other findings suggest that the neural substrate of binocular rivalry must involve high levels, perhaps the same levels involved in reversible figure alternations. RESULTS: We present evidence that activation or disruption of a single hemisphere in human subjects affects the perceptual alternations of binocular rivalry. Unilateral caloric vestibular stimulation changed the ratio of time spent in each competing perceptual state. Transcranial magnetic stimulation applied to one hemisphere disrupted normal perceptual alternations when the stimulation was timed to occur at one phase of the perceptual switch, but not at the other. Furthermore, activation of a single hemisphere by caloric stimulation affected the perceptual alternations of a reversible figure, the Necker cube. CONCLUSIONS: Our findings suggest that interhemispheric switching mediates perceptual rivalry. Thus, competition for awareness in both binocular rivalry and reversible figures occurs between, rather than within, each hemisphere. This interhemispheric switch hypothesis has implications for understanding the neural mechanisms of conscious experience and also has clinical relevance as the rate of both types of perceptual rivalry is slow in bipolar disorder (manic depression).     

Unusual alternations of floral organs in <Emphasis Type="Italic">Paeonia</Emphasis>: Structure and possible mechanism of formation

Morphological analysis of flowers was carried out in Paeonia L. cultivars. Some unusual alternations of floral organs were described: sepal-(petal-stamen) × n-carpel, where 2 ≤ n ≤ 4 (appearance of an additional zone of petal and stamen formation in the medial flower part). The identity of floral organs was not affected in the flowers with this unusual alternation. It was shown on the basis of mathematical simulation of the genes responsible for flower development that these alternations may be determined by increased pool of stem cells, which may lead to delayed termination of flower development.     

SARS-CoV-2 and the Nucleus

The ongoing COVID-19 pandemic is caused by an RNA virus, SARS-CoV-2. The genome of SARS-CoV-2 lacks a nuclear phase in its life cycle and is replicated in the cytoplasm. However, interfering with nuclear trafficking using pharmacological inhibitors greatly reduces virus infection and virus replication of other coronaviruses is blocked in enucleated cells, suggesting a critical role of the nucleus in virus infection. Here, we summarize the alternations of nuclear pathways caused by SARS-CoV-2, including nuclear translocation pathways, innate immune responses, mRNA metabolism, epigenetic mechanisms, DNA damage response, cytoskeleton regulation, and nuclear rupture. We consider how these alternations contribute to virus replication and discuss therapeutic treatments that target these pathways, focusing on small molecule drugs that are being used in clinical studies.     

Visual perception of ambiguous figures: synchronization based neural models

We develop and study two neural network models of perceptual alternations. Both models have a star-like architecture of connections with a central element connected to a set of peripheral elements. A particular perception is simulated in terms of partial synchronization between the central element and some sub-group of peripheral elements. The first model is constructed from phase oscillators and the mechanism of perceptual alternations is based on chaotic intermittency under fixed parameter values. Similar to experimental evidence, the distribution of times between perceptual alternations is represented by the gamma distribution. The second model is built of spiking neurons of the Hodgkin–Huxley type. The mechanism of perceptual alternations is based on plasticity of inhibitory synapses which increases the inhibition from the central unit to the neural assembly representing the current percept. As a result another perception is formed. Simulations show that the second model is in good agreement with behavioural data on switching times between percepts of ambiguous figures and with experimental results on binocular rivalry of two and four percepts. This article is part of a special issue on Neuronal Dynamics of Sensory Coding. This special issue is in honour of Professor Pepe Segundo who is one of the pioneers in the study of neural coding. Pepe has been an active participant in many Neural Coding Workshops sharing his great knowledge and experience of research in this field. I (R. Borisyuk) was very happy to meet Pepe for the first time in Prague when attending the first Neural Coding Workshop in 1995. From that time we regularly met at Neural Coding Workshops and these meetings have always been very stimulating and fruitful for my research. Remarkably, the first paper I studied at the beginning of my scientific career was a seminal paper by Moore et al. (1970). For me, this paper provided a great opportunity to learn the basic statistical techniques for the analysis of multiple spike trains and neural coding. According to the Institute of Scientific Information, this paper has been cited 380 times! This exciting paper has inspired my research into the synaptic and functional connectivity of neural circuits derived from spike-train recordings (Borisyuk et al. 1985; Stuart et al. 2005) and guided my search for new ideas on neural coding.     

Temporal dynamics of auditory and visual bistability reveal common principles of perceptual organization

When dealing with natural scenes, sensory systems have to process an often messy and ambiguous flow of information. A stable perceptual organization nevertheless has to be achieved in order to guide behavior. The neural mechanisms involved can be highlighted by intrinsically ambiguous situations. In such cases, bistable perception occurs: distinct interpretations of the unchanging stimulus alternate spontaneously in the mind of the observer. Bistable stimuli have been used extensively for more than two centuries to study visual perception. Here we demonstrate that bistable perception also occurs in the auditory modality. We compared the temporal dynamics of percept alternations observed during auditory streaming with those observed for visual plaids and the susceptibilities of both modalities to volitional control. Strong similarities indicate that auditory and visual alternations share common principles of perceptual bistability. The absence of correlation across modalities for subject-specific biases, however, suggests that these common principles are implemented at least partly independently across sensory modalities. We propose that visual and auditory perceptual organization could rely on distributed but functionally similar neural competition mechanisms aimed at resolving sensory ambiguities.     

Evidence for perceptual "trapping" and adaptation in multistable binocular rivalry

When a different pattern is presented to each eye, the perceived image spontaneously alternates between the two patterns (binocular rivalry); the dynamics of these bistable alternations are known to be stochastic. Examining multistable binocular rivalry (involving four dominant percepts), we demonstrated path dependence and on-line adaptation, which were equivalent whether perceived patterns were formed by single-eye dominance or by mixed-eye dominance. The spontaneous perceptual transitions tended to get trapped within a pair of related global patterns (e.g., opponent shapes and symmetric patterns), and during such trapping, the probability of returning to the repeatedly experienced patterns gradually decreased (postselection pattern adaptation). These results suggest that the structure of global shape coding and its adaptation play a critical role in directing spontaneous alternations of visual awareness in perceptual multistability.     

The Effect on the Growth of Sclerotinia fructigena of Alternating Periods of Light and Darkness of Equal Length

Apparatus has been designed to enable Sclerotinia fructigenato be grown at a constant temperature and under various equalalternating periods of light and darkness ranging from alternationsof 0·3 second to twelve hours. Diameters of the fungalcolonies were determined after three days' growth in the apparatus. In darkness and in twelve-hourly alternations the fungus producedan irregular colony, in the latter case showing some zonation.Under all other conditions the growth was regular. Growth wasslowest in total darkness, and faster in continuous light thanin twelve-hourly alternations. The rate of spread under twelve-hourlyalternations was slower than with any other of the alternatingtreatments. With the shortening of the period of alternationthe growth increased. It reached a maximum at about one-minutealternations, decreased to a minimum at five-second alternations,and subsequently rose again. The effect of alternating light of different periodicities onthe growth rate of the fungus is compared with its effect onchlorophyllous plants. It is concluded that the effect of alternatinglight on the growth of plants cannot be interpreted solely byits influence on the photosynthetic mechanism, but that in additionthere is an action on some photochemical mechanism present innon-green plants or there is some direct effect of light onthe protoplasm. In conclusion it gives me much pleasure to express my appreciationof the interest and criticism which Professor V. H. Blackmanhas shown during the course of these experiments.     

Alternate muscle activity observed between knee extensor synergists during low-level sustained contractions.

To determine quantitatively the features of alternate muscle activity between knee extensor synergists during low-level prolonged contraction, a surface electromyogram (EMG) was recorded from the rectus femoris (RF), vastus lateralis (VL), and vastus medialis (VM) in 11 subjects during isometric knee extension exercise at 2.5% of maximal voluntary contraction (MVC) for 60 min (experiment 1). Furthermore, to examine the relation between alternate muscle activity and contraction levels, six of the subjects also performed sustained knee extension at 5.0, 7.5, and 10.0% of MVC (experiment 2). Alternate muscle activity among the three muscles was assessed by quantitative analysis on the basis of the rate of integrated EMG sequences. In experiment 1, the number of alternations was significantly higher between RF and either VL or VM than between VL and VM. Moreover, the frequency of alternate muscle activity increased with time. In experiment 2, alternating muscle activity was found during contractions at 2.5 and 5.0% of MVC, although not at 7.5 and 10.0% of MVC, and the number of alternations was higher at 2.5 than at 5.0% of MVC. Thus the findings of the present study demonstrated that alternate muscle activity in the quadriceps muscle 1) appears only between biarticular RF muscle and monoarticular vasti muscles (VL and VM), and its frequency of alternations progressively increases with time, and 2) emerges under sustained contraction with force production levels < or =5.0% of MVC.