Interactions among Toxins That Inhibit N-type and P-type Calcium Channels

A number of peptide toxins from venoms of spiders and cone snails are high affinity ligands for voltage-gated calcium channels and are useful tools for studying calcium channel function and structure. Using whole-cell recordings from rat sympathetic ganglion and cerebellar Purkinje neurons, we studied toxins that target neuronal N-type (CaV2.2) and P-type (CaV2.1) calcium channels. We asked whether different toxins targeting the same channels bind to the same or different sites on the channel. Five toxins (ω-conotoxin-GVIA, ω-conotoxin MVIIC, ω-agatoxin-IIIA, ω-grammotoxin-SIA, and ω-agatoxin-IVA) were applied in pairwise combinations to either N- or P-type channels. Differences in the characteristics of inhibition, including voltage dependence, reversal kinetics, and fractional inhibition of current, were used to detect additive or mutually occlusive effects of toxins. Results suggest at least two distinct toxin binding sites on the N-type channel and three on the P-type channel. On N-type channels, results are consistent with blockade of the channel pore by ω-CgTx-GVIA, ω-Aga-IIIA, and ω-CTx-MVIIC, whereas grammotoxin likely binds to a separate region coupled to channel gating. ω-Aga-IIIA produces partial channel block by decreasing single-channel conductance. On P-type channels, ω-CTx-MVIIC and ω-Aga-IIIA both likely bind near the mouth of the pore. ω-Aga-IVA and grammotoxin each bind to distinct regions associated with channel gating that do not overlap with the binding region of pore blockers. For both N- and P-type channels, ω-CTx-MVIIC binding produces complete channel block, but is prevented by previous partial channel block by ω-Aga-IIIA, suggesting that ω-CTx-MVIIC binds closer to the external mouth of the pore than does ω-Aga-IIIA

Filter Bank Design based on Minimization of Individual Aliasing Terms for Minimum Mutual Information Subband Adaptive Beamforming

This paper presents new filter bank design methods for sub- band adaptive beamforming. In this work, we design analysis and synthesis prototypes for modulated filter banks so as to minimize each aliasing term individually. We then drive the total response error to null by constraining these prototypes to be Nyquist(M) filters. Thereafter those modulated filter banks are applied to a speech separation system which extracts a target speech signal. In our system, speech signals are first transformed into the subband domain with our filter banks, and the subband components are then processed with a beamforming algorithm. Following beamforming, post-filtering and binary masking are further performed to remove residual noises. We show that our filter banks can suppress the residual aliasing distortion more than conventional ones. Furthermore, we demonstrate the effectiveness of our design techniques through a set of automatic speech recognition experiments on the multi-channel speech data from the PASCAL Speech Separation Challenge. The experimental results prove that our beamforming system with the proposed filter banks achieves the best recognition performance, a 39.6 % word error rate (WER), with half the amount of computation of that of the conventional filter banks while the perfect reconstruction filter banks provided a 44.4 % WER

Filter Bank Design for Subband Adaptive Beamforming and Application to Speech Recognition

\begin{abstract} We present a new filter bank design method for subband adaptive beamforming. Filter bank design for adaptive filtering poses many problems not encountered in more traditional applications such as subband coding of speech or music. The popular class of perfect reconstruction filter banks is not well-suited for applications involving adaptive filtering because perfect reconstruction is achieved through alias cancellation, which functions correctly only if the outputs of individual subbands are \emph{not} subject to arbitrary magnitude scaling and phase shifts. In this work, we design analysis and synthesis prototypes for modulated filter banks so as to minimize each aliasing term individually. We then show that the \emph{total response error} can be driven to zero by constraining the analysis and synthesis prototypes to be \emph{Nyquist($M$)} filters. We show that the proposed filter banks are more robust for aliasing caused by adaptive beamforming than conventional methods. Furthermore, we demonstrate the effectiveness of our design technique through a set of automatic speech recognition experiments on the multi-channel, far-field speech data from the \emph{PASCAL Speech Separation Challenge}. In our system, speech signals are first transformed into the subband domain with the proposed filter banks, and thereafter the subband components are processed with a beamforming algorithm. Following beamforming, post-filtering and binary masking are performed to further enhance the speech by removing residual noise and undesired speech. The experimental results prove that our beamforming system with the proposed filter banks achieves the best recognition performance, a 39.6\% word error rate (WER), with half the amount of computation of that of the conventional filter banks while the perfect reconstruction filter banks provided a 44.4\% WER. \end{abstract

Applications of various range shifters for proton pencil beam scanning radiotherapy

Background A range pull-back device, such as a machine-related range shifter (MRS) or a universal patient-related range shifter (UPRS), is needed in pencil beam scanning technique to treat shallow tumors. Methods Three UPRS made by QFix (Avondale, PA, USA) allow treating targets across the body: U-shaped bolus (UB), anterior lateral bolus (ALB), and couch top bolus. Head-and-neck (HN) patients who used the UPRS were tested. The in-air spot sizes were measured and compared in this study at air gaps: 6 cm, 16 cm, and 26 cm. Measurements were performed in a solid water phantom using a single-field optimization pencil beam scanning field with the ALB placed at 0, 10, and 20 cm air gaps. The two-dimensional dose maps at the middle of the spread-out Bragg peak were measured using ion chamber array MatriXX PT (IBA-Dosimetry, Schwarzenbruck, Germany) located at isocenter and compared with the treatment planning system. Results A UPRS can be consistently placed close to the patient and maintains a relatively small spot size resulting in improved dose distributions. However, when a UPRS is non-removable (e.g. thick couch top), the quality of volumetric imaging is degraded due to their high Z material construction, hindering the value of Image-Guided Radiation Therapy (IGRT). Limitations of using UPRS with small air gaps include reduced couch weight limit, potential collision with patient or immobilization devices, and challenges using non-coplanar fields with certain UPRS. Our experience showed the combination of a U-shaped bolus exclusively for an HN target and an MRS as the complimentary device for head-and-neck targets as well as for all other treatment sites may be ideal to preserve the dosimetric advantages of pencil beam scanning proton treatments across the body. Conclusion We have described how to implement UPRS and MRS for various clinical indications using the PBS technique, and comprehensively reviewed the advantage and disadvantages of UPRS and MRS. We recommend the removable UB only to be employed for the brain and HN treatments while an automated MRS is used for all proton beams that require RS but not convenient or feasible to use UB

To separate speech! a system for recognizing simultaneous speech

Abstract. The PASCAL Speech Separation Challenge (SSC) is based on a corpus of sentences from the Wall Street Journal task read by two speakers simultaneously and captured with two circular eight-channel microphone arrays. This work describes our system for the recognition of such simultaneous speech. Our system has four principal components: A person tracker returns the locations of both active speakers, as well as segmentation information for each utterance, which are often of unequal length; two beamformers in generalized sidelobe canceller (GSC) configuration separate the simultaneous speech by setting their active weight vectors according to a minimum mutual information (MMI) criterion; a postfilter and binary mask operating on the outputs of the beamformers further enhance the separated speech; and finally an automatic speech recognition (ASR) engine based on a weighted finite-state transducer (WFST) returns the most likely word hypotheses for the separated streams. In addition to optimizing each of these components, we investigated the effect of the filter bank design used to perform subband analysis and synthesis during beamforming. On the SSC development data, our system achieved a word error rate of 39.6%

Scientific concepts and methods for moving persistence assessments into the 21st century

The evaluation of a chemical substance's persistence is key to understanding its environmental fate, exposure concentration, and, ultimately, environmental risk. Traditional biodegradation test methods were developed many years ago for soluble, nonvolatile, single-constituent test substances, which do not represent the wide range of manufactured chemical substances. In addition, the Organisation for Economic Co-operation and Development (OECD) screening and simulation test methods do not fully reflect the environmental conditions into which substances are released and, therefore, estimates of chemical degradation half-lives can be very uncertain and may misrepresent real environmental processes. In this paper, we address the challenges and limitations facing current test methods and the scientific advances that are helping to both understand and provide solutions to them. Some of these advancements include the following: (1) robust methods that provide a deeper understanding of microbial composition, diversity, and abundance to ensure consistency and/or interpret variability between tests; (2) benchmarking tools and reference substances that aid in persistence evaluations through comparison against substances with well-quantified degradation profiles; (3) analytical methods that allow quantification for parent and metabolites at environmentally relevant concentrations, and inform on test substance bioavailability, biochemical pathways, rates of primary versus overall degradation, and rates of metabolite formation and decay; (4) modeling tools that predict the likelihood of microbial biotransformation, as well as biochemical pathways; and (5) modeling approaches that allow for derivation of more generally applicable biotransformation rate constants, by accounting for physical and/or chemical processes and test system design when evaluating test data. We also identify that, while such advancements could improve the certainty and accuracy of persistence assessments, the mechanisms and processes by which they are translated into regulatory practice and development of new OECD test guidelines need improving and accelerating. Where uncertainty remains, holistic weight of evidence approaches may be required to accurately assess the persistence of chemicals. Integr Environ Assess Manag 2022;18:1454-1487. © 2022 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC). Keywords: Bioavailability; Biodegradability; Biodegradation; Degradation half-lives; Persistence assessment

Bacillus anthracis edema factor substrate specificity: evidence for new modes of action

Since the isolation of Bacillus anthracis exotoxins in the 1960s, the detrimental activity of edema factor (EF) was considered as adenylyl cyclase activity only. Yet the catalytic site of EF was recently shown to accomplish cyclization of cytidine 5'-triphosphate, uridine 5'-triphosphate and inosine 5'-triphosphate, in addition to adenosine 5'-triphosphate. This review discusses the broad EF substrate specificity and possible implications of intracellular accumulation of cyclic cytidine 3':5'-monophosphate, cyclic uridine 3':5'-monophosphate and cyclic inosine 3':5'-monophosphate on cellular functions vital for host defense. In particular, cAMP-independent mechanisms of action of EF on host cell signaling via protein kinase A, protein kinase G, phosphodiesterases and CNG channels are discussed

Scientific concepts and methods for moving persistence assessments into the 21st century

34 páginas.- 2 figuras.- 3 tablas.- 225 referenciasThe evaluation of a chemical substance's persistence is key to understanding its environmental fate, exposure concentration, and, ultimately, environmental risk. Traditional biodegradation test methods were developed many years ago for soluble, nonvolatile, single-constituent test substances, which do not represent the wide range of manufactured chemical substances. In addition, the Organisation for Economic Co-operation and Development (OECD) screening and simulation test methods do not fully reflect the environmental conditions into which substances are released and, therefore, estimates of chemical degradation half-lives can be very uncertain and may misrepresent real environmental processes. In this paper, we address the challenges and limitations facing current test methods and the scientific advances that are helping to both understand and provide solutions to them. Some of these advancements include the following: (1) robust methods that provide a deeper understanding of microbial composition, diversity, and abundance to ensure consistency and/or interpret variability between tests; (2) benchmarking tools and reference substances that aid in persistence evaluations through comparison against substances with well-quantified degradation profiles; (3) analytical methods that allow quantification for parent and metabolites at environmentally relevant concentrations, and inform on test substance bioavailability, biochemical pathways, rates of primary versus overall degradation, and rates of metabolite formation and decay; (4) modeling tools that predict the likelihood of microbial biotransformation, as well as biochemical pathways; and (5) modeling approaches that allow for derivation of more generally applicable biotransformation rate constants, by accounting for physical and/or chemical processes and test system design when evaluating test data. We also identify that, while such advancements could improve the certainty and accuracy of persistence assessments, the mechanisms and processes by which they are translated into regulatory practice and development of new OECD test guidelines need improving and accelerating. Where uncertainty remains, holistic weight of evidence approaches may be required to accurately assess the persistence of chemicals. Integr Environ Assess Manag 2022;1–34. © 2022 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).Peer reviewe

Cluster K Mycobacteriophages: Insights into the Evolutionary Origins of Mycobacteriophage TM4

Five newly isolated mycobacteriophages –Angelica, CrimD, Adephagia, Anaya, and Pixie – have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision into three subclusters: K1, K2, and K3. Although the overall genome architectures of these phages are similar, TM4 appears to have lost at least two segments of its genome, a central region containing the integration apparatus, and a segment at the right end. This suggests that TM4 is a recent derivative of a temperate parent, resolving a long-standing conundrum about its biology, in that it was reportedly recovered from a lysogenic strain of Mycobacterium avium, but it is not capable of forming lysogens in any mycobacterial host. Like TM4, all of the Cluster K phages infect both fast- and slow-growing mycobacteria, and all of them – with the exception of TM4 – form stable lysogens in both Mycobacterium smegmatis and Mycobacterium tuberculosis; immunity assays show that all five of these phages share the same immune specificity. TM4 infects these lysogens suggesting that it was either derived from a heteroimmune temperate parent or that it has acquired a virulent phenotype. We have also characterized a widely-used conditionally replicating derivative of TM4 and identified mutations conferring the temperature-sensitive phenotype. All of the Cluster K phages contain a series of well conserved 13 bp repeats associated with the translation initiation sites of a subset of the genes; approximately one half of these contain an additional sequence feature composed of imperfectly conserved 17 bp inverted repeats separated by a variable spacer. The K1 phages integrate into the host tmRNA and the Cluster K phages represent potential new tools for the genetics of M. tuberculosis and related species

The relevance of rich club regions for functional outcome post-stroke is enhanced in women

This study aimed to investigate the influence of stroke lesions in predefined highly interconnected (rich-club) brain regions on functional outcome post-stroke, determine their spatial specificity and explore the effects of biological sex on their relevance. We analyzed MRI data recorded at index stroke and similar to 3-months modified Rankin Scale (mRS) data from patients with acute ischemic stroke enrolled in the multisite MRI-GENIE study. Spatially normalized structural stroke lesions were parcellated into 108 atlas-defined bilateral (sub)cortical brain regions. Unfavorable outcome (mRS > 2) was modeled in a Bayesian logistic regression framework. Effects of individual brain regions were captured as two compound effects for (i) six bilateral rich club and (ii) all further non-rich club regions. In spatial specificity analyses, we randomized the split into "rich club" and "non-rich club" regions and compared the effect of the actual rich club regions to the distribution of effects from 1000 combinations of six random regions. In sex-specific analyses, we introduced an additional hierarchical level in our model structure to compare male and female-specific rich club effects. A total of 822 patients (age: 64.7[15.0], 39% women) were analyzed. Rich club regions had substantial relevance in explaining unfavorable functional outcome (mean of posterior distribution: 0.08, area under the curve: 0.8). In particular, the rich club-combination had a higher relevance than 98.4% of random constellations. Rich club regions were substantially more important in explaining long-term outcome in women than in men. All in all, lesions in rich dub regions were associated with increased odds of unfavorable outcome. These effects were spatially specific and more pronounced in women.Peer reviewe