ResearchPad - old-world-monkeys https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Conservation laws by virtue of scale symmetries in neural systems]]> https://www.researchpad.co/article/elastic_article_14657 Considerations of the way in which a dynamical system changes under transformation of scale offer insight into its operational principles. Scale freeness is a paradigm that has been observed in a variety of physical and biological phenomena and describes a situation in which appropriately scaling the space and time coordinates of any evolution of the system yields another possible evolution. In the brain, scale freeness has drawn considerable attention, as it has been associated with optimal information transmission capabilities. Scale symmetry describes a special case of scale freeness, in which a system is perfectly unchanged under transformation of scale. Noether’s theorem tells us that in a system that possesses such a symmetry, an associated conservation law must also exist. Here we show that scale symmetry can be identified, and the related conserved quantities measured, in both simulations and real-world data. We achieve this by deriving a generalised equation of motion that leaves the action invariant under spatiotemporal scale transformations and using a modified version of Noether’s theorem to write the associated family of conservation laws. Our contribution allows for the first such statistical characterisation of the quantity that is conserved purely by virtue of scale symmetry.

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<![CDATA[Maximizing viral detection with SIV droplet digital PCR (ddPCR) assays]]> https://www.researchpad.co/article/elastic_article_14590 Highly sensitive detection of HIV-1 nucleic acids is of critical importance for evaluating treatment interventions superimposed on combination antiretroviral therapy (cART) in HIV-1 infected individuals. SIV infection of rhesus macaques models many key aspects of human HIV-1 infection and plays a key role in evaluation of approaches for prevention, treatment and attempted eradication of HIV infection. Here we describe two droplet digital PCR (ddPCR) assays, a ddPCR DNA assay and an RT-ddPCR RNA assay for detecting simian immunodeficiency virus (SIV) on the RainDance platform. We demonstrate that RainDance ddPCR can tolerate significantly higher cell DNA input without inhibition on a per reaction basis (compared to both qPCR and Bio-Rad ddPCR), thus allowing a large quantity of sample to be analyzed in each reaction. In addition, the combination of a high processivity RT enzyme and RainDance ddPCR could overcome inhibition in severely inhibited (99.99% inhibition in qPCR quantification) viral RNA samples. These assays offer valuable tools for assessing low level viral production/replication and strategies for targeting residual virus in the setting of cART suppression of viral replication. The methodologies presented here can be adapted for a broad range of applications where highly sensitive nucleic acid detection is required.

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<![CDATA[Increasing sika deer population density may change resource use by larval dung beetles]]> https://www.researchpad.co/article/N8cd3ee58-c057-4e17-9e0d-6a1ba00b0cfd

Because animal feces contain organic matter and plant seeds, dung beetles (Scarabaeinae) are important for the circulation of materials and secondary seed dispersal through burying feces. Dung beetles are usually generalists and use the feces of various mammals. Additionally, the larval stages have access to feces from only one mammal species leaving them susceptible to changes in animal fauna and variations in animal populations. Here, we explain the effects of resource availability changes associated with sika deer (Cervus nippon) overabundance on dung beetle larvae feeding habits in Japan. δ15N values were notably higher in raccoon dog and badger dung than in that of other mammals. A dung beetle breeding experiment revealed that the δ15N values of dung beetle exoskeletons that had fed on deer feces during their larval stage were significantly lower than those of beetles that had fed on raccoon dog feces. The δ15N values of the adult exoskeleton were significantly lower in a deer high-density area than in a low-density area in large dung beetles only. It is possible that the high-quality feces, such as those of omnivores, preferred by the large beetles decrease in availability with an increase in deer dung; large beetles may therefore be unable to obtain sufficient high-quality feces and resort to using large amounts of low-quality deer feces. Small dung beetles may use the easily obtained feces that is in high abundance and they may also use deer feces more frequently with increases in deer density. These findings suggest that a larval resource shift associated with deer overabundance may affect ecosystem functions such as soil nutrient cycling and seed dispersal.

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<![CDATA[High capacity reversible data hiding with interpolation and adaptive embedding]]> https://www.researchpad.co/article/5c897722d5eed0c4847d2525

A new Interpolation based Reversible Data Hiding (IRDH) scheme is reported in this paper. For different applications of an IRDH scheme to the digital image, video, multimedia, big-data and biological data, the embedding capacity requirement usually varies. Disregarding this important consideration, existing IRDH schemes do not offer a better embedding rate-distortion performance for varying size payloads. To attain this varying capacity requirement with our proposed adaptive embedding, we formulate a capacity control parameter and propose to utilize it to determine a minimum set of embeddable bits in a pixel. Additionally, we use a logical (or bit-wise) correlation between the embeddable pixel and estimated versions of an embedded pixel. Thereby, while a higher range between an upper and lower limit of the embedding capacity is maintained, a given capacity requirement within that limit is also attained with a better-embedded image quality. Computational modeling of all new processes of the scheme is presented, and performance of the scheme is evaluated with a set of popular test-images. Experimental results of our proposed scheme compared to the prominent IRDH schemes have recorded a significantly better-embedding rate-distortion performance.

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<![CDATA[Late effects of total body irradiation on hematopoietic recovery and immune function in rhesus macaques]]> https://www.researchpad.co/article/5c6dc9f6d5eed0c48452a5fd

While exposure to radiation can be lifesaving in certain settings, it can also potentially result in long-lasting adverse effects, particularly to hematopoietic and immune cells. This study investigated hematopoietic recovery and immune function in rhesus macaques Cross-sectionally (at a single time point) 2 to 5 years after exposure to a single large dose (6.5 to 8.4 Gray) of total body radiation (TBI) derived from linear accelerator-derived photons (2 MeV, 80 cGy/minute) or Cobalt 60-derived gamma irradiation (60 cGy/min). Hematopoietic recovery was assessed through measurement of complete blood counts, lymphocyte subpopulation analysis, and thymus function assessment. Capacity to mount specific antibody responses against rabies, Streptococcus pneumoniae, and tetanus antigens was determined 2 years after TBI. Irradiated macaques showed increased white blood cells, decreased platelets, and decreased frequencies of peripheral blood T cells. Effects of prior radiation on production and export of new T cells by the thymus was dependent on age at the time of analysis, with evidence of interaction with radiation dose for CD8+ T cells. Irradiated and control animals mounted similar mean antibody responses to proteins from tetanus and rabies and to 10 of 11 serotype-specific pneumococcal polysaccharides. However, irradiated animals uniformly failed to make antibodies against polysaccharides from serotype 5 pneumococci, in contrast to the robust responses of non-irradiated controls. Trends toward decreased serum levels of anti-tetanus IgM and slower peak antibody responses to rabies were also observed. Taken together, these data show that dose-related changes in peripheral blood cells and immune responses to both novel and recall antigens can be detected 2 to 5 years after exposure to whole body radiation. Longer term follow-up data on this cohort and independent validation will be helpful to determine whether these changes persist or whether additional changes become evident with increasing time since radiation, particularly as animals begin to develop aging-related changes in immune function.

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<![CDATA[Monotherapy with a low-dose lipopeptide HIV fusion inhibitor maintains long-term viral suppression in rhesus macaques]]> https://www.researchpad.co/article/5c61e93ed5eed0c48496fa7b

Combination antiretroviral therapy (cART) dramatically improves survival of HIV-infected patients, but lifelong treatment can ultimately result in cumulative toxicities and drug resistance, thus necessitating the development of new drugs with significantly improved pharmaceutical profiles. We recently found that the fusion inhibitor T-20 (enfuvirtide)-based lipopeptides possess dramatically increased anti-HIV activity. Herein, a group of novel lipopeptides were designed with different lengths of fatty acids, identifying a stearic acid-modified lipopeptide (LP-80) with the most potent anti-HIV activity. It inhibited a large panel of divergent HIV subtypes with a mean IC50 in the extremely low picomolar range, being > 5,300-fold more active than T-20 and the neutralizing antibody VRC01. It also sustained the potent activity against T-20-resistant mutants and exhibited very high therapeutic selectivity index. Pharmacokinetics of LP-80 in rats and monkeys verified its potent and long-acting anti-HIV activity. In the monkey, subcutaneous administration of 3 mg/kg LP-80 yielded serum concentrations of 1,147 ng/ml after injection 72 h and 9 ng/ml after injection 168 h (7 days), equivalent to 42,062- and 330-fold higher than the measured IC50 value. In SHIV infected rhesus macaques, a single low-dose LP-80 (3 mg/kg) sharply reduced viral loads to below the limitation of detection, and twice-weekly monotherapy could maintain long-term viral suppression.

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<![CDATA[Information integration in large brain networks]]> https://www.researchpad.co/article/5c65dcadd5eed0c484dec021

An outstanding problem in neuroscience is to understand how information is integrated across the many modules of the brain. While classic information-theoretic measures have transformed our understanding of feedforward information processing in the brain’s sensory periphery, comparable measures for information flow in the massively recurrent networks of the rest of the brain have been lacking. To address this, recent work in information theory has produced a sound measure of network-wide “integrated information”, which can be estimated from time-series data. But, a computational hurdle has stymied attempts to measure large-scale information integration in real brains. Specifically, the measurement of integrated information involves a combinatorial search for the informational “weakest link” of a network, a process whose computation time explodes super-exponentially with network size. Here, we show that spectral clustering, applied on the correlation matrix of time-series data, provides an approximate but robust solution to the search for the informational weakest link of large networks. This reduces the computation time for integrated information in large systems from longer than the lifespan of the universe to just minutes. We evaluate this solution in brain-like systems of coupled oscillators as well as in high-density electrocortigraphy data from two macaque monkeys, and show that the informational “weakest link” of the monkey cortex splits posterior sensory areas from anterior association areas. Finally, we use our solution to provide evidence in support of the long-standing hypothesis that information integration is maximized by networks with a high global efficiency, and that modular network structures promote the segregation of information.

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<![CDATA[Zika virus infection at mid-gestation results in fetal cerebral cortical injury and fetal death in the olive baboon]]> https://www.researchpad.co/article/5c4b7f5dd5eed0c4848412b9

Zika virus (ZIKV) infection during pregnancy in humans is associated with an increased incidence of congenital anomalies including microcephaly as well as fetal death and miscarriage and collectively has been referred to as Congenital Zika Syndrome (CZS). Animal models for ZIKV infection in pregnancy have been developed including mice and non-human primates (NHPs). In macaques, fetal CZS outcomes from maternal ZIKV infection range from none to significant. In the present study we develop the olive baboon (Papio anubis), as a model for vertical transfer of ZIKV during pregnancy. Four mid-gestation, timed-pregnant baboons were inoculated with the French Polynesian ZIKV isolate (104 ffu). This study specifically focused on the acute phase of vertical transfer. Dams were terminated at 7 days post infection (dpi; n = 1), 14 dpi (n = 2) and 21 dpi (n = 1). All dams exhibited mild to moderate rash and conjunctivitis. Viremia peaked at 5–7 dpi with only one of three dams remaining mildly viremic at 14 dpi. An anti-ZIKV IgM response was observed by 14 dpi in all three dams studied to this stage, and two dams developed a neutralizing IgG response by either 14 dpi or 21 dpi, the latter included transfer of the IgG to the fetus (cord blood). A systemic inflammatory response (increased IL2, IL6, IL7, IL15, IL16) was observed in three of four dams. Vertical transfer of ZIKV to the placenta was observed in three pregnancies (n = 2 at 14 dpi and n = 1 at 21 dpi) and ZIKV was detected in fetal tissues in two pregnancies: one associated with fetal death at ~14 dpi, and the other in a viable fetus at 21 dpi. ZIKV RNA was detected in the fetal cerebral cortex and other tissues of both of these fetuses. In the fetus studied at 21 dpi with vertical transfer of virus to the CNS, the frontal cerebral cortex exhibited notable defects in radial glia, radial glial fibers, disorganized migration of immature neurons to the cortical layers, and signs of pathology in immature oligodendrocytes. In addition, indices of pronounced neuroinflammation were observed including astrogliosis, increased microglia and IL6 expression. Of interest, in one fetus examined at 14 dpi without detection of ZIKV RNA in brain and other fetal tissues, increased neuroinflammation (IL6 and microglia) was observed in the cortex. Although the placenta of the 14 dpi dam with fetal death showed considerable pathology, only minor pathology was noted in the other three placentas. ZIKV was detected immunohistochemically in two placentas (14 dpi) and one placenta at 21 dpi but not at 7 dpi. This is the first study to examine the early events of vertical transfer of ZIKV in a NHP infected at mid-gestation. The baboon thus represents an additional NHP as a model for ZIKV induced brain pathologies to contrast and compare to humans as well as other NHPs.

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<![CDATA[The molecular biology and HPV drug responsiveness of cynomolgus macaque papillomaviruses support their use in the development of a relevant in vivo model for antiviral drug testing]]> https://www.researchpad.co/article/5c57e6c2d5eed0c484ef3d31

Due to the extreme tissue and species restriction of the papillomaviruses (PVs), there is a great need for animal models that accurately mimic PV infection in humans for testing therapeutic strategies against human papillomaviruses (HPVs). In this study, we present data that demonstrate that in terms of gene expression during initial viral DNA amplification, Macaca fascicularis PV (MfPV) types 5 and 8 appear to be similar to mucosal oncogenic HPVs, while MfPV1 (isolated from skin) resembles most high-risk cutaneous beta HPVs (HPV5). Similarities were also observed in replication properties during the initial amplification phase of the MfPV genomes. We demonstrate that high-risk mucosal HPV-specific inhibitors target the transient replication of the MfPV8 genomes, which indicates that similar pathways are used by the high-risk HPVs and MfPVs during their genome replication. Taking all into account, we propose that Macaca fascicularis may serve as a highly relevant model for preclinical tests designed to evaluate therapeutic strategies against HPV-associated lesions.

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<![CDATA[A viral video and pet lemurs on Twitter]]> https://www.researchpad.co/article/5c3fa5b1d5eed0c484ca76f7

Content shared on social media platforms can impact public perceptions of wildlife. These perceptions, which are in part shaped by context (e.g. non-naturalistic setting, presence of a human), can influence people’s desires to interact with or acquire wild animals as pets. However, few studies have examined whether this holds true for wild animals featured in viral videos. This study reports on opportunistic data collected on Twitter before, during, and after a video that featured a habituated ring-tailed lemur (Lemur catta), called “Sefo”, in southern Madagascar went ‘viral’ (i.e. circulated rapidly on the internet). Our dataset of 13,953 tweets (from an 18.5-week time period in early 2016) referencing lemurs was collected using targeted keywords on the Twitonomy Service. We identified 613 individual tweets about people wanting a lemur as a pet. In addition, 744 tweets that were captured in our dataset linked to the Sefo viral video. We found that as the number of tweets about the viral video increased, so did the number of tweets where an individual wanted to have a lemur as a pet. Most tweets (91%) did not make reference to a specific species of lemur, but when they did, they often (82%) referenced ring-tailed lemurs (L. catta), ruffed lemurs (Varecia spp.), and mouse lemurs (Microcebus spp.). This study serves as a case study to consider how viral content can impact how wild animals are perceived. We close by noting that social media sites like Twitter, which are increasingly providing their users with news and information, should carefully consider how information about wild animals is shared on their platforms, as it may impact animal welfare.

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<![CDATA[Coastal complexity: Ancient human diets inferred from Bayesian stable isotope mixing models and a primate analogue]]> https://www.researchpad.co/article/5c2544e3d5eed0c48442baa9

An extensive ecological literature applies stable isotope mixing models to derive quantitative dietary reconstructions from isotope ratios of consumer tissues. While this approach works well for some organisms, it is challenging for consumers with complex, varied diets, including humans; indeed, many archaeologists have avoided the use of mixing models because uncertainties in model outputs are sufficiently large that the findings are not helpful in understanding ancient lifeways. Here, we exploit an unparalleled opportunity to evaluate the feasibility of dietary quantification in a nutritionally and isotopically complex context on the Cape Peninsula, South Africa. Delta values (δ13C and δ15N) of 213 indigenous food samples enable us to characterise four food groups: terrestrial plants, terrestrial vertebrates, marine invertebrates and marine vertebrates. A recent study of baboons that consumed marine and terrestrial foods provides insight into the relationship between such foods and consumer tissue isotopes. We use this information to refine our interpretation of δ15N and especially δ13C in bone collagen from 35 archaeological hunter-gatherers, achieving better estimates of the relative importance of marine and terrestrial foods in the diet than has hitherto been possible. Based on Bayesian stable isotope mixing model (SIMM) outputs, we infer that the trophic enrichment factor (TEF) for δ13Cbone collagen in these coastal humans is closer to +3 than +5‰. In the most 13C- and 15N-rich individuals, 65–98% of bone collagen (95% credible intervals) derived from marine foods. Conversely, in 13C and 15N-poor individuals, 7–44% of bone collagen derived from marine foods. The uncertainties discussed here highlight the need for caution when implementing SIMMs in studies of consumers with complex diets. To our knowledge, this work constitutes the most detailed and most tightly constrained study of this problem to date.

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<![CDATA[Vectored delivery of anti-SIV envelope targeting mAb via AAV8 protects rhesus macaques from repeated limiting dose intrarectal swarm SIVsmE660 challenge]]> https://www.researchpad.co/article/5c117b9ed5eed0c484699e2f

Gene based delivery of immunoglobulins promises to safely and durably provide protective immunity to individuals at risk of acquiring infectious diseases such as HIV. We used a rhesus macaque animal model to optimize delivery of naturally-arising, autologous anti-SIV neutralizing antibodies expressed by Adeno-Associated Virus 8 (AAV8) vectors. Vectored transgene expression was confirmed by quantitation of target antibody abundance in serum and mucosal surfaces. We tested the expression achieved at varying doses and numbers of injections. Expression of the transgene reached a saturation at about 2 x 1012 AAV8 genome copies (gc) per needle-injection, a physical limitation that may not scale clinically into human trials. In contrast, expression increased proportionately with the number of injections. In terms of anti-drug immunity, anti-vector antibody responses were universally strong, while those directed against the natural transgene mAb were detected in only 20% of animals. An anti-transgene antibody response was invariably associated with loss of detectable plasma expression of the antibody. Despite having atypical glycosylation profiles, transgenes derived from AAV-directed muscle cell expression retained full functional activity, including mucosal accumulation, in vitro neutralization, and protection against repeated limiting dose SIVsmE660 swarm challenge. Our findings demonstrate feasibility of a gene therapy-based passive immunization strategy against infectious disease, and illustrate the potential for the nonhuman primate model to inform clinical AAV-based approaches to passive immunization.

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<![CDATA[Reinvestigating the status of malaria parasite (Plasmodium sp.) in Indian non-human primates]]> https://www.researchpad.co/article/5c12cf05d5eed0c484913d41

Many human parasites and pathogens have closely related counterparts among non-human primates. For example, non-human primates harbour several species of malaria causing parasites of the genus Plasmodium. Studies suggest that for a better understanding of the origin and evolution of human malaria parasites it is important to know the diversity and evolutionary relationships of these parasites in non-human primates. Much work has been undertaken on malaria parasites in wild great Apes of Africa as well as wild monkeys of Southeast Asia however studies are lacking from South Asia, particularly India. India is one of the major malaria prone regions in the world and exhibits high primate diversity which in turn provides ideal setting for both zoonoses and anthropozoonoses. In this study we report the molecular data for malaria parasites from wild populations of Indian non-human primates. We surveyed 349 fecal samples from five different Indian non-human primates, while 94 blood and tissue samples from one of the Indian non-human primate species (Macaca radiata) and one blood sample from M. mulatta. Our results confirm the presence of P. fragile, P. inui and P. cynomolgi in Macaca radiata. Additionally, we report for the first time the presence of human malarial parasite, P. falciparum, in M. mulatta and M. radiata. Additionally, our results indicate that M. radiata does not exhibit population structure probably due to human mediated translocation of problem monkeys. Human mediated transport of macaques adds an additional level of complexity to tacking malaria in human. This issue has implications for both the spread of primate as well as human specific malarias.

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<![CDATA[Antibody responses to Zika virus proteins in pregnant and non-pregnant macaques]]> https://www.researchpad.co/article/5c06f04ad5eed0c484c6d62b

The specificity of the antibody response against Zika virus (ZIKV) is not well-characterized. This is due, in part, to the antigenic similarity between ZIKV and closely related dengue virus (DENV) serotypes. Since these and other similar viruses co-circulate, are spread by the same mosquito species, and can cause similar acute clinical syndromes, it is difficult to disentangle ZIKV-specific antibody responses from responses to closely-related arboviruses in humans. Here we use high-density peptide microarrays to profile anti-ZIKV antibody reactivity in pregnant and non-pregnant macaque monkeys with known exposure histories and compare these results to reactivity following DENV infection. We also compare cross-reactive binding of ZIKV-immune sera to the full proteomes of 28 arboviruses. We independently confirm a purported ZIKV-specific IgG antibody response targeting ZIKV nonstructural protein 2B (NS2B) that was recently reported in ZIKV-infected people and we show that antibody reactivity in pregnant animals can be detected as late as 127 days post-infection (dpi). However, we also show that these responses wane over time, sometimes rapidly, and in one case the response was elicited following DENV infection in a previously ZIKV-exposed animal. These results suggest epidemiologic studies assessing seroprevalence of ZIKV immunity using linear epitope-based strategies will remain challenging to interpret due to susceptibility to false positive results. However, the method used here demonstrates the potential for rapid profiling of proteome-wide antibody responses to a myriad of neglected diseases simultaneously and may be especially useful for distinguishing antibody reactivity among closely related pathogens.

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<![CDATA[Laboratory challenges of Plasmodium species identification in Aceh Province, Indonesia, a malaria elimination setting with newly discovered P. knowlesi]]> https://www.researchpad.co/article/5c0ae437d5eed0c4845892c2

The discovery of the life-threatening zoonotic infection Plasmodium knowlesi has added to the challenges of prompt and accurate malaria diagnosis and surveillance. In this study from Aceh Province, Indonesia, a malaria elimination setting where P. knowlesi endemicity was not previously known, we report the laboratory investigation and difficulties encountered when using molecular detection methods for quality assurance of microscopically identified clinical cases. From 2014 to 2015, 20 (49%) P. falciparum, 16 (39%) P. vivax, 3 (7%) P. malariae, and 2 (5%) indeterminate species were identified by microscopy from four sentinel health facilities. At a provincial-level reference laboratory, loop-mediated isothermal amplification (LAMP), a field-friendly molecular method, was performed and confirmed Plasmodium in all samples though further species-identification was limited by the unavailability of non-falciparum species-specific testing with the platform used. At a national reference laboratory, several molecular methods including nested PCR (nPCR) targeting the 18 small sub-unit (18S) ribosomal RNA, nPCR targeting the cytochrome-b (cytb) gene, a P. knowlesi-specific nPCR, and finally sequencing, were necessary to ultimately classify the samples as: 19 (46%) P. knowlesi, 8 (20%) P. falciparum, 14 (34%) P. vivax. Microscopy was unable to identify or mis-classified up to 56% of confirmed cases, including all cases of P. knowlesi. With the nPCR methods targeting the four human-only species, P. knowlesi was missed (18S rRNA method) or showed cross-reactivity for P. vivax (cytb method). To facilitate diagnosis and management of potentially fatal P. knowlesi infection and surveillance for elimination of human-only malaria in Indonesia and other affected settings, new detection methods are needed for testing at the point-of-care and in local reference laboratories.

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<![CDATA[Altering alpha-frequency brain oscillations with rapid analog feedback-driven neurostimulation]]> https://www.researchpad.co/article/5c117b82d5eed0c4846997e0

Oscillations of the brain’s local field potential (LFP) may coordinate neural ensembles and brain networks. It has been difficult to causally test this model or to translate its implications into treatments, because there are few reliable ways to alter LFP oscillations. We developed a closed-loop analog circuit to enhance brain oscillations by feeding them back into cortex through phase-locked transcranial electrical stimulation. We tested the system in a rhesus macaque with chronically implanted electrode arrays, targeting 8–15 Hz (alpha) oscillations. Ten seconds of stimulation increased alpha oscillatory power for up to 1 second after stimulation offset. In contrast, open-loop stimulation decreased alpha power. There was no effect in the neighboring 15–30 Hz (beta) LFP rhythm or on a neighboring array that did not participate in closed-loop feedback. Analog closed-loop neurostimulation might thus be a useful strategy for altering brain oscillations, both for basic research and the treatment of neuro-psychiatric disease.

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<![CDATA[Extensive editing of cellular and viral double-stranded RNA structures accounts for innate immunity suppression and the proviral activity of ADAR1p150]]> https://www.researchpad.co/article/5c2400b4d5eed0c484098ac6

The interferon (IFN)-mediated innate immune response is the first line of defense against viruses. However, an IFN-stimulated gene, the adenosine deaminase acting on RNA 1 (ADAR1), favors the replication of several viruses. ADAR1 binds double-stranded RNA and converts adenosine to inosine by deamination. This form of editing makes duplex RNA unstable, thereby preventing IFN induction. To better understand how ADAR1 works at the cellular level, we generated cell lines that express exclusively either the IFN-inducible, cytoplasmic isoform ADAR1p150, the constitutively expressed nuclear isoform ADAR1p110, or no isoform. By comparing the transcriptome of these cell lines, we identified more than 150 polymerase II transcripts that are extensively edited, and we attributed most editing events to ADAR1p150. Editing is focused on inverted transposable elements, located mainly within introns and untranslated regions, and predicted to form duplex RNA structures. Editing of these elements occurs also in primary human samples, and there is evidence for cross-species evolutionary conservation of editing patterns in primates and, to a lesser extent, in rodents. Whereas ADAR1p150 rarely edits tightly encapsidated standard measles virus (MeV) genomes, it efficiently edits genomes with inverted repeats accidentally generated by a mutant MeV. We also show that immune activation occurs in fully ADAR1-deficient (ADAR1KO) cells, restricting virus growth, and that complementation of these cells with ADAR1p150 rescues virus growth and suppresses innate immunity activation. Finally, by knocking out either protein kinase R (PKR) or mitochondrial antiviral signaling protein (MAVS)—another protein controlling the response to duplex RNA—in ADAR1KO cells, we show that PKR activation elicits a stronger antiviral response. Thus, ADAR1 prevents innate immunity activation by cellular transcripts that include extensive duplex RNA structures. The trade-off is that viruses take advantage of ADAR1 to elude innate immunity control.

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<![CDATA[Functional architecture of the foveola revealed in the living primate]]> https://www.researchpad.co/article/5c0841b8d5eed0c484fca8ba

The primate foveola, with its high cone density and magnified cortical representation, is exquisitely specialized for high-resolution spatial vision. However, uncovering the wiring of retinal circuitry responsible for this performance has been challenging due to the difficulty in recording receptive fields of foveal retinal ganglion cells (RGCs) in vivo. In this study, we use adaptive optics scanning laser ophthalmoscopy (AOSLO) to image the calcium responses of RGCs in the living primate, with a stable, high precision visual stimulus that allowed us to localize the receptive fields of hundreds of foveal ganglion cells. This approach revealed a precisely radial organization of foveal RGCs, despite the many distortions possible during the extended developmental migration of foveal cells. By back projecting the line connecting RGC somas to their receptive fields, we have been able to define the ‘physiological center’ of the foveola, locating the vertical meridian separating left and right hemifields in vivo.

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<![CDATA[Exploring attentional bias towards threatening faces in chimpanzees using the dot probe task]]> https://www.researchpad.co/article/5c08421dd5eed0c484fcbd18

Primates have evolved to rapidly detect and respond to danger in their environment. However, the mechanisms involved in attending to threatening stimuli are not fully understood. The dot-probe task is one of the most widely used experimental paradigms to investigate these mechanisms in humans. However, to date, few studies have been conducted in non-human primates. The aim of this study was to investigate whether the dot-probe task can measure attentional biases towards threatening faces in chimpanzees. Eight adult chimpanzees participated in a series of touch screen dot-probe tasks. We predicted faster response times towards chimpanzee threatening faces relative to neutral faces and faster response times towards faces of high threat intensity (scream) than low threat intensity (bared teeth). Contrary to prediction, response times for chimpanzee threatening faces relative to neutral faces did not differ. In addition, we found no difference in response times for faces of high and low threat intensity. In conclusion, we found no evidence that the touch screen dot-probe task can measure attentional biases specifically towards threatening faces in our chimpanzees. Methodological limitations of using the task to measure emotional attention in human and non-human primates, including stimulus threat intensity, emotional state, stimulus presentation duration and manual responding are discussed.

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<![CDATA[Preclinical IV busulfan dose-finding study to induce reversible myeloablation in a non-human primate model]]> https://www.researchpad.co/article/5c2400ced5eed0c48409930e

In this study we utilized a large animal model to identify a dose of intravenous busulfan that can cause reversible myelosuppression. Nine baboons (Papio anubis) were treated with IV busulfan at 6.4 (Group A), 8 (Group B), or 9.6 mg/kg (Group C). Peripheral blood counts were measured up to 90 days after treatment and serial bone marrow samples were obtained to analyze CD34+ cell content and colony forming units. Overall, the highest grade of peripheral blood cytopenia was observed 15 days after treatment in all three groups (n = 3/group). In particular, we observed a notable reduction of neutrophil and platelet counts in the blood and the number of marrow CD34+ cells and colony forming units. In contrast, the effect of busulfan on hemoglobin levels was mild. Baboons who received the highest dose of busulfan showed only a 25–35% recovery of marrow CD34+ cells and colony forming units after 90 days of busulfan administration. However, all three groups of animals showed a full recovery of peripheral blood counts and normal marrow cellularity and tri-lineage hematopoiesis after treatment. Notably, all three doses of busulfan were tolerated well without significant extra-medullary toxicity. These results validate the hierarchy of blood cells likely targeted by busulfan, and based on these findings, clinical trials using myelotoxic but not myeloablative doses of intravenous busulfan will be designed for patients with myeloid malignancies.

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