rudyvdbrink/CitationDatabase huggingface dataset:
Dynamic evolution of transposable elements, demographic history, and gene content of paleognathous birds.
Zoological research, 2021

Palaeognathae includes ratite and tinamou species that are important for understanding early avian evolution. Here, we analyzed the whole-genome sequences of 15 paleognathous species to infer their demographic histories, which are presently unknown. We found that most species showed a reduction of population size since the beginning of the last glacial period, except for those species distributed in Australasia and in the far south of South America. Different degrees of contraction and expansion of transposable elements (TE) have shaped the paleognathous genome architecture, with a higher transposon removal rate in tinamous than in ratites. One repeat family, AviRTE, likely underwent horizontal transfer from tropical parasites to the ancestor of little and undulated tinamous about 30 million years ago. Our analysis of gene families identified rapid turnover of immune and reproduction-related genes but found no evidence of gene family changes underlying the convergent evolution of flightlessness among ratites. We also found that mitochondrial genes have experienced a faster evolutionary rate in tinamous than in ratites, with the former also showing more degenerated W chromosomes. This result can be explained by the Hill-Robertson interference affecting genetically linked W chromosomes and mitochondria. Overall, we reconstructed the evolutionary history of the Palaeognathae populations, genes, and TEs. Our findings of co-evolution between mitochondria and W chromosomes highlight the key difference in genome evolution between species with ZW sex chromosomes and those with XY sex chromosomes.
Reinforcing effectiveness of midazolam, ethanol, and sucrose: behavioral economic comparison of a mixture relative to its component solutions.
Behavioural pharmacology, 2017

Benzodiazepines (BZs) are relatively safe when administered alone. However, these drugs can produce severe side effects when coadministered with ethanol. Despite these adverse consequences, rates of concurrent BZ and ethanol misuse are increasing, and it is unclear whether this behavior is maintained by an enhanced reinforcing effect of the mixture. To address this issue, the current study compared the reinforcing effectiveness of sucrose solutions mixed with midazolam, ethanol, or both. Eight male rats were trained to orally self-administer solutions of either sucrose (S), sucrose+midazolam (SM), sucrose+ethanol (SE), or sucrose+midazolam+ethanol (SME). The response requirement was increased between sessions until the number of reinforcers earned was zero and the relationship between response requirement and reinforcers earned was analyzed using the exponential model of demand. Although baseline intake was similar across drug conditions, consumption of SM was least affected by increases in cost, indicating that it possessed the highest reinforcing effectiveness (i.e. least elastic). The reinforcing effectiveness of S, SE, and SME did not differ significantly. The finding that the reinforcing effectiveness of the SME was less than that of SM does not support the supposition that BZ and ethanol coadministration is maintained by a higher reinforcing effectiveness of the mixture.
The Relationship of Rapid Eye Movement Sleep Behavior Disorder and Freezing of Gait in Parkinson's Disease.
Cureus, 2020

Rapid eye movement sleep behavior disorder (RBD) contributes to injury due to the alteration of the expected atonia during rapid eye movement (REM) sleep. It occurs before the overt signs of Parkinson's disease (PD). The co-expression of PD and RBD is characterized by non-tremor predominant subtype and higher incidence of freezing. Freezing of gait (FOG) is a debilitating symptom seen in PD patients that lead to falls. While this phenomenon is understood poorly, the involvement of the pedunculopontine nucleus (PPN) and the neural circuits that control locomotion and gait have been examined. This network has also the same control for REM sleep and arousal. The close relationship between PD and RBD and FOG's consequences has led us to explore the relationship between RBD and PD with FOG. This review provides an overview of the neural connections that control gait, locomotion, and REM sleep. The neural changes were seen in PD with FOG and RBD, and sensory and motor changes observed in these two diseases. The functional neuroanatomy that controls REM sleep, arousal, and locomotion overlap significantly with multiple neural circuits affected in RBD and PD with FOG. Visual perception dysfunction and motor symptoms that primarily affect gait initiation are common to both patients with RBD and FOG in PD, leading to freezing episodes. Prospective studies should be conducted to elucidate the relationship of RBD and PD with FOG subtype and find innovative treatment approaches and diagnostic tools for PD with FOG.
Feasibility of Real Time Internet-Based Teleconsultation in Patients With Multiple Sclerosis: Interventional Pilot Study.
Journal of medical Internet research, 2020

Telemedicine (TM) is currently flourishing in rural and emergency settings, but its implementation in the routine management of chronic neurological disorders has developed with more hesitation. Limited access to specialized care facilities and expanding patient populations, combined with unprecedented mobility restrictions imposed by the coronavirus disease pandemic, are currently stressing the need for remote solutions in this field. Studies in patients with multiple sclerosis (MS) have been heterogeneous in objectives and methodology but generally support the concept that TM interventions produce clinical benefits, cost-effectiveness, and user satisfaction. Nonetheless, data on live interaction between patients and health care providers for MS teleconsultation purposes remain scarce.
Designing a hands-on brain computer interface laboratory course.
Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference, 2016

Devices and systems that interact with the brain have become a growing field of research and development in recent years. Engineering students are well positioned to contribute to both hardware development and signal analysis techniques in this field. However, this area has been left out of most engineering curricula. We developed an electroencephalography (EEG) based brain computer interface (BCI) laboratory course to educate students through hands-on experiments. The course is offered jointly by the Biomedical Engineering, Electrical Engineering, and Computer Science Departments of Columbia University in the City of New York and is open to senior undergraduate and graduate students. The course provides an effective introduction to the experimental design, neuroscience concepts, data analysis techniques, and technical skills required in the field of BCI.
Motor neuron disease associated with multiple myeloma.
The International journal of neuroscience, 2008

The association between Amyotrophic Lateral Sclerosis or other Motor Neuron Diseases (MNDs) with Lymphoproliferative Disorders (LPDs) and plasma cell neoplasias (such as Hodgkin's or non-Hodgkin's lymphoma, Waldenstrom's macroglobulinemia, multiple myeloma, chronic lymphocytic leukemia) has been described. It is not clear whether LPDs play a role in the pathogenesis of MND; however it is possible that patients might have antibodies against motor neurons. An association between motor neuron disease and Multiple myeloma (MM) is rarely reported in the literature. This article reports a case of a 75-year-old male with MM and MND. Interestingly, the patient was in complete remission for MM when he was diagnosed as MND and he died due to progressive MND.
The clinical significance of histone deacetylase-8 in human breast cancer.
Pathology, research and practice, 2021

Recent studies have shown that the histone deacetylase-8 (HDAC8), as one of the HDACs, regulates the expression and activity of various genes involved in cancer initiation and progression. The HDAC8 plays an epigenetic role to dysregulate expressions or to interact with transcription factors. Most researchers had focused on the HDAC 1-3 and 6, but today the HDAC8 isotype is a promising target in cancer therapy. Different studies, on breast cancer (BC) cells, have recently shown the HDAC8 overexpression and suggested its oncogenic potential. It seems that the HDAC8 could be a novel and promising target in breast cancer treatment. Some studies on BC demonstrated therapeutic properties of the inhibitors of HDAC8 such as suberoylanilide hydroxamic acid (SAHA), Trichostatin A, valproic acid, sodium butyrate, 1,3,4 oxadiazole with alanine hybrid [(R)-2-amino-N-((5-phenyl-1,3,4-oxadiazol-2-yl) methyl) propanamide (10b)], N-(2-Hydroxyphenyl)-2propylpentanamide (compound 2) and PCI-34051. In this review, we highlight the role and existing inhibitors of HDAC8 in BC pathogenesis and therapy.
RETRACTED: Early hyperbaric oxygen therapy may improve the long term neurological consequences of diabetic patients suffering from hemorrhagic stroke.
Neuroscience letters, 2017

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of Neuroscience Letters has learned that text throughout this paper duplicates, or nearly duplicates, text in an earlier paper by others (Rusyniak DE, Kirk MA, May JD, Kao LW, Brizendine EJ, Welch JL, Cordell WH, Alonso RJ; Hyperbaric Oxygen in Acute Ischemic Stroke Trial Pilot Study, Stroke. 2003 Feb;34(2):571-4).
Reduced Independence in Daily Living Is Associated with the Gut Microbiome in People with HIV and HCV.
mSystems, 2020

Alterations in the gut microbiome are associated with neurocognition and related disorders, including in the context of human immunodeficiency virus (HIV) and hepatitis C virus (HCV) infection. However, the connection between the gut microbiome and cognitive decline, gauged by increased dependence in instrumental activities of daily living (IADL), remains largely unexplored in the context of these diseases. Here we characterized the gut microbiome using 16S rRNA amplicon sequencing and untargeted metabolomics with liquid chromatography-mass spectrometry from 347 people with HIV, HIV and HCV, or neither, all of whom underwent a comprehensive neuropsychiatric assessment. We observed that IADL-dependent and -independent HIV-monoinfected (HIV-positive [HIV+]/HCV-negative [HCV-]) and coinfected (HIV+/HCV+) individuals have distinct gut microbiomes. Moreover, we found that dependent individuals with HIV or HIV and HCV were enriched in
Hemorrhage and ischemia in different hemispheres in a child with moyamoya disease: Case report and review of literature.
Annals of Indian Academy of Neurology, 2013

Hemorrhagic type of moyamoya disease (MMD) is extremely rare in children. Ischemia following hemorrhage is very rare in MMD. There are only 11 reports of mixed-type of MMD, with the patient having both hemorrhage and ischemia in the same hemisphere at the time of presentation, or at different time periods. The ischemia is usually secondary to a precipitating cause. However, there are no reports of a child presenting with both ischemia and hemorrhage in different hemispheres. We present a previously unreported phenomenon of MMD, presenting as hemorrhage and ischemia in opposite hemispheres and review the relevant literature.
New neurophysiological human thermal model based on thermoreceptor responses.
International journal of biometeorology, 2020

A new neurophysiological human thermal model based on thermoreceptor responses, the NHTM model, has been developed to predict regulatory responses and physiological variables in asymmetric transient environments. The passive system is based on Wissler's model, which is more complex and refined. Wissler's model segments the human body into 21 cylindrical parts. Each part is divided into 21 layers, 15 for the tissues and 6 for clothes, and each layer is divided into 12 angular sectors. Thus, we have 3780 nodes for the tissues and 1512 for clothes. The passive system simulates heat exchange within the body and between the body and the surroundings. The active system is composed of the thermoregulatory mechanisms, i.e., skin blood flow, shivering thermogenesis, and sweating. The skin blood flow model and the shivering model are based on thermoreceptor responses. The sweating model is that of Fiala et al. and is based on error signals. The NHTM model was compared with Wissler's model, and the results showed that a calculation based on neurophysiology can improve the performance of the thermoregulation model. The NHTM model was more accurate in the prediction of mean skin temperature, with a mean absolute error of 0.27 °C versus 0.80 °C for the original Wissler model. The prediction accuracy of the NHTM model for local skin temperatures and core temperature could be improved via an optimization method to prove the ability of the new thermoregulation model to fit with the physiological characteristics of different populations.
Overexpression of HDAC6, but not HDAC3 and HDAC4 in the penumbra after photothrombotic stroke in the rat cerebral cortex and the neuroprotective effects of α-phenyl tropolone, HPOB, and sodium valproate.
Brain research bulletin, 2020

Epigenetic processes play important roles in brain responses to ischemic injury. We studied effects of photothrombotic stroke (PTS, a model of ischemic stroke) on the intracellular level and cellular localization of histone deacetylases HDAC3, HDAC4 and HDAC6 in the rat brain cortex, and tested the potential neuroprotector ability of their inhibitors. The background level of HDAC3, HDAC4 and HDAC6 in the rat cerebral cortex was relatively low. HDAC3 localized in the nuclei of some neurons and few astrocytes. HDAC4 was found in the neuronal cytoplasm. After PTS, their levels in penumbra did not change, but HDAC4 appeared in the nuclei of some cells. Its level in the cytoplasmic, but not nuclear fraction of penumbra decreased at 24, but not 4 h after PTS. HDAC6 was upregulated in neurons and astrocytes in the PTS-induced penumbra, especially in the nuclear fraction. Unlike HDAC3 and HDAC4, HDAC6 co-localized with TUNEL-positive apoptotic cells. Inhibitory analysis confirmed the involvement of HDAC6, but not HDAC3 and HDAC4 in neurodegeneration. HDAC6 inhibitor HPOB, HDAC2/8 inhibitor α-phenyl tropolone, and non-specific histone deacetylase inhibitor sodium valproate, but not HDAC3 inhibitor BRD3308, or HDAC4 inhibitor LMK235, decreased PTS-induced infarction volume in the mouse brain, reduced apoptosis, and recovered the motor behavior. HPOB also restored PTS-impaired acetylation of α-tubulin. α-phenyl tropolone restored acetylation of histone H4 in penumbra cells. These results suggest that histone deacetylases HDAC6 and HDAC2 are the possible molecular targets for anti-ischemic therapy, and their inhibitors α-phenyl tropolone, HBOP and sodium valproate can be considered as promising neuroprotectors.
Optimizing techniques for injecting DiI into the brain nuclei of neonatal mice P6 - C57Bl6/CBA.
Journal of neuroscience methods, 2019

DiI (1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine perchlorate) is a lipophilic dye used to research the intracerebral connections of neonatal animals. This dye is most frequently used in the form of dry crystals, but injections of the marker in this state into the mouse brain nuclei, such as MHb (2 cases), LHbM (2 cases), LPA (3 cases) and TS (1 case), clearly revealed excessive lateral diffusion marker into the tissue. Eventually, all the investigated cases except the LPA gave a false positive result. To find the optimal method of marker injection,DiI-kerosene liquid films (3 cases in the MHb); DiI-kerosene gelatinous paste (3 cases in the MHb); injections of insoluble DiI crystals from a solution of 99% dmso (3 cases in the MHb) and 70% ethanol (3 cases in the MHb, 2 cases in the LHbM, 4 cases in the TS) were tested. Injections of DiI in the form of undissolved crystals from a 70% ethanol solution gave a minimal level of side diffusion in all the studied cases. This method of injection is optimal and recommended for use.
CLR01 protects dopaminergic neurons in vitro and in mouse models of Parkinson's disease.
Nature communications, 2020

Parkinson's disease (PD) affects millions of patients worldwide and is characterized by alpha-synuclein aggregation in dopamine neurons. Molecular tweezers have shown high potential as anti-aggregation agents targeting positively charged residues of proteins undergoing amyloidogenic processes. Here we report that the molecular tweezer CLR01 decreased aggregation and toxicity in induced pluripotent stem cell-derived dopaminergic cultures treated with PD brain protein extracts. In microfluidic devices CLR01 reduced alpha-synuclein aggregation in cell somas when axonal terminals were exposed to alpha-synuclein oligomers. We then tested CLR01 in vivo in a humanized alpha-synuclein overexpressing mouse model; mice treated at 12 months of age when motor defects are mild exhibited an improvement in motor defects and a decreased oligomeric alpha-synuclein burden. Finally, CLR01 reduced alpha-synuclein-associated pathology in mice injected with alpha-synuclein aggregates into the striatum or substantia nigra. Taken together, these results highlight CLR01 as a disease-modifying therapy for PD and support further clinical investigation.
[A virologist visits the Papuan anthropophagists].
Virologie (Montrouge, France), 2009

In the 1950's, the American Carleton Gajdusek (1923-2008) was able to find the cause for kuru, a systematically fatal neurological disease, observed mainly on the Western Highlands of New Guinea. While living for a long period with the local indigenous population and studying their customs, he evidenced the infectious origin of this pathology and its transmission mechanism, cannibalism. He also demonstrated the transmissible nature of the agent of Creutzfeldt-Jakob. His works opened an important prospective field of research in neuroscience. A Nobel prize rewarded this outstanding scientific and human adventure.
Effects of C-Peptide Replacement Therapy on Bone Microarchitecture Parameters in Streptozotocin-Diabetic Rats.
Calcified tissue international, 2020

C-peptide therapy protects against diabetic micro- and macrovascular damages and neuropatic complications. However, to date, the role of C-peptide in preventing diabetes-related bone loss has not been investigated. Our aim was to evaluate if C-peptide infusion improves bone quality in diabetic rats. Twenty-three male Wistar rats were randomly divided into three groups: normal control group; sham diabetic control group; diabetic plus C-peptide group. Diabetes was induced by streptozotocin injection and C-peptide was delivered subcutaneously for 6 weeks. We performed micro-CT and histological testing to assess several trabecular microarchitectural parameters. At the end, diabetic plus C-peptide rats had a higher serum C-peptide (p = 0.02) and calcium (p = 0.04) levels and tibia weight (p = 0.02) than the diabetic control group. The diabetic plus C-peptide group showed a higher trabecular thickness and cross-sectional thickness than the diabetic control group (p = 0.01 and p = 0.03). Both the normal control and diabetic plus C-peptide groups had more Runx-2 and PLIN1 positive cells in comparison with the diabetic control group (p = 0.045 and p = 0.034). Diabetic rats receiving C-peptide had higher quality of trabecular bone than diabetic rats not receiving this treatment. If confirmed, C-peptide could have a role in improving bone quality in diabetes.
Single-nucleus transcriptome analysis reveals dysregulation of angiogenic endothelial cells and neuroprotective glia in Alzheimer's disease.
Proceedings of the National Academy of Sciences of the United States of America, 2020

Alzheimer's disease (AD) is the most common form of dementia but has no effective treatment. A comprehensive investigation of cell type-specific responses and cellular heterogeneity in AD is required to provide precise molecular and cellular targets for therapeutic development. Accordingly, we perform single-nucleus transcriptome analysis of 169,496 nuclei from the prefrontal cortical samples of AD patients and normal control (NC) subjects. Differential analysis shows that the cell type-specific transcriptomic changes in AD are associated with the disruption of biological processes including angiogenesis, immune activation, synaptic signaling, and myelination. Subcluster analysis reveals that compared to NC brains, AD brains contain fewer neuroprotective astrocytes and oligodendrocytes. Importantly, our findings show that a subpopulation of angiogenic endothelial cells is induced in the brain in patients with AD. These angiogenic endothelial cells exhibit increased expression of angiogenic growth factors and their receptors (i.e.,
HARDI-ZOOMit protocol improves specificity to microstructural changes in presymptomatic myelopathy.
Scientific reports, 2020

Diffusion magnetic resonance imaging (dMRI) proved promising in patients with non-myelopathic degenerative cervical cord compression (NMDCCC), i.e., without clinically manifested myelopathy. Aim of the study is to present a fast multi-shell HARDI-ZOOMit dMRI protocol and validate its usability to detect microstructural myelopathy in NMDCCC patients. In 7 young healthy volunteers, 13 age-comparable healthy controls, 18 patients with mild NMDCCC and 15 patients with severe NMDCCC, the protocol provided higher signal-to-noise ratio, enhanced visualization of white/gray matter structures in microstructural maps, improved dMRI metric reproducibility, preserved sensitivity (SE = 87.88%) and increased specificity (SP = 92.31%) of control-patient group differences when compared to DTI-RESOLVE protocol (SE = 87.88%, SP = 76.92%). Of the 56 tested microstructural parameters, HARDI-ZOOMit yielded significant patient-control differences in 19 parameters, whereas in DTI-RESOLVE data, differences were observed in 10 parameters, with mostly lower robustness. Novel marker the white-gray matter diffusivity gradient demonstrated the highest separation. HARDI-ZOOMit protocol detected larger number of crossing fibers (5-15% of voxels) with physiologically plausible orientations than DTI-RESOLVE protocol (0-8% of voxels). Crossings were detected in areas of dorsal horns and anterior white commissure. HARDI-ZOOMit protocol proved to be a sensitive and practical tool for clinical quantitative spinal cord imaging.
Microbial metabolites and immune regulation: New targets for major depressive disorder.
Brain, behavior, & immunity - health, 2020

Treatments for depression and mood disorders have been singularly targeted at the brain without consideration for the context of the rest of the body. As evidence mounts for a role of autoimmunity and inflammation as risk factors and contributors to mood disorders, attention has shifted to one of the primary immunoregulatory organs in the body--the gut. Gut-brain interactions have been established and correlative links between the microbiome and mood have been examined, but with novel tools and a base of understanding, focus shifts to the mechanisms of these communications. In this review, we examine how the small molecules produced by metabolic processes of bacteria in the gut influence the host immune system. The gaps in knowledge discussed here include the under characterized diversity of small molecules crossing the gut walls, as well as the need to close the logical loop connecting the microbiome to the immune system, and the immune system to behavior and mood. As we move past the dawn of this field, more precise understanding using novel tools and techniques will help move toward a more informed and systematic process for clinically evaluating the efficacy of probiotics and bacterially derived compounds as antidepressants and mood regulators.