gebhart/patrepeval huggingface dataset:
Relationships among low-frequency local field potentials, spiking activity, and three-dimensional reach and grasp kinematics in primary motor and ventral premotor cortices (2011)

A prominent feature of motor cortex field potentials during movement is a distinctive low-frequency local field potential (lf-LFP) (<4 Hz), referred to as the movement event-related potential (mEP). The lf-LFP appears to be a global signal related to regional synaptic input, but its relationship to nearby output signaled by single unit spiking activity (SUA) or to movement remains to be established. Previous studies comparing information in primary motor cortex (MI) lf-LFPs and SUA in the context of planar reaching tasks concluded that lf-LFPs have more information than spikes about movement. However, the relative performance of these signals was based on a small number of simultaneously recorded channels and units, or for data averaged across sessions, which could miss information of larger-scale spiking populations. Here, we simultaneously recorded LFPs and SUA from two 96-microelectrode arrays implanted in two major motor cortical areas, MI and ventral premotor (PMv), while monkeys freely reached for and grasped objects swinging in front of them. We compared arm end point and grip aperture kinematics' decoding accuracy for lf-LFP and SUA ensembles. The results show that lf-LFPs provide enough information to reconstruct kinematics in both areas with little difference in decoding performance between MI and PMv. Individual lf-LFP channels often provided more accurate decoding of single kinematic variables than any one single unit. However, the decoding performance of the best single unit among the large population usually exceeded that of the best single lf-LFP channel. Furthermore, ensembles of SUA outperformed the pool of lf-LFP channels, in disagreement with the previously reported superiority of lf-LFP decoding. Decoding results suggest that information in lf-LFPs recorded from intracortical arrays may allow the reconstruction of reach and grasp for real-time neuroprosthetic applications, thus potentially supplementing the ability to decode these same features from spiking populations.
Joint capacity assignment to state-independent working and spare paths for enchanced network survivability (2002)

To develop survivable and cost-efficient networks, it is important to consider practical restoration control in network design. We propose a design for joint capacity assignment to state-independent working paths and state-independent spare paths. The assignment is formulated as an integer programming problem. The use of state-independent paths simplifies the restoration process and shortens the restoration time, and our design is especially suitable to pre-planned distributed restoration schemes. We further apply it to a strategy in which all paths are state-dependent, and to one whose spare paths are state-dependent. A numerical comparison of capacity costs, in which our design was applied to specific network examples, shows that costs for a state-independent approach are only slightly higher than those for state-dependent approach.
Genetic knockout of porcine GGTA1 or CMAH/GGTA1 is associated with the emergence of neo‐glycans (2023)

Genetic deletion of GGTA1 or GGTA1/CMAH removes specific epitopes providing a more human-like glycosylation pattern, but at the same time changes distribution and levels of other porcine glycans that are potentially immunogenic.
Finite-Temperature Critical Behavior of Mutual Information (2011)

We study mutual information for Renyi entropy of arbitrary index n, in interacting quantum systems at finite-temperature critical points, using high-temperature expansion, quantum Monte Carlo simulations and scaling theory. We find that, for n>1, the critical behavior is manifest at two temperatures T(c) and nT(c). For the XXZ model with Ising anisotropy, the coefficient of the area law has a t lnt singularity, whereas the subleading correction from corners has a logarithmic divergence, with a coefficient related to the exact results of Cardy and Peschel. For T<nT(c) there is a constant term associated with broken symmetries that jumps at both T(c) and nT(c), which can be understood in terms of a scaling function analogous to the boundary entropy of Affleck and Ludwig.
Suppressed Surface‐Recombination Structure and Surface Passivation for Improving Current Gain of 4H‐SiC BJTs (2009)

This chapter contains sections titled: Introduction Survey of the conventional BJTs with high common emitter current gain Basic structure and operating principle of the proposed BJTs Evaluation of surface passivation for improving current gain Design and fabrication of the SSR-BJTs Characteristics of the SSR-BJTs Conclusion References
Constitutional activation of IL-6-mediated JAK/STAT pathway through hypermethylation of SOCS-1 in human gastric cancer cell line (2004)

The interleukin-mediated Janus kinase (JAK)/STAT pathway plays a crucial role in carcinogenesis. Recently, increased STAT3 activity was found in hepatocellular carcinoma and multiple myeloma in which there was silencing of SOCS-1 (suppressor of cytokine signalling-1) by gene promoter hypermethylation. We investigated the expression level of interleukin-6 (IL-6) and SOCS-1 in gastric cancer cell lines. Expression of SOCS-1 correlated with IL-6 level in most of the cell lines, except for AGS cells in which SOCS-1 was absent despite a high level of IL-6 production. Methylation analysis by methylation-specific polymerase chain reaction and bisulphite sequencing revealed that CpG island of SOCS-1 was densely methylated in AGS cells. Demethylation treatment by 5'aza-deoxycytidine restored SOCS-1 expression and also suppressed constitutive STAT3 phosphorylation in AGS cells. Moreover, methylation of SOCS-1 was detected in 27.5% (11 of 40) of primary gastric tumours samples, 10% (one of 10) of adjacent noncancer tissues but not in any (zero of nine) normal gastric mucosa. Methylation of SOCS-1 also correlated with the loss of mRNA expression in some primary gastric cancers. In conclusion, this is the first report to demonstrate that hypermethylation of SOCS-1 led to gene silencing in gastric cancer cell line and primary tumour samples. Downregulation of SOCS-1 cooperates with IL-6 in the activation of JAK/STAT pathway in gastric cancer.
Draft Genome Sequence of Linfuranone Producer Microbispora sp. GMKU 363 (2015)

Here, we report the draft genome sequence of Microbispora sp. GMKU 363, a plant-derived actinomycete that produces linfuranone A, a linear polyketide modified with a furanone ring possessing adipocyte differentiation inducing activity. The biosynthetic gene cluster for linfuranone was identified by analyzing polyketide synthase genes in the genome.
Higher-order resonant modes in a photonic heterostructure nanocavity (2008)

We investigated the optical characteristics of higher-order resonant modes for a heterostructure nanocavity formed in a two-dimensional photonic-crystal silicon slab. Two kinds of resonant modes were observed, the nanocavity modes and the Fabry–Pérot modes. High quality factors of more than 1.0×106 were obtained not only for the nanocavity mode but also for the Fabry–Pérot modes.
Solution-State Structure and Affinities of Cyclodextrin:Fentanyl Complexes by Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation (2016)

Cyclodextrins (CDs) are investigated for their ability to form inclusion complexes with the analgesic fentanyl and three similar molecules: acetylfentanyl, thiofentanyl, and acetylthiofentanyl. Stoichiometry, binding strength, and complex structure are revealed through nuclear magnetic resonance (NMR) techniques and discussed in terms of molecular dynamics (MD) simulations. It was found that β-cyclodextrin is generally capable of forming the strongest complexes with the fentanyl panel. Two-dimensional NMR data and computational chemical calculations are used to derive solution-state structures of the complexes. Binding of the fentanyls to the CDs occurs at the amide phenyl ring, leaving the majority of the molecule solvated by water, an observation common to all four fentanyls. This finding suggests a universal binding behavior, as the vast majority of previously synthesized fentanyl analogues contain this structural moiety. This baseline study serves as the most complete work on CD:fentanyl complexes to date and provides the insights into strategies for producing future generations of designer cyclodextrins capable of stronger and more selective complexation of fentanyl and its analogues.
Impacts of the Statewide COVID-19 Lockdown Interventions on Excess Mortality, Unemployment, and Employment Growth (2022)

There was no statistical relationship between excess mortality and openness scores, while there were strong relationships with employment measures. These results suggest that lockdowns are not sufficiently beneficial for future use in this pandemic and raise concerns for use in future pandemics.
Solubilization of the catecholamine carrier of chromaffin granule membranes in a form that binds substrates and inhibitors of uptake (1983)

The component of bovine chromaffin granule membrane responsible for the binding of [2-3H]dihydrotetrabenazine has been solubilized by treatment with detergents. The binding activity of the soluble material was measured either by equilibrium dialysis or by precipitation of the protein by poly(ethylene glycol) and filtration of the precipitate. The best yields and activities were obtained with sodium cholate, which solubilized more than 70% of the binding sites; deoxycholate had deleterious effects on the soluble activity, and among nonionic detergents, octyl beta-glucoside was the most efficient. With cholate, [3H]dihydrotetrabenazine binding occurred on soluble sites as judged by centrifugation of the bound material and by filtration on Sepharose 6B columns. Binding could be measured in the presence of cholate, but high detergent concentrations had a reversible inhibitory effect. The [3H]dihydrotetrabenazine binding characteristics of the soluble material were similar to those of the granule membrane, with one class of binding sites (KD = 23 nM, Bmax = 90 pmol/mg of protein). The association and dissociation rate constants were 0.072 X 10(6) M-1 s-1 and 1.1 X 10(-3) s-1, respectively. The pharmacological properties of the binding sites were also similar to those of the membranes. Our results thus support the view that the catecholamine carrier has been solubilized in an active conformation that binds substrates and inhibitors of uptake.
NR3C1 (nuclear receptor subfamily 3, group C, member 1/glucocorticoid receptor) (2017)

NR3C1 gene encodes the human glucocorticoid receptor(hGR), which is a ligand-dependent transcription factor and activates transcription of glucocorticoid-responsive genes through binding directly to glucocorticoid response elements(GREs) in their promoter region, or modulating transcriptional activity of other transcription factors through protein-protein interactions. hGR is implicated in a broad spectrum of biochemical physiologic functions, which are essential for life, and has also a key role in the maintenance of basal and stress-related homeostasis. Almost 20% of the genes expressed in human leukocytes are regulated positively or negatively by the hGR. Approximately every cellular, molecular and other physiologic network in the human body are influenced by this receptor and more specifically growth, reproduction, intermediary metabolism, immune and inflammatory reactions, as well as central nervous system and cardiovascular functions and lymphoproliferative disorders, cellular proliferation and differentiation in target tissues and normal renal tubular function and thus water and electrolyte homeostasis are only some of the examples where hGR is implicated(Nicolaides, Galata, Kino, Chrousos, and Charmandari, 2010).
Dynamic self-organization and clustering in distributed networked systems for performance improvement (2009)

We consider two closely related dynamic self-organization problems in networked control systems. Both are forms of dynamic clustering of nodes. The structure of networked control systems is often abstracted using graph theory. In this abstraction, the nodes of the graph represent the agents and the edges between them represent the relation(s) or the possibility of communication between the corresponding agents. The topology of the communication network supporting a networked control system has critical consequences for its performance. The first problem we address is the development of a distributed self-organization algorithm, resulting into a dynamic two level hierarchy of leader and regular agents, which substantially improves the convergence speed of distributed algorithms utilized by the networked control system. For the second problem, we consider the collaborative control of a group of autonomous mobile agents (e.g. vehicles, robots) supported by a mobile wireless network, consisting of many ground and a few aerial nodes. The agents collaborate to achieve a common goal or objective, like to move in a particular area and cover it, while avoiding obstacles and collisions. Building upon our earlier work on deterministic, randomized and hybrid distributed coordination algorithms we consider the communication needs of the agents, and in particular the connectivity of their communication network as they move. We develop distributed algorithms that automatically select some agents and move them appropriately so as to maintain certain degree of desired connectivity among the moving agents. We characterize the trade-off between the gain from maintaining a certain degree of connectivity vs. the combined cost of communications and the associated dynamic re-positioning of agents. We also describe classes of efficient communication topologies and in particular their similarity to dynamic small world topologies and extensions.
Impact of age at diagnosis on disease progression in patients with primary sclerosing cholangitis (2017)

Patients with later age at diagnosis of PSC displayed a different clinical phenotype with a different sex ratio, immune status and an increased risk for progressive liver failure and biliary malignancies.
Polyphenols suppress hydrogen peroxide‐induced oxidative stress in human bone‐marrow derived mesenchymal stem cells (2012)

Human mesenchymal stem cells (hMSCs) are considered a highly promising candidate cell type for cell-based tissue engineering and regeneration because of their self-renewal and multi-lineage differentiation characteristics. Increased levels of reactive oxygen/nitrogen species (ROS/RNS) are associated with tissue injury and inflammation, impact a number of cellular processes, including cell adhesion, migration, and proliferation, and have been linked to cellular senescence in MSCs, potentially compromising their activities. Naturally occurring polyphenolic compounds (polyphenols), epigallocatechin-3-gallate (EGCG), and curcumin, block ROS/RNS and are potent inflammation-modulating agents. However, their potential protective effects against oxidative stress in hMSCs have not been examined. In this study, we carried out a systematic analysis of the effects of polyphenols on hMSCs in their response to oxidative stress in the form of treatment with H(2)O(2) and S-nitroso-N-acetylpenicillamine (SNAP), respectively. Parameters measured included colony forming activity, apoptosis, and the levels of antioxidant enzymes and free reactive species. We found that polyphenols reversed H(2)O(2) -induced loss of colony forming activity in hMSCs. In a dose-dependent manner, polyphenols inhibited increased levels of ROS and NO, produced by H(2)O(2) or SNAP, respectively, in MSCs. Notably, polyphenols rapidly and almost completely blocked H(2)O(2) -induced ROS in the absence of significant direct effect on H(2)O(2) itself. Polyphenols also protected the antioxidant enzymes and reduced apoptotic cell death caused by H(2)O(2) exposure. Taken together, these findings demonstrate that EGCG and curcumin are capable of suppressing inducible oxidative stress in hMSCs, and suggest a possible new approach to maintain MSC viability and potency for clinical application.
Nicotine therapy for ulcerative colitis: a review of rationale, mechanisms, pharmacology, and clinical results (1999)

Smoking is protective against developing ulcerative colitis. Nicotine may be the cause of this protective effect. Controlled trials have demonstrated efficacy of transdermal nicotine for active ulcerative colitis. Side effects observed with transdermal nicotine include contact dermatitis, nausea, and lightheadedness. Topical administration of nicotine to the colon reduces nicotine blood concentrations and side effects, and may be of clinical benefit.
Metabolism of 2,4,6-Trinitrotoluene by Pseudomonas sp. JLR11 (1998)

The main contaminant at many military sites is 2,4,6-trinitrotoluene (TNT). This explosive remains stable in the environment, and because it is toxic, there is an urgent need for remediation to clean up contaminated sites. Pseudomonas sp. JLR11 is a soil isolate able to use nitrate, TNT, or both as the N source under anaerobic conditions. At least two polypeptides were detected in cell-free extracts of TNT-grown cells that were not present in the cell-free extracts of nitrate-grown cells. Mass balances with unlabeled TNT revealed that about 85% of total N-TNT was incorporated as cell biomass, whereas only about 1% of [14C]TNT was recovered as 14CO2. Analyses of culture supernatants detected some pathway intermediates in the productive removal of nitro groups from TNT, such as 2,4,6-trinitrobenzaldehyde, 2-nitro-4-hydroxybenzoic acid, 4-hydroxybenzaldehyde, and 4-hydroxybenzoic acid. This strain reduced a small fraction of the total TNT to monoaminodinitrotoluenes and diaminomononitrotoluenes, but these products accumulated with time and were not used by the strain as an N source. We discuss how the productive metabolism of TNT may occur.
Abstract B91: RNAi knockdown of Mek2, but not Mek1, increases proliferation of malignant and non-malignant human breast cells (2009)

Abstract We are using shRNAs against Mek1 and/or Mek2 to determine the individual contributions of Mek1 and Mek2 to proliferation, migration and Mek inhibitor sensitivity in malignant and non-malignant human breast epithelial cell lines. We found in both malignant (MCF7 and MDAMB231) and non-malignant immortalized (184vTERT and MCF10A) breast cell lines that, despite significant shRNA-mediated reductions (&amp;gt;95%) in the expression of Mek1, Mek2, or both kinases, the cells maintained long-term growth. In fact, the shMek2 lines grew significantly faster and were more motile than controls, suggesting that in some breast cancers, drugs that specifically target Mek1 might be more effective than those which target both Mek1 and 2. In MCF7 cells, levels of phosphorylated (P)-Erk1 and 2 were significantly decreased or undetectable in the presence of Mek shRNAs, indicating that Erk phosphorylation may be dispensable for cell proliferation in these cells. In contrast, in 184vTERT and MCF10A, phosphorylated Erk levels remained constant despite the knockdown of both Mek1 and Mek2. This latter result indicated that, in some breast cells, another kinase is likely to phosphorylate Erk1/2 in the absence of Mek1 and Mek2. The Mek5 kinase is genetically most similar to Mek1 and Mek2, making it an attractive candidate for further investigation. Mek5 is expressed in 184vTERT, and its total protein levels are not altered when Mek1 and 2 are knocked down. A preliminary experiment indicates that siRNA induced knockdown of Mek5 expression leads to decreased ERK1/2 phosphorylation in 184v-TERT cells independently of Mek1/2 expression. We are currently investigating whether this occurs in other breast cell lines. Collectively, our data indicate that in at least some breast cells, both Mek1 and Mek2 are dispensable for proliferation and survival, and that parallel pathways are sufficient for relaying signals from cell surface receptors, independently of Mek1/2 and/or P-Erk1/2. This data may explain why Mek inhibitors, which target both Mek1 and Mek2, have not done well clinically. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):B91.
Potential Use of Tannin Extracts as Additives in Semen Destined for Cryopreservation: A Review (2022)

Cryopreservation and storage of semen for artificial insemination (AI) result in excessive accumulation of reactive oxygen species (ROS). This leads to a shortened life span and reduced motility of spermatozoa post-thawing, with consequent impairment of their function. However, certain levels of ROS are essential to facilitate the capacitation of spermatozoa required for successful fertilisation. Tannins, as well-known antioxidant compounds, may act as ROS binders/acceptors/scavengers to inhibit the damaging effects of ROS. This review comprises an analysis of the semen cryopreservation protocol and health functions of tannins, as well as the effects of ROS on fresh and cryopreserved semen's longevity and fertilisation. Additionally, we surveyed available evidence of the effects of tannin extract feed supplementation on male fertility. We furthermore interrogated existing theories on tannin use as a potential additive to semen extenders, its relationship with semen quality, and to what degree existing theories have been investigated to develop testable new hypotheses. Emphasis was placed on the effects of tannins on ROS, their involvement in regulating sperm structure and function during cryopreservation, and on post-thaw sperm motility, capacitation, and fertilising ability. The diverse effects of tannins on the reproductive system as a result of their potential metal ion chelation, protein precipitation, and biological antioxidant abilities have been identified. The current data are the first to support the further investigation of the incorporation of tannin-rich plant extracts into semen extenders to enhance the post-thaw survival, motility, and fertilising ability of cryopreserved spermatozoa.
Development of a Clinical Grade Procedure for Generation of mRNA Transfected Dendritic Cells from Purified Frozen CD34+ Blood Progenitor Cells (2004)

Enriched CD34(+) peripheral blood progenitor cells (PBPC) are frequently used as stem cell support in cancer patients following high dose therapy. Since precursor dendritic cells (DCs) originate from haematopoietic progenitor cells, purified CD34(+) cells might also serve as starting cells for ex- vivo production of DC. In the present study we developed a clinical grade procedure for ex- vivo production of DC derived from enriched CD34(+) cells. Different concentrations of CD34(+) cells were grown in gas-permeable Teflon bags with different serum-free and serum-containing media supplemented with GM-CSF, IL-4, TNF-alpha, SCF, Flt-3L and INF-alpha. Serum-free CellGroSCGM medium for 7 days followed by CellGroDC medium in 7 days gave the same results as serum-containing medium. After incubation the cultured cells containing immature DCs were concentrated and transfected with tumour mRNA from human prostate cancer cell lines employing a highly efficient electroporation procedure. Thawed transfected DCs were able to elicit primary T-cell responses in vitro against antigens encoded by the prostate cancer mRNA as shown by ELISPOT assay using mock-transfected DCs as control. Our results show that frozen enriched CD34(+) cells can be an alternative and efficient source for production of DCs for therapeutic purpose.