gebhart/patrepeval huggingface dataset:
Oct‐4 : Gatekeeper in the Beginnings of Mammalian Development (2001)

The Oct-4 POU transcription factor is expressed in mouse totipotent embryonic stem and germ cells. Differentiation of totipotent cells to somatic lineages occurs at the blastocyst stage and during gastrulation, simultaneously with Oct-4 downregulation. Stem cell lines derived from the inner cell mass and the epiblast of the mouse embryo express Oct-4 only if undifferentiated. When embryonic stem cells are triggered to differentiate, Oct-4 is downregulated thus providing a model for the early events linked to somatic differentiation in the developing embryo. In vivo mutagenesis has shown that loss of Oct-4 at the blastocyst stage causes the cells of the inner cell mass to differentiate into trophectoderm cells. Recent experiments indicate that an Oct-4 expression level of roughly 50%-150% of the endogenous amount in embryonic stem cells is permissive for self-renewal and maintenance of totipotency. However, upregulation above these levels causes stem cells to express genes involved in the lineage differentiation of primitive endoderm. These novel advances along with latest findings on Oct-4-associated factors, target genes, and dimerization ability, provide new insights into the understanding of the early steps regulating mammalian embryogenesis.
High density lipoprotein loses its effect to stimulate efflux of cholesterol from foam cells after oxidative modification. (1991)

In this study, we performed oxidative modification of high density lipoprotein (HDL) in vitro. The amount of lipid peroxide increased when either HDL2 or HDL3 was incubated with phosphate-buffered saline containing 5 microM CuSO4 for 24 h at 37 degrees C, indicating that both fractions of HDL were oxidatively modified. This modification resulted in denaturation of apolipoprotein AI on SDS/PAGE and increased the negative charge on agarose gel electrophoresis. When incubated with macrophage-derived foam cells, native HDL caused a marked efflux of cholesterol from them, leading to a decrease in the amount of cholesteryl ester in the cells. However, oxidized HDL showed a lessened effect on the decrease of cholesteryl ester in foam cells. These data suggest that oxidative modification of HDL may stimulate development of atherosclerosis by limiting efflux of cholesterol from foam cells.
Riluzole inhibits the persistent sodium current in mammalian CNS neurons (2000)

The effects of 0.1-100 microM riluzole, a neuroprotective agent with anticonvulsant properties, were studied on neurons from rat brain cortex. Patch-clamp whole-cell recordings in voltage-clamp mode were performed on thin slices to examine the effects of the drug on a noninactivating (persistent) Na+ current (INa,p). INa,p was selected because it enhances neuronal excitability near firing threshold, which makes it a potential target for anticonvulsant drugs. When added to the external solution, riluzole dose-dependently inhibited INa,p up to a complete blocking of the current (EC50 2 microM), showing a significant effect at therapeutic drug concentrations. A comparative dose-effect study was carried out in the same cells for the other main known action of riluzole, the inhibitory effect on the fast transient sodium current. This effect was confirmed in our experiments, but we found that it was achieved at levels much higher than putative therapeutic concentrations. Only the effect on INa,p, and not that on fast sodium current, can account for the reduction in neuronal excitability observed in cortical neurons following riluzole treatment at therapeutic concentrations, and this might represent a novel mechanism accounting for the anticonvulsant and neuroprotective properties of riluzole.
Effects of electric fields on transmembrane potential and excitability of turtle cerebellar Purkinje cells in vitro. (1988)

1. Transmembrane potential (TMP) responses of Purkinje cells (PCs) in isolated turtle cerebellum to externally applied quasi-steady-state electric fields aligned with the dendritic axis were continuously measured using simultaneous intracellular and extracellular recording. TMP was obtained by subtraction of extracellular voltage fields from intracellular potential recorded at the same depth in the cerebellum. 2. The applied field changed the TMP with the polarity and amplitude dependent on the location on the PC membrane. This response at a given location increased linearly with external field up to a threshold level, beyond which active responses appeared. 3. The basic effect on TMP consisted of depolarization in the half of the dendrite towards which the fields were directed, and hyperpolarization in the other half. A pooled TMP depth-profile shows a steady increase in polarization from the middle of the molecular layer towards each end. This profile correlates with that predicted from previously proposed cable models, giving them empirical support for the first time. 4. Active responses were triggered by the field-induced depolarization. Tetrodotoxin (TTX)-sensitive action potentials arose with the primary depolarization in the somatic region. Notched, Ca2+-dependent action potentials arose with primary depolarization in the distal and mid-dendritic regions. 5. A TTX-sensitive voltage plateau was triggered by TMP-depolarization in the proximal region. It in turn activated Na+-spike trains. The frequency of spiking was proportional to the external field. At around 160 spikes/s, the Na+ spikes inactivated, and the TMP level rose to a more depolarized plateau. This latter plateau was also TTX-sensitive. 6. During depolarization of the distal dendritic region, sometimes a Ca2+-dependent plateau was observed. It appears to be associated with a small conductance increase. 7. Field-induced hyperpolarization suppressed local spiking and voltage plateaux, but remote Ca2+ spikes with reduced amplitude appeared in recordings from the proximal region. Similarly, in the distal region, low-amplitude, remote Na+ spikes and a Na+ plateau were observed superimposed on the hyperpolarizing baseline. The Na+ plateau apparently did not contribute to shunting of membrane currents in the distal dendrite. 8. The phase characteristics of the action potentials correlate with the modulation pattern noted in our extracellular study (Chan & Nicholson, 1986). Thus, the extracellular units ("giant spikes") were probably Na+ spikes activated in the soma and spread distally. Occasionally Ca2+ spikes, with a higher threshold, might also be activated to give dual-phase response.(ABSTRACT TRUNCATED AT 400 WORDS)
Optical Control of CRISPR/Cas9 Gene Editing (2015)

The CRISPR/Cas9 system has emerged as an important tool in biomedical research for a wide range of applications, with significant potential for genome engineering and gene therapy. In order to achieve conditional control of the CRISPR/Cas9 system, a genetically encoded light-activated Cas9 was engineered through the site-specific installation of a caged lysine amino acid. Several potential lysine residues were identified as viable caging sites that can be modified to optically control Cas9 function, as demonstrated through optical activation and deactivation of both exogenous and endogenous gene function.
Optimizing the dose of zolmitriptan (Zomig,* 311C90) for the acute treatment of migraine (1997)

This study investigated the efficacy of zolmitriptan (Zomig, formerly 311C90) in acute migraine therapy. Patients with a history of migraine were randomized in a double-blind, multicenter, placebo-controlled, dose range-finding study of oral zolmitriptan 1, 2.5, 5, or 10 mg versus placebo for the treatment of a severe or moderate migraine headache. Patients with persistent or recurrent headache 4 to 24 hours after the initial dose, who did not take escape medication, were eligible to receive a second blinded dose of either zolmitriptan or placebo. Of 1,144 patients treated, 999 evaluable patients completed the study. The headache response rates with zolmitriptan doses > or = 2.5 mg were 44 to 51% at 1 hour, 65 to 67% at 2 hours, and 75 to 78% at 4 hours (all significantly superior to placebo). Also, zolmitriptan effectively relieved migraine-associated symptoms such as nausea, photophobia and phonophobia, and reduced activity impairment. Rates of headache recurrence, headache persistence, and use of escape medication were lower with zolmitriptan doses > or = 2.5 mg than with placebo. In patients with persistent or recurrent headache, a second zolmitriptan dose effectively treated both headache and nonheadache symptoms. Zolmitriptan was well tolerated, with a lower incidence of adverse events being reported with doses < or = 2.5 mg than with those > or = 5 mg. Zolmitriptan is a well tolerated and effective acute migraine therapy providing rapid relief of migraine headache within 1 hour. A clear dose-response relationship between efficacy and tolerability suggests that 2.5 mg is the optimal initial dose for the acute treatment of a migraine attack.
Effects of dietary omega-3 polyunsaturated fatty acids on brain gene expression (2004)

Polyunsaturated fatty acids (PUFA) are essential structural components of the central nervous system. Their role in controlling learning and memory has been well documented. A nutrigenomic approach with high-density microarrays was used to reveal brain gene-expression changes in response to different PUFA-enriched diets in rats. In aged rats fed throughout life with PUFA-enriched diets, genes with altered expressions included transthyretin, alpha-synuclein, and calmodulins, which play important roles in synaptic plasticity and learning. The effect of perinatal omega-3 PUFA supply on gene expression later in life also was studied. Several genes showed similar changes in expression in rats fed omega-3-deficient diets in the perinatal period, regardless of whether they or their mothers were fed omega-3 PUFA-sufficient diets after giving birth. In this experiment, among the down-regulated genes were a kainate glutamate receptor and a DEAD-box polypeptide. Among the up-regulated genes were a chemokine-like factor, a tumor necrosis factor receptor, and cytochrome c. The possible involvement of the genes with altered expression attributable to different diets in different brain regions in young and aged rats and the possible mode of regulatory action of PUFA also are discussed. We conclude that PUFA-enriched diets lead to significant changes in expression of several genes in the central nervous tissue, and these effects appear to be mainly independent of their effects on membrane composition. The direct effects of PUFA on transcriptional modulators, the downstream developmentally and tissue-specifically activated elements might be one of the clues to understanding the beneficial effects of the omega-3 PUFA on the nervous system.
The Related Adhesion Focal Tyrosine Kinase Is Tyrosine-phosphorylated after β1-Integrin Stimulation in B Cells and Binds to p130cas (1997)

Integrin ligation initiates intracellular signaling events, among which are the activation of protein tyrosine kinases. The related adhesion focal tyrosine kinase (RAFTK), also known as PYK2 and CAKbeta, is a tyrosine kinase that is homologous to the focal adhesion kinase (FAK) p125FAK. The structure of RAFTK is similar to p125FAK in that it lacks a transmembrane region, does not contain Src homology 2 or 3 domains, and has a proline-rich region in its C terminus. Here we report that RAFTK is a target for beta1-integrin-mediated tyrosine phosphorylation in both transformed and normal human B cells. Ligation of the B cell antigen receptor also induced tyrosine phosphorylation of RAFTK. Phosphorylation of RAFTK following integrin- or B cell antigen receptor-mediated stimulation was decreased by prior treatment of cells with cytochalasin B, indicating that this process was at least partially cytoskeleton-dependent. One of the tyrosine-phosphorylated substrates after integrin stimulation in fibroblasts is p130cas, which can associate with p125FAK. RAFTK also interacted constitutively with p130cas in B cells, since p130cas was detected in RAFTK immunoprecipitates. Although the function of RAFTK remains unknown, these data suggest that RAFTK may have a significant function in integrin-mediated signaling pathways in B cells.
Cell-Directed Assembly of Bio/Nano Interfaces—A New Scheme for Cell Immobilization (2007)

When lipid-directed assembly of silicic acid precursors is conducted in the presence of living cells, the cells intervene, surrounding themselves with a fluid, multilayered lipid vesicle that interfaces coherently with an ordered silica mesophase. This bio/nano interface is unique in that its uniform nanostructure prevents excessive drying of water, maintaining cell viability, yet provides accessibility of the cell surface to small molecules. In comparison to existing immobilization schemes, such as encapsulation within sol-gel matrices, we show this interface to form by an active interplay between the living cell and surrounding matrix, which we refer to as cell-directed assembly (CDA). Importantly and perhaps uniquely, CDA creates a localized nanostructured microenvironment within which three-dimensional chemical gradients are established and maintained.
Assembly and remodelling of myofibrils and intercalated discs in cultured neonatal rat heart cells (1986)

The reorganization of myofibrils and the re-formation of intercalated discs was examined in neonatal rat cardiac muscle cells during the first 72 h of culture. Rhodamine phalloidin was used to monitor the organizational state of the myofibrils and antibodies to desmoplakin and vinculin were used as markers for the presence of desmosomes and fasciae adherentes, respectively. Tiny punctate desmosomes were observed between muscle cells after 24 h and apparently increased in number and/or size between 24 and 48 h in culture. Fasciae adherentes were not detectable with antibodies to vinculin until after 48 h in culture. Well-defined sarcomeres were restored after 48 h in culture. Once formed the sarcomeric organization of the myofibrils was found to be stable provided they were attached to the sarcolemma via intercalated discs. However, if the myofibrils attached to regions of the membrane that lacked intercalated discs the sarcomeres appeared to break down gradually centripetally. When myofibrils attached to the membrane at the free edges of cells that were not in contact with other muscle cells, the striations stopped abruptly at a considerable distance before the myofibril attached to the membrane. These non-striated terminals elongated between 48 and 72 h and were associated with focal contacts that contained vinculin. Overall the results suggest that cell-cell contact may be critical for the stabilization of normal myofibrillar structure in the heart.
Bottom-Up Fill of Copper in Deep Submicrometer Holes by Electroless Plating (2004)

Bottom-up fill of Cu in deep submicrometer via holes was achieved through electroless plating alone for the first time. We investigated the effect of addition of inhibitor molecules to electroless Cu plating solution, and found that sulfopropyl sulfonate (SPS) was highly effective in promoting the bottom-up fill. The tendency for bottom-up filling was enhanced by shrinkage of the hole diameter. This suggests that the diffusion flux of SPS molecules to the bottom of holes was more suppressed for smaller holes. Thus, the Cu deposition rate near the hole bottom is larger than that outside the hole, leading to bottom-up filling. © 2004 The Electrochemical Society. All rights reserved.
Photocleavable peptide hydrogel arrays for MALDI-TOF analysis of kinase activity (2006)

We have developed an acrylamide copolymerization strategy to immobilize acrylamide labeled peptides and proteins into a hydrogel surface and detect their modifications using MALDI-TOF mass spectrometry. Copolymerization into hydrogels is robust, compatible with "off-the-shelf" chemistry, and yields materials and surfaces that are stable to aqueous or organic solvents, drying, high or low temperature, high or low pH, oxidizing agents, sonication, mechanical contact, etc. The use of acrylamide hydrogels allows immobilization of substrates in a hydrated environment that can be used both as a biological reaction matrix and as a MALDI target. In our strategy, a substrate peptide was designed in a modular fashion to include both modification site and affinity domains. It was labeled with an acrylamide functionality using a generalized chemistry and covalently attached to the surface with a photocleavable linker, allowing for aggressive washing to remove any fouling, followed by selective release for MALDI-TOF analysis. Using this system we were able to analyze and compare v-Abl (truncated) and c-Abl (full-length) kinase activity on a peptide substrate with an affinity domain specific for the full-length kinase, observing excellent overall reproducibility in the extent of phosphorylation detected. This work serves as proof of principle for modular substrate design strategies for mass spectrometry-readable biosensors.
Presence of a novel primary response gene ST2L, encoding a product highly similar to the interleukin 1 receptor type 1 (1993)

In the course of studying the ST2 gene, which was initially found to be expressed specifically at the G0/G1 transitional state in BALB/c-3T3 cells and was one of the primary response genes, we found another ST2-related mRNA, designated as ST2L, in serum-stimulated BALB/c-3T3 cells in the presence of cycloheximide. Nucleotide sequence analysis of the cloned ST2L cDNA revealed that it had an open reading frame encoding a polypeptide of 567 amino acids. A 5' region (1,028 nucleotides) of ST2L cDNA was identical with the ST2 cDNA, and a unique 3' region encoded a putative transmembrane domain of 24 amino acids and a cytoplasmic domain of 201 amino acids. The ST2 gene product is highly similar to the extracellular portion of IL-1 receptors type 1 and type 2, and the ST2L gene product shows a marked similarity with entire IL-1 receptor type 1.
Potent Inhibition of Ribonuclease A by Oligo(vinylsulfonic Acid) (2003)

Ribonuclease A (RNase A) can make multiple contacts with an RNA substrate. In particular, the enzymatic active site and adjacent subsites bind sequential phosphoryl groups in the RNA backbone through Coulombic interactions. Here, oligomers of vinylsulfonic acid (OVS) are shown to be potent inhibitors of RNase A that exploit these interactions. Inhibition is competitive with substrate and has Ki = 11 pm in assays at low salt concentration. The effect of salt concentration on inhibition indicates that nearly eight favorable Coulombic interactions occur in the RNase A.OVS complex. The phosphonic acid and sulfuric acid analogs of OVS are also potent inhibitors although slightly less effective. OVS is also shown to be a contaminant of MES and other buffers that contain sulfonylethyl groups. Oligomers greater than nine units in length can be isolated from commercial MES buffer. Inhibition by contaminating OVS is responsible for the apparent decrease in catalytic activity that has been observed in assays of RNase A at low salt concentration. Thus, OVS is both a useful inhibitor of RNase A and a potential bane to chemists and biochemists who use ethanesulfonic acid buffers.
Maximum-diversity transmissions over doubly selective wireless channels (2003)

High data rates and multipath propagation give rise to frequency-selectivity of wireless channels, while carrier frequency offsets and mobility-induced Doppler shifts introduce time-selectivity in wireless links. The resulting time- and frequency-selective (or doubly selective) channels offer joint multipath-Doppler diversity gains. Relying on a basis expansion model of the doubly selective channel, we prove that the maximum achievable multipath-Doppler diversity order is determined by the rank of the correlation matrix of the channel's expansion coefficients, and is multiplicative in the effective degrees of freedom that the channel exhibits in the time and frequency dimensions. Interestingly, it turns out that time-frequency reception alone does not guarantee maximum diversity, unless the transmission is also designed judiciously. We design such block precoded transmissions. The corresponding designs for frequency-selective or time-selective channels follow as special cases, and thorough simulations are provided to corroborate our theoretical findings.
Microring-resonator filter with doubled free-spectral-range by two-point coupling (2005)

Two-point coupling is used to double the free-spectral-range (FSR) of a microring-resonator filter. The filter, designed using rigorous electromagnetic simulations and fabricated using e-beam lithography, demonstrates 22 dB resonance suppression yielding a 40.8 nm FSR
Tendon and ligament regeneration and repair: Clinical relevance and developmental paradigm (2013)

As dense connective tissues connecting bone to muscle and bone to bone, respectively, tendon and ligament (T/L) arise from the somitic mesoderm, originating in a recently discovered somitic compartment, the syndetome. Inductive signals from the adjacent sclerotome and myotome upregulate expression of Scleraxis, a key transcription factor for tenogenic and ligamentogenic differentiation. Understanding T/L development is critical to establishing a knowledge base for improving the healing and repair of T/L injuries, a high-burden disease due to the intrinsically poor natural healing response. Current treatment of the three most common tendon injuries-tearing of the rotator cuff of the shoulder, flexor tendon of the hand, and Achilles tendon-include mostly surgical repair and/or conservative approaches, including biophysical modalities such as rehabilitation and cryotherapy. Unfortunately, the fibrovascular scar formed during healing possesses inferior mechanical and biochemical properties, resulting in compromised tissue functionality. Regenerative approaches have sought to augment the injured tissue with cells, scaffolds, bioactive agents, and mechanical stimulation to improve the natural healing response. The key challenges in restoring full T/L function following injury include optimal combination of these biological agents as well as their delivery to the injury site. A greater understanding of the molecular mechanisms involved in T/L development and natural healing, coupled with the capability of producing complex biomaterials to deliver multiple biofactors with high spatiotemporal resolution and specificity, should lead to regenerative procedures that more closely recapitulate T/L morphogenesis, thereby offering future patients the prospect of T/L regeneration, as opposed to simple tissue repair.
Viruses and Apoptosis (1999)

Successful viral replication requires not only the efficient production and spread of progeny, but also evasion of host defense mechanisms that limit replication by killing infected cells. In addition to inducing immune and inflammatory responses, infection by most viruses triggers apoptosis or programmed cell death of the infected cell. This cell response often results as a compulsory or unavoidable by-product of the action of critical viral replicative functions. In addition, some viruses seem to use apoptosis as a mechanism of cell killing and virus spread. In both cases, successful replication relies on the ability of certain viral products to block or delay apoptosis until sufficient progeny have been produced. Such proteins target a variety of strategic points in the apoptotic pathway. In this review we summarize the great amount of recent information on viruses and apoptosis and offer insights into how this knowledge may be used for future research and novel therapies.