gebhart/patrepeval huggingface dataset:
Binding of microtubule protein to DNA and chromatin: possibility of simultaneous linkage of microtubule to nucleic acid and assembly of the microtubule structure (1981)

Microtubule protein binds to DNA through microtubule associated polypeptides (MAPs). Among MAPs there is one high molecular weight polypeptide (MAP2) which interacts with DNA fundamentally through certain polynucleotide sequences. This interaction is not affected by the presence of histones and other chromosomal proteins. DNA can associate to assembled microtubules and when a determinate DNA/protein ratio is reached the nucleic acid behaves as a microtubule associated molecule. The nucleic acid fragments which preferentially bind to microtubules have been isolated and characterized. These fragments contain DNA regions enriched in repetitive sequences that hybridizes preferentially to the pericentromeric zone of metaphase chromosomes. These results give further support to the model of interaction microtubule-chromosome based upon the mediator function of the microtubule associated proteins.
Loss of a Single N-Linked Glycan Allows CD4-Independent Human Immunodeficiency Virus Type 1 Infection by Altering the Position of the gp120 V1/V2 Variable Loops (2001)

The gp120 envelope glycoprotein of primary human immunodeficiency virus type 1 (HIV-1) promotes virus entry by sequentially binding CD4 and the CCR5 chemokine receptor on the target cell. Previously, we adapted a primary HIV-1 isolate, ADA, to replicate in CD4-negative canine cells expressing human CCR5. The gp120 changes responsible for CD4-independent replication were limited to the V2 loop-V1/V2 stem. Here we show that elimination of a single glycosylation site at asparagine 197 in the V1/V2 stem is sufficient for CD4-independent gp120 binding to CCR5 and for HIV-1 entry into CD4-negative cells expressing CCR5. Deletion of the V1/V2 loops also allowed CD4-independent viral entry and gp120 binding to CCR5. The binding of the wild-type ADA gp120 to CCR5 was less dependent upon CD4 at 4 degrees C than at 37 degrees C. In the absence of the V1/V2 loops, neither removal of the N-linked carbohydrate at asparagine 197 nor lowering of the temperature increased the CD4-independent phenotypes. A CCR5-binding conformation of gp120, achieved by CD4 interaction or by modification of temperature, glycosylation, or variable loops, was preferentially recognized by the monoclonal antibody 48d. These results suggest that the CCR5-binding region of gp120 is occluded by the V1/V2 variable loops, the position of which can be modulated by temperature, CD4 binding, or an N-linked glycan in the V1/V2 stem.
Laser frequency stabilization by polarization spectroscopy of a reflecting reference cavity (1980)

We propose a new scheme for locking the frequency of a laser to a resonant reference cavity. A linear polarizer or Brewster plate is placed inside the reference cavity, so that the reflected light acquires a frequency-dependent elliptical polarization. A simple polarization analyzer detects dispersion shaped resonances which can provide the error signal for electronic frequency stabilization without any need for modulation techniques.
Angiosperm genome comparisons reveal early polyploidy in the monocot lineage (2009)

Although the timing and extent of a whole-genome duplication occurring in the common lineage of most modern cereals are clear, the existence or extent of more ancient genome duplications in cereals and perhaps other monocots has been hinted at, but remain unclear. We present evidence of additional duplication blocks of deeper hierarchy than the pancereal rho (rho) duplication, covering at least 20% of the cereal transcriptome. These more ancient duplicated regions, herein called sigma, are evident in both intragenomic and intergenomic analyses of rice and sorghum. Resolution of such ancient duplication events improves the understanding of the early evolutionary history of monocots and the origins and expansions of gene families. Comparisons of syntenic blocks reveal clear structural similarities in putatively homologous regions of monocots (rice) and eudicots (grapevine). Although the exact timing of the sigma-duplication(s) is unclear because of uncertainties of the molecular clock assumption, our data suggest that it occurred early in the monocot lineage after its divergence from the eudicot clade.
Fruit Polyphenolics and Brain Aging (2002)

Nutritional interventions, in this case, increasing dietary intake of fruits and vegetables, can retard and even reverse age-related declines in brain function and in cognitive and motor performance in rats. Our lab has shown that as Fischer 344 rats age their brains are increasingly vulnerable to oxidative stress. Dietary supplementation with fruit or vegetable extracts high in antioxidants (e.g., blueberry, BB, spinach, respectively) can decrease this vulnerability to oxidative stress as assessed in vivo by examining reductions in neuronal signaling and behavioral deficits and in vitro via H2O2-induced decrements in striatal synaptosomal calcium buffering. Examinations have also revealed that BB supplementations are effective in antagonizing other age-related changes in brain and behavior, as well as decreasing indices of inflammation and oxidative stress in gastrocnemius and quadriceps muscles. In ongoing studies we are attempting to determine the most effective BB polyphenolic components. To date, the anthocyanins show the most efficacy in penetrating the cell membrane and in providing antioxidant protection. In sum, our results indicate that increasing dietary intake of fruits and vegetables high in antioxidant activity may be an important component of a healthy living strategy designed to maximize neuronal and cognitive functioning into old age.
Expression Of Estrogen Receptors α And β By Sympathetic Ganglion Neurons Projecting To The Proximal Urethra Of Female Rats (2003)

Almost all examined sympathetic neurons projecting to the proximal urethra express estrogen receptor beta and a substantial subset expresses estrogen receptor alpha irrespective of estrogen titer. Therefore, estrogen may influence continence by acting not only on the urethral target, but also on its excitatory sympathetic innervation.
Early and Selective Impairments in Axonal Transport Kinetics of Synaptic Cargoes Induced by Soluble Amyloid β‐Protein Oligomers (2012)

The downstream targets of amyloid β (Aβ)-oligomers remain elusive. One hypothesis is that Aβ-oligomers interrupt axonal transport. Although previous studies have demonstrated Aβ-induced transport blockade, early effects of low-n soluble Aβ-oligomers on axonal transport remain unclear. Furthermore, the cargo selectivity for such deficits (if any) or the specific effects of Aβ on the motility kinetics of transported cargoes are also unknown. Toward this, we visualized axonal transport of vesicles in cultured hippocampal neurons treated with picomolar (pm) levels of cell-derived soluble Aβ-oligomers. We examined select cargoes thought to move as distinct organelles and established imaging parameters that allow organelle tracking with consistency and high fidelity - analyzing all data in a blinded fashion. Aβ-oligomers induced early and selective diminutions in velocities of synaptic cargoes but had no effect on mitochondrial motility, contrary to previous reports. These changes were N-methyl D-aspartate receptor/glycogen synthase kinase-3β dependent and reversible upon washout of the oligomers. Cluster-mode analyses reveal selective attenuations in faster-moving synaptic vesicles, suggesting possible decreases in cargo/motor associations, and biochemical experiments implicate tau phosphorylation in the process. Collectively, the data provide a biological basis for Aβ-induced axonal transport deficits.
Improving Safety and Stability of Large Containerships in Automated Stowage Planning (2011)

Stowage planning is an important task in the container transportation business. The quality of stowage plans generated for ships on a multiport voyage greatly affects a shipping line's operating cost which also directly affects the competitiveness of supply-chain companies that rely on it. This paper describes ongoing research and development of an automated system for generating quality stowage plans for large containerships. The system consists of three modules: stowage plan generator, stability module and optimization engine. The focus of the study is on the stability module, which automatically generates feasible stowage plans that conform to safety and stability requirements for large-scale vessels. The module can greatly reduce the amount of ballast required by the ship and lower the cost of shipping. The proposed system is tested on a real-world large containership with more than 7000 TEUs on a multiport voyage. Experimental results show that the proposed system is able to efficiently generate feasible stowage plans using only a fraction of the time required by human planners (<;2 min per plan versus 2 hours per plan). The quality of the generated plans is also comparable to human planners in terms of the number of rehandles, crane intensity, safety and stability, all of which are crucial to shipping operations.
Control of hepatocyte metabolism by sympathetic and parasympathetic hepatic nerves (2004)

More than any other organ, the liver contributes to maintaining metabolic equilibrium of the body, most importantly of glucose homeostasis. It can store or release large quantities of glucose according to changing demands. This homeostasis is controlled by circulating hormones and direct innervation of the liver by autonomous hepatic nerves. Sympathetic hepatic nerves can increase hepatic glucose output; they appear, however, to contribute little to the stimulation of hepatic glucose output under physiological conditions. Parasympathetic hepatic nerves potentiate the insulin-dependent hepatic glucose extraction when a portal glucose sensor detects prandial glucose delivery from the gut. In addition, they might coordinate the hepatic and extrahepatic glucose utilization to prevent hypoglycemia and, at the same time, warrant efficient disposal of excess glucose.
Development of the retinotectal projection in zebrafish embryos under TTX-induced neural-impulse blockade (1990)

The influence of neural activity on the morphology of retinal-axon-terminal arbors and the precision of the developing retinotectal projection in zebrafish embryos was explored. Terminal-arbor morphology and their distribution in the tectum was determined with anatomical fiber-tracing methods using the fluorescent dyes dil and diO. To allow development under activity-deprived conditions, TTX was injected into the eyes of 30-38-hr-old zebrafish embryos at concentrations that effectively blocked neural activity both in retinal ganglion cells and throughout the CNS. Much like axons with normal neural-activity patterns, activity-deprived axons from dorsal and ventral and from temporal and nasal regions in the retina terminated over retinotopically appropriate and nonoverlapping regions of the tectum. Even after ablation of 1 hemiretina at the time of axonal outgrowth, activity-deprived axons from the remaining hemiretina grew directed toward and arborized selectively within their retinotopically appropriate tectal half in the same way as would nondeprived axons. Besides being retinotopic, the area over which small populations of activity-deprived axons from neighboring ganglion cells arborize is as small as that of active axons. The size of terminal arbors of retinal ganglion cell axons was unaffected by blockade of neural activity. The mean terminal-arbor size was 27 x 18 microns for the TTX-injected and 31 x 22 microns for the control embryos. The tectal coverage of TTX-blocked and control axons was equally small, with values of 1.4% and 1.6%, respectively. These data show that a precisely organized retinotopic map in developing zebrafish forms independent of neural-impulse activity.
Fibrin sealant promotes migration and proliferation of human articular chondrocytes: Possible involvement of thrombin and protease-activated receptors (2006)

Fibrin sealant (FS), a biological adhesive material, has been recently recommended as an adjunct in autologous chondrocyte implantation (ACI). While FS has been shown to possess osteoinductive potential, little is known about its effects on chondrogenic cells. In this study, we assessed the bioactivity of FS (Tisseel) on the migration and proliferation of human articular chondrocytes in vitro. Using a co-culture assay to mimic matrix-induced ACI (MACI), chondrocytes were found to migrate from collagen membranes towards FS within 12 h of culture, with significant migratory activity evident by 24 h. In addition, 5-bromo-2'-deoxyuridine (BrdU) incorporation experiments revealed that thrombin, the active component of the tissue glue, stimulated chondrocyte proliferation, with maximal efficacy observed at 48 h post-stimulation (1-10 U/ml). In an effort to elucidate the molecular mechanisms underlying these thrombin-induced effects, we examined the expression and activation of protease-activated receptors (PARs), established thrombin receptors. Using a combination of RT-PCR and immunohistochemistry, all four PARs were detected in human chondrocytes, with PAR-1 being the major isoform expressed. Moreover, thrombin and a PAR-1, but not other PAR-isotype-specific peptide agonists, were found to induce rapid intracellular Ca2+ responses in human chondrocytes in calcium mobilization assays. Together, these data demonstrate that FS supports both the migration and proliferation of human chondrocytes. We propose that these effects are mediated, at least in part, via thrombin-induced PAR-1 signalling in human chondrocytes.
Treg Depletion Inhibits Efficacy of Cancer Immunotherapy: Implications for Clinical Trials (2008)

Our data demonstrate for the first time, that although Treg depletion inhibits the progression/eliminates GBM tumors, its efficacy is dependent on tumor burden. We conclude that this approach will be useful in a setting of minimal residual disease. Further, we also demonstrate that Treg depletion, using PC61 in combination with immunotherapy, inhibits clonal expansion of tumor antigen-specific T cells, suggesting that new, more specific targets to block Tregs will be necessary when used in combination with therapies that activate anti-tumor immunity.
Double-Blinded Randomized Study of High-Dose Calcitriol Plus Docetaxel Compared With Placebo Plus Docetaxel in Androgen-Independent Prostate Cancer: A Report From the ASCENT Investigators (2007)

This study suggests that DN-101 treatment was associated with improved survival, but this will require confirmation because survival was not a primary end point. The addition of weekly DN-101 did not increase the toxicity of weekly docetaxel.
Microemulsions: A Novel Approach to Enhanced Drug Delivery (2008)

Microemulsions are isotropic, thermodynamically stable transparent (or translucent) systems of oil, water and surfactant, frequently in combination with a cosurfactant with a droplet size usually in the range of 20-200 nm. They can be classified as oil-in-water (o/w), water-in-oil (w/o) or bicontinuous systems depending on their structure and are characterized by ultra low interfacial tension between oil and water phases. These versatile systems are currently of great technological and scientific interest to the researchers because of their potential to incorporate a wide range of drug molecules (hydrophilic and hydrophobic) due to the presence of both lipophilic and hydrophilic domains. These adaptable delivery systems provide protection against oxidation, enzymatic hydrolysis and improve the solubilization of lipophilic drugs and hence enhance their bioavailability. In addition to oral and intravenous delivery, they are amenable for sustained and targeted delivery through ophthalmic, dental, pulmonary, vaginal and topical routes. Microemulsions are experiencing a very active development as reflected by the numerous publications and patents being granted on these systems. They have been used to improve the oral bioavailability of various poorly soluble drugs including cyclosporine and paclitaxel as professed by Hauer et al., US patent 7235248, and Gao et al., US patent 7115565, respectively. Furthermore, they can be employed for challenging tasks such as carrying chemotherapeutic agents to neoplastic cells and oral delivery of insulin as diligently described by Maranhao, US patent 5578583 and Burnside et al., US patent 5824638 respectively. The recent commercial success of Sandimmune Neoral (Cyclosporine A), Fortovase (Saquinavir), Norvir (Ritonavir), etc. also reflects the tremendous potential of these newer drug therapeutic systems. A critical evaluation of recent patents claiming different approaches to improve the drug delivery is the focus of the current review.
Aberrant structures of fecal bacterial community in allergic infants profiled by 16S rRNA gene pyrosequencing (2011)

We investigated the correlation between fecal bacteria composition in early infancy and the prevalence of allergic diseases in late infancy. The fecal microbiota in the first 2 months was profiled using the 16S rRNA V6 short-tag sequences in the community and statistically compared between two groups of subjects who did and did not show allergic symptoms in the first 2 years (n = 11 vs. 11). In the allergic group, genus Bacteroides at 1 month and genera Propionibacterium and Klebsiella at 2 months were more abundant, and genera Acinetobacter and Clostridium at 1 month were less abundant than in the nonallergic group. Allergic infants who showed high colonization of Bacteroides and/or Klebsiella showed less colonization of Clostridium perfringens/butyricum, suggesting antagonism between these bacterial groups in the gastrointestinal tract. It was also remarkable that the relative abundance of total Proteobacteria, excluding genus Klebsiella, was significantly lower in the allergic than in the nonallergic group at the age of 1 month. These results indicate that pyrosequence-based 16S rRNA gene profiling is valid to find the intestinal microbiotal disorder that correlates with allergy development in later life.
Viewpoint invariant 3D landmark model inference from monocular 2D images using higher-order priors (2011)

In this paper, we propose a novel one-shot optimization approach to simultaneously determine both the optimal 3D landmark model and the corresponding 2D projections without explicit estimation of the camera viewpoint, which is also able to deal with misdetections as well as partial occlusions. To this end, a 3D shape manifold is built upon fourth-order interactions of landmarks from a training set where pose-invariant statistics are obtained in this space. The 3D-2D consistency is also encoded in such high-order interactions, which eliminate the necessity of viewpoint estimation. Furthermore, the modeling of visibility improves further the performance of the method by handling missing correspondences and occlusions. The inference is addressed through a MAP formulation which is naturally transformed into a higher-order MRF optimization problem and is solved using a dual-decomposition-based method. Promising results on standard face benchmarks demonstrate the potential of our approach.
Structure and Enzymology of ADP-ribosyl Cyclases: Conserved Enzymes that Produce Multiple Calcium Mobilizing Metabolites (2004)

Cyclic ADP-ribose is an important calcium mobilizing metabolite produced by the ADP-ribosyl cyclase (cyclases) family of enzymes. Three evolutionarily conserved ADP-ribosyl cyclase superfamily members have been identified, one from the invertebrate Aplysia californica and two from mammalian tissues, CD38 and CD157. CD38 regulates calcium signaling in a number of cell types, and it was recently shown that cyclic ADP-ribose produced by CD38 modulates calcium mobilization induced upon chemokine receptor engagement. Excitingly, because immunocytes deficient in CD38 are unable to migrate to inflammatory sites in vivo, this enzyme has now become an attractive target for drug development. To rationally design inhibitors it is critical to understand the mechanism(s) by which CD38 catalyzes the transformation of its substrate NAD+ into cyclic ADP-ribose. Likewise, it is necessary to identify the CD38 substrate-binding site. Importantly, significant progress has been made in these two areas and much is now known about the structure and enzymology of CD38 and the other ADP-ribosyl cyclase superfamily members. In this review, we will outline the critical data demonstrating a role for CD38 in regulating calcium mobilization in mammalian cells. We will also describe the crystallographic data and site-directed mutagenesis studies that have helped to elucidate the CD38 structure and the identification of its active site and key catalytic residues. Finally, we will address the important advances in our understanding of the kinetic and molecular mechanisms that control cyclic ADP-ribose production by CD38.
Surveillance in hereditary nonpolyposis colorectal cancer (1993)

During its second meeting at Amsterdam in 1990, the International Collaborative Group on Hereditary Non-Polyposis Colorectal Cancer (ICG-HNPCC) decided to carry out a pilot study on colorectal cancer surveillance in HNPCC. The objectives of the study were to ascertain in each of the participating centers the number of HNPCC families, the recommended screening procedures, the age at diagnosis of colorectal cancer (CRC), and the occurrence of interval cancers. Nine centers in seven countries including Denmark, Finland, Italy, Japan, The Netherlands, Switzerland, and the United States participated. Data were derived from a total of 165 families. With respect to screening, half of the centers advise colonoscopy as the only procedure. The interval between the consecutive examinations varies from one to three years. In the majority of the centers, screening begins at 20 to 25 years. Lifelong screening is recommended by three centers, while the rest advise discontinuation at age 60 to 75 years. The family material included 840 patients with colorectal cancer. The mean age at diagnosis was 45 years, and about 15 percent were diagnosed at age 60 or later. A total of 682 high-risk relatives are being followed. After the follow-up of 1 to 10 years in these families, only six cases of interval cancers were encountered.