gebhart/patrepeval huggingface dataset:
Quantal entry of diphtheria toxin to the cytosol. (1985)

The rate-limiting step in diphtheria toxin (DT) intoxication of Vero cells has been determined utilizing cycloheximide as an inhibitor of the intoxication process. Cycloheximide is shown to inhibit the toxin catalyzed ADP-ribosylation of elongation factor 2 (EF-2). The inhibition is blocked by puromycin thus establishing the ribosome as the location of cycloheximide protection. Washing cells free of cycloheximide rapidly reverses the protective effect. The initial rates of protein synthesis inhibition observed after removal of cycloheximide from DT-intoxicated cells are 5 to 12-fold greater than rates observed in unprotected cells and are shown to reflect ADP-ribosylation of EF-2 by cytosolic DT. Ten to thirty minutes after cycloheximide removal, the rate of protein synthesis inhibition abruptly changes to values identical to those of unprotected cells. Both the initial rates and extent of the initial rapid inactivation are directly related to toxin concentration and time of incubation with DT in the presence of cycloheximide. We concluded that: the rate-limiting step in protein synthesis inhibition by DT is not the ADP-ribosylation of EF-2 by cytosolic toxin but rather the earlier entry step of DT into the cytosol. DT enters the cytosol as a bolus of sufficient size to rapidly inactivate all EF-2 in that cell. It is inferred from 1 and 2 that the first order inactivation rate exhibited by DT is the result of the probability of the release of a bolus of toxin to the cytosol of any cell in the population per unit time. Autoradiographic analysis of intoxicated cell populations support this two-population state model. The size of a single bolus or quantum of DT is calculated from data over the range of 10(-11) to 10(-9) M DT and is found to remain constant. We suggest that the cytosolic entry mechanism of DT results from a unique ability of the internalized toxin molecules to destabilize the vesicular membrane resulting in a random release of a bolus of toxin into the cytosol. Because the bolus size remains constant over a 50-fold change in receptor occupancy the possibility is raised that DT undergoes a post-receptor packaging process, package size remaining a constant and package number increasing with receptor occupancy.
THE IMPACT OF INSECTICIDES AND HERBICIDES ON THE BIODIVERSITY AND PRODUCTIVITY OF AQUATIC COMMUNITIES (2005)

Pesticides constitute a major anthropogenic addition to natural communities. In aquatic communities, a great majority of pesticide impacts are determined from single‐species experiments conducted under laboratory conditions. Although this is an essential protocol to rapidly identify the direct impacts of pesticides on organisms, it prevents an assessment of direct and indirect pesticide effects on organisms embedded in their natural ecological contexts. In this study, I examined the impact of four globally common pesticides (two insecticides, carbaryl [Sevin] and malathion; two herbicides, glyphosate [Roundup] and 2,4‐D) on the biodiversity of aquatic communities containing algae and 25 species of animals. Species richness was reduced by 15% with Sevin, 30% with malathion, and 22% with Roundup, whereas 2,4‐D had no effect. Both insecticides reduced zooplankton diversity by eliminating cladocerans but not copepods (the latter increased in abundance). The insecticides also reduced the diversity and biomass of predatory insects and had an apparent indirect positive effect on several species of tadpoles, but had no effect on snails. The two herbicides had no effects on zooplankton, insect predators, or snails. Moreover, the herbicide 2,4‐D had no effect on tadpoles. However, Roundup completely eliminated two species of tadpoles and nearly exterminated a third species, resulting in a 70% decline in the species richness of tadpoles. This study represents one of the most extensive experimental investigations of pesticide effects on aquatic communities and offers a comprehensive perspective on the impacts of pesticides when nontarget organisms are examined under ecologically relevant conditions.
External Guide Sequences for an RNA Enzyme (1990)

Ribonuclease P (RNase P) from Escherichia coli or its catalytic RNA subunit can efficiently cleave small RNA substrates that lack the conserved features of natural substrates of RNase P if an additional small RNA is also present. This additional RNA must contain a sequence complementary to the substrate [external guide sequence (EGS)] and a 3'-proximal CCA sequence to ensure cleavage. The aminoacyl acceptor stem and some additional 5'- and 3'-terminal sequences of a precursor transfer RNA are sufficient to allow efficient cleavage by RNAase P, and the 2'-hydroxyl group at the cleavage site is not absolutely necessary for cleavage. In principle, any RNA could be targeted by a custom-designed EGS RNA for specific cleavage by RNase P in vitro or in vivo.
Analysis of maize brittle-1 alleles and a defective Suppressor-mutator-induced mutable allele. (1991)

A mutant allele of the maize brittle-1 (bt1) locus, brittle-1-mutable (bt1-m), was shown genetically and molecularly to result from the insertion of a defective Suppressor-mutator (dSpm) transposable element. An Spm-hybridizing restriction enzyme fragment, which cosegregates with the bt1-m allele and is absent from wild-type revertants of bt1-m, was identified and cloned. Non-Spm portions of it were used as probes to identify wild-type (Bt1) cDNAs in an endosperm library. The 4.3-kb bt1-m genomic clone contains a 3.3-kb dSpm, which is inserted in an exon and is composed of Spm termini flanking non-Spm sequences. RNA gel blot analyses, using a cloned Bt1 cDNA probe, indicated that Bt1 mRNA is present in the endosperm of developing kernels and is absent from embryo or leaf tissues. Several transcripts are produced by bt1-m. The deduced translation product from a 1.7-kb Bt1 cDNA clone has an apparent plastid transit peptide at its amino terminus and sequence similarity to several mitochondrial inner-envelope translocator proteins, suggesting a possible role in amyloplast membrane transport.
Anatomy of orofacial structures (1977)

Part 1 Introduction: oral cavity. Part 2 Oral histology and embryology: basic tissues development of orofacial complex dental lamina and enamel organ enamel, dentin and pulp root formation and attachment apparatus eruption and shedding of teeth oral mucous membrane the tongue salivary glands test for Parts 1 and 2. Part 3 Head and neck anatomy: osteology of the skull nose, nasal cavity and paranasal sinuses muscles of mastication, hyoid muscles, and sternocleidomastoid and trapezius muscle temporomandibular joint muscles of facial expression soft palate and pharynx arterial supply and venous drainage salivary glands nervous system lymphatics and spread of dental infection test for Part 3. Part 4 Dental anatomy: the tooth - functions and terms fundamental and preventive curvatures - proximal alignment of the teeth and protection of the periodontium dentition development, form and eruption occlusion dental anomalies supporting structures - the periodontium clinical considerations tooth identification incisors canines premolars molars deciduous dentition test for Part 4 test answers.
Beat-To-Beat Variations of Heart Rate Reflect Modulation of Cardiac Autonomic Outflow (1990)

What is most intriguing about heart rate (HR) variability is that there is so much of it. HR is constantly responding both rapidly and slowly to various physiological perturbations. We now understand that the frequency and amplitude of these HR fluctuations are indicative of the autonomic control systems underlying the response.
Limits of control flow on parallelism (1992)

This paper discusses three techniques useful in relaxing the constraints imposed by control flow on parallelism: control dependence analysis, executing multiple flows of control simultaneously, and speculative execution. We evaluate these techniques by using trace simulations to find the limits of parallelism for machines that employ different combinations of these techniques. We have three major results. First, local regions of code have limited parallelism, and control dependence analysis is useful in extracting global parallelism from different parts of a program. Second, a superscalar processor is fundamentally limited because it cannot execute independent regions of code concurrently. Higher performance can be obtained with machines, such as multiprocessors and dataflow machines, that can simultaneously follow multiple flows of control. Finally, without speculative execution to allow instructions to execute before their control dependences are resolved, only modest amounts of parallelism can be obtained for programs with complex control flow.
Infliximab in the treatment of adult Still's disease refractory to conventional therapy. (2001)

In this study we evaluated the efficacy of Infliximab in the treatment of adult Still's disease (ASD) refractory to conventional therapy. Three patients with chronic and active ASD unresponsive to corticosteroids and methotrexate were given intravenous Infliximab infusions at a dosage of 3 mg/kg at weeks 0, 2, 6 and then once every 8 weeks. Methotrexate was maintained in all cases at a dosage of 15 mg/week, whereas the prednisone dose was modified according to disease activity. The follow-up lasted 50 weeks and disease activity improved in all cases during Infliximab therapy. Two patients presented arthralgias and sore throat at 20 and 28 weeks, that was rapidly controlled by Infliximab reinfusion every 4 weeks. One patient relapsed at 18 weeks and dropped out at 22 weeks due to an urticarioid rash after the beginning of the fifth infusion. Infliximab may be effective in the treatment of relapse of ASD refractory to conventional therapy and requiring continuous high dose corticosteroid medication. Further studies are needed to evaluate the long-term safety, efficacy and the optimal schedule of infusion.
Genetically targeted radiotherapy for multiple myeloma (2003)

Multiple myeloma is a disseminated neoplasm of terminally differentiated plasma cells that is incurable with currently available therapies. Although the disease is radiosensitive, external beam radiation leads to significant toxicity due to sensitive end-organ damage. Thus, genetic approaches for therapy are required. We hypothesized that the incorporation of immunoglobulin promoter and enhancer elements in a self-inactivating (SIN) lentiviral vector should lead to specific and high-level transgene expression in myeloma cells. A SIN lentivector with enhanced green fluorescent protein (EGFP) expression under the control of a minimal immunoglobulin promoter as well as the Kappa light chain intronic and 3' enhancers transduced myeloma cell lines with high efficiency (30%-90%). EGFP was expressed at a high level in myeloma cells but silent in all nonmyeloma cell lines tested compared with the cytomegalovirus (CMV) promoter/enhancer. Transduction of myeloma cells with the targeted vector coding for the human sodiumiodide symporter (hNIS) led to hNIS expression by these cells allowing them to concentrate radioiodine up to 18-fold compared with controls. Tumor xenografts in severe combined immunodeficiency mice expressing hNIS could be imaged using iodine-123 (123I) and shown to retain iodide for up to 48 hours. These tumor xenografts were completely eradicated by a single dose of the therapeutic isotope iodine-131 (131I) without evidence of recurrence up to 5 months after therapy. We conclude that lentivectors can be transcriptionally targeted for myeloma cells and the use of hNIS as a therapeutic gene for myeloma in combination with 131I needs further exploration.
Time-hopping sequence design for narrowband interference suppression (2005)

In this paper, we present a simple interference mitigation solution for the coexistence of ultra-wideband (UWB) systems with other wireless systems. Specifically, we consider the design of time-hopping (TH) codes for UWB systems that deploy an impulse radio architecture. We give a methodology for the construction of TH sequences that minimize the imposed UWB interference on a given narrowband system. To illustrate the effectiveness of our designed codes, we conduct physical layer simulations of the interference induced by UWB signals on close proximity wireless local area networks (WLANs) that deploy the IEEE 802.11a standard. Our performance measure is the IEEE 802.11a client rate degradation vs. distance from its access point. Our results show that, when using optimized TH codes, UWB systems can have no impact on the achievable data-rates and range of IEEE 802.11a WLAN devices; regardless of the position of the UWB system with respect to these devices.
Longevity Regulation by Drosophila Rpd3 Deacetylase and Caloric Restriction (2002)

Genetic studies of single gene mutations are revealing mechanisms and pathways that regulate longevity across distant species ([1][1]). One such mechanism is an alteration in histone deacetylase activity. Abolishing expression of the Rpd3 deacetylase ([2][2]) or increasing expression of the Sir2
The Ca2+-sensing receptor: a target for polyamines (1997)

The Ca2+-sensing receptor (CaR) is activated at physiological levels of external Ca2+ (Ca(o)) but is expressed in a number of tissues that do not have well-established roles in the control of Ca(o), including several regions of the brain and the intestine. Polyamines are endogenous polyvalent cations that can act as agonists for the CaR, as shown by our current studies of human embryonic kidney (HEK-293) cells transfected with the human CaR. Cellular parameters altered by polyamines included cytosolic free Ca2+ (Ca(i)), inositol phosphate production, and the activity of a nonselective cation channel. Spermine stimulated Ca(i) transients in CaR-transfected HEK cells, with a concentration producing a half-maximal response (EC50) of approximately 500 microM in the presence of 0.5 mM Ca2+, whereas sustained increases in Ca(i) had an EC50 of approximately 200 microM. The order of potency was spermine > spermidine >> putrescine. Elevation of Ca(o) shifted the EC50 for spermine sharply to the left, with substantial stimulation below 100 microM. Addition of subthreshold concentrations of spermine increased the sensitivity of CaR-expressing HEK cells to Ca(o). Parathyroid hormone secretion from bovine parathyroid cells was inhibited by 50% in the presence of 200 microM spermine, a response similar to that elicited by 2.0 mM Ca(o). These data suggest that polyamines could be effective agonists for the CaR, and several tissues, including the brain, may use the CaR as a target for the actions of spermine and other endogenous polycationic agonists.
The Practical Synthesis of a Methylenebisphosphonate Analogue of Benzamide Adenine Dinucleotide:  Inhibition of Human Inosine Monophosphate Dehydrogenase (Type I and II) (1997)

beta-Methylene-BAD (8), a nonhydrolyzable analogue of benzamide adenine dinucleotide (BAD), was synthesized as potential inhibitor of human inosine monophosphate dehydrogenase (IMPDH). Treatment of 2',3'-O-isopropylideneadenosine 5'-methylenebisphosphonate (15) with DCC afforded P1,P4-bis(2',3'-O-isopropylideneadenosine) 5'-P1,P2:P3,P4-dimethylenetetrakisphosphonate (17). This compound was further converted with DCC to an active intermediate 18 which upon reaction with 3-(2',3'-O-isopropylidene-beta-D-ribofuranosyl)benzamide (19) gave, after hydrolysis and deisopropylidenation, the desired beta-methylene-BAD (8) in 95% yield. In a similar manner, treatment of 18 with 2',3'-O-isopropylidenetiazofurin (21) followed by hydrolysis and deprotection afforded beta-methylene-TAD (5) in 91% yield. Compound 8 (IC50 = 0.665 microM) was found to be a 6-8 times less potent inhibitor of IMPDH than 5 (IC50 = 0.107 microM) and was almost equally potent against IMPDH type I and type II. Although TAD and beta-methylene-TAD were bound by LADH with the same affinity, the binding affinity of 8 toward LADH (Ki = 333 microM) was found to be 50-fold lower than that of the parent pyrophosphate 7 (Ki = 6.3 microM).
Characterization of medroxyprogesterone and DMBA‐induced multilineage mammary tumors by gene expression profiling (2005)

Mouse mammary tumors arising during medroxyprogesterone-DMBA-mediated mammary carcinogenesis comprised three distinct phenotypes: adenocarcinoma, squamous cell carcinoma, and myoepithelial carcinoma. The molecular signature for each of the three tumor subsets was characterized by gene microarray analysis, and three distinct sets of gene expression profiles were obtained that were corroborated in part by quantitative RT-PCR and immunohistochemistry. These results suggest that this carcinogenesis and gene expression model will be useful for rapidly assessing the histopathological differences arising in mammary carcinogenesis and the effects of tumor promoting or chemoprevention agents.
Finding paths through the world's photos (2008)

When a scene is photographed many times by different people, the viewpoints often cluster along certain paths. These paths are largely specific to the scene being photographed, and follow interesting regions and viewpoints. We seek to discover a range of such paths and turn them into controls for image-based rendering. Our approach takes as input a large set of community or personal photos, reconstructs camera viewpoints, and automatically computes orbits, panoramas, canonical views, and optimal paths between views. The scene can then be interactively browsed in 3D using these controls or with six degree-of-freedom free-viewpoint control. As the user browses the scene, nearby views are continuously selected and transformed, using control-adaptive reprojection techniques.
Lung cancer secreted microvesicles: Underappreciated modulators of microenvironment in expanding tumors (2009)

Microvesicles (MVs) are shed from cell membranes of several cell types and have an important function in cell-to-cell communication. Exponentially growing lung cancer cells secrete large quantities of MVs and we were interested in their role in tumor progression. We observed that both human and murine lung cancer cell lines secrete more MVs in response to non-apoptotic doses of hypoxia and irradiation. These tumor-derived (t)MVs activate and chemoattract stroma fibroblasts and endothelial cells. Furthermore, they induce expression of several pro-angiopoietic factors in stromal cells such as IL-8, VEGF, LIF, OSM, IL-11 and MMP-9. We also noticed that conditioned media harvested from stroma cells stimulated by tMVs enhanced the metastatic potential of both human and murine lung cancer cells in vivo. Thus, we postulated that tMVs are underappreciated constituents of the tumor microenvironment and play a pivotal role in tumor progression, metastasis and angiogenesis.
Enteric Bacterial Catalysts for Fuel Ethanol Production (1999)

The technology is available to produce fuel ethanol from renewable lignocellulosic biomass. The current challenge is to assemble the various process options into a commercial venture and begin the task of incremental improvement. Current process designs for lignocellulose are far more complex than grain to ethanol processes. This complexity results in part from the complexity of the substrate and the biological limitations of the catalyst. Our work at the University of Florida has focused primarily on the genetic engineering of Enteric bacteria using genes encoding Zymomonas mobilis pyruvate decarboxylase and alcohol dehydrogenase. These two genes have been assembled into a portable ethanol production cassette, the PET operon, and integrated into the chromosome of Escherichia coli B for use with hemicellulose-derived syrups. The resulting strain, KO11, produces ethanol efficiently from all hexose and pentose sugars present in the polymers of hemicellulose. By using the same approach, we integrated the PET operon into the chromosome of Klebsiella oxytoca to produce strain P2 for use in the simultaneous saccharification and fermentation (SSF) process for cellulose. Strain P2 has the native ability to ferment cellobiose and cellotriose, eliminating the need for one class of cellulase enzymes. Recently, the ability to produce and secrete high levels of endoglucanase has also been added to strain P2, further reducing the requirement for fungal cellulase. The general approach for the genetic engineering of new biocatalysts using the PET operon has been most successful with Enteric bacteria but was also extended to Gram positive bacteria, which have other useful traits for lignocellulose conversion. Many opportunities remain for further improvements in these biocatalysts as we proceed toward the development of single organisms that can be used for the efficient fermentation of both hemicellulosic and cellulosic substrates.
The structure and function of the brown fat uncoupling protein UCP1: current status (1998)

The uncoupling protein of brown adipose tissue (UCP1) is a transporter that allows the dissipation as heat of the proton gradient generated by the respiratory chain. The discovery of new UCPs in other mammalian tissues and even in plants suggests that the proton permeability of the mitochondrial inner membrane can be regulated and its control is exerted by specialised proteins. The UCP1 is regulated both at the gene and the mitochondrial level to ensure a high thermogenic capacity to the tissue. The members of the mitochondrial transporter family, which includes the UCPs, present two behaviours with carrier and channel transport modes. It has been proposed that this property reflects a functional organization in two domains: a channel and a gating domain. Mounting evidence suggest that the matrix loops contribute to the formation of the gating domain and thus they are determinants to the control of transport activity.
Rabies virus glycoprotein can fold in two alternative, antigenically distinct conformations depending on membrane-anchor type (2002)

Rabies virus glycoprotein (G) is a trimeric type I transmembrane glycoprotein that mediates both receptor recognition and low pH-induced membrane fusion. We have previously demonstrated that a soluble form of the ectodomain of G (G(1-439)), although secreted, is folded in an alternative conformation, which is monomeric and antigenically distinct from the native state of the complete, membrane-anchored glycoprotein. This has raised questions concerning the role of the transmembrane domain (TMD) in the correct native folding of the ectodomain. Here, we show that an ectodomain anchored in the membrane by a glycophosphatidylinositol is also folded in an alternative conformation, whereas replacement of the TMD of G by other peptide TMDs results in correct antigenicity of G. However, mutants with an insertion of a hydrophilic linker between the ectodomain and the TMD also fold in an alternative conformation. The influence of the membrane-anchor type on G ectodomain trimerization and folding is discussed.
Laboratory-scale method for enzymatic saccharification of lignocellulosic biomass at high-solids loadings (2009)

Effective initial mixing to promote good enzyme distribution and continued, but not necessarily continuous, mixing is necessary in order to facilitate high biomass conversion rates. The simplicity and robustness of the bench-scale RBR system, combined with its ability to accommodate numerous reaction vessels, will be useful in screening new biomass pretreatments and advanced enzyme systems at high-solids loadings.