gebhart/patrepeval huggingface dataset:
Replication Study: Coadministration of a tumor-penetrating peptide enhances the efficacy of cancer drugs (2017)

In 2015, as part of the Reproducibility Project: Cancer Biology, we published a Registered Report (Kandela et al., 2015) that described how we intended to replicate selected experiments from the paper "Coadministration of a tumor-penetrating peptide enhances the efficacy of cancer drugs" (Sugahara et al., 2010). Here we report the results of those experiments. We found that coadministration with iRGD peptide did not have an impact on permeability of the chemotherapeutic agent doxorubicin (DOX) in a xenograft model of prostate cancer, whereas the original study reported that it increased the penetrance of this cancer drug (Figure 2B; Sugahara et al., 2010). Further, in mice bearing orthotopic 22Rv1 human prostate tumors, we did not find a statistically significant difference in tumor weight for mice treated with DOX and iRGD compared to DOX alone, whereas the original study reported a decrease in tumor weight when DOX was coadministered with iRGD (Figure 2C; Sugahara et al., 2010). In addition, we did not find a statistically significant difference in TUNEL staining in tumor tissue between mice treated with DOX and iRGD compared to DOX alone, while the original study reported an increase in TUNEL positive staining with iRGD coadministration (Figure 2D; Sugahara et al., 2010). Similar to the original study (Supplemental Figure 9A; Sugahara et al., 2010), we did not observe an impact on mouse body weight with DOX and iRGD treatment. Finally, we report meta-analyses for each result.
Bioconversion of plant biomass to ethanol. Annual report and revised research plan, January 1977--January 1978 (1978)

The objective of this research is to demonstrate on a laboratory scale the technical feasibility of the direct microbial conversion of pretreated wood to ethanol. During the first year of this contract, we investigated the feasibility of biologically delignifying wood with C. pruinosum and directly fermenting the pretreated wood to ethanol with a mixed culture. Bench-top fermentations of a thermophilic bacillus growing on glucose and of a mixed culture of thermophilic sporocytophaga (US) and a thermophilic bacillus growing on microcrystalline and amorphous cellulose were evaluated for growth and ethanol production. In the mixed culture fermentation of amorphous and microcrystalline cellulose, the specific rate of substrate depletion was calculated to be 0.087 hr/sup -1/ and 0.0346 hr/sup -1/, respectively. However, defining the growth requirements of C. pruinosum and sporocytophaga (US) proved more difficult than originally anticipated. In order to achieve the program objectives within the contract period, a revised research plan was developed based upon chemical pretreatment and the direct fermentation of pretreated hardwood to ethanol. In place of the biological delignification pretreatment step, we have substituted a chemically supplemented steam pretreatment step to partially delignify wood and to enhance its accessibility to microbial utilization. Clostridium thermocellum, which ferments cellulose directly to ethanol and acetic acid, has replaced the mixed culture fermentation stage for ethanol production. Research on the production of ethanol from xylose by the thermophilic bacillus ZB-B2 is retained as one means of utilizing the hemicellulose fraction of hardwood. Work on the genetic improvement of the ethanol yields of both cultures by suppressing acetic acid production is also retained. The rationale, experimental approach, and economic considerations of this revised research plan are also presented.
Very rapid tuning of cw dye laser (1975)

A method is described which allows the cw dye laser to be tuned over hundreds of angstroms on a nanosecond time scale in spite of the 100-nsec cavity decay and buildup time. Data are provided to verify the proposed method. This tuning rate is fast enough to do, for example, chemical kinetic studies on a nanosecond time scale.
Invasive Group A Streptococcal Infection Concurrent with 2009 H1N1 Influenza (2010)

We describe 10 patients with 2009 H1N1 influenza and concurrent invasive group A streptococcal infection with marked associated morbidity and mortality. Seven patients required intensive care, 8 required mechanical ventilation, and 7 died. Five of the patients, including 4 of the fatalities, were previously healthy.
Overexpression of oncogenic STK15/BTAK/Aurora A kinase in human pancreatic cancer. (2003)

These results show that STK15 is overexpressed in pancreatic tumors and carcinoma cell lines and suggest that overexpression of STK15 may play a role in pancreatic carcinogenesis.
Impact of chip-level integration on performance of OLTP workloads (2002)

With increasing chip densities, future microprocessor designs have the opportunity to integrate many of the traditional system-level modules onto the same chip as the processor. Some current designs already integrate extremely large on-chip caches, and there are aggressive next-generation designs that attempt to also integrate the memory controller, coherence hardware, and network router all onto a single chip. The tight coupling of these modules will enable efficient memory systems with substantially better latency and bandwidth characteristics relative to current designs. Among the important application areas for high-performance servers, online transaction processing (OLTP) workloads are likely to benefit most from these trends due to their large instruction and data footprints and high communication miss rates. This paper examines the design trade-offs that arise as more system functionality is integrated onto the processor chip, and identifies a number of important architectural choices that are influenced by chip-level integration. In addition, the paper presents a detailed study of the performance impact of chip-level integration in the context of OLTP workloads. Our results are based on full system simulations of the Oracle commercial database engine running on both in-order and out-of-order issue processors used in uniprocessor and multiprocessor configurations. The results show that chip-level integration can improve the performance of both configurations by about 1.4 to 1.5 times, though for different reasons. For uniprocessors, integration of the L2 cache and the resulting lower hit latency is the primary factor in performance improvement. For multiprocessors, the improvement comes from both the integration of the L2 cache (lower L2 hit latency) and the integration of the other memory system components (better dirty remote latency). Furthermore, we find that the higher associativity afforded by integrating the L2 cache plays a critical role in counteracting the loss of capacity relative to larger off-chip caches. Finally, we find that the relative gains from chip-level integration are virtually identical for in-order and out-of-order processors.
TX-004HR Improves Sexual Function as Measured by the Female Sexual Function Index in Postmenopausal Women with Vulvar and Vaginal Atrophy: The REJOICE Trial (2016)

TX-004HR improved FSFI scores in a dose-dependent manner. The observed improvements in sexual function suggest that TX-004HR is a promising treatment option for postmenopausal VVA with a potential added beneficial effect on female sexual dysfunction.
Optical Nanoantennas with Tunable Radiation Patterns (2013)

We address new optical nanoantenna systems with tunable highly directional radiation patterns. The antenna comprises a regular linear array of metal nanoparticles in the proximity of an interface with high dielectric contrast. We show that the radiation pattern of the system can be controlled by changing parameters of the excitation, such as the polarization and/or incidence angles. In the case of excitation under the total reflection condition, the system operates as a nanoscopic source of radiation, converting the macroscopic incident plane wavefront into a narrow beam of light with adjustable characteristics. We derive also simple analytical formulas which give an excellent description of the radiation pattern and provide a useful tool for analysis and antenna design.
Expression of gicerin enhances the invasive and metastatic activities of a mouse mammary carcinoma cell line (2003)

Gicerin, an immunoglobulin superfamily protein, is expressed abundantly in the embryonic tissues and plays an important role in development through its cell adhesive activity. Interestingly, re-expression of gicerin is found in a variety of tumors. In the present study, the possible role of gicerin in the progression of mammary carcinoma was investigated. The normal mammary glands of mice were negative for gicerin, but sporadic mammary carcinoma cells expressed gicerin strongly on their surface. A mouse mammary carcinoma cell line, JYG-B, which is gicerin-negative was employed for introducing gicerin cDNA and the resultant gicerin transfectants were subsequently analyzed. In vitro, self-aggregation activity of the gicerin-transfectants progressed. For an in vivo study, invasive and metastatic potential of the cells was examined by a subcutaneous implantation into nude mice. The invasion of gicerin transfectants into the surrounding tissue was enhanced and severe metastasis to the lungs occurred. These findings suggest that gicerin is an effector for the malignant progression of mammary carcinoma.
A Conditional Generative Adversarial Network to Fuse Sar And Multispectral Optical Data For Cloud Removal From Sentinel-2 Images (2018)

In this paper, we present the first conditional generative adversarial network (cGAN) architecture that is specifically designed to fuse synthetic aperture radar (SAR) and optical multi-spectral (MS) image data to generate cloud- and haze-free MS optical data from a cloud-corrupted MS input and an auxiliary SAR image. Experiments on Sentinel-2 MS and Sentinel-l SAR data confirm that our extended SAR-Opt-cGAN model utilizes the auxiliary SAR information to better reconstruct MS images than an equivalent model which uses the same architecture but only single-sensor MS data as input.
Effectiveness of Live, Attenuated Intranasal Influenza Virus Vaccine in Healthy, Working Adults (1999)

Intranasal trivalent LAIV vaccine was safe and effective in healthy, working adults in a year in which a drifted influenza A virus predominated.
A dynamic object replication and migration protocol for an Internet hosting service (2003)

The paper proposes a protocol suite for dynamic replication and migration of Internet objects. It consists of an algorithm for deciding on the number and location of object replicas and an algorithm for distributing requests among currently available replicas. Our approach attempts to place replicas in the vicinity of a majority of requests, while ensuring at the same time that no servers are overloaded. The request distribution algorithm uses the same simple mechanism to take into account both server proximity and load, without actually knowing the latter. The replica placement algorithm executes autonomously on each node, without the knowledge of other object replicas in the system. The proposed algorithms rely on the information available in databases maintained by Internet routers. A simulation study using synthetic workloads and the network backbone of UUNET, one of the largest Internet service providers, shows that the proposed protocol is effective in eliminating hot spots and achieves a significant reduction in backbone traffic and server response time at the expense of creating only a small number of extra replicas.
Role of vesicles during adenovirus 2 internalization into HeLa cells (1985)

In this investigation, the early period of adenovirus type 2 (Ad2)-HeLa cell interaction was analyzed by electron microscopy and biochemical techniques. Events observed in this period ranged from the disappearance of virions from the cell surface to their subsequent association with the cell nucleus. Destabilization of the virions attached to the intact cell was necessary for virions to escape from intracellular vesicles. Strong temperature dependence and rapid escape from a vesicular compartment were shown in temporal kinetic experiments. These vesicles appeared to be acidic, since lysosomotropic agents partly inhibited the release of virions from vesicles. Studies of Ad2 binding to cells in buffers of different pH values suggested that adenovirus binds to cells by two different mechanisms. At low pH the binding was most probably mediated by the penton base and at neutral pH by the fiber protein. The number of receptor sites per cell was 25,000 and 6,000 at low and neutral pH, respectively. This study suggests that the low-pH affinity between the penton base and a vesicular membrane is important inside acid vesicles when Ad2 quickly enters the cytoplasm. However, a significant fraction of the virions was possibly internalized by a pathway not requiring a passage through such vesicles.
Enhancing the anticancer properties of cardiac glycosides by neoglycorandomization (2005)

Glycosylated natural products are reliable platforms for the development of many front-line drugs, yet our understanding of the relationship between attached sugars and biological activity is limited by the availability of convenient glycosylation methods. When a universal chemical glycosylation method that employs reducing sugars and requires no protection or activation is used, the glycorandomization of digitoxin leads to analogs that display significantly enhanced potency and tumor specificity and suggests a divergent mechanistic relationship between cardiac glycoside-induced cytotoxicity and Na+/K+-ATPase inhibition. This report highlights the remarkable advantages of glycorandomization as a powerful tool in glycobiology and drug discovery.
CD74–NRG1 Fusions in Lung Adenocarcinoma (2014)

CD74–NRG1 fusions may represent a therapeutic opportunity for invasive mucinous lung adenocarcinomas, a tumor with no effective treatment that frequently presents with multifocal unresectable disease.
Direct syntheses of ordered SBA-15 mesoporous materials containing arenesulfonic acid groups (2002)

SBA-15 mesoporous silica has been functionalized with arenesulfonic acid groups by means of a one-step simple synthesis approach involving co-condensation of tetraethoxysilane (TEOS) and 2-(4-chlorosulfonylphenyl)ethyltrimethoxysilane (CSPTMS) in the presence of a poly(alkylene oxide) block copolymer (Pluronic 123) under acid silica-based catalysis. The resultant materials show hexagonal mesoscopic order and pores sizes up to 60 Å, with acid exchange capacities of ca. 1.3 mequiv. H+ per g SiO2 and surface areas up to 600 m2 g−1. The sulfonic groups anchored to the silica surface of the pore walls are thermally stable to temperatures up to 380 °C and resistant to leaching in organic and aqueous solutions under mild conditions. 31P MAS NMR measurements of chemically adsorbed triethylphosphine oxide and the catalytic properties confirm the presence of Brönsted acid centers in these mesoporous materials containing arenesulfonic acid groups that are stronger than those found in propanesulfonic-modified SBA-15 and Al-MCM-41.
Mechanically flexible thin film transistors and logic gates on plastic substrates by use of single-crystal silicon wires from bulk wafers (2010)

This letter presents a method to fabricate single-crystal silicon wires from (100) wafer and print them onto thin plastic substrates for high-performance, mechanically flexible, thin-film transistors by dry transfer printing. Electrical measurements indicate excellent performance, with a per ribbon mobility of 580 cm2/V s, subthreshold voltage of 100 mV/dec and on/off ratios &amp;gt;107. The inverter shows good performance and voltage gains of ∼2.5 at 3 V supply voltage. In addition, these devices revealed stable performance at bending configuration, an important feature essential for flexible electronic systems.
The Control of Experimental Escherichia coli Diarrhoea in Calves by Means of Bacteriophages (1987)

Seven phages highly active in vitro and in vivo against one or other of seven bovine enteropathogenic strains of Escherichia coli belonging to six different serotypes were isolated from sewage. Severe experimentally induced E. coli diarrhoea in calves could be cured by a single dose of 10(5) phage organisms. It could be prevented by doses as low as 10(2), by spraying the litter in the calf rooms with aqueous phage suspensions or simply by keeping the calves in uncleaned rooms previously occupied by calves whose E. coli infections had been treated with phage. Microbiological examinations of calves used in these experiments revealed that the phage organisms multiplied rapidly and profusely after gaining entry to the E. coli-infected small intestine, quickly reducing the E. coli to numbers that were virtually harmless. The only phage-resistant E. coli that emerged in the studies on calves infected with one or other of the seven E. coli strains were K-. These organisms were much less virulent than the K+ organisms from which they were derived and did not present a serious problem in calves given adequate amounts of colostrum. Infections produced by oral inoculation of a mixture of six strains of the E. coli could be controlled by administration of a pool of the six phages that were active against them but, in general, the control was less complete than that observed in the single-strain infections. K+ phage-resistant bacteria emerged in some of the calves used in these mixed infections and they were as virulent as their parent organisms; evidence from in vitro studies suggested that they might have arisen by genetic transfer between organisms of the different infecting strains. Infections produced by these K+ mutants and their parents could be controlled by the use of mutant phages derived from phages that were active on their parents. During the experiments with mixed E. coli infection, an extraneous phage active against one of the six E. coli strains suddenly appeared in calves kept in the same rooms. Microbiological examinations revealed that this phage was effectively controlling the multiplication of organisms of that particular strain of E. coli in the small intestines of the calves.
Diffusion maps and coarse-graining: a unified framework for dimensionality reduction, graph partitioning, and data set parameterization (2006)

We provide evidence that nonlinear dimensionality reduction, clustering, and data set parameterization can be solved within one and the same framework. The main idea is to define a system of coordinates with an explicit metric that reflects the connectivity of a given data set and that is robust to noise. Our construction, which is based on a Markov random walk on the data, offers a general scheme of simultaneously reorganizing and subsampling graphs and arbitrarily shaped data sets in high dimensions using intrinsic geometry. We show that clustering in embedding spaces is equivalent to compressing operators. The objective of data partitioning and clustering is to coarse-grain the random walk on the data while at the same time preserving a diffusion operator for the intrinsic geometry or connectivity of the data set up to some accuracy. We show that the quantization distortion in diffusion space bounds the error of compression of the operator, thus giving a rigorous justification for k-means clustering in diffusion space and a precise measure of the performance of general clustering algorithms.
Radiation patterns of a shear-wave vibrator in near-surface shale (1983)

Abstract Two shallow, surface-to-borehole field tests were conducted to investigate the radiation patterns of a shear-wave vibrator in near-surface shale. In the in-line direction, for which baseplate motion is transverse to the source-geophone raypath, the vibrator produces a broadband, high-amplitude signal of the SH type and virtually no signal of the SV or P types. The amplitude of the SH radiation is approximately constant as a function of polar angle, but it falls off as the cosine of the azimuthal angle measured with respect to the in-line direction. In the broadside direction, the vibrator produces a strong, uncontaminated signal of the SV type. The radiation pattern of the SV signature is lobate in the polar plane and peaks at an incident angle of 30 to 35 degrees. In the horizontal plane, the SV radiation varies as the sine of the azimuthal angle measured with respect to the in-line direction. The field tests were conducted on a Permian shale in Oklahoma and an Eocene shale in East Texas. Comparison between SH and SV wave surfaces indicates that both shales behave approximately like transversely isotropic solids with a vertical axis of symmetry. Theoretical wave surfaces are fit to the observed data by using elastic moduli determined from the field measurements and by making the assumption that the near-surface shale at each field site is a single, homogeneous, inherently transversely isotropic material. The analyses indicate that horizontal SH group velocity is about 30 percent greater than horizontal SV group velocity in the Permian shale and about 25 percent greater in the Eocene shale.
Cadherin switching: essential for behavioral but not morphological changes during an epithelium-to-mesenchyme transition (2005)

Epithelium-to-mesenchyme transitions (EMTs) are characterized by morphological and behavioral changes in cells. During an EMT, E-cadherin is downregulated while N-cadherin is upregulated. The goal of this study was to understand the role cadherin switching plays in EMT using a classical model system: transforming growth factor beta1 (TGF-beta1)-mediated EMT in mammary epithelial cells. We showed that stress fibers and focal adhesions are increased, and cell-cell junctions are decreased in response to TGF-beta1. Moreover, these changes were reversible upon removal of TGF-beta1. Downregulation of E-cadherin and upregulation of N-cadherin were both transcriptional. Neither experimental knockdown nor experimental overexpression of N-cadherin interfered with the morphological changes. In addition, the morphological changes associated with EMT preceded the downregulation of E-cadherin. Interestingly, TGF-beta1-induced motility in N-cadherin-knockdown cells was significantly reduced. Together, these data suggest that cadherin switching is necessary for increased motility but is not required for the morphological changes that accompany EMT.
Taxonomy, biology, and periodontal aspects of Fusobacterium nucleatum. (1996)

The pathogenic potential of Fusobacterium nucleatum and its significance in the development of periodontal diseases, as well as in infections in other organs, have gained new interest for several reasons. First, this bacterium has the potential to be pathogenic because of its number and frequency in periodontal lesions, its production of tissue irritants, its synergism with other bacteria in mixed infections, and its ability to form aggregates with other suspected pathogens in periodontal disease and thus act as a bridge between early and late colonizers on the tooth surface. Second, of the microbial species that are statistically associated with periodontal disease, F. nucleatum is the most common in clinical infections of other body sites. Third, during the past few years, new techniques have made it possible to obtain more information about F. nucleatum on the genetic level, thereby also gaining better knowledge of the structure and functions of the outer membrane proteins (OMPs). OMPs are of great interest with respect to coaggregation, cell nutrition, and antibiotic susceptibility. This review covers what is known to date about F. nucleatum in general, such as taxonomy and biology, with special emphasis on its pathogenic potential. Its possible relationship to other periodontal bacteria in the development of periodontal diseases and the possible roles played by OMPs are considered.