gebhart/patrepeval huggingface dataset:
Cell manipulation in microfluidics (2013)

Recent advances in the lab-on-a-chip field in association with nano/microfluidics have been made for new applications and functionalities to the fields of molecular biology, genetic analysis and proteomics, enabling the expansion of the cell biology field. Specifically, microfluidics has provided promising tools for enhancing cell biological research, since it has the ability to precisely control the cellular environment, to easily mimic heterogeneous cellular environment by multiplexing, and to analyze sub-cellular information by high-contents screening assays at the single-cell level. Various cell manipulation techniques in microfluidics have been developed in accordance with specific objectives and applications. In this review, we examine the latest achievements of cell manipulation techniques in microfluidics by categorizing externally applied forces for manipulation: (i) optical, (ii) magnetic, (iii) electrical, (iv) mechanical and (v) other manipulations. We furthermore focus on history where the manipulation techniques originate and also discuss future perspectives with key examples where available.
In Vivo Evaluation of Safety and Toxicity of a Lactobacillus jensenii Producing Modified Cyanovirin-N in a Rhesus Macaque Vaginal Challenge Model (2013)

Sexual transmission of human immunodeficiency virus type 1 (HIV-1) across the cervicovaginal mucosa in women is influenced by many factors including the microbiota and the presence of underlying inflammation. It is important that potential HIV preventative agents do not alter the mucosal environment in a way that enhances HIV acquisition. We examined the impact of a "live" microbicide on the vaginal mucosal environment in a rhesus macaque repeated vaginal simian-HIV (SHIVSF162P3) challenge model. The microbicide contained a human vaginal Lactobacillus jensenii expressing the HIV-1 entry inhibitor, modified Cyanovirin-N (mCV-N), and henceforth called LB-mCV-N. Macaques were colonized vaginally each week with LB-mCV-N and sampled six days after colonization for culturable bacteria, pH and cervical-vaginal cytokines during the duration of the six-week study. We show that macaques that retained the engineered LB-mCV-N strain in their vaginal microbiota, during SHIV challenge, had lower pH, when colonization levels were higher, and had no evidence of inflammatory cytokines. Indeed, Interleukin-13, a mediator of inflammation, was detected less often in LB-mCV-N colonized macaques than in controls and we found higher levels of Interleukin 1 receptor antagonist (IL-1RA) in LB-mCV-N colonized macaques during the SHIV challenge period. We noted an inverse correlation between levels of mucosal IL-1RA and peak plasma viral load, thus higher IL-1RA correlated with lower viral load in LB-mCV-N treated macaques. These data support the use of LB-mCV-N as a safe "live" microbicide and suggest that lactobacilli themselves may positively impact the mucosal environment.
Structure of medicinal chemistry (1976)

The great advances in biochemistry and molecular biology, the development of physical organic chemistry, and the availability of large computers are creating opportunities for restructuring medicinal chemistry. The enormous volume of scientific results relevant to medicinal chemistry which appear with each new round of the journals forces us to make greater efforts to bring the information together in more meaningful patterns. The QSAR paradigm redirects our thinking about structuring medicinal chemistry.
A physiologic function for alkaline phosphatase: endotoxin detoxification. (1997)

Alkaline phosphatase (AP), a common enzyme present in many species including humans, has been studied extensively. Although the enzyme is routinely applied as a marker for liver function, its biologic relevance is poorly understood. The reason for this is obvious: the pH optimum of AP in vitro, as measured with the usual test substrates (+/-10.5), greatly exceeds the physiologic pH range as it occurs in biologic tissues. We now hypothesize that this relatively high pH optimum in vitro is related to dissociation of acidic groups in the protein preparation, which leads to the formation of negatively charged groups in the vicinity of the active site of the enzyme. These negatively charged groups may promote the activity of AP. We examined the possibility that endotoxin is a natural substrate for this enzyme because this phosphorylated substance is able to supply multiple negatively charged residues in the microenvironment of the enzyme at a physiologic pH level. Phosphate groups in the endotoxin molecule are known to be essential for the biologic activities of this bacterial product. The present study demonstrates that in intestinal and renal tissue specimens in vitro, AP is endowed with endotoxin dephosphorylating activity at pH levels closer to the physiologic range. This is also illustrated by our experiments in vivo showing that the toxicity of endotoxin is significantly reduced after exposure to AP preparations, as tested by inducing a local intradermal inflammatory reaction in rats. Collectively, our data suggest that the ubiquitous enzyme AP may accomplish protection against endotoxin, an equally ubiquitous product of Gram-negative bacteria that may cause lethal complications after an infection with these micro organisms.
Generation of a Tn5 promoter probe and its use in the study of gene expression in Caulobacter crescentus. (1984)

A promoter probe, Tn5-VB32, was constructed and placed in a P group R plasmid containing bacteriophage Mu sequences, allowing transfer of the transposon to bacteria such as Caulobacter, Rhizobium, and Agrobacterium without retention of the plasmid. The probe carries an altered Tn5 transposon that allows detection of chromosomal promoter regions by virtue of acquired kanamycin resistance. A fragment of DNA containing the neomycin phosphotransferase II (NPT II) gene from Tn5, lacking its promoter region but retaining its translation initiation signal, was inserted into a Tn5 derivative that lacked the entire NPT II gene and a large portion of the IS50L sequence while retaining its ability to transpose. This Tn5 derivative also contained the intact tetracycline resistance-encoding region of the transposon Tn10. Transposition of the Tn5-VB32 promoter probe into the Caulobacter crescentus chromosome generated auxotrophic and motility mutants and Southern blot analysis of DNA from these mutants showed Tn5-VB32 sequences in random-sized chromosomal restriction fragments. Transcriptional regulation by exogenous cysteine of NPT II gene expression was demonstrated in a cysteine auxotroph generated by Tn5-VB32 insertional inactivation. NPT II synthesis, measured by agar plate assays of kanamycin resistance and by immunoprecipitation of the NPT II protein, was repressed in the presence of cysteine and derepressed in its absence. Several fla- mutants were also isolated by Tn5-VB32 mutagenesis and shown to confer kanamycin resistance. Insertions within temporally regulated genes, such as those involved in flagellar biosynthesis and chemotaxis functions, can now be used directly to monitor transcriptional regulation from Caulobacter promoter sequences.
Starch and Microbial α-Amylases: From Concepts to Biotechnological Applications (2012)

Starch is a polymer of glucose linked to one another through the C1 oxygen, known as the glycosidic bond. Amylases are capable of digesting these glycosidic linkages found in starch. Amylases have been isolated from diversified sources including plants, animals, and microbes, where they play a dominant role in carbohydrate metabolism. In spite of the wide distribution of α-amylase, microbial sources are used for the industrial production. This is due to their advantages such as cost effectiveness, consistency, less time and space required for production as well as ease of process modification and optimization.
Plastic optical fiber star coupler (1986)

A new plastic optical fiber star coupler and the means of fabricating it have been developed. This coupler has been realized by twisting and pulling the waist region of a biconical tapered fiber bundle made by pretapered fibers while heating. Controlling the biconical tapered shape has been achieved by jetting gas on the fiber surface while heating the fiber bundle. By using this fabrication method, the desired diameter mixing portion can be formed without breakage from melting. Low-cost optical star couplers with large port number, low excess loss, and small power deviation can be obtained.
A randomized approximation of the MDL for stochastic models with hidden variables (1996)

Article Free Access Share on A randomized approximation of the MDL for stochastic models with hidden variables Author: Kenji Yamanishi C&C Research Laboratories, NEC Corporation, 1-1, 4-chome, Miyazaki, Miyamae-ku, Kawasaki, Kanagawa 216, Japan C&C Research Laboratories, NEC Corporation, 1-1, 4-chome, Miyazaki, Miyamae-ku, Kawasaki, Kanagawa 216, JapanView Profile Authors Info & Claims COLT '96: Proceedings of the ninth annual conference on Computational learning theoryJanuary 1996 Pages 99–109https://doi.org/10.1145/238061.238074Online:01 January 1996Publication History 4citation241DownloadsMetricsTotal Citations4Total Downloads241Last 12 Months3Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Closed-loop production and automation scheduling in RMSs (2011)

Highly reconfigurable and agile production systems are selected to operate in production contexts often characterized by changes of the production requirements or changes of the part family demand. The operational level for such system architecture is expected to manage the short term production planning while guaranteeing the automation layer enables physical devices to exploit logic control tasks within the specific time buckets. The proposed work outlines an integrated approach supporting the operational level for RMSs in which the scheduling of production jobs and the scheduling of corresponding automation tasks are dynamically coupled. Connections with consolidated constraint-based representation and solving techniques are also discussed. The integrated scheduling approach has been validated with reference to a Finishing Robotic Cell (FRC) operating in a pilot assembly line.
Three-dimensional electromagnetic diffraction of a Gaussian beam by a perfectly conducting half-plane (2002)

Formulas are derived for the diffraction of a three-dimensional electromagnetic Gaussian beam by a perfectly conducting half-plane. The beam can be incident from any direction, and the main component of the electric field can point in any direction on the plane of the beam waist. The center of the beam waist is on the edge of the half-plane. The incident beam is constructed as a superposition of plane waves, and the total diffracted field is obtained from a superposition of the diffracted fields that are due to each plane wave. Physical constraints that limit the size and direction of the beam relative to the half-plane are described and incorporated into the theory. The scattered field in the far zone is obtained by asymptotic evaluation of the general formulas. Graphical results for the near-field as well as far-field patterns are presented and discussed.
Zone-based color flow imaging (2004)

A zone-based technique for real-time color flow imaging is described. The technique utilizes a broad transmit beam which is equivalent to 20-50 focused transmit beams, such that the full field of view can be scanned using only 3-5 firings, times the flow sample count (FSC) required for color flow estimation. On receive, the channel domain RF data is pre-processed and accumulated in memory, and then transferred to a software-based image formation system, which performs dynamic receive focusing, clutter filtering, mean velocity estimation and scan conversion. Various methods of compensating for the lack of transmit focusing gain are discussed, including a larger FSC, over-sampling pulsed repetition frequencies, and coded excitation using FM chirp, Barker and Golay codes. Both 7.5 MHz linear array and 3 MHz curved array images obtained using a research platform show very good agreement with the predicted signal-to-noise-ratio (SNR) gain for a 5-chip Barker coded signal.
Reducing SAR and enhancing cerebral signal‐to‐noise ratio with high permittivity padding at 3 T (2010)

Previous works have shown that placement of a high-dielectric pad can improve image intensity in a region adjacent to the pad, or that placement of dielectric pads around a large surface of the head can improve image homogeneity on an entire plane through the head in high-field MRI. Here, experimental results show that use of high-dielectric pads around the human head can reduce the required input radiofrequency power by 50% while enhancing image signal-to-noise ratio by 20-40% throughout the cerebrum at 3 T. Thus, dielectric pads may be used to provide a relatively simple and low-cost method for improving quality and safety of MRI in a variety of applications at 3 T.
Breast adenocarcinoma liver metastases, in contrast to colorectal cancer liver metastases, display a non-angiogenic growth pattern that preserves the stroma and lacks hypoxia (2004)

Although angiogenesis is a prerequisite for the growth of most human solid tumours, alternative mechanisms of vascularisation can be adopted. We have previously described a non-angiogenic growth pattern in liver metastases of colorectal adenocarcinomas (CRC) in which tumour cells replace hepatocytes at the tumour-liver interface, preserving the liver architecture and co-opting the sinusoidal blood vessels. The aim of this study was to determine whether this replacement pattern occurs during liver metastasis of breast adenocarcinomas (BC) and whether the lack of an angiogenic switch in such metastases is due to the absence of hypoxia and subsequent vascular fibrinogen leakage. The growth pattern of 45 BC liver metastases and 28 CRC liver metastases (73 consecutive patients) was assessed on haematoxylin- and eosin-stained tissue sections. The majority of the BC liver metastases had a replacement growth pattern (96%), in contrast to only 32% of the CRC metastases (P<0.0001). The median carbonic anhydrase 9 (CA9) expression (M75 antibody), as a marker of hypoxia, (intensity x % of stained tumour cells) was 0 in the BC metastases and 53 in the CRC metastases (P<0.0001). There was CA9 expression at the tumour-liver interface in only 16% of the BC liver metastases vs 54% of the CRC metastases (P=0.002). There was fibrin (T2G1 antibody) at the tumour-liver interface in only 21% of the BC metastases vs 56% of the CRC metastases (P=0.04). The median macrophage count (Chalkley morphometry; KP-1 anti-CD68 antibody) at the interface was 4.3 and 7.5, respectively (P<0.0001). Carbonic anhydrase 9 score and macrophage count were positively correlated (r=0.42; P=0.002) in all metastases. Glandular differentiation was less in the BC liver metastases: 80% had less than 10% gland formation vs only 7% of the CRC metastases (P<0.0001). The liver is a densely vascularised organ and can host metastases that exploit this environment by replacing the hepatocytes and co-opting the vasculature. Our findings confirm that a non-angiogenic pattern of liver metastasis indeed occurs in BC, that this pattern of replacement growth is even more prevalent than in CRC, and that the process induces neither hypoxia nor vascular leakage.
Phenotypic and Genotypic Characteristics of Novel Mouse Cell Line (NIH/3T3)-Adapted Human Enterovirus 71 Strains (EV71:TLLm and EV71:TLLmv) (2014)

Since its identification in 1969, Enterovirus 71 (EV71) has been causing periodic outbreaks of infection in children worldwide and most prominently in the Asia-Pacific Region. Understanding the pathogenesis of Enterovirus 71 (EV71) is hampered by the virus's inability to infect small animals and replicate in their derived in vitro cultured cells. This manuscript describes the phenotypic and genotypic characteristics of two selected EV71 strains (EV71:TLLm and EV71:TLLmv), which have been adapted to replicate in mouse-derived NIH/3T3 cells, in contrast to the original parental virus which is only able to replicate in primate cell lines. The EV71:TLLm strain exhibited productive infection in all primate and rodent cell lines tested, while EV71:TLLmv exhibited greater preference for mouse cell lines. EV71:TLLmv displayed higher degree of adaptation and temperature adaptability in NIH/3T3 cells than in Vero cells, suggesting much higher fitness in NIH/3T3 cells. In comparison with the parental EV71:BS strain, the adapted strains accumulated multiple adaptive mutations in the genome resulting in amino acid substitutions, most notably in the capsid-encoding region (P1) and viral RNA-dependent RNA polymerase (3D). Two mutations, E167D and L169F, were mapped to the VP1 canyon that binds the SCARB2 receptor on host cells. Another two mutations, S135T and K140I, were located in the VP2 neutralization epitope spanning amino acids 136-150. This is the first report of human EV71 with the ability to productively infect rodent cell lines in vitro.
A novel treatment approach for paediatric Gorham–Stout syndrome with chylothorax (2011)

Abstract Aim: To expand the treatment options in paediatric Gorham–Stout syndrome (GSS) when conventional therapy is ineffective. Method: Two children with biopsy confirmed GSS, a rare disorder with progressive lymphangiomatosis, were treated with a combination of interferon‐α‐2b, low anticoagulant, low molecular weight heparin, radiotherapy and surgery. Results: The combined therapy resolved the symptoms in the acute phase, and both patients have since been free of symptoms for >2 years. Conclusion: The successful addition of a low anticoagulant, low molecular weight heparin (tafoxiparin) to the treatment protocol in two paediatric cases of the GSS may justify the use of this approach in similar cases.
Coherent Detection of Terahertz via Laser Induced Plasma with Controlled Optical Bias (2013)

Common air-breakdown coherent detection techniques rely on either large DC bias across plasma or second harmonic contribution from the supercontinuum to provide a local oscillator field. Here we report coherent detection by purposely injecting second harmonic.
'Fuels Plus' from the Forest (2007)

We live in an oil-based economy! But how long we can continue to do so is an open question at this time. The pessimistic view is that oil reserves are limited and that within the next ten years world demand for crude oil will exceed supply, while the optimistic view is that current estimates of the crude oil reserves understate the quantity that can be extracted, albeit at a higher cost. Whichever scenario prevails, however, it seems likely that oil prices will edge steadily upwards over the next ten to fifteen years (prices up to USD 400 per barrel by 2015 have been suggested) with peaks at irregular intervals caused by periods of exceptionally heavy demand eg. because of a cold winter in the northern hemisphere, a Hurricane Katrina, or interruptions to supply due to shut down of an oilfield or factors such as the current unrest in the Middle East. Other factors that will have an influence include the availability of alternative liquid fuels and concerns about carbon dioxide emission from the combustion of natural or synthetic fossil fuels. One outcome of the recent price rises and increasing concern about the level of CO2 in the atmosphere has been an upsurge of interest in wood as a source of fuels and chemicals as shown by the World Bioenergy Conference held in Sweden in June 2006, the International Energy and Forest Products Industry Seminar, held in Rome in October, as well as a flurry of articles in forestry, pulp and paper industry journals and general science magazines, on this topic.
Parathyroid Hormone and Teriparatide for the Treatment of Osteoporosis: A Review of the Evidence and Suggested Guidelines for Its Use (2005)

All therapies currently recommended for the management of osteoporosis act mainly to inhibit bone resorption and reduce bone remodeling. PTH and its analog, teriparatide [recombinant human PTH(1-34)], represent a new class of anabolic therapies for the treatment of severe osteoporosis, having the potential to improve skeletal microarchitecture. Significant reductions in both vertebral and appendicular fracture rates have been demonstrated in the phase III trial of teriparatide, involving elderly women with at least one prevalent vertebral fracture before the onset of therapy. However, there is as yet no evidence that the antifracture efficacy of PTH will be superior to the bisphosphonates, whereas cost-utility estimates suggest that teriparatide is significantly more expensive. Teriparatide should be considered as treatment for postmenopausal women and men with severe osteoporosis, as well as for patients with established glucocorticoid-induced osteoporosis who require long-term steroid treatment. Teriparatide should also be considered for the management of individuals at particularly high risk for fractures, including subjects who are younger than age 65 and who have particularly low bone mineral density measurements (T scores < or = 3.5). Teriparatide therapy is not recommended for more than 2 yr, based, in part, on the induction of osteosarcoma in a rat model of carcinogenicity. Total daily calcium intake from both supplements and dietary sources should be limited to 1500 mg together with adequate vitamin D intake (< or =1000 U/d). Monitoring of serum calcium may be safely limited to measurement after 1 month of treatment; mild hypercalcemia may be treated by withdrawing dietary calcium supplements, reducing the dosing frequency of PTH, or both. At present, concurrent therapy with antiresorptive therapy, particularly bisphosphonates, should be avoided, although sequential therapy with such agents may consolidate the beneficial effects upon the skeleton after PTH is discontinued.
Bootstrapping pay-as-you-go data integration systems (2008)

Data integration systems offer a uniform interface to a set of data sources. Despite recent progress, setting up and maintaining a data integration application still requires significant upfront effort of creating a mediated schema and semantic mappings from the data sources to the mediated schema. Many application contexts involving multiple data sources (e.g., the web, personal information management, enterprise intranets) do not require full integration in order to provide useful services, motivating a pay-as-you-go approach to integration. With that approach, a system starts with very few (or inaccurate) semantic mappings and these mappings are improved over time as deemed necessary.