gebhart/patrepeval huggingface dataset:
The Use of Mudlac Transposons as Tools for Vital Staining to Visualize Clonal and Non-clonal Patterns of Organization in Bacterial Growth on Agar Surfaces (1984)

When a histochemical stain for beta-galactosidase activity is applied to growth of Gram-negative bacteria on agar medium, the pigmentation is non-uniform and capable of revealing internal colony organization into different cell types. Use of an Escherichia coli strain with a thermosensitive lac repressor indicates that colonies expand by addition of new cells at the periphery and that older cells which have synthesized beta-galactosidase early in development remain in the centre. Mixed inocula of different strains show clonal exclusiveness as they proliferate outwards. Mudlac transposons can create genetic fusions that place beta-galactosidase expression under a variety of regulatory systems. Stained surface cultures of E. coli and Pseudomonas putida strains carrying Mudlac insertions in plasmids reveal a variety of flower-like staining patterns. These patterns display both clonal (i.e. sectorial) and non-clonal (circular and radial) features which are heritable within a given strain. The non-clonal aspects of the patterns reflect phenotypic differentiation without genetic change. These observations indicate that bacterial growth on agar surfaces is a highly regulated process similar, in many respects, to the development of specific multicellular tissues and organisms.
Inhibition of dopamine beta-hydroxylase by aromatic and alkyl thioureas. (1969)

Severall aromatic and alkyl thioureas were effective inhibitors of a purified bovine adrenal dopamine β-hydroxylase preparation. Inhibition of the enzyme by U-10,157 (1, 1-dimethyl-3-phenyl-2-thiourea) was competitive with the substrate after a 5-minute preincubation of inhibitor with the enzyme. Increased substrate concentration did not overcome the inhibition with U-10,157 after 15-minute preincubation. Seven of the 21 thioureas which demonstrated in vitro enzyme inhibition were administered i.p. to mice at 200 or 100 mg/kg. Only two of the inhibitors failed to decrease mouse brain norepinephrine. The effects of the inhibitors upon the dopamine content of mouse brain varied greatly, but dopamine levels were generally elevated consistent with inhibition of brain dopamine β-hydroxylase in vivo. Maximum depletion of rat brain norepinephrine reached 40% of control four to seven hours after U-10,157, 200 mg/kg. A chelating mechanism for in vitro and in vivo enzyme inhibition is briefly discussed.
PCR-Based Methods for the Enrichment of Minority Alleles and Mutations (2009)

This review summarizes technologies available for detecting minority DNA mutations, placing an emphasis on newer methods that facilitate the enrichment of unknown low-level DNA variants such that the mutation can subsequently be sequenced. The enrichment of minority alleles is imperative in clinical and diagnostic applications, especially in those related to cancer detection, and continued technology development is warranted.
Modeling and optimal design of piezoelectric cantilever microactuators (1997)

A novel model is described for predicting the static behavior of a piezoelectric cantilever actuator with an arbitrary configuration of elastic and piezoelectric layers. The model is compared to deflection measurements obtained from 500-/spl mu/m-long ZnO cantilever actuators fabricated by surface micromachining. Modeled and experimental results demonstrate the utility of the model for optimizing device design. A discussion of design considerations and optimization of device performance is presented.
Change detection in streetscapes from GPS coordinated omni-directional image sequences (2006)

As part of ITS technology, to achieve quick map updates, we propose a method for automatically detecting changes in streetscapes from images captured by car-mounted omnidirectional cameras. It comprises two stages; accurate alignment of a map and street images taken at various times, and detection of changes in streetscapes from the aligned data. The system will collect data via many free-running cars fitted with low-cost equipment to obtain images at various times and along routes. In the first stage, we process the alignment of the image frames taken at same locations and determine the accurate position information of each frame by a method composed of dimension reduction and DP matching. Then in the second stage, we detect changes in streetscapes from images taken at various times. Experiments with 44 data items which were collected over about a year, demonstrate the effectiveness of our method.
Isocitrate dehydrogenase mutations: A challenge to traditional views on the genesis and malignant progression of gliomas (2011)

Isocitrate dehydrogenases (IDHs) convert isocitrate to α-ketoglutarate by oxidative decarboxylation and are thereby involved in multiple metabolic processes. Mutations in the genes encoding IDH1 and IDH2 were first reported in human gliomas in 2008 and later on also identified in a minority of patients with acute myeloid leukemia. The mutations universally affect codons 132 in IDH1 and 172 in IDH2 and result in decreased enzymatic activity. The oncogenic pathway triggered by IDH mutations may involve the activation of hypoxia-inducible factor pathway as well as the acquisition of a novel (gain of enzymatic) function consuming NADPH and generating α-hydroxyglutarate. Most intriguingly, IDH mutations are observed in ∼70-80% of grade II/III gliomas and the majority of secondary glioblastomas, but only 10% of primary glioblastomas, suggesting a different cellular origin of the gliomas, which had previously been viewed as a multistep process of malignant progression. Understanding the oncogenic pathway mediated by mutant IDH might result in the development of novel, tailored pharmacological therapies for human glioma patients.
Enhancing therapeutic vaccination by blocking PD-1–mediated inhibitory signals during chronic infection (2008)

Therapeutic vaccination is a potentially promising strategy to enhance T cell immunity and viral control in chronically infected individuals. However, therapeutic vaccination approaches have fallen short of expectations, and effective boosting of antiviral T cell responses has not always been observed. One of the principal reasons for the limited success of therapeutic vaccination is that virus-specific T cells become functionally exhausted during chronic infections. We now provide a novel strategy for enhancing the efficacy of therapeutic vaccines. In this study, we show that blocking programmed death (PD)-1/PD-L1 inhibitory signals on exhausted CD8(+) T cells, in combination with therapeutic vaccination, synergistically enhances functional CD8(+) T cell responses and improves viral control in mice chronically infected with lymphocytic choriomeningitis virus. This combinatorial therapeutic vaccination was effective even in the absence of CD4(+) T cell help. Thus, our study defines a potent new approach to augment the efficacy of therapeutic vaccination by blocking negative signals. Such an approach may have broad applications in developing treatment strategies for chronic infections in general, and perhaps also for tumors.
Oncogenic Adenomatous Polyposis Coli Mutants Impair the Mitotic Checkpoint through Direct Interaction with Mad2 (2009)

The majority of colorectal tumors are aneuploid because of the underlying chromosome instability (CIN) phenotype, in which a defective mitotic checkpoint is implicated. Adenomatous polyposis coli (APC), a tumor suppressor gene that is commonly mutated in colon cancers, has been suggested in causing CIN; however, the molecular mechanism remains unresolved. In this study, we report an interaction of tumor-associated N-terminal APC fragments (N-APC) with Mad2, an essential mitotic checkpoint protein, providing a direct molecular support for linking APC mutations to the generation of CIN. N-APC interacts with Mad2 in Xenopus egg extracts, colon cancer cells, and in vitro with purified components. The interaction between N-APC and Mad2 decreases the soluble pool of Mad2, which is essential for Mad2 cycling and releasing from unattached kinetochores to produce a diffusible |P;wait anaphase|P' signal. Addition of such an N-APC mutant of egg extracts inactivates the mitotic checkpoint. Expressing a tumor-associated N-APC mutant in mammalian cells with an intact mitotic checkpoint produces premature anaphase onset with missegregated chromosomes.
OPPORTUNITIES FOR DEMAND PARTICIPATION IN NEW ENGLAND CONTINGENCY-RESERVE MARKETS (2003)

The Federal Energy Regulatory Commission (FERC 2002a), in its notice on StandardMarket Design (SMD), is clear that it wants loads to participate in wholesale power marketsand much prefers this to special load-reduction programs: “We believe the direct approach ofletting demand bid in the market will be less costly than a program where an end-user receivespayments greater than the market clearing price to reduce its demand.” To date, however, the primary mechanism through which retail loads respond towholesale prices and reliability concerns is via special demand-response programs, not theexisting markets for energy, congestion management, and ancillary services. Nevertheless,direct participation of retail loads in wholesale power markets is likely to expand the scope ofthese markets, lower prices (especially price spikes), reduce the opportunities for the exerciseof market power, and improve reliability. Encouraging such demand participation requires acareful review of existing reliability rules and market designs to ensure they do not unfairlyexclude resources that can provide valuable services to the grid. This paper deals with the issues and opportunities New England faces in getting retailloads to provide some of the real-power ancillary services and to participate in the markets forthese services. The paper focuses on the three contingency reserves that are deployedthroughout the Northeast: 10-minute spinning reserve, 10-minute nonspinning (supplemental)reserve, and 30-minute (replacement) reserve. The paper explains what these services are, thetechnical and reliability requirements imposed on resources that provide these services, thedesign and results of markets for contingency reserves, the desirable characteristics of retailloads that might provide reserves, and recommendations to NEDRI and ISO New England toencourage demand participation in reserve markets.
Velocity model building for variable-depth streamer data: Brunei case study (2013)

The computation of velocity by tomography using Residual Move-Out (RMO) curves is widely used in the industry. The semblance-based, automatic dense picking of RMO has proved to be a very efficient technique for conventional data. However, in the case of variable-depth streamer acquisition, this technique is poorly adapted due to the presence of ghosts in the data. We present here a robust, automatic, high-order dense picking technique based on a cross-semblance criteria using the migrated and mirrormigrated common image gathers that eliminates the need for pre-stack deghosting prior to velocity update. This paper focuses on velocity model building using our method. It is applied to a complex 2D variable-depth streamer acquisition from Brunei, which is characterized by noisy data where faults and gas pockets coexist. We show that our method allows us to obtain an accurate velocity function conformable to structure that improves the focusing.
Region-Based Shape Matching for Automatic Image Annotation and Query-by-Example (1997)

We present a method for automatic image annotation and retrieval based on query-by-example by region-based shape matching. The proposed method consists of two parts: region selection and shape matching. In the first part, the image is partitioned into disjoint, connected regions with more-or-less uniform color, whose boundaries coincide with spatial edge locations. Each region or valid combinations of neighboring regions constitute “potential objects.” In the second part, the shape of each potential object is tested to determine whether it matches one from a set of given templates. To this effect, we propose a new shape matching method, which is translation-, rotation-, and isotropic scale-invariant, where the boundary of each potential object, as well as of each template, is represented by a B-spline. We, then, identify correspondences between the joint points of the B-splines of potential objects and templates by using a modal matching method. These correspondences are used to estimate the parameters of an affine mapping to register the object with the template. A proximity measure is then computed between the two contours based on the Hausdorff distance. We demonstrate the performance of the proposed method on a variety of images.
The deadman theory of suture anchors: observations along a South Texas fence line (1995)

Suture anchors are being increasingly reported as a means of fixation of torn rotator cuff tendons to bone. The author has developed a mechanical model for the suture anchor-rotator cuff construct based on an analogy to the deadman system used to stabilize a corner fence post. Using this model, one can demonstrate a mechanically favorable angle of insertion of the suture anchor (theta 1) such that the anchor's pullout strength is increased at low angles of theta 1. In addition, the angle that the suture makes with the direction of pull of the rotator cuff (theta 2) has a direct effect on tension in the suture. A low angle of theta 2 minimizes the total tension in the suture, thereby minimizing the chance of suture breakage.
Evolution and resolution of stimulation-induced axonal injury in peripheral nerve (1999)

We describe the evolution of axonal injury following the induction of neural damage by electrical stimulation. The sciatic nerves of cats were stimulated continuously for 8 h with charge-balanced waveforms at high intensities, 50 Hz and 2100-4500 microA, using circumneural helical electrodes. Computer-assisted morphometric and ultrastructural studies indicate that many of the damaged fibers had not regenerated by 125 days after stimulation. Functional deficits were not observed in any of the animals, and most of the fibers appeared to be histologically normal at 125 days after stimulation. These findings indicate that there is relatively little late-onset injury associated with the stimulation. However, the slow, and possibly incomplete, recovery of the damaged axons emphasizes the importance of using stimulus protocols with adequate margins of safety.
Rapid ("warm") autopsy study for procurement of metastatic prostate cancer. (2000)

In this report, we describe the distribution of metastases from 14 patients who had hormone-refractory adenocarcinoma of the prostate and agreed while alive to undergo directed autopsies after their deaths. These autopsies were undertaken specifically to document the distribution of metastases, characterize tumors phenotypically and immunohistochemically, harvest fresh and snap frozen tumor and normal control tissues suitable for molecular examination, and establish cell lines via passages through generations of severe combined immunodeficient and athymic mice. Achievement of these goals was obtained through the development of a multidisciplinary team approach. Team members included a medical oncologist, pathologists, urologists, and researchers. The autopsy and tissue procurement teams were available on a round-the-clock basis. The tissues harvested from these autopsies yielded high-quality tumor samples, as evidenced by excellent preservation seen by light microscopy, strong prostate-specific antigen immunostaining, and the successful development of xenografts. The development and expansion of this program represent a valuable resource for molecular and clinical researchers.
Randomized clinical trial of non-specific immunotherapy with cell-wall skeleton of Nocardia rubra. (1984)

A randomized clinical trial of intrapleural Nocardia rubra cell-wall skeleton (N-CWS) followed by intradermal N-CWS was performed against lung cancer patients from November, 1977 to June, 1981. Totally, 190 patients were entered into this trial. The N-CWS treatment was effective in terms of prolongation of remission duration against not only operable but also inoperable patients. However, significant improvement of survival rate was observed only in operable patients, especially curative operation group (p less than 0.05). The mode of recurrence was classified as local recurrence and distant metastasis in the curative operation group. The rates of distant metastasis were 34.1 and 17.6% respectively, in the control and the N-CWS groups. The rate of local recurrence was 13.6% in the control group, although no local recurrence was observed in the N-CWS group. These results indicate the clinical effectiveness of the N-CWS treatment especially in curatively resectable lung cancer. Major and frequent side-effects of the N-CWS treatment were fever up to 40 degrees C with an average duration of 2 days following intrapleural instillation and skin reaction at the site of intradermal injections. No serious side effect was experienced during this trial.
Effects of Bofu-tsusho-san, a traditional Chinese medicine, on body fat accumulation in fructose-loaded rats. (2001)

The effects of Bofu-tsusho-san (BOF), a traditional Chinese medicine, on fructose-induced hypertriglyceridemia and body fat accumulation were investigated in female SD rats. Rats were allowed to drink ad libitum 25% (w/w) fructose solution for 6 weeks. BOF was administered to the rats as an experimental diet containing 1.5% or 4.5% (w/w) of BOF during the fructose-loading period. BOF suppressed body weight gain and prevented the elevation of serum triglyceride levels and body fat accumulation in fructose-loaded rats without affecting food and fructose intake. Furthermore, BOF prevented the increase of triglyceride content in the liver and the reduction of mitochondrial cytochome c oxidase activity in the brown adipose tissue induced by fructose. From these results, it has been suggested that BOF has a preventive effect against the body fat accumulation caused by excess intake of sugar or other fructose-containing foods. The inhibition of triglyceride synthesis in the liver, and the enhancement of lipolysis in adipocytes and of thermogenesis in brown adipose tissue have been presumed as the mechanisms of action of BOF.
Cleaning of Silicon Surfaces by NF3-Added Hydrogen and Water-Vapor Plasma Downstream Treatment (1996)

Native oxide was removed from silicon surfaces by NF 3 -added hydrogen and water-vapor plasma downstream treatment. It took 45 s to remove native oxide from a 6-inch silicon wafer. Fourier transform infrared attenuated total reflection (FT-IR ATR) measurement revealed that the surface roughness after the downstream treatment was the same as that after wet cleaning with 2% HF solution. A silicon epitaxial layer was grown on the surface cleaned by the downstream treatment. Although process temperature was as low as 100°C, the present downstream treatment induced the same effect as in situ hydrogen annealing.
Discovery of 2-[4-{{2-(2S,5R)-2-Cyano-5-ethynyl-1-pyrrolidinyl]-2-oxoethyl]amino]- 4-methyl-1-piperidinyl]-4-pyridinecarboxylic Acid (ABT-279):  A Very Potent, Selective, Effective, and Well-Tolerated Inhibitor of Dipeptidyl Peptidase-IV, Useful for the Treatment of Diabetes (2006)

Dipeptidyl peptidase-IV (DPP-IV) inhibitors are poised to be the next major drug class for the treatment of type 2 diabetes. Structure-activity studies of substitutions at the C5 position of the 2-cyanopyrrolidide warhead led to the discovery of potent inhibitors of DPP-IV that lack activity against DPP8 and DPP9. Further modification led to an extremely potent (Ki(DPP)(-)(IV) = 1.0 nM) and selective (Ki(DPP8) > 30 microM; Ki(DPP9) > 30 microM) clinical candidate, ABT-279, that is orally available, efficacious, and remarkably safe in preclinical safety studies.
Secreted antagonists of the Wnt signalling pathway (2003)

The extracellular antagonists of the Wnt signalling pathway can be divided into two broad classes. Both classes of molecule prevent ligand-receptor interactions, but by different mechanisms: members of the first class, which include the sFRP (secreted Frizzled-related protein) family, WIF (Wnt inhibitory factor)-1 and Cerberus, primarily bind to Wnt proteins; the second class comprises certain members of the Dickkopf (Dkk) family, which bind to one subunit of the Wnt receptor complex. In addition, there are other protein interactions that contribute to Wnt antagonist function. Moreover, certain sFRPs and Dkks do not antagonise Wnt function, which suggests that these families have as-yet-undiscovered functions.
Multivalent Rituximab Lipid Nanoparticles as Improved Lymphoma Therapies: Indirect Mechanisms of Action and In Vivo Activity (2011)

Although indirect and direct mechanisms of multivalent Ritux are enhanced, its further development requires methods to improve its circulation lifetime.
Targeting Methanopterin Biosynthesis ToInhibitMethanogenesis (2003)

This paper describes the design, synthesis, and successful employment of inhibitors of 4-(beta-D-ribofuranosyl)aminobenzene-5'-phosphate (RFA-P) synthase, which catalyzes the first committed step in the biosynthesis of methanopterin, to specifically halt the growth of methane-producing microbes. RFA-P synthase catalyzes the first step in the synthesis of tetrahydromethanopterin, a key cofactor required for methane formation and for one-carbon transformations in methanogens. A number of inhibitors, which are N-substituted derivatives of p-aminobenzoic acid (pABA), have been synthesized and their inhibition constants with RFA-P synthase have been determined. Based on comparisons of the inhibition constants among various inhibitors, we propose that the pABA binding site in RFA-P synthase has a relatively large hydrophobic pocket near the amino group. These enzyme-targeted inhibitors arrest the methanogenesis and growth of pure cultures of methanogens. Supplying pABA to the culture relieves the inhibition, indicating a competitive interaction between pABA and the inhibitor at the cellular target, which is most likely RFAP synthase. The inhibitors do not adversely affect the growth of pure cultures of the bacteria (acetogens) that play a beneficial role in the rumen. Inhibitors added to dense ruminal fluid cultures (artificial rumena) halt methanogenesis; however, they do not inhibit volatile fatty acid (VFA) production and, in some cases, VFA levels are slightly elevated in the methanogenesis-inhibited cultures. We suggest that inhibiting methanopterin biosynthesis could be considered in strategies to decrease anthropogenic methane emissions, which could have an environmental benefit since methane is a potent greenhouse gas.
Blind Multi-user Detection for Autonomous Grant-free High-Overloading MA without Reference Signal (2017)

In this paper, a novel blind multi-user detection(MUD) framework for autonomous grant-free high-overloading non-orthogonal multiple access is introduced in detail aimed at fulfilling the requirements of fifth-generation massive Machine Type Communications. From the perspective of the transmitter side, pros and cons regarding diverse types of emerging grant-free transmission, particularly autonomous grant-free, are elaborated and presented in a comparative manner. In the receiver end,code word-level successive interference cancellation (CL-SIC) is revealed as the main framework to perform MUD. In addition, underpinning state-of-art blind ideas such as blind activation detection taking advantage of the statistical metric of the aggregate signals, blind equalization based on the constellation's simple geometric character of low order modulation symbols, and blind channel estimation employing solely the successfully decoded code words are explained.