gebhart/patrepeval huggingface dataset:
Vincristine-induced allodynia in the rat (2001)

The aims of this study were two-fold: first, to simplify the method for creating a recently described neuropathic pain model in the rat, and second, to evaluate the effects of a number of drugs with analgesic or antihyperalgesic properties, in this model. Continuous intravenous vincristine infusion (1-100 microg kg(-1) day (-1)) for 14 days resulted in a dose dependent tactile allodynia (as measured by von Frey filaments) by 7 days at doses between 30 - 100 microg kg(-1) day (-1), with a hindlimb motor deficit observed at doses greater than 50 microg kg(-1) day (-1). No thermal hyperalgesia was observed. Systemic morphine, lidocaine, mexiletine and pregabalin (given intraperitoneally) produced significant reduction of the allodynia, while tetrodotoxin was without effect. Continuous intravenous infusion of vincristine in rats thus provides a reliable model of chemotherapy induced neuropathy which may be used in defining the mechanism and pharmacology of this clinically relevant condition.
Biochemical and genetic characterization of the action of triclosan on Staphylococcus aureus (2001)

Triclosan, a widely used antibacterial agent, possesses potent activity against Staphylococcus aureus. This study reports on an investigation of the antibacterial target of triclosan in this pathogen. A strain of S. aureus overexpressing the enoyl-[acyl-carrier-protein] reductase (FabI), demonstrated by Western immunoblotting, gave rise to an increase in the MIC of triclosan, while susceptibilities to a range of unrelated antibacterials were unaffected. There are approximately 12 000 molecules of FabI per cell in mid-log phase growth. This number increased by approximately three- to four-fold in the S. aureus FabI overexpressor. Triclosan selectively inhibited the incorporation of [(14)C]acetate into TCA-precipitable product, an indicator of fatty acid biosynthesis. Furthermore, it inhibited de novo fatty acid biosynthesis in this organism. In vitro, triclosan inhibited recombinant, purified S. aureus FabI with an IC(50) of approximately 1 microM. The combination of these biochemical and genetic data provide further evidence that the mode of action of triclosan in S. aureus is via inhibition of FabI.
CD141+ dendritic cells produce prominent amounts of IFN-α after dsRNA recognition and can be targeted via DEC-205 in humanized mice (2013)

Functional differences between human dendritic cell (DC) subsets and the potential benefits of targeting them with vaccines remain poorly defined. Here we describe that mice with reconstituted human immune system components (huNSG mice) develop all human conventional and plasmacytoid DC compartments in lymphoid organs. Testing different Toll-like receptor agonists for DC maturation in vivo, we found that IL-12p70 and interferon (IFN)-α production correlated with the maturation of CD141+ (BDCA3+) conventional DCs in huNSG mice. Furthermore, depletion of CD141+ DCs before stimulation significantly reduced IFN-α levels in vivo. This DC subset produced similar total amounts but different subtypes of IFN-α in response to synthetic double-stranded RNA compared with plasmacytoid DCs in response to a single-stranded RNA equivalent. Moreover, synthetic double-stranded RNA as adjuvant and antigen targeting to the endocytic receptor DEC-205, a combination that focuses antigen presentation for T-cell priming on CD141+ DCs, stimulated antigen-specific human CD4+ T-cell responses. Thus, the human CD141+ DC subset is a prominent source of IFN-α and interleukin-12 production and should be further evaluated for vaccine development.
[Use of vasopressin analogues and antagonist in clinical practice]. (2004)

Vasopressin is an endogenous peptide hormone with the antidiuretic and vasoactive action. Its mechanisms of action on vasal smooth muscles and kidney collective tubules are well known. This hormone also plays a role in the central nervous system and influences smooth muscles of the gastrointestinal tract. The recent research results indicated much more extensive effects of endogenous vasopressin action on the circulation than appeared from the water-electrolyte balance regulation only. The use of this hormone is actually an alternative for catecholamine in treatment of the shock. This paper presents short review of vasopressin action, actual clinical use and perspectives in use of vasopressin antagonists in the heart failure.
Programming by demonstration: a machine learning approach (2001)

Programming by demonstration (PBD) enables users to construct programs to automate repetitive tasks without writing a line of code. The key idea in PBD is to generalize from the user&amp;apos;s demonstration of the program on a concrete example to a robust program that will work in new situations. Previous approaches to PBD have employed heuristic, domain-specific algorithms to generalize from a small number of examples. In this thesis, we formalize programming by demonstration as a machine learning problem: given the changes in the application state that result from the user&amp;apos;s demonstrated actions, learn the sequence of instructions that map from one application state to the next. We propose a domain-independent machine learning approach to PBD that is capable of learning useful programs from a small number of examples. This approach addresses two difficult questions: (1) How do we construct the search space of possible program statements? (2) How do we search this large space efficiently? Our solution is based on the concept of version space algebra. Mitchell [55] formalized concept learning as a search through a version space of hypotheses consistent with the examples. Concept learning may be thought of as learning functions that map from an instance to a binary classification. In this work, we extend version spaces to apply to complex functions: functions that map from one complex object to another. We then present version space algebra, a means for combining several small spaces in order to construct complex version s...
Detection of β cell death in diabetes using differentially methylated circulating DNA (2011)

In diabetes mellitus, β cell destruction is largely silent and can be detected only after significant loss of insulin secretion capacity. We have developed a method for detecting β cell death in vivo by amplifying and measuring the proportion of insulin 1 DNA from β cells in the serum. By using primers that are specific for DNA methylation patterns in β cells, we have detected circulating copies of β cell-derived demethylated DNA in serum of mice by quantitative PCR. Accordingly, we have identified a relative increase of β cell-derived DNA after induction of diabetes with streptozotocin and during development of diabetes in nonobese diabetic mice. We have extended the use of this assay to measure β cell-derived insulin DNA in human tissues and serum. We found increased levels of demethylated insulin DNA in subjects with new-onset type 1 diabetes compared with age-matched control subjects. Our method provides a noninvasive approach for detecting β cell death in vivo that may be used to track the progression of diabetes and guide its treatment.
ABySS: A parallel assembler for short read sequence data (2009)

Widespread adoption of massively parallel deoxyribonucleic acid (DNA) sequencing instruments has prompted the recent development of de novo short read assembly algorithms. A common shortcoming of the available tools is their inability to efficiently assemble vast amounts of data generated from large-scale sequencing projects, such as the sequencing of individual human genomes to catalog natural genetic variation. To address this limitation, we developed ABySS (Assembly By Short Sequences), a parallelized sequence assembler. As a demonstration of the capability of our software, we assembled 3.5 billion paired-end reads from the genome of an African male publicly released by Illumina, Inc. Approximately 2.76 million contigs > or =100 base pairs (bp) in length were created with an N50 size of 1499 bp, representing 68% of the reference human genome. Analysis of these contigs identified polymorphic and novel sequences not present in the human reference assembly, which were validated by alignment to alternate human assemblies and to other primate genomes.
Reduction in recombinant human erythropoietin doses by the use of chronic intravenous iron supplementation (1995)

We have compared the efficacy of oral to intravenous iron for the chronic maintenance of iron stores in hemodialysis patients. Fifty-two hemodialysis patients with initial serum ferritin greater than 100 ng/mL and transferrin saturation greater than 15% were randomly assigned to one of two groups: those receiving oral iron therapy (n = 32) and those receiving intravenous iron dextran (100 mg twice weekly) (n = 20). At study completion (4 months), the mean hematocrit was significantly higher in the intravenous group than in the oral iron group (34.4% ± 0.7% v 31.8% ± 0.4%, respectively; P < 0.05), the final mean recombinant human erythropoietin dose was 46% lower in the intravenous iron group than in the oral group (4,050 ± 634 U/treatment v 7,563 ± 378 U/ treatment; P < 0.05), and the mean serum ferritin was significantly higher in the intravenous group than in the oral iron group (753.9 ± 30.2 ng/mL v 157.3 ± 15.4 ng/mL, respectively; P < 0.05). We have found that administering iron intravenously instead of orally for chronic maintenance iron supplementation in hemodialysis patients resulted in improved erythropoiesis. We hypothesize that most hemodialysis patients have inadequate iron stores for optimal erythropoiesis when currently recommended levels of ferritin and transferrin saturation are used to guide therapy, and that the chronic use of intravenous iron could reduce recombinant human erythropoietin requirements by maximizing iron stores. The improvement in erythropoiesis was accompanied, however, by an increase in iron indices to levels that could be indicative of tissue iron overload. Future studies must be performed to determine whether lower doses of intravenous iron dextran would improve erythropoiesis without causing potential organ iron overload.
A randomized controlled trial of prednisone in Alzheimer’s disease (2000)

A low-dose regimen of prednisone is not useful in the treatment of AD.
Photoconversion of Riboflavin to Lumichrome in Plant Tissues (1972)

Free flavins have been extracted from shoots of etiolated corn (Zea mays L., var. Burpee Snowcross) and from yeast cells and separated from other substances by absorption on resorcinol-formaldehyde resin and talc columns and by thin layer chromatography. Riboflavin was the only free flavin present. Extracts of etiolated shoots of oats (Avena sativa L., var. Multiline E-69 and Clinford) yielded riboflavin plus a second free flavin previously demonstrated in oats. The areas of the chromatograms expected to contain lumichrome were completely clear. After illumination of any of the three organisms with artificial light (1100 ft-c) or sunlight for 6 hours, lumichrome (7,8-dimethylalloxazine) was found. In corn shoots after irradiation by sunlight, the amount of lumichrome present was equivalent to 2.5% of the total free flavin. Lumichrome was identified by thin layer chromatography in six solvent systems (including two two-dimensional systems), by its characteristic fluorescence in acetic acid, by its absorption spectrum, and by formation of a characteristic hydrate in ammonia-containing solutions. A comparison was made with in vitro photolysis of riboflavin and the possible role of photolysis of riboflavin (either free or bound) and of lumichrome formation in photo-responses of plants is discussed. Placing the shoots in the dark for 4 hours after irradiation in sunlight for 6 hours led to no detectable loss of the lumichrome which had been formed.
A prefetching protocol for continuous media streaming in wireless environments (2001)

Streaming of continuous media over wireless links is a notoriously difficult problem. This is due to the stringent quality of service (QoS) requirements of continuous media and the unreliability of wireless links. We develop a streaming protocol for the real-time delivery of prerecorded continuous media from (to) a central base station to (from) multiple wireless clients within a wireless cell. Our protocol prefetches parts of the ongoing continuous media streams into prefetch buffers in the clients (base station). Our protocol prefetches according to a join-the-shortest-queue (JSQ) policy. By exploiting rate adaptation techniques of wireless data packet protocols, the JSQ policy dynamically allocates more transmission capacity to streams with small prefetched reserves. Our protocol uses channel probing to handle the location-dependent, time-varying, and bursty errors of wireless links. We evaluate our prefetching protocol through extensive simulations with VBR MPEG and H.263 encoded video traces. Our simulations indicate that for bursty VBR video with an average rate of 64 kb/s and typical wireless communication conditions our prefetching protocol achieves client starvation probabilities on the order of 10/sup -4/ and a bandwidth efficiency of 90% with prefetch buffers of 128 kbytes.
Fully Automatic Segmentation of the Proximal Femur Using Random Forest Regression Voting (2013)

Extraction of bone contours from radiographs plays an important role in disease diagnosis, preoperative planning, and treatment analysis. We present a fully automatic method to accurately segment the proximal femur in anteroposterior pelvic radiographs. A number of candidate positions are produced by a global search with a detector. Each is then refined using a statistical shape model together with local detectors for each model point. Both global and local models use Random Forest regression to vote for the optimal positions, leading to robust and accurate results. The performance of the system is evaluated using a set of 839 images of mixed quality. We show that the local search significantly outperforms a range of alternative matching techniques, and that the fully automated system is able to achieve a mean point-to-curve error of less than 0.9 mm for 99% of all 839 images. To the best of our knowledge, this is the most accurate automatic method for segmenting the proximal femur in radiographs yet reported.
Engineering Herbicide Tolerance in Transgenic Plants (1986)

The herbicide glyphosate is a potent inhibitor of the enzyme 5-enolpyruvylshikimate- 3-phosphate (EPSP) synthase in higher plants. A complementary DNA (cDNA) clone encoding EPSP synthase was isolated from a complementary DNA library of a glyphosate-tolerant Petunia hybrida cell line (MP4-G) that overproduces the enzyme. This cell line was shown to overproduce EPSP synthase messenger RNA as a result of a 20-fold amplification of the gene. A chimeric EPSP synthase gene was constructed with the use of the cauliflower mosaic virus 35S promoter to attain high level expression of EPSP synthase and introduced into petunia cells. Transformed petunia cells as well as regenerated transgenic plants were tolerant to glyphosate.
Oral Sumatriptan: Effect of a Second Dose, and Incidence and Treatment of Headache Recurrences (1994)

Oral sumatriptan in a dose of 100 mg aborts about 60% of migraine attacks within 2 h, but the headache may recur within 24 h. We investigated: (i) the incidence of headache recurrence after oral sumatriptan (ii) whether a second tablet of sumatriptan at 2 h increases initial efficacy and/or (iii) prevents headache recurrence and (iv) whether a further tablet of sumatriptan treats headache recurrence. In a randomized parallel-group clinical trial, 1246 patients treated one to three migraine attacks (with or without aura), with 100 mg oral sumatriptan. Two hours later they all took a double-blind randomized second table of sumatriptan (group I) or placebo (group II). Patients who initially improved, but then experienced headache recurrence took a further double-blind randomized tablet of sumatriptan or placebo. Proportions of patients who improved from moderate/severe headache to mild/none were similar in groups I and III at 2 h (55 vs 56%) and 4 h (80 vs 77%). Incidences of headache recurrence (moderate/severe-any grade of headache) and median times to headache recurrence were also similar: 22-32% at 16 h in group I and 25-33% at 16.5 h in group II. Sumatriptan was superior to placebo in treating headache recurrence: 74 vs 49% (p = 0.017) in group I and 70 vs 30% (p = 0.0001) in group II. Thus, one-fourth of patients experience headache recurrence at about 16 h after successful treatment of a migraine attack with 100 mg oral sumatriptan. A second tablet of sumatriptan at 2 h does not increase initial efficacy and neither prevents nor delays headache recurrence.(ABSTRACT TRUNCATED AT 250 WORDS)
In vitro pharmacokinetics of anti-psoriatic fumaric acid esters (2004)

Together, these in vitro data indicate that hydrolysis of DMF to MMF rapidly occurs at pH 8, resembling that within the small intestines, but not at pH 1 resembling the pH in the stomach. At both pHs MMF and MEF remained intact. These data explain the observation that after oral FAE intake MMF and MEF, but not DMF, can be readily detected in the circulation of human healthy volunteers and psoriasis patients.
Synthesis of progressively-variant textures on arbitrary surfaces (2003)

We present an approach for decorating surfaces with progressively-variant textures. Unlike a homogeneous texture, a progressively-variant texture can model local texture variations, including the scale, orientation, color, and shape variations of texture elements. We describe techniques for modeling progressively-variant textures in 2D as well as for synthesizing them over surfaces. For 2D texture modeling, our feature-based warping technique allows the user to control the shape variations of texture elements, making it possible to capture complex texture variations such as those seen in animal coat patterns. In addition, our feature-based blending technique can create a smooth transition between two given homogeneous textures, with progressive changes of both shapes and colors of texture elements. For synthesizing textures over surfaces, the biggest challenge is that the synthesized texture elements tend to break apart as they progressively vary. To address this issue, we propose an algorithm based on texton masks, which mark most prominent texture elements in the 2D texture sample. By leveraging the power of texton masks, our algorithm can maintain the integrity of the synthesized texture elements on the target surface.
Characterization of a Family of Chimpanzee Adenoviruses and Development of Molecular Clones for Gene Transfer Vectors (2004)

The high prevalence of preexisting immunity to the commonly used adenoviral vectors, as well as the requirement for readministration of vector for multiple therapeutic applications, necessitates the development of a panel of immunologically distinct adenoviral vectors against which neutralizing antibodies are rare in human populations. We have completely sequenced three chimpanzee-derived adenoviruses, Pan 5, Pan 6, and Pan 7, and have molecularly cloned E1-deleted vector genomes from each as bacterial plasmids. All the E1-deleted vectors were grown to high titer in HEK 293 cells. Neutralizing antibodies to the chimpanzee adenoviral vectors were not detected in serum samples from human subjects. In vitro cross-neutralization using rabbit antisera and in vivo readministration experiments in mice demonstrated that antibodies against Pan 5, Pan 7, or Pan 9 cross-neutralize one another but do not neutralize Pan 6. These results indicate that chimpanzee adenoviral vectors may be useful as vaccines or gene therapy vectors in human populations and should allow applications that require multiple vector administrations.
Compressed fluid technology: Application to RIE‐developed resists (1987)

Abstract A novel plasma‐developed resist lithographic process is described that uses compressed CO 2 to extract nonvolatile siloxane molecules from host organic polymers. The process is capable of at least 0.75 μm resolution with an X‐ray sensitive guest siloxane‐host polymer system. A processing window was investigated and defined to eliminate or minimize film damage during compressed fluid extraction. Polymer deformation was usually avoided by using supercritical CO 2 rather than liquid CO 2 , provided that film thicknesses were ≤1 μm. Increased solute concentrations in the host polymer also adversely affected the quality of extracted films. An in situ capacitance process monitoring scheme was developed which indicated that film damage, when observed, was primarily caused by explosive decompression of the solvent from the host polymer.
Expression of the α‐thionin gene from barley in tobacco confers enhanced resistance to bacterial pathogens (1993)

Thionins are cysteine-rich, 5 kDa polypeptides which are toxic to plant pathogens in vitro. Expression of the gene encoding alpha-thionin from barley endosperm, under the 35S promoter from cauliflower mosaic virus, conferred to transgenic tobacco enhanced resistance to the bacterial plant pathogens Pseudomonas syringae pv. tabaci 153 and P. syringae pv. syringae. The barley alpha-thionin gene, which has two introns, was correctly spliced in tobacco. The alpha-thionin in transgenic plants had the expected mobility in the gradient, when separated by high-performance liquid chromatography, reacted with monospecific antibodies and showed the expected antibiotic properties in vitro.
Modification of the siRNA Passenger Strand by 5‐Nitroindole Dramatically Reduces its Off‐Target Effects (2012)

During the formation of RNA-induced silencing complex (RISC), the passenger and guide strand of an siRNA duplex separate from each other to generate an active RISC complex. Accumulating evidence shows that an siRNA passenger strand can also assemble into a RISC complex and mediate RNA interference, thereby causing undesired off-target effects. To reduce this effect, the so-called "universal base" 5-nitroindole nucleotides were incorporated into an siRNA passenger strand. Melting temperature and circular dichroism spectrum measurements showed no significant changes compared to the unmodified duplex, thus indicating the formation of normal A-form conformation. Using a dual luciferase reporter assay, we have further shown that 5-nitroindole modification at position 15 of the siRNA passenger strand drastically decreased the RNAi (RNA interfering) potency of this strand, whereas the potency of the RNA guide strand was not much affected. These results could provide a practical approach for reducing off-target effects mediated by the siRNA passenger strand.