gebhart/patrepeval huggingface dataset:
Protein 3D Structure Prediction by Improved Tabu Search in Off-Lattice AB Model (2008)

Tabu Search (TS) algorithm is one of optimization search methods and has been applied for a large number of combinatorial optimization problems. In the paper, an improved TS algorithm is proposed for protein 3D folding structure prediction in off-lattice AB model. Experimental results show that the lowest energies computed by the improved TS algorithm are better than those obtained by the previous methods. Given a protein sequence, its lowest-energy conformation obtained by our improved TS method forms a single hydrophobic core, which suggests that AB model in three dimensions appears to reflect the real protein reasonably. Compared with the previous heuristic approaches, the improved TS algorithm has higher performance and can be effectively used to predict 3D structure prediction of proteins.
High-resolution fluorescence imaging via pattern-illuminated Fourier ptychography (2014)

Fluorescence microscopy plays a vital role in modern biological research and clinical diagnosis. Here, we report an imaging approach, termed pattern-illuminated Fourier ptychography (FP), for fluorescence imaging beyond the diffraction limit of the employed optics. This approach iteratively recovers a high-resolution fluorescence image from many pattern-illuminated low-resolution intensity measurements. The recovery process starts with one low-resolution measurement as the initial guess. This initial guess is then sequentially updated by other measurements, both in the spatial and Fourier domains. In the spatial domain, we use the pattern-illuminated low-resolution images as intensity constraints for the sample estimate. In the Fourier domain, we use the incoherent optical-transfer-function of the objective lens as the object support constraint for the solution. The sequential updating process is then repeated until the sample estimate converges, typically for 5-20 times. Different from the conventional structured illumination microscopy, any unknown pattern can be used for sample illumination in the reported framework. In particular, we are able to recover both the high-resolution sample image and the unknown illumination pattern at the same time. As a demonstration, we improved the resolution of a conventional fluorescence microscope beyond the diffraction limit of the employed optics. The reported approach may provide an alternative solution for structure illumination microscopy and find applications in wide-field, high-resolution fluorescence imaging.
Syntheses of Click PEG−Dexamethasone Conjugates for the Treatment of Rheumatoid Arthritis (2010)

A novel linear multifunctional polyethylene glycol (PEG)-dexamethasone (Dex) conjugate (click PEG-Dex) was synthesized using facile Cu(I)-catalyzed Huisgen 1,3-dipolar cycloaddition (a click reaction). Dex was conjugated to the click PEG via an acid-labile hydrazone bond to allow the drug release in a pathophysiological environment. To evaluate click PEG's potential as a versatile drug delivery platform, the click PEG-Dex conjugates were tested in an adjuvant-induced arthritis (AA) rat model. In vivo optical imaging data confirmed the arthrotropism of the conjugates in the arthritic rats. A long-term treatment study revealed that a single click PEG-Dex conjugate administration provided sustained (>15 days) amelioration of ankle joint inflammation to the AA rats. Treatment with an equivalent dose of dexamethasone phosphate sodium (free Dex) only provided temporal resolution of the arthritis, which recurred upon treatment withdrawal. Further histological and bone mineral density comparison between the ankle joints from both click PEG-Dex and free Dex treatment groups confirmed the superior anti-inflammatory and disease modifying effects of the novel polymer-drug conjugates.
Hepatocellular Carcinoma in Italian Patients with Cirrhosis (1991)

In the West, as in Asia, patients with cirrhosis of the liver are at substantial risk for hepatocellular carcinoma, with a yearly incidence rate of 3 percent. Our screening program did not appreciably increase the rate of detection of potentially curable tumors.
The value of a single combined measurement of VEGF, glycodelin, progesterone, PAPP-A, HPL and LIF for differentiating between ectopic and abnormal intrauterine pregnancy (2005)

VEGF serum levels might be a useful marker in differentiating between EPs and aIUPs.
Hypotensive Effect of a Newly Identified Peptide, ProadrenomedullinN-Terminal 20 Peptide (1996)

Proadrenomedullin N-terminal 20 peptide (PAMP) and adrenomedullin (AM), which are both derived from proadrenomedullin, exhibit marked hypotensive effects. We recently reported that PAMP but not AM reduced the release of norepinephrine from peripheral sympathetic nerve endings. Our present objective was to clarify the involvement of the sympathetic nervous system in the hypotensive action of PAMP and AM. Intravenous administration of PAMP (10, 20, and 50 nmol/kg) to conscious rats induced less reflex tachycardia (5 +/- 5, 10 +/- 5, and 14 +/- 6 beats per minute [bpm]) than that of AM in 0.1, 0.5, and 1.0 nmol/kg doses (5 +/- 8, 20 +/- 7, and 38 +/- 5 bpm, P < .01) although both agents showed similar hypotensive effects. We evaluated the effect of PAMP on blood pressure in pithed rats whose sympathetic nervous systems were abolished. In pithed rats, AM (-2 +/- 1, -7 +/- 1, and -10 +/- 3 mm Hg; NS, P < .05, and P < .01, respectively) but not PAMP evoked hypotension. In contrast, administration of PAMP (-3 +/- 1, -11 +/- 2, and -14 +/- 4 mm Hg; P < .05, P < .01, and P < .01, respectively) as well as adrenomedullin (-2 +/- 2, -10 + 3, and -15 +/- 4 mm Hg; NS, P < .01, and P < .01) significantly reduced blood pressure in electrically stimulated, pithed rats, which had reached almost the same levels as in conscious rats. In electrically stimulated, pithed rats, plasma norepinephrine level was reduced by PAMP but not by vehicle or AM. These findings suggest that the hypotensive effect of PAMP is mainly due to inhibition of peripheral sympathetic nerve activity.
Norovirus gastroenteritis causes severe and lethal complications after chemotherapy and hematopoietic stem cell transplantation (2011)

Norovirus (NV) infections are a frequent cause of gastroenteritis (GE), but data on this disease in immunocompromised patients are limited. We analyzed an NV outbreak, which affected immunosuppressed patients in the context of chemotherapy or HSCT. On recognition, 7 days after admission of the index patient, preventive measures were implemented. Attack rates were only 3% (11/334) and 10% (11/105) among patients and staff members, respectively. The median duration of symptoms was 7 days in patients compared with only 3 days in staff members (P = .02). Three patients died of the NV infection. Commonly used clinical diagnostic criteria (Kaplan-criteria) were unsuitable because they applied to 11 patients with proven NV-GE but also to 15 patients without NV-GE. With respect to the therapeutic management, it is important to differentiate intestinal GVHD from NV-GE. Therefore, we analyzed the histopathologic patterns in duodenal biopsies, which were distinctive in both conditions. Stool specimens in patients remained positive for NV-RNA for a median of 30 days, but no transmission was observed beyond an asymptomatic interval of 48 hours. NV-GE is a major threat to patients with chemotherapy or HSCT, and meticulous measures are warranted to prevent transmission of NV to these patients.
Selectable traits to increase crop photosynthesis and yield of grain crops (2000)

The grain yield of cereals has almost doubled this century as a result of genetic manipulation by plant breeding. Surprisingly, there has been no change in the rate of photosynthesis per unit leaf area to accompany these increases. However, total photosynthesis has increased as a result of an increase in leaf area, daily duration of photosynthesis or leaf area duration. There remain substantial opportunities to continue to improve total photosynthesis and crop yield genetically using conventional breeding practices. Selectable traits are discussed here in the context of increasing total above-ground biomass under favourable conditions. Opportunities exist to alter crop duration and the timing of crop development to match it better to radiation, temperature and vapour pressure during crop growth, and to increase the rate of development of early leaf area to achieve rapid canopy closure. The importance of these traits will depend on the environment in which the crop is grown. Increases in crop photosynthesis through breeding are also likely to come via indirect means. Selection for a high and sustained stomatal conductance during the period of stem elongation is one way. Increasing assimilate allocation to the reproductive primordia so as to establish a large potential sink should also indirectly increase total crop photosynthesis. Evidence in the major grain crops suggests that by anthesis the capacity for photosynthesis is high and that photosynthesis is not limiting during grain filling. To use this surplus capacity it is suggested that carbon and nitrogen partitioning to the reproductive meristem be increased so as to establish a high potential grain number and the potential for a large grain size. It is then expected that additional photosynthesis will follow, either by a longer daily duration of photosynthesis or by an extended leaf area duration.
Swainsonine Inhibition of Spontaneous Metastasis (1989)

We have previously shown that swainsonine, administered systemically to C57BL/6 mice, inhibited the pulmonary metastasis of iv injected B16-F10 melanoma cells by a mechanism involving interleukin-2 production and augmentation of natural killer cell activity. From this finding, which uses an "experimental metastasis" model system, we considered: (a) whether swainsonine would be effective in the inhibition of authentic or spontaneous metastasis; (b) whether the drug would also inhibit metastasis formation in organs other than the lungs; and (c) whether the drug would block the metastasis of tumor cells of different histological type or origin. Our data indicated that swainsonine effectively inhibited the spontaneous metastasis of B16-BL6 melanoma (by 88%) and M5076 reticulum sarcoma (by 95%) murine tumor cells to the lung and liver, respectively. In both cases, the antimetastatic activity of the drug increased as a function of the concentration in drinking water up to 3 micrograms/mL. These findings indicate that the antimetastatic activity of swainsonine is not limited to artificial or experimentally induced metastasis nor to a single tumor type or specific organ. The inhibition of metastasis is likely due to a combination of events, which are currently under investigation.
Slow response to loss of glycemic control in type 2 diabetes mellitus. (2003)

The level of HbA1c that seemed to trigger glucose-lowering action was 9.0% or higher, not 8.0% as recommended by the ADA. A substantial hyperglycemic peak preceded change in therapy even in this relatively tightly controlled population with type 2 diabetes mellitus. Earlier therapeutic changes, but not more frequent testing, would prevent the glycemic excursions we observed. Low mean HbA1c levels in populations do not necessarily indicate that loss of glycemic control is being rapidly addressed for most patients. More research is needed to estimate the impact of these peaks on current well-being and future complications.
A comparison of media synchronization quality among reactive control schemes (2002)

This paper assesses the quality of media synchronization of recovery control schemes from asynchrony, which are referred to as reactive control schemes here, in terms of objective and subjective measures. We deal with four reactive control techniques: skipping, discarding, shortening and extension of output duration, and virtual time-contraction and time-expansion. We have carried out subjective and objective assessment of the media synchronization quality of nine schemes, which consist of combinations of the four techniques. The paper makes a comparison of media synchronization quality among the schemes. It also clarifies the relations between the two kinds of quality measures.
β-Peptidic Peptidomimetics (2008)

For more than a decade now, a search for answers to the following two questions has taken us on a new and exciting journey into the world of beta- and gamma-peptides: What happens if the oxygen atoms in a 3i-helix of a polymeric chain composed of (R)-3-hydroxybutanoic acid are replaced by NH units? What happens if one or two CH2 groups are introduced into each amino acid building block in the chain of a peptide or protein, thereby providing homologues of the proteinogenic alpha-amino acids? Our journey has repeatedly thrown up surprises, continually expanding the potential of these classes of compound and deepening our understanding of the structures, properties, and multifaceted functions of the natural "models" to which they are related. Beta-peptides differ from their natural counterparts, the alpha-peptides, by having CH2 groups inserted into every amino acid residue, either between the C=O groups and the alpha-carbon atoms (beta(3)) or between the alpha-carbon and nitrogen atoms (beta(2)). The synthesis of these homologated proteinogenic amino acids and their assembly into beta-peptides can be performed using known methods. Despite the increased number of possible conformers, the beta-peptides form secondary structures (helices, turns, sheets) even when the chain lengths are as short as four residues. Furthermore, they are stable toward degrading and metabolizing enzymes in living organisms. Linear, helical, and hairpin-type structures of beta-peptides can now be designed in such a way that they resemble the characteristic and activity-related structural features ("epitopes") of corresponding natural peptides or protein sections. This Account presents examples of beta-peptidic compounds binding, as agonists or antagonists (inhibitors), to (i) major histocompatibility complex (MHC) proteins (immune response), (ii) the lipid-transport protein SR-B1 (cholesterol uptake from the small intestine), (iii) the core (1-60) of interleukin-8 (inflammation), (iv) the oncoprotein RDM2, (v) the HIVgp41 fusion protein, (vi) G-protein-coupled somatostatin hsst receptors, (vii) the TNF immune response receptor CD40 (apoptosis), and (viii) DNA. Short-chain beta-peptides may be orally bioavailable and excreted from the body of mammals; long-chain beta-peptides may require intravenous administration but will have longer half-lives of clearance. It has been said that an interesting field of research distinguishes itself in that the results always throw up new questions; in this sense, the structural and biological investigation of beta-peptides has been a gold mine. We expect that these peptidic peptidomimetics will play an increasing role in biomedical research and drug development in the near future.
Adaptive Rendering Based on Weighted Local Regression (2014)

Monte Carlo ray tracing is considered one of the most effective techniques for rendering photo-realistic imagery, but requires a large number of ray samples to produce converged or even visually pleasing images. We develop a novel image-plane adaptive sampling and reconstruction method based on local regression theory. A novel local space estimation process is proposed for employing the local regression, by robustly addressing noisy high-dimensional features. Given the local regression on estimated local space, we provide a novel two-step optimization process for selecting bandwidths of features locally in a data-driven way. Local weighted regression is then applied using the computed bandwidths to produce a smooth image reconstruction with well-preserved details. We derive an error analysis to guide our adaptive sampling process at the local space. We demonstrate that our method produces more accurate and visually pleasing results over the state-of-the-art techniques across a wide range of rendering effects. Our method also allows users to employ an arbitrary set of features, including noisy features, and robustly computes a subset of them by ignoring noisy features and decorrelating them for higher quality.
Liquid crystal thermography as a screening test for deep vein thrombosis in patients with cerebral infarction (1991)

Abstract. Pulmonary embolism secondary to deep vein thrombosis is a frequent cause of death in stroke patients. In a multicentre study of deep vein thrombosis prophylaxis, 112 patients with cerebral infarction and leg paresis were given aspirin 300 mg three times a day (t.d.s.) alone or with dipyridamole 100 mg t.d.s. To screen for deep vein thrombosis liquid crystal thermography of the legs was performed daily for 15 days on all patients. Those patients with positive thermography underwent immediate X‐ray venography of the appropriate limb as the definitive investigation for venous thrombosis. Twenty‐two patients had positive thermograms, of whom 16 had confirmed deep vein thrombosis as demonstrated by X‐ray venography. Only 8 of the 22 had clinical signs of deep vein thrombosis and 2 of those had a negative venogram. Of the 14 patients with positive thermography but negative clinical signs 10 had positive venograms. Difference in the incidence of deep vein thrombosis in the two treatment groups was not demonstrated. It is concluded that occult deep venous thrombosis is common after ischaemic stroke and it can occur without clinical signs. Liquid crystal thermography is a simple, rapid and cheap screening test that will allow the detection of clinically unrecognized thrombosis.
Fighting infection using immunomodulatory agents (2001)

The last decade has seen the emergence of immunomodulators as promising therapeutic agents in infectious diseases. A diverse array of recombinant, synthetic and natural immunomodulatory preparations for prophylaxis and treatment of various infections are available today. Some of these substances, such as granulocyte colony-stimulating factor (G-CSF), interferons, imiquimod and bacterial-derived preparations are already licensed for use in patients. Others including IL-12, various chemokines, synthetic cytosine phosphate-guanosine (CpG) oligodeoxynucleotides and glucans are being investigated extensively in clinical and preclinical studies. Immunomodulatory regimens offer an attractive approach as an adjunct modality for control of microbial diseases in the era of antibiotic resistance. Practical application of the advances in molecular biology, bioinformatics, genomic mining and high-throughput peptide synthesis should foster future discovery and development of novel immunomodulators contingent upon scientific evidence rather than dictates of discursive empiricism.
Identification of endometrial genes important for conceptus survival and development in sheep (2005)

Recurrent early pregnancy loss in the ovine uterine gland knockout (UGKO) ewe model manifests on Day 14 of pregnancy, indicating that endometrial secretions are critical for peri-implantation conceptus development. Therefore, the following studies were conducted with fertile ewes and infertile UGKO ewes to identify candidate endometrial factors essential for normal conceptus survival, utilizing both genomics and proteomics approaches. \nThe first study used transcriptional profiling of endometrium from Day 14 cyclic, pregnant, and bred UGKO ewes, as well as ewes treated with interferon tau (IFN??) and progesterone, to identify genes important for conceptus development. A number of novel and previously known IFN??-stimulated genes, as well as progesterone-stimulated genes were identified that are higher in fertile ewes, such as galectin-15. Interactive effects of progesterone and IFN?? regulate endometrial gene expression in a temporal and cell-type specific manner. \nThe second study characterized the endometrial expression and hormonal regulation of galectin-15, a member of the galectin family of secreted ??-galactoside lectins. Galectin-15 was secreted into the uterine lumen by the lumenal (LE) and superficial glandular epithelium (sGE), where it may promote adhesion during implantation, as well as was phagocytosed by the trophectoderm and formed intracellular crystals. \nThe third study determined the endometrial expression of galectin-15 throughout gestation. Galectin-15 was secreted into the uterine lumen, where it was phagocytosed \nby the trophectoderm/chorion, transferred through placental vasculature to the fetus, and cleared through the fetal kidney to be stored in allantoic fluid. The fourth study utilized proteomic analysis of uterine flushes and endometrial explant cultures from Day 14 cyclic, pregnant and UGKO ewes to identify differences in uterine secretions. Analyses identified several genes that were expressed by the LE and sGE and may be involved in prostaglandin production and/or pH regulation. Collectively, results of these studies suggest that transcriptional profiling and analysis of uterine secretions are effective tools to determine genes important for early pregnancy. Further, identified genes are expected to reveal novel endometrial factors and metabolic pathways for support of conceptus survival and implantation, as well as provide improvements for embryo culture methods and diagnose endometrial dysfunctions leading to infertility.
A simple and fast method to extract RNA from tissue culture cells. (1990)

We describe here a simple and fast method for the extraction of total cellular RNA from cultured mammalian cells. With this procedure, it takes less than 90 min to extract RNA from up to 18 samples. This method is very reproducible and gives RNA suitable for hybridization assays. In addition, it requires only equipment and reagents that are commonly found in any laboratory working with eukaryotic RNA
A Novel Multicontext Coarse-Grained Join Accelerator for Column-Oriented Databases. (2009)

Reconfigurable Logic (RL) coprocessors may be a promising solution for hardware acceleration of column-oriented databases. In this paper, we describe a multicontext, coarsegrained Reconfigurable coprocessor Unit (RU) that can be used to accelerate the join operator in column-oriented databases. We then evaluate the performance of this hardware accelerator using a microbenchmark query. Our results indicate that the query execution of the hardware join operator on the proposed RU model is one to two orders of magnitude faster than the software only query execution.