gebhart/patrepeval huggingface dataset:
Enhancement of Insect Antifreeze Protein Activity by Solutes of Low Molecular Mass (1998)

Antifreeze proteins (AFPs) lower the non-equilibrium freezing point of water (in the presence of ice) below the melting point, thereby producing a difference between the freezing and melting points that has been termed thermal hysteresis. In general, the magnitude of the thermal hysteresis depends upon the specific activity and concentration of the AFP. This study describes several low-molecular-mass solutes that enhance the thermal hysteresis activity of an AFP from overwintering larvae of the beetle Dendroides canadensis. The most active of these is citrate, which increases the thermal hysteresis nearly sixfold from 1.2 degrees C in its absence to 6.8 degrees C. Solutes which increase activity approximately fourfold are succinate, malate, aspartate, glutamate and ammonium sulfate. Glycerol, sorbitol, alanine and ammonium bicarbonate increased thermal hysteresis approximately threefold. Interestingly, 0.5 mol l-1 sodium sulfate eliminated activity. Solute concentrations between 0.25 and 1 mol l-1 were generally required to elicit optimal thermal hysteresis activity. Glycerol is the only one of these enhancing solutes that is known to be present at these concentrations in overwintering D. canadensis, and therefore the physiological significance of most of these enhancers is unknown. The mechanism(s) of this enhancement is also unknown. The AFP used in this study (DAFP-4) is nearly identical to previously described D. canadensis AFPs. The mature protein consists of 71 amino acid residues arranged in six 12- or 13-mer repeats with a consensus sequence consisting of Cys-Thr-X3-Ser-X5-X6-Cys-X8-X9-Ala-X11-Thr-X1 3, where X3 and X11 tend to be charged residues, X5 tends to be Thr or Ser, X6 to be Asn or Asp, X9 to be Asn or Lys and X13 to be Ala in the 13-mers. DAFP-4 is shorter by one repeat than previously described D. canadensis AFPs.
Linear Compression of Digital Ink via Point Selection (2012)

We present a method to compress digital ink based on piecewise-linear approximation within a given error threshold. The objective is to achieve good compression ratio with very fast execution. The method is especially effective on types of handwriting that have large portions with nearly linear parts, e.g. hand drawn geometric objects. We compare this method with an enhanced version of our earlier functional approximation method, finding the new technique to give slightly worse compression while performing significantly faster. This suggests the presented method can be used in applications where speed of processing is of higher priority than the compression ratio.
Effect of Ceria Structure on Oxygen Migration for Rh/Ceria Catalysts (1996)

The adsorption and reaction properties of Rh particles supported on a CeO2(100) surface and on polycrystalline CeO2 films annealed at low (LT, 970 K) and high (HT, 1720 K) temperatures were studied using temperature-programmed desorption (TPD) and steady-state, CO oxidation kinetics. SEM and XRD of the polycrystalline samples showed significant growth of the ceria crystallite size and change in the surface morphology upon high-temperature annealing. In TPD, a substantial fraction of the CO adsorbed on Rh supported on the LT polycrystalline film was found to desorb as CO2, with the oxygen coming from the CeO2 support. In contrast, oxidation of CO to CO2 was not observed in significant amounts during TPD from Rh on the CeO2(100) sample or the HT film. In agreement with the adsorption measurements, steady-state CO oxidation exhibited a second, ceria-mediated process for Rh on the LT film which was not observed on the HT film. These results indicate that the structure of ceria plays an important role in the r...
Blue 470-nm Light Kills Methicillin-Resistant Staphylococcus aureus (MRSA) in Vitro (2009)

At practical dose ranges, 470-nm blue light kills HA-MRSA and CA-MRSA in vitro, suggesting that a similar bactericidal effect may be attained in human cases of cutaneous and subcutaneous MRSA infections.
Selective solvent delignification for fermentation enhancement (1983)

Cellulose and hemicellulose in renewable biomass resources such as cornstover and wheat straw have been examined as substrates for the production of ethanol. A mixed culture of selected strains of Clostridium thermocellum and Clostridium thermosaccharolyticum are used to accomplish both the hydrolysis and fermentation of these carbohydrates in a single step. However, lignin and related phenolic materials are shown to diminish the rate, extent, and yield at which these carbohydrates can be utilized for ethanol production. In order to overcome this problem, a selective solvent pretreatment with alkaline-ethanol-water mixtures was examined for the delignification of cellulosic biomass under conditions where very little loss of fermentable carbohyrates results. Under optimal conditions, up to 67% of the initial lignin in cornstover can be extracted while 95% of the alpha-cellulose and pentosan carbohydrates remain insoluble. Subsequent mixed culture fermentation of the treated material has shown a 400% increase in the rate of degradation and greater than 85% utilization of the substrate. The effects of various extraction parameters on delignification kinetics and subsequent fermentation performance are discussed.
Bcl-xL and Bcl-2 expression in squamous cell carcinoma of the head and neck (1999)

These results suggest that disruption of apoptotic control pathways is an important event in the evolution of squamous cell carcinoma of the head and neck. A common mechanism for this disruption involves overexpression of Bcl-xL, Patients whose tumors demonstrate Bcl-2 positivity, even with locoregionally advanced disease, appear to have a high likelihood of cure with aggressive combined modality therapy and may be treated successfully with less toxic therapy.
Efficacy and safety of secukinumab in patients with generalized pustular psoriasis: A 52‐week analysis from phase III open‐label multicenter Japanese study (2016)

Generalized pustular psoriasis (GPP) is a severe inflammatory skin disease characterized by the presence of sterile pustules covering almost the entire body and systemic symptoms such as fever. Secukinumab, a fully human-recombinant anti-interleukin-17A monoclonal antibody was indicated for psoriasis vulgaris and psoriatic arthritis in Japan but is not yet investigated for GPP. In this phase III, open-label multicenter single arm study, the efficacy and safety of secukinumab as monotherapy or with co-medication was evaluated in 12 Japanese patients with GPP. All the patients received secukinumab 150 mg s.c. at baseline, week 1, 2, 3 and 4, and then every 4 weeks. Two non-responders were up-titrated to 300 mg. Change in GPP severity from baseline was evaluated by clinical global impression (CGI) categorized as "worsened", "no change", "minimally improved", "much improved" or "very much improved". Treatment success was achieved by 83.3% (n = 10) of patients at week 16 (primary end-point) with CGI evaluated as "very much improved" (n = 9) and "much improved" (n = 1). Moreover, the area of erythema with pustules improved as early as week 1 and resolved by week 16 in most of the patients. The improvements were sustained throughout 52 weeks. Over the 52-week treatment period, secukinumab was well tolerated with no unexpected safety signals. Nasopharyngitis, urticaria, diabetes mellitus and arthralgia were the frequent adverse events reported. The data from this study shows that secukinumab can become one of the potent treatment options for GPP.
Inhibition of specific IgE response in vivo by allergen-gene transfer (1996)

DNA immunization has been an attractive approach in altering the host immune response to antigen. To examine the utility of DNA immunization in allergic response, we examined the in vivo efficacy of an 'allergen-gene immunization' approach in the modulation of allergen-specific IgE responses in mice. Our results showed first that I.m. injection of a gene construct (pCMVD) containing an important house dust mite allergen gene (Dermatophagoides pteronyssinus group 5 allergen; Der p 5) results in the induction of Der p 5-specific IgG antibodies, but not IgE antibody. We next examined the effect of transduced allergen gene on the expression of specific IgE response in mice after i.p. challenge with recombinant Der p 5 (rDer p 5). Both vector (mock) control- and pCMVD-treated mice were i.p. sensitized with rDer p 5 at 3 weeks after injection of gene construct. Results showed that there is a 90% reduction in the level of specific IgE in pCMVD-treated mice when compared with mock-treated mice. Furthermore, the suppression of specific IgE response can be adoptively transferred with CD8+ T cells from pCMVD-treated mice and such inhibition is in an antigen-specific manner, since the level of specific IgE to an irrelevant allergen, Der p 1, remained unchanged in comparison to that of the mock-treated group. In addition, Der p 5-specific CD8+ T cells could produce high levels of IFN-gamma which probably inhibit allergen-specific IgE responses. Taken together, our results suggest that allergen-gene transfer is effective in the modulation of allergen-specific IgE responses and may provide a novel therapeutic approach.
Analysis of the 10q11 Cancer Risk Locus Implicates MSMB and NCOA4 in Human Prostate Tumorigenesis (2010)

Genome-wide association studies (GWAS) have established a variant, rs10993994, on chromosome 10q11 as being associated with prostate cancer risk. Since the variant is located outside of a protein-coding region, the target genes driving tumorigenesis are not readily apparent. Two genes nearest to this variant, MSMB and NCOA4, are strong candidates for mediating the effects of rs109939934. In a cohort of 180 individuals, we demonstrate that the rs10993994 risk allele is associated with decreased expression of two MSMB isoforms in histologically normal and malignant prostate tissue. In addition, the risk allele is associated with increased expression of five NCOA4 isoforms in histologically normal prostate tissue only. No consistent association with either gene is observed in breast or colon tissue. In conjunction with these findings, suppression of MSMB expression or NCOA4 overexpression promotes anchorage-independent growth of prostate epithelial cells, but not growth of breast epithelial cells. These data suggest that germline variation at chromosome 10q11 contributes to prostate cancer risk by influencing expression of at least two genes. More broadly, the findings demonstrate that disease risk alleles may influence multiple genes, and associations between genotype and expression may only be observed in the context of specific tissue and disease states.
Chelating Agents Used for Plutonium and Uranium Removal in Radiation Emergency Medicine (2005)

The prospects of using chelating agents for increasing the excretion of actinides are reviewed. The removal of plutonium by chelating agents is of great importance because plutonium is extremely dangerous and induces cancer due to radiation toxicity. Similarly, uranium is a radionuclide, which causes severe renal dysfunction within a short time period due to chemical toxicity. It may also induce cancers such as leukemia and osteosarcoma in cases of long-term internal radiation exposure. Investigations on chelating agents for the removal of plutonium were initiated in the 1960's and 1970's. Diethylenetriaminepentaacetic acid (DTPA) is recognized as a chelating agent that accelerates the excretion of plutonium in early treatment after an accident. Thereafter, there has long been an interest in finding new chelating agents with radionuclide removal properties for use in therapy, and many chelating agents such as 3,4,3-LIHOPO and CBMIDA have been studied for their ability to remove plutonium and uranium. Recently, the focus has turned to drugs that have been used successfully in the treatment of a variety of other diseases, for example the iron chelating drug deferiprone or 1,2-dimethyl-3-hydroxypyrid-4-one (L1), which is used in thalassaemia and ethane-1-hydroxy-1,1-bisphosphonate (EHBP), which is used in osteoporosis. Within this context, it is important to examine the clinical use of these two drugs as well as the properties of the experimental chelators 3,4,3-LIHOPO and CBMIDA in order to identify possible uses in the treatment of radiation workers contaminated with plutonium and uranium.
2010 Adaptive management report (2010)

The Desert Conservation Program administers the incidental take permit issued in 2001 by the United States Fish and Wildlife Service in accordance with the Endangered Species Act. Compliance with the permit requires implementation of the Clark County Multiple Species Habitat Conservation Plan. This plan requires an adaptive management program and a biennial report by an independent science advisor to assess the status of the plan and make recommendations for future funding. This 2010 Adaptive Management Report reviews current data on land use trends, habitat loss, species status and plan implementation, and makes recommendations for the future.
Reovirus-Specific Ribonucleic Acid from Polysomes of Infected L Cells (1972)

Polysomes from reovirus-infected L cells were analyzed. Although all 10 transcription products of the viral genome were represented in polysomes and presumably can be translated, fewer than 10 reovirus-specific polypeptides were detected in infected cells. The 5'-terminal sequence of all species of reovirus ribonucleic acid (RNA) from polysomes was ppGpYp, as previously found for the genome double-stranded RNA and the in vitro single-stranded products of the virion-associated RNA polymerase. RNA isolated from both heavy (>30 ribosomes) and light (5 to 8 ribosomes) polysomes includes similar amounts of large, medium, and small classes of reovirus single-stranded RNA, suggesting that linkage of the genome segments observed in virions may occur at the single-strand stage of RNA replication.
HDAC4 Protein Regulates HIF1α Protein Lysine Acetylation and Cancer Cell Response to Hypoxia (2011)

Hypoxia-inducible factor 1 α (HIF1α) is an essential part of the HIF-1 transcriptional complex that regulates angiogenesis, cellular metabolism, and cancer development. In von Hippel-Lindau (VHL)-null kidney cancer cell lines, we reported previously that HIF1α proteins can be acetylated and inhibited by histone deacetylase (HDAC) inhibitors or specific siRNA against HDAC4. To investigate the mechanism and biological consequence of the inhibition, we have generated stable HDAC4 knockdown via shRNA in VHL-positive normal and cancer cell lines. We report that HDAC4 regulates HIF1α protein acetylation and stability. Specifically, the HIF1α protein acetylation can be increased by HDAC4 shRNA and decreased by HDAC4 overexpression. HDAC4 shRNA inhibits HIF1α protein stability. In contrast, HDAC1 or HDAC3 shRNA has no such inhibitory effect. Mutations of the first five lysine residues (lysine 10, 11, 12, 19, and 21) to arginine within the HIF1α N terminus reduce protein acetylation but render the mutant HIF1α protein resistant to HDAC4 and HDACi-mediated inhibition. Functionally, in VHL-positive cancer cell lines, stable inhibition of HDAC4 decreases both the HIF-1 transcriptional activity and a subset of HIF-1 hypoxia target gene expression. On the cellular level, HDAC4 inhibition reduces the hypoxia-related increase of glycolysis and resistance to docetaxel chemotherapy. Taken together, the novel biological relationship between HDAC4 and HIF1α presented here suggests a potential role for the deacetylase enzyme in regulating HIF-1 cancer cell response to hypoxia and presents a more specific molecular target of inhibition.
Calnexin, calreticulin and the folding of glycoproteins (1997)

Calnexin and calreticulin are molecular chaperones in the endoplasmic reticulum (ERJ. They are lectins that interact with newly synthesized glycoproteins that have undergone partial trimming of their core N-linked oligosaccharides. Together with the enzymes responsible for glucose removal and a glucosyltransferase that re-glucosylates already-trimmed glycoproteins, they provide a novel mechanism for promoting folding, oligomeric assembly and quality control in the ER.
Exploiting Product Related Review Features for Fake Review Detection (2016)

Product reviews are now widely used by individuals for making their decisions. However, due to the purpose of profit, reviewers game the system by posting fake reviews for promoting or demoting the target products. In the past few years, fake review detection has attracted significant attention from both the industrial organizations and academic communities. However, the issue remains to be a challenging problem due to lacking of labelling materials for supervised learning and evaluation. Current works made many attempts to address this problem from the angles of reviewer and review. However, there has been little discussion about the product related review features which is the main focus of our method. This paper proposes a novel convolutional neural network model to integrate the product related review features through a product word composition model. To reduce overfitting and high variance, a bagging model is introduced to bag the neural network model with two efficient classifiers. Experiments on the real-life Amazon review dataset demonstrate the effectiveness of the proposed approach.
Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types (2010)

A significant modification to the additive all-atom CHARMM lipid force field (FF) is developed and applied to phospholipid bilayers with both choline and ethanolamine containing head groups and with both saturated and unsaturated aliphatic chains. Motivated by the current CHARMM lipid FF (C27 and C27r) systematically yielding values of the surface area per lipid that are smaller than experimental estimates and gel-like structures of bilayers well above the gel transition temperature, selected torsional, Lennard-Jones and partial atomic charge parameters were modified by targeting both quantum mechanical (QM) and experimental data. QM calculations ranging from high-level ab initio calculations on small molecules to semiempirical QM studies on a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer in combination with experimental thermodynamic data were used as target data for parameter optimization. These changes were tested with simulations of pure bilayers at high hydration of the following six lipids: DPPC, 1,2-dimyristoyl-sn-phosphatidylcholine (DMPC), 1,2-dilauroyl-sn-phosphatidylcholine (DLPC), 1-palmitoyl-2-oleoyl-sn-phosphatidylcholine (POPC), 1,2-dioleoyl-sn-phosphatidylcholine (DOPC), and 1-palmitoyl-2-oleoyl-sn-phosphatidylethanolamine (POPE); simulations of a low hydration DOPC bilayer were also performed. Agreement with experimental surface area is on average within 2%, and the density profiles agree well with neutron and X-ray diffraction experiments. NMR deuterium order parameters (S(CD)) are well predicted with the new FF, including proper splitting of the S(CD) for the aliphatic carbon adjacent to the carbonyl for DPPC, POPE, and POPC bilayers. The area compressibility modulus and frequency dependence of (13)C NMR relaxation rates of DPPC and the water distribution of low hydration DOPC bilayers also agree well with experiment. Accordingly, the presented lipid FF, referred to as C36, allows for molecular dynamics simulations to be run in the tensionless ensemble (NPT), and is anticipated to be of utility for simulations of pure lipid systems as well as heterogeneous systems including membrane proteins.
Role of Arachidonic Acid in the Regulation of the Inflammatory Response in TNF‐α‐treated Rats (1998)

These results suggest that fish oil is anti-inflammatory principally through a reduction in the AA content of phospholipids.
Autologous chondrocyte implantation in the knee using fibrin (2009)

Autologous chondrocyte implantation (ACI) is widely used to treat symptomatic articular cartilage injury of the knee. Fibrin ACI is a new tissue-engineering technique for the treatment of full-thickness articular cartilage defects, in which autologous chondrocytes are inserted into a three-dimensional scaffold provided by fibrin gel. The objective of this study is to document and compare mean changes in overall clinical scores at both baseline and follow-up. Fibrin ACI was used to treat deep cartilage defects of the femoral condyle in 30 patients. There were 24 men and 6 women with a median age of 35 years (range 15-55) and with a mean defect size of 5.8 cm(2) (range 2.3-12). Clinical and functional knee evaluations were performed using different scoring systems, MRI was performed 24 months postoperatively, and arthroscopy was performed 12 months postoperatively. All patients achieved clinical and functional status improvements following surgery (P < 0.01). The mean scores of the Henderson classification (MRI evaluation) significantly improved from 14.4 to 7 (P = 0.001), and no graft-associated complications were noted. Arthroscopic assessments performed 12 months postoperatively produced nearly normal (grade II) International Cartilage Repair Society scores in 8 of the 10 study patients. Fibrin ACI offers the advantages of technical simplicity, minimal invasiveness, a short surgery time, and easier access to difficult sites than classical ACI. Based on the findings of this clinical pilot study, we conclude that fibrin ACI offers a reliable means of treating articular cartilage defects of the knee.
Dynamic and Static Quenching of Fluorescence by 1−4 nm Diameter Gold Monolayer-Protected Clusters (2006)

How the efficiency of molecular quenching by Au nanoparticles depends on nanoparticle size is reported for (a) dynamic (collisional) quenching of four different fluorophores by three Au nanoparticles having similar protective layers but differing core diameters (1.1, 1.6, and 2.0 nm) and (b) static quenching in the electrostatic association between [Ru(bpy)3]2+ and five tiopronin-protected Au nanoparticles having core diameters from 1.3 to 3.9 nm. The quenching constants systematically increase with core size. In (a), the dynamic constants scale with the molar absorbance coefficients of the nanoparticles, showing the essentially of the absorbance/emission spectral overlap, and the associated nanoparticle core density of electronic states, in energy-transfer quenching. In (b), the fluorescence of the Au nanoparticle itself was enhanced by energy transfer from the [Ru(bpy)3]2+ fluorophore.
Molecular cloning and characterization of human DDX36 and mouse Ddx36 genes, new members of the DEAD/H box superfamily. (2002)

With the strategy of homologue molecular cloning using the sequence of the maleless gene (mle) of Drosophila, the novel homologous human and mouse genes with longer DNA/RNA helicase box (DEAD/DEAH box), named DDX36 and Ddx36 genes, respectively, were cloned as new members of the DEAD/H box superfamily. The predicted protein encoded by human DDX36 gene has a sequence identity of 37% and similarity of 58% with the MLE protein of Drosophila and 91% and 94% with the predicted protein encoded by mouse Ddx36 gene, respectively. Northern blotting of DDX36 shows a single strong signal of 3.8 kb in the hybridization pattern in human testis but no or very weak signal in other tissues. The DDX36 gene is mapped to chromosome 3q25.1-3q25.2, in which 26 exons and 25 introns have been identified. DDX36 and Ddx36 genes may be involved in sex development, spermatogenesis and male reproduction.