gebhart/patrepeval huggingface dataset:
Templating effect in DNA proximity ligation enables use of non-bioorthogonal chemistry in biological fluids (2012)

Here we describe the first example of selective reductive amination in biological fluids using split aptamer proximity ligation (StAPL). Utilizing the cocaine split aptamer, we demonstrate small-molecule-dependent ligation that is dose-dependent over a wide range of target concentrations in buffer, human blood serum and artificial urine medium. We explore the substrate binding preferences of the split aptamer and find that the cinchona alkaloids quinine and quinidine bind to the aptamer with higher affinity than cocaine. This increased affinity leads to improved detection limits for these small-molecule targets. We also demonstrate that linker length and hydrophobicity impact the efficiency of split aptamer ligation. The ability to carry out selective chemical transformations using non-bioorthogonal chemistry in media where competing reactive groups are present highlights the power of the increased effective molarity provided by DNA assembly. Obviating the need for bioorthogonal chemistry would dramatically expand the repertoire of chemical transformations available for use in templated reactions such as proximity ligation assays, in turn enabling the development of novel methods for biomolecule detection.
Solution Structure and Adenylyl Cyclase Stimulating Activities of C-Terminal Truncated Human Parathyroid Hormone Analogs (1995)

Analogues of human parathyroid hormone (hPTH) truncated at the C-terminal end have been studied for adenylyl cyclase (AC) activity and for solution conformation by circular dichroism (CD) spectroscopy. Analogues of hPTH-(1-34)-NH2, containing the first 28-31 residues, had only a slightly diminished ability to stimulate AC in rat osteosarcoma (ROS) cells as compared to that of the parent analogue. CD data on hPTH-(16-34)-NH2 and C-terminal deletion mutants of hPTH-(1-34)-NH2 supported the presence of a partially stable alpha-helix over residues 17-28. A carboxyl-terminal mutant, hPTH-(1-30)-OH, showed both reduced helix and greatly reduced AC-stimulating activity as compared to the corresponding amide analogue. In contrast, both of these analogues, in the presence of palmitoyloleoylphosphatidylserine (POPS) vesicles, showed an equal stabilization of alpha-helix. All other analogues showed at least some enhancement of alpha-helix in the presence of POPS. However, both in neutral, aqueous buffer and in POPS, the relative amount of alpha-helix decreased greatly as the peptide was shortened below the 1-28 sequence. These data provide additional support for an amphiphilic alpha-helix over residues 21-28 being the conformation for receptor binding of hPTH for stimulation of AC activity. Modeling human parathyroid hormone-related peptide as an alpha-helix over this same region, and comparison to hPTH, suggests that both may bind via the hydrophobic face to the receptor.
Growth suppression induced by wild-type p53 protein is accompanied by selective down-regulation of proliferating-cell nuclear antigen expression. (1991)

The p53 gene is a frequent target of mutation in a wide variety of human cancers. Previously, it was reported that conditional expression of wild-type p53 protein in a cell line (GM47.23) derived from a human glioblastoma multiform tumor had a negative effect on cell proliferation. We have now investigated the effect that induction of wild-type p53 protein in this cell line has on the expression of the proliferating-cell nuclear antigen gene. The proliferating-cell nuclear antigen gene encodes a nuclear protein that is an auxiliary factor of DNA polymerase delta and part of the DNA replication machinery of the cell. We show that inhibition of cell cycle progression into S-phase after induction of wild-type p53 protein is accompanied by selective down-regulation of proliferating-cell nuclear antigen mRNA and protein expression.
Variability of clinical manifestation of factor VII-deficiency in homozygous and heterozygous subjects of the European F7 gene mutation A294V (2008)

Inherited factor VII deficiency (FVIID) is a rare autosomal bleeding disorder. Subjects with reduced FVII activity and identified F7 gene mutation are registered in the International Greifswald registry of FVIID.[1][1] The mutation A294V is the most frequent among 717 FVIID patients in Central and
Adjuvanticity and protective immunity elicited by Bordetella pertussis antigens encapsulated in poly(DL-lactide-co-glycolide) microspheres (1995)

Purified Bordetella pertussis antigens, encapsulated in biodegradable poly(DL-lactide-co-glycolide) (DL-PLG) microspheres, were evaluated for their immunogenicity and ability to elicit a protective immune response against B. pertussis respiratory infection. Microencapsulated pertussis toxoid, filamentous hemagglutinin, and pertactin all retained their immunogenicity when administered parenterally. Intranasal immunization with a low dose (1 micrograms) of encapsulated filamentous hemagglutinin, pertussis toxoid, or pertactin elicited strong specific immunoglobulin G and immunoglobulin A antibody responses in respiratory secretions that were greater in magnitude than the responses elicited by the same doses of unencapsulated antigen. Intranasal immunization with as little as 1 micrograms of encapsulated pertussis antigen prior to infection reduced the bacterial recovery by 3 log10 CFU. However, intranasal immunization with the same low doses of unencapsulated antigens did not reduce infection. Intranasal administration of a combination of 1 micrograms of each of the microencapsulated pertussis antigens was more effective in reducing bacterial infection than administration of any single microencapsulated antigen. Intranasal administration of microencapsulated B. pertussis antigens elicits high levels of specific antibody coinciding with protection against infection when these microspheres are administered to the respiratory tract. These data provide evidence of the respiratory adjuvanticity of three different DL-PLC microsphere preparations, each of which contains a unique B. pertussis antigen.
Strain effects and band offsets in GaAs/InGaAs strained layered quantum structures (1989)

Strained single quantum wells composed of GaAs/InGaAs/GaAs were grown by molecular beam epitaxy and characterized at room temperature by photoreflectance and at 6 and 77 K by photoluminescence spectroscopy. For the InGaAs/GaAs heterojunction, utilizing a band offset ratio of 85:15 (conduction band:valence band) for the intrinsic (nonstrained) interface and a contribution of the hydrostatic compression to the valence band movement corresponding to the pressure sensitivity of the spin orbit band, excellent agreement is found between calculated excitonic transition energies and those found by experiment at all temperatures studied. Our analysis indicates that material parameters and the combined strain components used to calculate band structure are not temperature dependent to our degree of sensitivity. An empirical equation, which differs slightly from that for bulk InGaAs crystals, describing the nonstrained band-gap energy as a function of In fraction at 77 K is presented. The difference between band offset ratios for the intrinsic and strained heterojunction are found to be significant and the relative merits of each are discussed.
Discriminability objective for training descriptive captions (2018)

One property that remains lacking in image captions generated by contemporary methods is discriminability: being able to tell two images apart given the caption for one of them. We propose a way to improve this aspect of caption generation. By incorporating into the captioning training objective a loss component directly related to ability (by a machine) to disambiguate image/caption matches, we obtain systems that produce much more discriminative caption, according to human evaluation. Remarkably, our approach leads to improvement in other aspects of generated captions, reflected by a battery of standard scores such as BLEU, SPICE etc. Our approach is modular and can be applied to a variety of model/loss combinations commonly proposed for image captioning.
Lentiviral delivery of short hairpin RNAs protects CD4 T cells from multiple clades and primary isolates of HIV (2005)

Viral heterogeneity is a major hurdle for potential therapeutic use of RNA interference (RNAi) against HIV-1. To determine the extent of RNAi tolerance to mutations, we tested 3 viral target sites with differing propensity for mutations: a highly variable rev sequence, a gag sequence conserved only among clade B isolates, and a vif sequence highly conserved across clades. Lentiviral expression of all 3 shRNAs inhibited replication of the homologous HIV(IIIB) strain. However, they differed in their ability to protect primary CD4 T cells against multiple isolates within and across HIV clades. The least conserved rev sequence inhibited only 2 of 5 clade B isolates. The gag sequence (conserved within clade B) protected 5 of 5 clade B isolates but not other clade viruses with 2 or 3 mutations in the central region. In contrast, the vif sequence, which was conserved across clades except for single mutations at positions 14 and 17, inhibited viruses from 5 different clades. Moreover, siRNAs with introduced mutations at sites of gag sequence polymorphisms showed reduced antiviral activity, whereas mutations in vif siRNA only modestly decreased silencing. Thus, although 1 or 2 mutations at peripheral sites are tolerated, mutations in the central target cleavage region abolish RNAi activity.
Ultrastructural localization of vascular permeability factor/vascular endothelial growth factor (VPF/VEGF) to the abluminal plasma membrane and vesiculovacuolar organelles of tumor microvascular endothelium. (1995)

Vascular permeability factor/vascular endothelial growth factor (VPF/VEGF) is a cytokine secreted by many animal and human tumors, activated macrophages, keratinocytes, rheumatoid synovial cells, embryonic tissues, and by cultured epithelial and mesenchymal cell lines. It acts selectively on vascular endothelial cells to increase their permeability to circulating macromolecules and to stimulate their replication. Although not detectably expressed by vascular cells in the human and animal tumors we have studied, VPF/VEGF accumulates in the microvessels supplying tumors and certain inflammatory reactions in which VPF/VEGF is also overexpressed. Light microscopic immunohistochemistry lacked the resolution necessary to localize VPF/VEGF precisely in such vessels. Therefore, we used a pre-embedding immunocytochemical method to localize VPF/VEGF at the ultrastructural level in the new blood vessels that are elicited in the peritoneal walls of mice bearing a transplantable mouse ascites tumor of ovarian origin. Intense immunostaining for VPF/VEGF was observed on the abluminal plasma membrane of tumor-associated microvascular endothelial cells and in vesiculovacuolar organelles (VVOs) present in these same endothelial cells. (VVOs are recently described cytoplasmic organelles present in tumor vascular endothelium that provide an important pathway for extravasation of circulating macromolecules.) In contrast to labeling of the abluminal plasma membrane and VVO vesicles and vacuoles, endothelial cytoplasmic organelles, such as multivesicular bodies and Weibel-Palade bodies, and the underlying basal lamina, did not stain with antibodies to VPF/VEGF. The distribution of VPF/VEGF here described corresponds to that anticipated for high-affinity VFP/VEGF receptors, although binding of VPF/VEGF to other endothelial cell surface structures, such as plasma membrane proteoglycans, is also a possibility.
Hand Tracking Based on Behavioral Analysis for Users (2014)

人手结构的高维性而导致粒子滤波跟踪方法中采样数目非常庞大,是实现运动人手的实时性跟踪研究的主要障碍之一.以降低粒子数目为目标,以行为分析和建模为切入点,提出一种手势跟踪方法.首先分析操作者在手势操作过程中的行为特征,建立人手运动的动态模型;其次,研究动态模型的基本特征,并给出一种描述方法;然后,建立人手运动的时段模型,分析了手势状态的时间-空间关系.在此基础上,提出了状态变量微观结构的概念,重点给出了基于状态变量微观结构的手势跟踪算法;最后,设计和完成了实验,并与相关参考文献方法的实验结果进行对比.结果表明,采用该算法,用少量粒子就可以得到比较精确的跟踪结果.提出的核心算法已经用于一个基于自然手势交互的三维虚拟装配原型系统.
Digital Breast Tomosynthesis–guided Vacuum-assisted Breast Biopsy: Initial Experiences and Comparison with Prone Stereotactic Vacuum-assisted Biopsy (2014)

Clinical performance of DBT VAB was significantly superior to PS VAB. Because DBT VAB allows use of the full detector size for imaging and provides immediate lesion depth information without requiring triangulation, it facilitates target lesion reidentification and sampling of even low-contrast targets, such as uncalcified masses.
Role of human longevity assurance gene 1 and C18-ceramide in chemotherapy-induced cell death in human head and neck squamous cell carcinomas (2007)

In this study, quantitative isobologram studies showed that treatment with gemcitabine and doxorubicin, known inducers of ceramide generation, in combination, supra-additively inhibited the growth of human UM-SCC-22A cells in situ. Then, possible involvement of the human homologue of yeast longevity assurance gene 1 (LASS1)/C(18)-ceramide in chemotherapy-induced cell death in these cells was examined. Gemcitabine/doxorubicin combination treatment resulted in the elevation of mRNA and protein levels of LASS1 and not LASS2-6, which was consistent with a 3.5-fold increase in the endogenous (dihydro)ceramide synthase activity of LASS1 for the generation of C(18)-ceramide. Importantly, the overexpression of LASS1 (both human and mouse homologues) enhanced the growth-inhibitory effects of gemcitabine/doxorubicin with a concomitant induction of caspase-3 activation. In reciprocal experiments, partial inhibition of human LASS1 expression using small interfering RNA (siRNA) prevented cell death by about 50% in response to gemcitabine/doxorubicin. In addition, LASS1, and not LASS5, siRNA modulated the activation of caspase-3 and caspase-9, but not caspase-8, in response to this combination. Treatment with gemcitabine/doxorubicin in combination also resulted in a significant suppression of the head and neck squamous cell carcinoma (HNSCC) tumor growth in severe combined immunodeficiency mice bearing the UM-SCC-22A xenografts. More interestingly, analysis of endogenous ceramide levels in these tumors by liquid chromatography/mass spectroscopy showed that only the levels of C(18)-ceramide, the main product of LASS1, were elevated significantly (about 7-fold) in response to gemcitabine/doxorubicin when compared with controls. In conclusion, these data suggest an important role for LASS1/C(18)-ceramide in gemcitabine/doxorubicin-induced cell death via the activation of caspase-9/3 in HNSCC.
Phenotypic and genetic diversity of Paenibacillus azotofixans strains isolated from the rhizoplane or rhizosphere soil of different grasses (1998)

Fifty‐three strains identified as Paenibacillus azotofixans were isolated from the rhizoplane and rhizosphere of different grasses and from soil. To study the diversity within this species, four approaches were used: assessment of homology with a nifKDH probe in hybridization experiments; use of a selected 20‐mer primer to produce RAPD profiles and of BOX‐PCR to generate genomic fingerprintings; and phenotypic tests using the API50CH system. The API tests performed with the 53 P. azotofixans strains showed that all strains produced acid from 15 carbohydrates; using six other carbohydrates (sorbitol, dulcitol, tagatose, starch, glycogen and D‐arabitol), the strains could be divided in five groups of related strains. All strains tested showed homology to Klebsiella pneumoniae nifKDH genes, resulting in 14 different hybridization patterns with this probe. Using RAPD‐fingerprinting with one appropriate primer, 23 different amplification patterns were observed. The BOX‐PCR approach confirmed the grouping suggested by the RAPD fingerprinting. A comparison of the 53 strains by similarity matrix analysis using the data obtained in all approaches resulted in a phenogram, grouping them into five broad groups at 74% similarity and into 27 subgroups at 94% similarity. At 100% similarity, 31 groups of strains could be formed, indicating a high degree of diversity among the strains tested. Overall, the diversity was independent from the origin of strains, since a variety of different groups was isolated from each plant studied. However, some clusters were dominant in wheat and sugarcane samples. The results indicated that the methods used here are sensitive indicators of diversity among the strains studied and can be applied as efficient and reliable means for further ecological and biogeographical studies.
Polar anchoring energy measurement of vertically aligned liquid-crystal cells (2005)

An electric-field method is developed for measuring the polar anchoring energy of vertically aligned nematic liquid-crystal cells. Both theoretical analyses and confirming experimental results are presented. Vertically aligned liquid-crystal cells with buffed polyimide alignment layers are used to investigate the measurement techniques. Based on the voltage-dependent transmittance of the liquid-crystal cells, a linear fitting can be obtained, leading to a precise determination of the anchoring energy. If some specific liquid-crystal material parameters are known, measuring of the cell capacitance is not necessary.
Interleukin‐11 and IL‐17 and the Pathogenesis of Periodontal Disease (2004)

Gingival concentrations of IL-11 and IL-17 are different in diseased gingiva adjacent to 3, 4 to 5, and > or = 6 mm pockets, suggesting that their concentrations change as a consequence of the progression of gingivitis to periodontitis and that both cytokines could have a significant role in this progression. These data may be useful for the design of procedures for prevention of periodontal disease.
Bacterial Adhesion: Genetics, Biogenesis, and Role in Pathogenesis of Fimbrial Adhesins of Escherichia coli (1991)

Microbial pathogenicity is a complex phenomenon encompassing many varied mechanisms. There are, however, several common strategies that pathogenic organisms use to sustain themselves and overcome host barriers. In one of these strategies, the first step is the firm adhesion of the microorganism to host cells. Adhesion is frequently mediated by organelles called fimbriae. A surprising variety of fimbrial adhesins have been found in Escherichia coli, and several have been extensively characterized. The genetics and regulation of the various fimbrial structures are reviewed, and strategies for preventing the adhesion of harmful bacteria to host surfaces are discussed.
Lipids of Plasma Membrane and Outer Acrosomal Membrane from Bovine Spermatozoa (1987)

Plasma membrane (PM), primarily from the anterior sperm head, and outer acrosomal membrane (OAM), were isolated from ejaculated bovine spermatozoa, and the major lipid classes were characterized. Whole sperm (WS) lipids were analyzed for comparison. PM was removed by nitrogen cavitation and purified by sucrose density-gradient centrifugation. The OAM was removed by centrifugation through hyperosmotic sucrose and recovered by sucrose density-gradient centrifugation. The PM contained primarily spherical vesicles from the region overlying the OAM and was enriched 9- and 13-fold in 5'-nucleotidase and alkaline phosphatase activity, respectively, compared to the original cavitate. The OAM was recovered as caplike structures with associated ground substance. Protein, phospholipid, and cholesterol (PR, PL, and CH as micrograms/5 x 10(9) sperm) were 300, 467, and 93 for PM and 276, 111, and 25 for OAM, respectively. Corresponding values for WS (mg/5 x 10(9) sperm) were 31.4, 6.63, and 0.72. The PR/PL (w/w) and CH/PL (mol/mol) ratios were 0.66 and 0.38 for PM; 2.48 and 0.26 for OAM; and 4.39 and 0.22 for WS. Cholesterol was the only free sterol detected by gas/liquid chromatography in WS, PM, and OAM, with traces of CH sulfate present in all three preparations. Glycolipid tentatively identified as sulfogalactolipid was detected by thin-layer chromatography (TLC) in PM but not OAM. Phospholipid composition of WS and membranes was determined by TLC. Cardiolipin (3% of total PL) was present in WS only. Choline, ethanolamine, and inositol phosphoglycerides (CP, EP, PI, PIP, PIPP); sphingomyelin (SP); phosphatidylserine (PS); and lysophosphatidylcholine (LPC) were present in WS, PM, and OAM. Approximately 50% of total PL was CP in all preparations; SP was 13% of PL in PM and 17% in OAM (p less than 0.05); EP was 7% of PL in PM and 10% in OAM (p less than 0.05). The differences in composition between PM and OAM is discussed with respect to capacitation and ability of sperm to undergo the acrosome reaction.
Carbohydrates as recognition molecules in macrophage activities. (1989)

Mononuclear phagocyte functions are critically dependent on cell surface recognition events. This review describes a number of receptors that appear to recognize simple sugars and function in the clearance of foreign or effete material or in the stimulation of other cellular processes.
Crystal Structure of Severe Acute Respiratory Syndrome Coronavirus Spike Protein Fusion Core (2004)

Severe acute respiratory syndrome coronavirus is a newly emergent virus responsible for a recent outbreak of an atypical pneumonia. The coronavirus spike protein, an enveloped glycoprotein essential for viral entry, belongs to the class I fusion proteins and is characterized by the presence of two heptad repeat (HR) regions, HR1 and HR2. These two regions are understood to form a fusion-active conformation similar to those of other typical viral fusion proteins. This hairpin structure likely juxtaposes the viral and cellular membranes, thus facilitating membrane fusion and subsequent viral entry. The fusion core protein of severe acute respiratory syndrome coronavirus spike protein was crystallized, and the structure was determined at 2.8 A of resolution. The fusion core is a six-helix bundle with three HR2 helices packed against the hydrophobic grooves on the surface of central coiled coil formed by three parallel HR1 helices in an oblique antiparallel manner. This structure shares significant similarity with the fusion core structure of mouse hepatitis virus spike protein and other viral fusion proteins, suggesting a conserved mechanism of membrane fusion. Drug discovery strategies aimed at inhibiting viral entry by blocking hairpin formation, which have been successfully used in human immunodeficiency virus 1 inhibitor development, may be applicable to the inhibition of severe acute respiratory syndrome coronavirus on the basis of structural information provided here. The relatively deep grooves on the surface of the central coiled coil will be a good target site for the design of viral fusion inhibitors.
“Clicking” Functionality onto Electrode Surfaces (2004)

We demonstrate the applicability of Sharpless “click” chemistry, specifically Huisgen 1,3-dipolar cycloadditions, as a general methodology for functionalizing surfaces coated with self-assembled monolayers. Ferrocene immobilization was used as our model, and the resulting monolayers were analyzed using traditional surface analytical techniques. Our preliminary results indicate that this reaction proceeds to completion at room temperature in aqueous solvent. The triazole group is a thermally and hydrolytically stable, conjugated linkage. The reactants, acetylenes and azides, are independently stable; they do not react with common organic reagents or with themselves. Thus the potential for this reaction to immobilize a wide range of functionally complex substances on metal surfaces is significant. To our knowledge this is the first report of the use of “click” chemistry to modify a well-defined electrode surface.