gebhart/patrepeval huggingface dataset:
Molecular Analysis of the Distal Enhancer of the Mouse α-Fetoprotein Gene (1995)

The mouse alpha-fetoprotein (AFP) gene is transcribed at high levels in the visceral endoderm of the yolk sac and fetal liver and at much lower rates in the endoderm of the fetal gut. Expression of the gene in vivo requires the presence of at least one of three enhancers which lie in its 5' flanking region. In this report, we establish that the most distal AFP enhancer directed consistent expression of a linked AFP minigene in all three endodermal tissues in transgenic mice. The enhancer is composed of three domains, each of which is essential for full enhancer function by transient transfection assays. DNase I footprinting identified three regions of the enhancer which are protected by human hepatoma nuclear extracts, one of which corresponded to a consensus site for HNF-3 binding. Site-directed mutations in this site caused a 10-fold reduction in enhancer function by transient transfection. In transgenic mice, however, the mutation resulted in sporadic expression of the transgene, dependent on the site of integration. A similar acquisition of position-dependent sporadic expression of the transgene was observed with a mutation in a second protein binding site, despite the fact that this mutation had very little effect on enhancer function as assessed by transient transfection. These studies underscore the value of examining the functions of specific protein binding sites in vivo.
Identification and cloning of two isoforms of human high-temperature requirement factor A3 (HtrA3), characterization of its genomic structure and comparison of its tissue distribution with HtrA1 and HtrA2 (2003)

In the present study, we identified an additional member of the human high-temperature requirement factor A (HtrA) protein family, called pregnancy-related serine protease or HtrA3, which was most highly expressed in the heart and placenta. We cloned the full-length sequences of two forms (long and short) of human HtrA3 mRNA, located the gene on chromosome 4p16.1, determined its genomic structure and revealed how the two mRNA variants are produced through alternative splicing. The alternative splicing was also verified by Northern blotting. Four distinct domains were found for the long form HtrA3 protein: (i) an insulin/insulin-like growth factor binding domain, (ii) a Kazal-type S protease-inhibitor domain, (iii) a trypsin protease domain and (iv) a PDZ domain. The short form is identical to the long form except it lacks the PDZ domain. Comparison of all members of human HtrA proteins, including their isoforms, suggests that both isoforms of HtrA3 represent active serine proteases, that they may have different substrate specificities and that HtrA3 may have similar functions to HtrA1. All three HtrA family members showed very different mRNA-expression patterns in 76 human tissues, indicating a specific function for each. Interestingly, both HtrA1 and HtrA3 are highly expressed in the placenta. Identification of the tissue-specific function of each HtrA family member is clearly of importance.
Unsupervised Learning of 3D Structure from Images (2016)

A key goal of computer vision is to recover the underlying 3D structure from 2D observations of the world. In this paper we learn strong deep generative models of 3D structures, and recover these structures from 3D and 2D images via probabilistic inference. We demonstrate high-quality samples and report log-likelihoods on several datasets, including ShapeNet [2], and establish the first benchmarks in the literature. We also show how these models and their inference networks can be trained end-to-end from 2D images. This demonstrates for the first time the feasibility of learning to infer 3D representations of the world in a purely unsupervised manner.
An efficient remote use authentication scheme using smart cards (2000)

Based on the discrete logarithm problem, Hwang and Li (see ibid., vol.46, no.1, p.28-30, Feb. 2000) proposed a remote user authentication scheme using smart cards. Their scheme is very novel because no password table is required to keep in a system. In this paper, we further propose an efficient and practical remote user authentication scheme using smart cards. The proposed scheme not only provides the same advantages as that of Hwang and Li's scheme, but also significantly reduces the communication and computation costs.
Keeping found things found on the web (2001)

This paper describes the results of an observational study into the methods people use to manage web information for re-use. People observed in our study used a diversity of methods and associated tools. For example, several participants emailed web addresses (URLs) along with comments to themselves and to others. Other methods observed included printing out web pages, saving web pages to the hard drive, pasting the address for a web page into a document and pasting the address into a personal web site. Ironically, two web browser tools that have been explicitly developed to help users track web information - the bookmarking tool and the history list - were not widely used by participants in this study. A functional analysis helps to explain the observed diversity of methods. Methods vary widely in the functions they provide. For example, a web address pasted into a self-addressed email can provide an important reminding function together with a context of relevance: The email arrives in an inbox which is checked at regular intervals and the email can include a few lines of text that explain the URL's relevance and the actions to be taken. On the other hand, for most users in the study, the bookmarking tool ("Favorites" or "Bookmarks" depending on the browser) provided neither a reminding function nor a context of relevance. The functional analysis can help to assess the likely success of various tools, current and proposed.
Site-directed mutagenesis of HIV-1 integrase demonstrates differential effects on integrase functions in vitro. (1993)

The retroviral integrase (IN) protein is essential for integration of retroviral DNA into the host cell genome. To identify functional domains within the protein and to assess the importance of conserved residues, we performed site-directed mutagenesis of HIV-1 IN and analyzed the mutants in vitro for IN-mediated activities: 3' processing (att site-specific nuclease activity), strand transfer (the joining of att site oligonucleotides to target DNA), disintegration (the reverse of strand transfer), and integration site selection. Changing the conserved residue His-16 either to Cys or to Val in a proposed zinc-finger region had minimal effect on IN activities. Alteration of two highly conserved amino acid residues, Asp-116-->Ile and Glu-152-->Gly, each resulted in complete or nearly complete loss of 3' processing, strand transfer, and disintegration, whereas alteration of another conserved residue, Trp-235-->Glu, had no demonstrable effect on any of the activities in vitro. Two mutants, Asp-64-->Val and Arg-199-->Cys delta, each demonstrated differential effects on IN activities. Asp-64-->Val has no demonstrable strand transfer or disintegration activity yet maintains 3' processing activity at a diminished level. Arg-199-->Cys delta, which lacks part of the carboxyl terminus of IN, has impaired strand transfer activity without loss of disintegration activity. Use of a target site selection assay showed that all of our mutants with strand transfer activity maintain the same integration pattern as wild type IN. We conclude that not all highly conserved IN residues are essential for IN activities in vitro, zinc coordination by the proposed zinc-finger domain may not be required for the activities assayed, alteration of single residues can yield differential effects on IN activities, and target site selection into naked DNA is not necessarily altered by changes in strand transfer activity.
Organic anion transport across the choroid plexus (2000)

Several organic anion transport systems have recently been identified and localized at the apical and basolateral plasma membrane domains of choroid plexus epithelial cells. These organic anion transporters include (1) indirectly coupled Na(+)/dicarboxylate cotransport and dicarboxylate/organic anion exchange, which is represented on the molecular level by a member of the "kidney"-type organic anion transporter (OAT) family at the apical plasma membrane domain; (2) the organic anion transporting polypeptide 1 (Oatp1) and Oatp2, which both mediate typical "liver"-like organic anion transport activities at the apical and basolateral plasma membrane domains, respectively; and (3) the multidrug resistance protein Mrp1/MRP1 at the basolateral plasma membrane domain, and the P-glycoprotein Mdr1/MDR1 at an apical and subapical membrane vesicle compartment. This cellular transport polarity can account, at least in part, for the previously suggested physiologic transport properties of the choroid plexus epithelium and provides a framework for the identification and localization of additional organic anion transporters involved in the absorption and/or excretion of drugs and drug metabolites at the choroid plexus.
MALE LUMPECTOMY: FOCAL THERAPY IS THE FUTURE OF PROSTATE CANCER TREATMENT (2014)

We &nd ourselves in a paradoxical situation. Early detection of prostate cancer has become di'cult, if not impossible, due to new guidelines against routine PSA screening. Why did the U.S. Preventive Services Task Force, a volunteer panel of medical professionals, rule against wide use of a simple and e(ective screening tool? First, men with suspicious or rising test results are sent for an unpleasant diagnostic procedure (TRUS biopsy) that has been proven to miss up to 30% of cancers. %ose with negative biopsies later have repeat biopsies, while expense (and anxiety) mount up. Second, this protocol &nds too many less aggressive cancers—and the cure may be worse than the disease.
Dynamic Spyware Analysis (2018)

Spyware is a class of malicious code that is surreptitiously installed on victims’ machines. Once active, it silently monitors the behavior of users, records their web surfing habits, and steals their passwords. Current anti-spyware tools operate in a way similar to traditional virus scanners. That is, they check unknown programs against signatures associated with known spyware instances. Unfortunately, these techniques cannot identify novel spyware, require frequent updates to signature databases, and are easy to evade by code obfuscation. In this paper, we present a novel dynamic analysis approach that precisely tracks the flow of sensitive information as it is processed by the web browser and any loaded browser helper objects. Using the results of our analysis, we can identify unknown components as spyware and provide comprehensive reports on their behavior. The techniques presented in this paper address limitations of our previouswork on spyware detection and significantly improve the quality and richness of our analysis. In particular, our approach allows a human analyst to observe the actual flows of sensitive data in the system. Based on this information, it is possible to precisely determine which sensitive data is accessed and where this data is sent to. To demonstrate the effectiveness of the detection and the comprehensiveness of the generated reports, we evaluated our system on a substantial body of spyware and benign samples.
Anti-inflammatory Properties of the Monoterpene 1.8-cineole: Current Evidence for Co-medication in Inflammatory Airway Diseases (2014)

1,8-cineole is a natural monoterpene, also known as eucalyptol. It is a major compound of many plant essential oils, mainly extracted from Eucalyptus globulus oil. As an isolated compound, 1,8-cineole is known for its mucolytic and spasmolytic action on the respiratory tract, with proven clinical efficacy. 1,8-cineole has also shown therapeutic benefits in inflammatory airway diseases, such as asthma and chronic obstructive pulmonary disease (COPD). This clinical evidence refers to its anti-inflammatory and anti-oxidant mode of action, which has been proven in numerous pre-clinical studies. In vitro studies found strong evidence that 1,8-cineole controls inflammatory processes and mediator production of infection- or inflammation-induced mucus hypersecretion by its action as anti-inflammatory modifier rather than a simple mucolytic agent. The aim of this review is to present these preclinical studies performed with the pure monoterpene, and to summarize the current knowledge on the mode of action of 1,8-cineole. The actual understanding of the pure 1,8-cineole compared to mixtures of natural volatile oils containing 1,8-cineole as a major compound and to mixtures of natural terpenes, known as essential oils, will be discussed. Based on the anti-oxidative and anti-inflammatory properties, recent clinical trials with 1,8-cineole have shown first evidence for the beneficial use of 1,8-cineole as long-term therapy in the prevention of COPD-exacerbations and to improve asthma control.
Freeze-Drying of Composite Core-Shell Nanoparticles (2006)

The effects of four sugars (glucose, saccharose, maltose, trehalose) and one surfactant (Poloxamer 188), on the freeze-drying of poly(isobutylcyanoacrylate) (PIBCA), poly(epsilon-caprolactone)-poly(ethylene glycol) (PCL-PEG), and novel core (mainly PIBCA)-shell (principally PEG) composite nanoparticles (CNP) obtained by co-precipitation were investigated. The efficiency of the additives against the adverse effect of freeze-drying on the redispersibility of the nanoparticles was evaluated, based on the visual appearance of the nanoparticle suspensions (Tyndall effect and aggregation), and on the determination of the mean diameter ratio of the nanoparticles before and after freeze-drying. The results indicated that the addition of both sugars and surfactant was essential for the good redispersion of freeze-dried nanoparticles displaying hydrophobic (PIBCA) or hydrophilic (PCL-PEG and CNP) surfaces.
Combination of Phagostimulant and Visual Lure as an Effective Tool in Designing House Fly Toxic Baits: A Laboratory Evaluation (2013)

House flies (Diptera: Muscidae), potential vectors of a variety of pathogens, characteristically search and feed on sugar sources just after emergence for their survival. Phagostimulants like sugars, and visual characteristics of feeding materials play an important role in foraging success in house flies. Therefore, development of toxic baits by using the combination of phagostimulant and visual lure may prove effective in localized control of house flies. In the present study, visual attraction of house flies to different fabric colors was studied in choice and no choice experiments. Dark blue was the most preferred color in both experiments. In toxicity experiments, insecticide solutions were prepared in 20% sugar solution. Dark blue fabric strips were prepared by moistening with 20% sugar water solution containing median lethal concentrations of one of the four insecticides viz., fipronil, Imidacloprid, indoxacarb and Spinosad. The fabric strips treated with fipronil and Imidacloprid took minimum time (7.66 and 7.81 h, respectively) to cause 50% mortality, while those treated with Spinosad and indoxacarb took relatively more time (13.62 and 17.91 h, respectively) to cause 50% mortality. In conclusion, the combination of phagostimulant and visual lure could be used in designing toxic baits for house flies.
Characterisation of a Monoclonal Antibody to von Willebrand Factor as a Potent Inhibitor of Ristocetin-Mediated Platelet Interaction and Platelet Adhesion (1987)

We studied a murine monoclonal antibody (211 A6) to von Willebrand factor (vWF) with a view to investigating structure-relationship of plasma vWF. The specificity of this antibody has been substantiated by ELISA tests and indirect immunofluorescence. It reacts with purified vWF, normal plasma but not with plasma or platelets from a severe von Willebrand's disease patient. Monoclonal antibody 211 A6 is a potent inhibitor of ristocetin-induced platelet aggregation. The 125I-FVIII/vWF binding to platelets in presence of ristocetin is totally inhibited by low 211 A6 concentrations. Thrombin-induced binding of vWF to platelets is not affected by 211 A6. The ability of this antibody to inhibit platelet adhesion to subendothelium and to collagen was investigated with a perfusion model. The complete inhibition of platelet adhesion by 211 A6 questions the similarity or the interrelationship in vWF domains involved in ristocetin-induced platelet functions and platelet adhesion.
Three dimensional optical angiography (2007)

With existing optical imaging techniques three-dimensional (3-D) mapping of microvascular perfusion within tissue beds is severely limited by the efficient scattering and absorption of light by tissue. To overcome these limitations we have developed a method of optical angiography (OAG) that can generate 3-D angiograms within millimeter tissue depths by analyzing the endogenous optical scattering signal from an illuminated sample. The technique effectively separates the moving and static scattering elements within tissue to achieve high resolution images of blood flow, mapped into the 3-D optically sectioned tissue beds, at speeds that allow for perfusion assessment in vivo. Its development has its origin in Fourier domain optical coherence tomography. We used OAG to visualize the cerebral microcirculation, of adult living mice through the intact cranium, measurements which would be difficult, if not impossible, with other optical imaging techniques.
Superlow Fouling Sulfobetaine and Carboxybetaine Polymers on Glass Slides (2006)

This work describes the superlow fouling properties of glass slides grafted with zwitterionic polymers to highly resist the adsorption of proteins and the adhesion of mammalian cells. Glass slides were first silanized using 2-bromo-2-methyl-N-3-[(triethoxysilyl)propyl]propanamide (BrTMOS). Two zwitterionic polymers, poly(sulfobetaine methacrylate) (polySBMA) and poly(carboxybetaine methacrylate) (polyCBMA), were then grafted from the silanized glass substrates using the atom-transfer radical polymerization (ATRP) method. X-ray photoelectron spectroscopy (XPS) was used to analyze the surfaces of the silanized glass substrates and the substrates grafted with the polymers. An enzyme-linked immonosobrbent assay (ELISA) using polyclonal antibodies was used to measure fibrinogen adsorption on these surfaces. The surfaces with polySBMA or polyCBMA layers were shown to reduce fibrinogen adsorption to a level comparable with that of adsorption on poly(ethylene glycol)-like films. Bovine aortic endothelial cells (BAECs) were seeded on these surfaces. The attachment and spreading of the cells were observed only on unpolymerized glass surfaces. This work further demonstrates that zwitterionic polymers highly resist nonspecific protein adsorption and cell adhesion and provides an effective method to modify glass slides or other oxide surfaces to achieve superlow fouling.
N-acetylcysteine (D- and L-stereoisomers) prevents apoptotic death of neuronal cells (1995)

In the present study we tested whether N-acetyl-L-cysteine (LNAC) affects apoptotic death of neuronal cells caused by trophic factor deprivation. LNAC, an antioxidant, elevates intracellular levels of glutathione. We used serum-deprived PC12 cells, neuronally differentiated PC12 cells deprived of serum and NGF, and NGF-deprived neonatal sympathetic neurons. In each case LNAC prevents apoptotic DNA fragmentation and maintains long-term survival in the absence of other trophic support. Unlike NGF, LNAC does not induce or maintain neurite outgrowth or somatic hypertrophy. To rule out actions of LNAC metabolic derivatives, we assessed N-acetyl-D-cysteine (DNAC). DNAC also prevents death of PC12 cells and sympathetic neurons. However, other antioxidants were ineffective in this regard. Since it has been hypothesized that trophic factors prevent neuronal death by either preventing or coordinating cell cycle progression, we tested whether LNAC or DNAC treatment can affect cell cycle. We found that both (but not other antioxidants) suppress proliferation and DNA synthesis by PC12 cells and do so at concentrations similar to those at which they prevent apoptotic death. Although the abilities of LNAC and DNAC to rescue cells from apoptosis triggered by trophic factor deprivation could derive from their direct influences on cellular responsiveness to oxidative stress, our observations raise the possibility of a mechanism involving cell cycle regulation.
USP chapter 797: Establishing a practice standard for compounding sterile preparations in pharmacy (2004)

Journal Article USP chapter 797: Establishing a practice standard for compounding sterile preparations in pharmacy Get access Eric S. Kastango, M.B.A., FASHP, Eric S. Kastango, M.B.A., FASHP President Clinical IQ, LLC, Florham Park, NJ Address correspondence to Mr. Kastango at Clinical IQ, LLC, 184 Columbia Turnpike #282, Florham Park, NJ 07932. Search for other works by this author on: Oxford Academic Google Scholar Brian D. Bradshaw, B.S.PHARM., FASCP Brian D. Bradshaw, B.S.PHARM., FASCP Project Manager Clinical IQ, LLC, Florham Park, NJ Search for other works by this author on: Oxford Academic Google Scholar American Journal of Health-System Pharmacy, Volume 61, Issue 18, 1 September 2004, Pages 1928–1938, https://doi.org/10.1093/ajhp/61.18.1928 Published: 15 September 2004
Analysis of culture filtrate and cell wall-associated antigens of Mycobacterium paratuberculosis with monoclonal antibodies (1997)

Proteins secreted by Mycobacterium species have been suggested as major immune targets in the early phase of infection. In this study, we sought to identify specific antigens in culture filtrates and in soluble cell extracts of Mycobacterium paratuberculosis. The release of antigens into the culture medium during growth of the bacilli and the distribution of specific epitopes within the Mycobacterium species were investigated by immunoblot analysis with monoclonal antibodies (MAbs) raised against M. paratuberculosis antigens. MAb B6A interacted with a cellular antigen with an apparent molecular mass of 34.5 kDa in lysates of M. paratuberculosis. MAb B6A did not interact with lysates from any other mycobacterial species, suggesting recognition of an M. paratuberculosis species-specific epitope. MAb FL1-A1 reacted with an antigen of 44.3 kDa in M. paratuberculosis and a 9-kDa antigen in Mycobacterium kansasii. MAb PII-B1 reacted with concanavalin A (ConA)-binding cellular and filtrate molecules of M. paratuberculosis and with lysates of Mycobacterium kansasii and Mycobacterium avium 18. The affinity-purified glycosylated antigens migrated as a diffuse band of between 35 and 45.6 kDa and reacted strongly with ovine and bovine paratuberculosis serum and polyclonal serum against M. tuberculosis lipoarabinomannan antigens. These glycoconjugates were the earliest antigens detected in culture filtrates of M. paratuberculosis. Deglycosylation of the ConA-binding molecules with alpha-mannosidase enzyme abolished the reaction with MAb PII-B1 and with bovine but not ovine paratuberculosis serum, suggesting selective immunogenicity in the different animal species.