gebhart/patrepeval huggingface dataset:
Identification of homologous regions in human immunodeficiency virus I gp41 and human MHC class II beta 1 domain. I. Monoclonal antibodies against the gp41-derived peptide and patients' sera react with native HLA class II antigens, suggesting a role for autoimmunity in the pathogenesis of acquired immune deficiency syndrome. (1988)

Homologous regions of five amino acids each, were identified in the NH2-terminal domain of human class II beta chains and the COOH terminus of HIV I envelope protein. The homologous regions are highly conserved among different DR and DQ alleles and also among different isolates of HIV. Septamers containing these sequences were synthesized and used for the generation of murine mAbs. The mAbs selected for this study were raised against the HIV I-derived peptide and reacted strongly not only with the immunizing peptide, but also with the homologous class II-derived peptide. These mAbs also reacted with native MHC class II antigens expressed on human B cell lines and on murine fibroblast L cell lines transfected with the genes coding for the alpha and beta chains of human class II antigens. Furthermore, sera from 36% of AIDS patients tested contained antibodies that reacted with the class II-derived peptide, as well as with intact class II molecule-rich cell extracts. Such antibodies in HIV I-infected individuals may recognize self class II antigens, triggering autoimmune mechanisms that could contribute to the development of immunodeficiency in AIDS patients.
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity (2012)

Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. We show here that in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand, whereas the Cas9 RuvC-like domain cleaves the noncomplementary strand. The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. Our study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing.
Pain Intensity on the First Day after Surgery (2013)

Several common minor- to medium-level surgical procedures, including some with laparoscopic approaches, resulted in unexpectedly high levels of postoperative pain. To reduce the number of patients suffering from severe pain, patients undergoing so-called minor surgery should be monitored more closely, and postsurgical pain treatment needs to comply with existing procedure-specific pain-treatment recommendations.
A wireless interface type for OSPF (2004)

We report on a new wireless interface type for the OSPF routing protocol that greatly improves performance in multihop wireless networks. In this paper, we describe how to adapt OSPF to adequately handle wireless networks in a scalable manner. Our simulation-based study first illustrates that the operation of legacy OSPF routers in mobile ad hoc network environments can generate prohibitive amounts of overhead for networks as small as 20 nodes. Next, we study the possibility of constraining the number of OSPF adjacencies formed in the wireless network, and find that, while scalability can be improved in this manner, the performance does not approach that of the OLSR protocol designed specifically for mobile networks. Consequently, we describe how OSPF can be extended to incorporate key design concepts from OLSR, such that the scaling performance of OLSR can be approached while maintaining backward compatibility with legacy OSPF routers. Our "wireless" interface type achieves bandwidth efficiency within a factor of two to three of OLSR, and allows wireless networks to be incorporated into larger heterogeneous networks. Finally, we describe some strategies and open issues regarding the composition of large heterogeneous networks including wireless subnets.
A semi-solid drug delivery system for epidermal growth factor in corneal epithelial wound healing (1997)

Treatment with EGF in a Carbopol gel carrier for a period of 8 hours results in significant wound healing enhancement (p < 0.05). The optimum EGF loading in the gel was determined to be 0.4%. A slow release gel may be an effective way to deliver EGF to the corneal surface.
Adjuvants of Immunity (2002)

Since Jules Freund reported that crude mycobacterial extracts greatly promoted immune responses to antigens ([1][1]), the use of adjuvants has become a widespread, but poorly understood practice to promote T and B cell responses ([2][2]). Recent studies have begun to identify the chemical nature of
Enhancing the Activity of Protein C by Mutagenesis To Improve the Membrane-Binding Site:  Studies Related to Proline-10 (1997)

Bovine and human protein C show high homology in the amino acids of their GLA domains (amino-terminal 44 residues), despite the about 10-fold higher membrane affinity of the human protein. A proposed membrane contact site and mechanism suggested that this difference was largely due to the presence of proline at position 10 of bovine protein C versus histidine at position 10 of human protein C [McDonald, J.F., Shah, A.M., Schwalbe, R.A., Kisiel, W., Dahlback, B., and Nelsestuen, G.L. (1997) Biochemistry, 36, 5120-5127]. This study examined the impact of replacing proline-10 in bovine protein C with histidine, and the reverse change in human protein C. In both cases, the protein containing proline-10 showed lower membrane affinity, about 10-fold lower for bovine protein C and 5-fold lower for human protein C. As expected, activated human protein C (hAPC) containing proline at position 10 showed 2.4-3.5-fold lower activity than wild type hAPC, depending on the assay used. Most interesting was that bovine APC containing histidine-10 displayed up to 15-fold higher activity than wild type bAPC. This demonstrated the ability to improve both membrane contact and activity by mutation. This general strategy should be applicable to other vitamin K-dependent proteins, providing opportunities to study function as well as to produce proteins that may find use as promoters and inhibitors of blood coagulation in pathological states.
Zinc Salts Inactivate Clinical Isolates of Herpes Simplex Virus In Vitro (2000)

Using a standard plaque assay and clinical isolates of herpes simplex virus (HSV), we have tested the ability of zinc salts to inactivate HSV. Virus was treated by incubation at 37 degrees C with zinc salts in morpholinepropanesulfonic acid-buffered culture medium and was then diluted and plated onto CV-1 cells for detection and quantitation of remaining infectious virus. Of 10 randomly chosen clinical isolates (five HSV type 1 [HSV-1] isolates and five HSV-2 isolates), seven were inactivated >98% by treatment in vitro with 50 mM zinc gluconate for 2 h and nine were inactivated >97% by treatment with zinc lactate. The effect was concentration dependent. With an HSV-1 isolate, 50 mM zinc gluconate or zinc lactate caused 100% inactivation, 15 mM caused 98 to 99% inactivation, and 5 mM caused 63 to 86% inactivation. With an HSV-2 isolate, 50 and 15 mM zinc gluconate caused 30% inactivation and 5 and 1 mM caused less than 9% inactivation, whereas 50 and 15 mM zinc lactate caused greater than 92% inactivation and 5 and 1 mM caused 37 and 26% inactivation, respectively. The ability of the zinc salts to inactivate HSV was not related to pH in the pH range of 6.1 to 7.6 since inactivation by zinc gluconate or zinc lactate in that pH range was 99.7 to 100% with a 2-h treatment with 50 mM zinc salt. Short (5-min) treatments of selected isolates with zinc gluconate, zinc lactate, zinc acetate, or zinc sulfate yielded inactivation rates of 0 to 55%.
Experimental implication of celiac ganglionotropic invasion of pancreatic-cancer cells bearing c-ret proto-oncogene with reference to glial-cell-line-derived neurotrophic factor (GDNF) (1999)

Perineural invasion is a prominent clinical feature of pancreatic cancer which causes difficulty in curative resection. In the present study, the human pancreatic cancer cell lines, PaCa-2, AsPC-1, SW1990 and Capan-2, were all found to express abundant c-ret proto-oncogene mRNA and RET protein, a member of the receptor-tyrosine-kinase superfamily, identified as being a receptor for glial-cell-line-derived neurotrophic factor (GDNF). In an invasion assay, the migration of pancreatic cancer cells was markedly induced by co-cultivation with human glioma cells, T98G or A172, capable of producing and secreting GDNF. Anti-GDNF antibody in conditioned media of glioma cells suppressed much of the migratory activity. Checkerboard analysis of the migration showed both chemotactic and chemokinetic activity of GDNF. There was no detectable expression of another GDNF receptor component, a glycosyl-phosphatidylinositol-linked receptor (GFR alpha-1), in pancreatic-cancer cell lines, suggesting that the neural invasion of pancreatic-cancer cells spreads along a concentration gradient of GDNF produced from peripheral ganglions through direct interaction of GDNF with its receptor, the c-ret proto-oncogene product. Immunochemical localization of GDNF in human celiac ganglionic tissue supported this contention.
The distribution of satellite cells and their relationship to specific fiber types in soleus and extensor digitorum longus muscles (1982)

Fiber type classification of p-phenylene-diamine-stained transverse sections of rat skeletal muscle correlated with electron microscopic observations demonstrate that satellite cells are not equally distributed among the various fiber types in either the EDL or soleus at 1 and 12 months of age. Of the three fiber types in the EDL, satellite cells are observed most frequently on Type IIA fibers, and at approximately equal frequencies on Type IIB and Type I fibers. Satellite cells in the soleus, in contrast to the EDL, are not often encountered on Type IIA fibers, but are preferentially associated with Type I fibers in that muscle. The frequency with which satellite cells are found on specific fiber types is distinct for the soleus and EDL and appears to correspond with their growth characteristics. The distribution of satellite cells according to fiber type does not provide an explanation for the differences in the percentage of satellite cell nuclei between the EDL and soleus.
Relationship of Patient and Medical Characteristics to Health Status in Children and Adolescents After the Fontan Procedure (2006)

There are deficits in health status in children and adolescents after the Fontan procedure. Strategies to address this problem might emphasize coordinated and effective prevention, detection, and management of noncardiac and psychosocial conditions, as well as specific targeting of patients from low-income households.
Interleukin-3 and interleukin-7 are alternative growth factors for the same B-cell precursors in the mouse (1995)

Clones and lines of precursor (pre) B cells can be established by limiting dilutions of unseparated cell suspensions of fetal liver or bone marrow on stromal cells in the presence of interleukin (IL)-7. When IL-3 is used instead of IL-7, cultures are regularly overgrown by different precursor cells of the myeloid lineage, as well as by adherent cells that inhibit pre-B-cell expansion. However, in the presence of either IL-7 or IL-3, clones of pre-B cells can be established on stroma cells at frequencies near one in one when the cultures are initiated with cell sorter purified CD45RO (B220)+/c-kit+ fetal liver or bone marrow derived pre-B cells. Clones grown on stromal cells in the presence of IL-7 can be regrown in IL-3, and vice versa. Pre-B cells that proliferate on stromal cells in the presence of IL-7 or IL-3 have the same phenotype, ie, are B220+ c-kit+, CD43+, and surrogate light chain+. Removal of the growth factors (IL-7, respectively IL-3) from the cultures results in differentiation to surface immunoglobulin (slg) positive, c-kit-, CD43-, surrogate light chain- B cells, a fraction of which is lipopolysaccharide (LPS) responsive as shown by IgM secretion. These results show that IL-7 and IL-3 stimulate largely overlapping populations of precursor B cells from bone marrow to proliferate for long periods of time in the presence of stromal cells. Thus, IL-7 and IL-3 are alternative growth factors for the same pre-BI cell.
COMBINING ABSOLUTE POSITIONING AND VISION FOR WIDE AREA AUGMENTED REALITY (2010)

One of the major limitations of vision based mapping and localisation is its inability to scale and operate over wide areas. This restricts its use in applications such as Augmented Reality. In this paper we demonstrate that the integration of a second absolute positioning sensor addresses this problem, allowing independent local maps to be combined within a global coordinate frame. This is achieved by aligning trajectories from the two sensors which enables estimation of the relative position, orientation and scale of each local map. The second sensor also provides the additional benefit of reducing the search space required for efficient relocalisation. Results illustrate the method working for an indoor environment using an ultrasound position sensor, building and combining a large number of local maps and successfully relocalising as users move arbitrarily within the map. To show the generality of the proposed method we also demonstrate the system building and aligning local maps in an outdoor environment using GPS as the position sensor.
A Randomized Trial of Deep-Brain Stimulation for Parkinson's Disease (2006)

In this six-month study of patients under 75 years of age with severe motor complications of Parkinson's disease, neurostimulation of the subthalamic nucleus was more effective than medical management alone. (ClinicalTrials.gov number, NCT00196911 [ClinicalTrials.gov].).
A nondestructive method for determining the spring constant of cantilevers for scanning force microscopy (1993)

The spring constant of microfabricated cantilevers used in scanning force microscopy (SFM) can be determined by measuring their resonant frequencies before and after adding small end masses. These masses adhere naturally and can be easily removed before using the cantilever for SFM, making the method nondestructive. The observed variability in spring constant—almost an order of magnitude for a single type of cantilever—necessitates calibration of individual cantilevers in work where precise knowledge of forces is required. Measurements also revealed that the spring constant scales with the cube of the unloaded resonant frequency, providing a simple way to estimate the spring constant for less precise work.
New approach for the selective chemical functionalization of porous silicon films with organic monolayers (2009)

Abstract A new approach for the selective chemical modification of porous silicon surfaces with organic monolayers is reported. The organic layers are first covalently grafted onto (100) surface of hydrogen terminated silicon via thermal hydrosilylation of alkene or functionalized alkene molecules yielding stable monolayers on flat Si surfaces. The functionalized silicon surfaces are then electrochemically etched in a hydrofluoric acid solution. (© 2009 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Cloning of the genes for degradation of the herbicides EPTC (S-ethyl dipropylthiocarbamate) and atrazine from Rhodococcus sp. strain TE1 (1995)

The degradation of the herbicides EPTC (S-ethyl dipropylthiocarbamate) and atrazine (2-chloro-4-ethyl-amino-6-isopropylamino-1,3,5-triazine) is associated with an indigenous plasmid in Rhodococcus sp. strain TE1. Plasmid DNA libraries of Rhodococcus sp. strain TE1 were constructed in a Rhodococcus-Escherichia coli shuttle vector, pBS305, and transferred into Rhodococcus sp. strain TE3, a derivative of Rhodococcus sp. strain TE1 lacking herbicide degradation activity, to select transformants capable of growing on EPTC as the sole source of carbon (EPTC+). Analysis of plasmids from the EPTC+ transformants indicated that the eptA gene, which codes for the enzyme required for EPTC degradation, residues on a 6.2-kb KpnI fragment. The cloned fragment also harbored the gene required for atrazine N dealkylation (atrA). The plasmid carrying the cloned fragment could be electroporated into a number of other Rhodococcus strains in which both eptA and atrA were fully expressed. No expression of the cloned genes was evident in E. coli strains. Subcloning of the 6.2-kb fragment to distinguish between EPTC- and atrazine-degrading genes was not successful.
Point spread function and two-point resolution in Fresnel incoherent correlation holography (2011)

Fresnel Incoherent Correlation Holography (FINCH) allows digital reconstruction of incoherently illuminated objects from intensity records acquired by a Spatial Light Modulator (SLM). The article presents wave optics model of FINCH, which allows analytical calculation of the Point Spread Function (PSF) for both the optical and digital part of imaging and takes into account Gaussian aperture for a spatial bounding of light waves. The 3D PSF is used to determine diffraction limits of the lateral and longitudinal size of a point image created in the FINCH set-up. Lateral and longitudinal resolution is investigated both theoretically and experimentally using quantitative measures introduced for two-point imaging. Dependence of the resolving power on the system parameters is studied and optimal geometry of the set-up is designed with regard to the best lateral and longitudinal resolution. Theoretical results are confirmed by experiments in which the light emitting diode (LED) is used as a spatially incoherent source to create object holograms using the SLM.
Increased levels of forkhead box M1B transcription factor in transgenic mouse hepatocytes prevent age-related proliferation defects in regenerating liver (2001)

The forkhead box (Fox) family of transcription factors share homology in the winged helix/forkhead DNA-binding domain and play important roles in regulating cellular proliferation, differentiation, longevity, and cellular transformation. Forkhead box M1B (FoxM1B) is a ubiquitously expressed member of the Fox transcription factor family whose expression is restricted to proliferating cells and that mediates hepatocyte entry into DNA synthesis and mitosis during liver regeneration. Recent cDNA microarray studies indicated that age-related defects in cellular proliferation are associated with diminished expression of the FoxM1B transcription factor. Here, we show that increased levels of FoxM1B in regenerating liver of old transgenic mice restore the sharp peaks in hepatocyte DNA replication and mitosis that are the hallmarks of young regenerating mouse liver. Restoration of the young regenerating liver phenotype is associated with increased expression of numerous cell cycle regulatory genes that include cyclin D1, cyclin A2, cyclin F, cyclin B1, cyclin B2, Cdc25B, and p55cdc. Cotransfection assays in the human hepatoma HepG2 cell line demonstrated that FoxM1B protein stimulated expression of both the cyclin B1 and cyclin D1 promoters, suggesting that these cyclin genes are a direct FoxM1B transcriptional target. These results suggest that FoxM1B controls the transcriptional network of genes that are essential for cell division and exit from mitosis. Our results indicate that reduced expression of the FoxM1B transcription factor contributes to the decline in cellular proliferation observed in the aging process.
Phagosomal Maturation, Acidification, and Inhibition of Bacterial Growth in Nonphagocytic Cells Transfected with FcγRIIA Receptors (1999)

Phagocytosis and killing of microbial pathogens by professional phagocytes is an essential component of the innate immune response. Recently, heterologous transfection of individual receptors into nonmyeloid cells has been used successfully to elucidate the early steps that signal phagosome formation. It is unclear, however, whether the vacuoles formed by such transfected cells are bona fide phagosomes, capable of fusion with endomembranes, of luminal acidification, and of controlling the growth of microorganisms. The aim of the current study was to determine whether COS-1 and Chinese hamster ovary cells, rendered phagocytic by expression of human FcgammaRIIA receptors, express the cellular machinery required to support phagosomal maturation. Immunolocalization studies demonstrated that early endosomes, as well as late endosomes and/or lysosomes, fuse sequentially with phagosomes in the transfectants. Microfluorescence ratio imaging of particles labeled with pH-sensitive dyes revealed that maturation of the phagosome was accompanied by luminal acidification. The drop in pH, which attained levels comparable to those reported in professional phagocytes, was prevented by inhibitors of vacuolar-type H(+)-ATPases. Optimal phagosomal acidification required elevation of cytosolic [Ca(2+)], suggesting that it results from fusion of endomembranes bearing proton pumps. Moreover, the transfected cells effectively internalized live bacteria. Opsonization was essential for bacterial internalization, implying that it occurred by FcgammaRIIA-mediated phagocytosis, as opposed to invasion. Uptake into phagolysosomes was associated with inhibition of bacterial growth, due at least in part to the low intraphagosomal pH. These studies indicate that the biochemical events that follow receptor-mediated particle internalization in cells transfected with FcgammaRIIA receptors closely resemble the process of phagosomal maturation in neutrophils and macrophages. FcgammaRIIA-transfected cells can, therefore, be used as a model for the study of additional aspects of phagocyte biology.
Synthesis of isoxazoles by hypervalent iodine-induced cycloaddition of nitrile oxides to alkynes (2011)

Treatment of oximes with hypervalent iodine leads to substituted isoxazoles via rapid formation of nitrile oxides. Reaction with terminal alkynes led to a series of 3,5-disubstituted isoxazoles with complete regioselectivity and high yield, in a procedure mild enough to prepare a range of nucleoside and peptide conjugates. Exceptionally high reaction rates were found for the formation of 3,4,5-trisubstituted isoxazoles from a cyclic alkyne.
MCARTA: A Malicious Code Automated Run-Time Analysis framework (2012)

This paper describes MCARTA, a new malware analysis framework which speeds up the velocity of investigation with run-time malware analysis. MCARTA (Malicious Code Automated Run-Time Analysis) is based on a new approach to cataloging, tracking, and comparing malware that does not depend on reverse engineering. Using MCARTA the malware analysts can quickly identify a small set of highly suspicious files to zoom in for further investigation using reverse-engineering tools. Using MCARTA and reverse-engineering tools in sequence, we will get the best of both worlds.