gebhart/patrepeval huggingface dataset:
Circulating Nef Induces Dyslipidemia in Simian Immunodeficiency Virus–Infected Macaques by Suppressing Cholesterol Efflux (2010)

Human immunodeficiency virus (HIV) infection and subsequent antiretroviral therapy have been associated with an increased incidence of dyslipidemia and cardiovascular disease and has been shown to suppress cholesterol efflux from virus-infected macrophages by inducing Nef-dependent down-regulation of adenosine triphosphate-binding cassette transporter A1 (ABCA1). Here, the simian immunodeficiency virus (SIV)-infected macaque model was used to examine the consequences and mechanisms involved. SIV infection drove a significant remodeling of high-density lipoprotein profiles, suggesting that systemic inhibition of the ABCA1-dependent reverse cholesterol transport pathway occurred. The ABCA1 cholesterol transporter was significantly down-regulated in the livers of the SIV-infected macaques, and the viral protein Nef could be detected in the livers as well as in the plasma of infected animals. Extracellular myristoylated HIV Nef inhibited cholesterol efflux from macrophages and hepatocytes. Moreover, serum samples from SIV-infected macaques also suppressed cholesterol efflux in a Nef-dependent fashion. These results indicate that SIV infection is a significant contributor to primary dyslipidemia, likely through the ability of Nef to suppress ABCA1-dependent reverse cholesterol transport.
File system usage in Windows NT 4.0 (1999)

We have performed a study of the usage of the Windows NT File System through long-term kernel tracing. Our goal was to provide a new data point with respect to the 1985 and 1991 trace-based File System studies, to investigate the usage details of the Windows NT file system architecture, and to study the overall statistical behavior of the usage data.In this paper we report on these issues through a detailed comparison with the older traces, through details on the operational characteristics and through a usage analysis of the file system and cache manager. Next to architectural insights we provide evidence for the pervasive presence of heavy-tail distribution characteristics in all aspect of file system usage. Extreme variances are found in session inter-arrival time, session holding times, read/write frequencies, read/write buffer sizes, etc., which is of importance to system engineering, tuning and benchmarking.
Expression of Interleukin-8 Correlates with Angiogenesis, Tumorigenicity, and Metastasis of Human Prostate Cancer Cells Implanted Orthotopically in Nude Mice (2001)

We determined whether the expression of interleukin-8 (IL-8) by human prostate cancer cells correlates with induction of angiogenesis, tumorigenicity, and production of metastasis. Low and high IL-8-producing clones were isolated from the heterogeneous PC-3 human prostate cancer cell line. The secretion of IL-8 protein correlated with transcriptional activity and levels of IL-8 mRNA. All PC-3 cells expressed both IL-8 receptors, CXCR1 and CXCR2. The low and high IL-8-producing clones were injected into the prostate of nude mice. Titration studies indicated that PC-3 cells expressing high levels of IL-8 were highly tumorigenic, producing rapidly growing, highly vascularized prostate tumors with and a 100% incidence of lymph node metastasis. Low IL-8-expressing PC-3 cells were less tumorigenic, producing slower growing and less vascularized primary tumors and a significantly lower incidence of metastasis. In situ hybridization (ISH) analysis of the tumors for expression of genes that regulate angiogenesis and metastasis showed that the expression level of IL-8, matrix metalloproteinases, vascular endothelial growth factor (VEGF), and E-cadherin corresponded with microvascular density and biological behavior of the prostate cancers in nude mice. Collectively, the data show that the expression level of IL-8 in human prostate cancer cells is associated with angiogenesis, tumorigenicity, and metastasis.
Navigating close to shore (1994)

The author describes a new marine chart display information system that pinpoints a ship's position to within 3 meters and could have as great an impact as radar. The system uses an oceanographic chart on a video screen presented by an electronic data display information system (Ecdis) which looks much like a paper chart prepared by the hydrographic office. For its accuracy in fixing a ship's position, Ecdis depends on a navigation system, the differential Global Positioning System (DGPS). DGPS is now being installed along the US coastline by the Coast Guard, and will include some 50 on-shore stations that should be in place by January 1996. Other nations, including Australia, Canada, Finland, Norway, Sweden, and the United Kingdom, are also building such stations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Glycosylation of an N-Terminal Extension Prolongs the Half-Life and Increases the in Vivo Activity of Follicle Stimulating Hormone (2003)

FSH is a key component in assisted reproductive technologies. Because of rapid clearance of the hormone, patients have to be treated with daily injections. To address this problem, a long-acting FSH mutein was created by introduction of additional N-linked glycosylation into the molecule. New glycosylation sites were introduced by two different approaches: structure-aided, site-directed introduction of sites within the FSH molecule and addition of N-terminal extensions. A mutein with the extension sequence ANITVNITV at the N terminus of the alpha-chain (FSH1208) was efficiently glycosylated at both new sites. This resulted in a molecule with increased size and charge, factors known to reduce renal clearance of proteins. FSH1208 was found to have a 3- to 4-fold increased serum half-life, compared with wild-type recombinant FSH. Furthermore, in spite of a lower in vitro activity, FSH1208 had a markedly increased in vivo potency, as shown by increased ability to augment the ovarian weight and stimulate the serum estradiol levels in rats. These characteristics make FSH1208 a possible candidate for improved infertility treatment.
Macroscopic 10-Terabit–per–Square-Inch Arrays from Block Copolymers with Lateral Order (2009)

Generating laterally ordered, ultradense, macroscopic arrays of nanoscopic elements will revolutionize the microelectronic and storage industries. We used faceted surfaces of commercially available sapphire wafers to guide the self-assembly of block copolymer microdomains into oriented arrays with quasi-long-range crystalline order over arbitrarily large wafer surfaces. Ordered arrays of cylindrical microdomains 3 nanometers in diameter, with areal densities in excess of 10 terabits per square inch, were produced. The sawtoothed substrate topography provides directional guidance to the self-assembly of the block copolymer, which is tolerant of surface defects, such as dislocations. The lateral ordering and lattice orientation of the single-grain arrays of microdomains are maintained over the entire surface. The approach described is parallel, applicable to different substrates and block copolymers, and opens a versatile route toward ultrahigh-density systems.
Approximations of Weighted Independent Set and Hereditary Subset Problems (2000)

The focus of this study is to clarify the approximability of the important versions of the maximum independent set problem, and to apply, where possible, the technique to related hereditary subgraph and subset problem. We report improved performance ratios for the Independent Set problem in weighted general graphs, weighted bounded-degree graphs, and in sparse graphs. Other problems with better than previously reported ratios include Weighted Set Packing, Longest Subsequence, Maximum Independent Sequence, and Independent Set in hypergraphs.
Indoor communications networks realized through hybrid free-space optical and wifi links (2018)

Recently, free-space optical (FSO) networks have been investigated as a potential replacement for traditional WiFi networks due to their large bandwidth potentials. However, FSO networks often suffer from a lack of mobility. We present a hybrid free-space optical and radio frequency (RF) system that we have named WiFO, which seamlessly integrates free-space optical links with pre-existing WiFi networks. The free-space optical link in this system utilizes infrared LEDs operating at a wavelength of 850nm and is capable of transmitting 50Mbps over a three-meter distance. In this hybrid system, optical transmitters are embedded periodically throughout the ceiling of a workspace. Each transmitter directs an optical signal downward in a diffuse light cone, establishing a line of sight optical link. Line of sight communications links have an intrinsic physical layer of security due to the fact that a user must be directly in the path of transmission to access the link; however, this feature also poses a challenge for mobility. In our system, if the free-space optical link is interrupted, a control algorithm redirects traffic over a pre-existing WiFi link ensuring uninterrupted transmissions. After data packets are received, acknowledgments are sent back to a central access point via a WiFi link. As the demand for wireless bandwidth continues to increase exponentially, utilizing the unregulated bandwidth contained within optical spectrum will become necessary. Our fully functional hybrid free-space optical and WiFi prototype system takes full advantage of the untapped bandwidth potential in the optical spectrum, while also maintaining the mobility inherent in WiFi networks.
Physicochemical characteristics of fluorine doped tin oxide films (2006)

In this work, relationships between chemical and physical properties of fluorine doped tin oxide films prepared by the chemical spray pyrolysis technique have been studied. Changes in the structural, optical and electrical properties of these films in relation to their doping concentrations determined by the resonant nuclear reaction analysis and x-ray photoelectron spectroscopy (XPS) techniques have been correlated. By XPS measurements, it was found that the fluorine content in the tin oxide films does not induce any chemical shift of the Sn and O core levels. At the same time, XPS measurements are carried out at low binding energy, shown that the valence band of heavy doped tin oxide changes with respect to that determined in SnO2 powder, due to the influence of the fluorine doping. In addition, it was shown that the formation of F–Sn complexes provides a decrease in both the concentration and mobility of the carriers.
A parathyroid hormone antagonist stimulates epidermal proliferation and hair growth in mice. (1994)

The biologic action of parathyroid hormone (PTH)-related peptide (PTHrP) in normal skin was investigated in cultured human keratinocytes and in SKH-1 hairless mice. The results indicate that the PTHrP agonists human PTHrP-(1-34) and PTH(1-34) are potent inhibitors of epidermal cell proliferation. [Nle8,18,Tyr34]bovine PTH-(7-34)-amide, an antagonist of the PTH/PTHrP receptor, blocked the inhibitory effect of PTH-(1-34) in cultured keratinocytes. In the SKH-1 mice, PTH-(7-34) caused a 244% increase of [3H]thymidine incorporation into isolated epidermal DNA and 246% and 180% increases in the number and length of hair shafts, respectively. Thus, PTH and PTHrP may play an important role in the normal physiology of skin, and their agonists and antagonists have potentially wide therapeutic applications in the treatment of hyperproliferative skin disorders and aging skin and could also be effective in stimulating and maintaining hair growth.
Flow cytometric measurements of fluorescence energy transfer using single laser excitation (1987)

Flow cytometric energy transfer (FCET) measurements between labeled specific sites of cell surface elements (Szöllosi et al., Cytometry, 5:210-216, 1984) have been extended in a simplified form using a flow cytometer equipped with single excitation beam. This versatile and easily applicable method has several advantages over any nonflow cytometric (i.e., spectrofluorimetric) energy transfer measurements on cell surfaces: The labeled ligands can be applied in excess, without washing, thereby enabling the investigation of relatively labile receptor-ligand complexes. Contributions of signals from cell debris, from cell aggregates, or from nonviable cells can be avoided by gating the data collection on the light scatter signal. The heterogeneity of the cell population with respect to the proximity of the labeled binding sites can be studied. In the cases of homologous ligands or of ligands binding to the same molecule but at different epitopes, the determination of fluorescence resonance energy transfer efficiency values can be carried out on a cell-by-cell basis, offering data on intramolecular conformational changes. This modified FCET method enabled us to demonstrate the uniform density of glycoproteins, specific for Con A binding, in the plasma membrane of normal and Gross virus leukemic mouse cells of different sizes. The utility of this procedure has also been demonstrated by using the mean fluorescence intensities of the distribution curves in the calculation of the fluorescence energy transfer efficiency.
Unlocking the opportunity of tight glycaemic control (2005)

As the incidence of diabetes reaches epidemic proportions, the use of new, alternative routes of insulin delivery to manage glycaemic control is becoming an ever more active area of research. The high permeability and large surface area of the lung make it an attractive alternative to subcutaneous (SC) insulin injections. This review discusses the technical factors that influence the efficacy of pulmonary drug delivery and describes how an appreciation of these issues has enabled the design of Exubera, a novel, non-invasive, pulmonary dry-powder human insulin delivery system currently in development by Pfizer and the Sanofi-Aventis Group in collaboration with Nektar Therapeutics. While clinical trials of this novel aerosol delivery of insulin are still ongoing in patients with diabetes, the results so far suggest it is simple to use and can provide reproducible doses of insulin in therapeutic amounts with only a few inhalations per dose. In addition, it has been shown to be comparable in terms of efficacy and safety to a conventional SC insulin injection regimen. Delivering aerosolized drugs via the lungs avoids the necessity for SC injections and thereby may increase the patient's acceptability of an insulin-based therapeutic regimen.
Evolution of cancer of the colon and rectum (1974)

In this paper the opportunity is taken to describe the personal position of the speaker with respect to the evolution of cancer of the colon and rectum. A general account of the predisposing causes is presented, with emphasis on the malignant potential of adenomatous polyps and villous adenomas. The significance of the polyp–cancer sequence is discussed, and some evidence given about how long it takes for polyps to become cancerous. Some reference is also made to the etiologic significance of the polyp–cancer sequence. Do all cancers of the colon and rectum arise from adenomatous polyps or villous adenomas? An attempt will be made to answer this question and to review the alternatives to this mode of histogenesis.
Worldwide experience shows horizontal well success (1989)

The convergence of technology and experience has made horizontal drilling an important tool in increasing production and solving a variety of completion problems. Since the early 1980s, horizontal drilling has been used to improve production on more than 700 oil and gas wells throughout the world. Approximately 200 horizontal wells were drilled in 1988 alone. Interest in horizontal drilling has been accelerating rapidly as service companies have developed and offered new technology for drilling and producing horizontal wells. Simultaneously, oil companies have developed better methods for evaluating reservoirs for potential horizontal applications, while their production departments have gained experience at completing and producing them. To date, most horizontal wells have been drilled in the United States. A major application is to complete naturally fractured formations, such as the Austin chalk in Texas, the Bakken shale in the Williston basin, the Spraberry in West Texas and the Devonian shale in the Eastern states. In addition, many horizontal wells have been drilled to produce the Niagaran reefs and the irregular Antrim shale reservoirs in Michigan.
Management of relapsing/remitting multiple sclerosis with copolymer I (Copaxone) (1996)

Copolymer I (Copazone) was evaluated in a multicenter, placebo-controlled, double-blind trial at 11 universities. Two hundred and fifty-one relapsing-remitting ambulatory MS patients were randomized to receive 20 mg of copolymer I or placebo by daily subcutaneous injection for approximately 30 months. At conclusion, the copolymer I group had 32% fewer relapses (P = 0.002) and significantly more were relapse-free (P = 0.035). Significantly, more patients were receiving copolymer I had improved during the study, while more patients on placebo showed neurological decline (P = 0.001). There were few side effects and no drug related laboratory abnormalities. Copolymer I is being considered by North American and European regulatory agencies for approval as commercially available agent for the control of multiple sclerosis.
A new shape segmentation approach for active vision systems (2002)

A solution to extract 3-D shapes from a structured light image is presented. The 2-D striped image is segmented into regions corresponding to quadratic surfaces. A fuzzy analysis of the stripe's properties allows one to locate discontinuities and to model stripe parts. These parts are tracked in consecutive images and matched in order to create regions. Segmentation results are presented which were obtained with a real scene consisting of multiple objects of arbitrary shapes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Design considerations in instrumenting and monitoring web-based information retrieval systems (1998)

The Internet Web environment opens up extraordinary opportunities for user access to information. Techniques for monitoring users and systems and for evaluating system design and performance have not kept pace with Web development. This article reviews concepts of Web operations (including browsers, clients, information retrieval applications, servers, and data communications systems) with specific attention given to how monitoring should take place and how privacy can be protected. It examines monitoring needs of users, systems designers, managers, and customer support staff and outlines measures of workload, capacity, and performance for hardware, software, and data communications systems. Finally, the article proposes a client-server design for monitoring, which involves creation of a series of server and client systems to obtain and process transaction and computer performance information. These systems include: A Log Server, which captures all levels of transactions and packets on the network; a Monitor Server, which synthesizes the log and packet data; an Assistance Server, which processes requests for information and help from the Web Server in real time; and an Accounting Server, which authenticates user access to the system. A special System Administrator Client is proposed to control the monitoring system, as is a System Information Client to receive real-time and on-demand reports of system activity. © 1998 John Wiley & Sons, Inc.
Hypermethylation in human cancers of the RIZ1 tumor suppressor gene, a member of a histone/protein methyltransferase superfamily. (2001)

The retinoblastoma protein-interacting zinc finger gene RIZ1 is a tumor suppressor gene and a member of a nuclear histone/protein methyltransferase superfamily. RIZ1 inactivation is commonly found in many types of human cancers and occurs through loss of mRNA expression, frameshift mutation, chromosomal deletion, and missense mutation. RIZ1 is also a tumor susceptibility gene in mice. We now show that loss of RIZ1 mRNA in human cancers is associated with DNA methylation of its promoter CpG island. Methylation of the RIZ1 promoter strongly correlated with lost or decreased RIZ1 mRNA expression in breast, liver, colon, and lung cancer cell lines as well as in liver cancer tissues. Treatment with the methylation inhibitor 5-aza-2'-deoxycytidine activated RIZ1 mRNA expression in cancer cells. Furthermore, methylation was found in 11 of 25 (44%) breast cancer specimens and 20 of 32 (62%) liver cancer specimens. Our results suggest that DNA methylation is a common mechanism in inactivating the RIZ1 tumor suppressor gene in human liver and breast cancers.
Comparative Analyses of Intracellularly Expressed Antisense RNAs as Inhibitors of Human Immunodeficiency Virus Type 1 Replication (1998)

The antiviral activities of intracellularly expressed antisense RNAs complementary to the human immunodeficiency virus type 1 (HIV-1) pol, vif, and env genes and the 3' long terminal repeat (LTR) sequence were evaluated in this comparative study. Retroviral vectors expressing the antisense RNAs as part of the Moloney murine leukemia virus LTR promoter-directed retroviral transcript were constructed. The CD4+ T-cell line CEM-SS was transduced with retroviral constructs, and Northern blot analyses showed high steady-state antisense RNA expression levels. The most efficient inhibition of HIV-1 replication was observed with the env antisense RNA, followed by the pol complementary sequence, leading to 2- to 3-log10 reductions in p24 antigen production even at high inoculation doses (4 x 10(4) 50% tissue culture infective doses) of the HIV-1 strain HXB3. The strong antiviral effect correlated with a reduction of HIV-1 steady-state RNA levels, and with intracellular Tat protein production, suggesting that antisense transcripts act at an early step of HIV-1 replication. A lower steady-state antisense RNA level was detected in transduced primary CD4+ lymphocytes than in CEM-SS cells. Nevertheless, replication of the HIV-1 JR-CSF isolate was reduced with both the pol and env antisense RNA. Intracellularly expressed antisense sequences demonstrated more pronounced antiviral efficacy than the transdominant RevM10 protein, making these antisense RNAs a promising gene therapy strategy for HIV-1.
tRNA-controlled Nuclear Import of a Human tRNA Synthetase (2012)

Aminoacyl-tRNA synthetases, essential components of the cytoplasmic translation apparatus, also have nuclear functions that continue to be elucidated. However, little is known about how the distribution between cytoplasmic and nuclear compartments is controlled. Using a combination of methods, here we showed that human tyrosyl-tRNA synthetase (TyrRS) distributes to the nucleus and that the nuclear import of human TyrRS is regulated by its cognate tRNA(Tyr). We identified a hexapeptide motif in the anticodon recognition domain that is critical for nuclear import of the synthetase. Remarkably, this nuclear localization signal (NLS) sequence motif is also important for interacting with tRNA(Tyr). As a consequence, mutational alteration of the hexapeptide simultaneously attenuated aminoacylation and nuclear localization. Because the NLS is sterically blocked when the cognate tRNA is bound to TyrRS, we hypothesized that the nuclear distribution of TyrRS is regulated by tRNA(Tyr). This expectation was confirmed by RNAi knockdown of tRNA(Tyr) expression, which led to robust nuclear import of TyrRS. Further bioinformatics analysis showed that to have nuclear import of TyrRS directly controlled by tRNA(Tyr) in higher organisms, the NLS of lower eukaryotes was abandoned, whereas the new NLS was evolved from an anticodon-binding hexapeptide motif. Thus, higher organisms developed a strategy to make tRNA a regulator of the nuclear trafficking of its cognate synthetase. The design in principle should coordinate nuclear import of a tRNA synthetase with the demands of protein synthesis in the cytoplasm.