gebhart/patrepeval huggingface dataset:
Introduction of foreign sequences into the genome of influenza A virus. (1994)

The ability to apply reverse genetics technologies to influenza virus now allows us to construct novel viruses containing heterologous sequences. We have engineered two neuraminidase (NA) genes of influenza A/WSN/33 virus containing additional sequences which were inserted downstream of the open reading frame of the NA. These NA genes, NA/EMC and NA/EMC-NS1, possess a 546 and a 917 nucleotide (nt) insertion respectively. Transfectant viruses were rescued following ribonucleoprotein (RNP) transfection of the engineered NA genes into influenza helper-virus-infected cells. The transfectant viruses maintained their artificially introduced sequences stably during three passages. The rescued virus containing the NA/EMC-NS1 gene produced one log fewer infectious virus particles in MDBK cells than did wild type A/WSN/33 virus. The growth characteristics in tissue culture of the virus containing the NA/EMC gene was indistinguishable from that of wild-type influenza virus. Based on these results we conclude that influenza A viruses can tolerate heterologous insertions of at least a kilobase in the NA gene.
Correlates of Actual and Perceived Knowledge of Prostate Cancer Among African Americans (2001)

While digital rectal examination, prostate-specific antigen, and transrectal ultrasound have been identified as effective means of early detection of prostate cancer, African American men tend to underuse these services as compared to white men. Using a nonrandom sample of 108 African American men, the authors conducted an exploratory investigation of the effects of education, income, age, and health insurance coverage on actual and perceived knowledge of prostate cancer. The extent to which the use of prostate cancer screening services may be attributed to actual and perceived knowledge of prostate cancer was also explored. Respondents demonstrated a poor knowledge of prostate cancer and less than 40% reported having had prostate cancer screening as part of their annual physical examination. The results of the study also revealed that (a) there was a moderately strong correlation between actual and perceived knowledge of prostate cancer, (b) use of prostate cancer screening service was positively associated with actual and perceived knowledge of the disease, (c) actual knowledge of prostate cancer was negatively correlated with education, age, and income, and (d) actual and perceived knowledge of prostate cancer were both correlated with having health insurance coverage.
Single‐marker identification of head and neck squamous cell carcinoma cancer stem cells with aldehyde dehydrogenase (2010)

ALDH(high) cells comprise a subpopulation cells in HNSCCs that are tumorigenic and capable of producing tumors at very low numbers. This finding indicates that ALDH activity on its own is a highly selective marker for CSCs in HNSCC.
Sialylated O-Glycans and Sulfated Tyrosines in the NH2-Terminal Domain of CC Chemokine Receptor 5 Contribute to High Affinity Binding of Chemokines (2001)

The chemokine receptor CCR5 plays an important role in leukocyte chemotaxis and activation, and also acts as a coreceptor for human and simian immunodeficiency viruses (HIV-1, HIV-2, and SIV). We provide evidence that CCR5 is O-glycosylated on serine 6 in the NH2 terminus. The O-linked glycans, particularly sialic acid moieties, significantly contribute to binding of the chemokine ligands. By contrast, removal of O-linked oligosaccharide exerted little effect on HIV-1 infection. Sulfation of specific tyrosine residues in the CCR5 NH2 terminus was important for efficient beta-chemokine binding. Thus, as has been observed for the binding of selectins and their ligands, O-linked carbohydrates and tyrosine sulfates play major roles in promoting the interaction of chemokines with CCR5. The resulting flexible arrays of negative charges on the CCR5 surface may allow specific, high-affinity interactions with diverse chemokine ligands. Although this is the first example of O-linked oligosaccharides and tyrosine sulfates playing a role in chemokine binding, the high density of serines, threonines and tyrosines in the N-termini of many CC chemokine receptors suggests that these posttranslational modifications may commonly contribute to chemokine binding.
The future of starch bioengineering: GM microorganisms or GM plants? (2015)

Plant starches regularly require extensive modification to permit subsequent applications. Such processing is usually done by the use of chemical and/or physical treatments. The use of recombinant enzymes produced by large-scale fermentation of GM microorganisms is increasingly used in starch processing and modification, sometimes as an alternative to chemical or physical treatments. However, as a means to impart the modifications as early as possible in the starch production chain, similar recombinant enzymes may also be expressed in planta in the developing starch storage organ such as in roots, tubers and cereal grains to provide a GM crop as an alternative to the use of enzymes from GM microorganisms. We here discuss these techniques in relation to important structural features and modifications of starches such as: starch phosphorylation, starch hydrolysis, chain transfer/branching and novel concepts of hybrid starch-based polysaccharides. In planta starch bioengineering is generally challenged by yield penalties and inefficient production of the desired product. However, in some situations, GM crops for starch bioengineering without deleterious effects have been achieved.
Cytokine Receptor-independent, Constitutively Active Variants of STAT5 (1997)

STAT (signal transducers and activators of transcription) proteins are dual function proteins, which participate in cytokine-mediated signal transduction events at the cell surface and transcriptional regulation in the nucleus. We have exploited insights into the activation mechanism of STAT factors to derive constitutively active variants. Chimeric genes encoding fusion proteins of STAT5 and the kinase domain of JAK2 have been derived. The functional properties of the fusion proteins have been investigated in transiently transfected COS cells or in HeLa cells stably transfected with STAT5-JAK2 gene constructs regulated by a tetracycline-sensitive promoter. The STAT5-JAK2 proteins exhibit tyrosine kinase activity and are phosphorylated on tyrosine. The molecules are activated through an intramolecular or a cross-phosphorylation reaction and exhibit constitutive, STAT5-specific DNA binding activity. The transactivation potentials of three constitutively activated STAT5-JAK2 variants comprising different transactivation domains (TADs) derived from STAT5, STAT6, and VP16 were compared. The chimeric molecule containing the STAT5 TAD had no or only a very low, the molecule with the STAT6 TAD a medium, and the molecule with the VP16 TAD a very high transactivation potential. Transcription from STAT5-responsive gene promoter regions of the beta-casein, oncostatin M, and the cytokine-inducible Src homology 2 domain-containing protein genes was observed. These chimeric STAT molecules allow the study of the function of STAT5 independent of cytokine receptors and the activation of other signal transduction pathways.
Redirected Perforin-Dependent Lysis of Colon Carcinoma by Ex Vivo Genetically Engineered CTL (2000)

The redirection of autologous lymphocytes to predefined tumor target Ags has considerable potential for the immunotherapeutic treatment of cancer; however, robust experimental systems for comparing various approaches have not been developed. Herein, we have generated a single chain variable domain anti-carcinoembryonic Ag (CEA) Fcepsilon receptor I gamma-chain fusion (scFv anti-CEA) receptor and demonstrated high-level expression of this chimeric receptor in naive mouse T lymphocytes by retroviral gene transduction. These gene-modified CTL were able to lyse CEA+ targets and secrete high levels of IFN-gamma following Ag stimulation. Depletion studies demonstrated that specific tumor cell cytotoxicity was mediated by gene-modified CD8+ T cells. Importantly, in increasingly stringent tests of efficacy in vivo, transduced CTL were sequentially shown to reject CEA+ colon carcinoma cells in a Winn assay and then reject established s.c. colon carcinoma in scid or syngeneic mice. Furthermore, using gene-targeted and scFv anti-CEA receptor-transduced donor CTL, perforin and IFN-gamma were demonstrated to be absolutely critical for the eradication of colon carcinoma in mice. In summary, we have developed a highly efficient gene transfer system for evaluating chimeric receptor expression in cytotoxic lymphocytes. This series of experiments has revealed the utility of scFv anti-CEA chimeras in providing mouse T cells the capacity to reject colon carcinoma in an Ag- and perforin-specific manner.
Intrusion detection in wireless ad-hoc networks (2000)

As the recent denial-of-service attacks on several major Internet sites have shown us, no open computer network is immune from intrusions. The wireless ad-hoc network is particularly vulnerable due to its features of open medium, dynamic changing topology, cooperative algorithms, lack of centralized monitoring and management point, and lack of a clear line of defense. Many of the intrusion detection techniques developed on a fixed wired network are not applicable in this new environment. How to do it differently and effectively is a challenging research problem. In this paper, we first examine the vulnerabilities of a wireless ad-hoc network, the reason why we need intrusion detection, and the reason why the current methods cannot be applied directly. We then describe the new intrusion detection and response mechanisms that we are developing for wireless ad-hoc networks.
Tunnel junctions of unconventional superconductors (1995)

The phenomenology of Josephson tunnel junctions between unconventional superconductors is developed further. In contrast to s-wave superconductors, for d-wave superconductors the direction dependence of the tunnel matrix elements that describe the barrier is relevant. We find the full I-V characteristics and comment on the thermodynamical properties of these junctions. They depend sensitively on the relative orientation of the superconductors. The I-V characteristics differ from the normal s-wave resistively-shunted-junction-like behavior.
A survey of architectures for volume rendering (1990)

Five hardware architectures for volume rendering, which requires efficiently handling a huge amount of volumetric data, are surveyed, categorized, and compared. They are Cube, Insight, PARCUM, Voxel Processor, and 3DP. General-purpose graphics systems that exploit their surface-based geometry engine to reduce the computational burden of the rendering process are briefly reviewed.
RF SOI Switch FET Design and Modeling Tradeoffs for GSM Applications (2010)

A single-pole double-throw novel switch device in0.18¹m SOI complementary metal-oxide semiconductor(CMOS) process is developed for 0.9 Ghz wireless GSMsystems. The layout of the device is optimized keeping inmind the parameters of interest for the RF switch. A subcircuitmodel, with the standard surface potential (PSP) modelas the intrinsic FET model along with the parasitic elementsis built to predict the Ron and Coff of the switch. Themeasured data agrees well with the model. The eight FETstacked switch achieved an Ron of 2.5 ohms and an Coff of180 fF.
Synthesis of 2,4-Disubstituted Oxazoles (1992)

Some 2-substituted methyl 1,3-oxazole-4-carboxylates (5) can be obtained by the one-step cyclization of N-acylserines (3) by the combined use of diphenyl sulfoxide and trifluoroacetic anhydride, and subsequent nickel peroxide oxidation of the oxazoline.
Die Geschichte der Postkarte (1988)

Seit dem 15. Jahrhundert sind kleine Karten mit christlichen Motiven bekannt, die man sich mit Glückwünschen zum Neujahrstag überreichte.
Parallelism in sequential functional languages (1995)

This paper formally studies the question of how much parallelism is available in cal-by-value functional languages with no parallel extensions (i. e., the functional sub;ets of ML or Scheme). In particular we are interested in placing bounds on how much parallelism is available for various problems. To do this we introduce a complexity model, the PAL, based on the call-by-value A-calculus. The model is defined in terms of a profiling semantics and measures complexity in terms of the total work and the parallel depth of a computation. We describe a simulation of the A-PAL (the PAL extended with arithmetic operations) on various parallel machine models, including the butterfly, hypercube, and PRAM models and prove simulation bounds. In particular the simulat ions are workeficient (the processor-time product on the machines is within a constant factor of the work on the A-PAL), and for p processors the slowdown (time on the machines divided by depth on the A-PAL) is proportional to at most O(log p). We also prove bounds for simulating the PRAM on the A-PAL. Based on the model, we describe and analyze tree-based versions of quicksort and merge sort. We show that for an input of size n these algorithms run on the A-PAL model with O(rI log n) work and 0(log2 n) depth (expected case for quicksort ).
Real-time L3 cache simulations using the Programmable Hardware-Assisted Cache Emulator (PHA$E) (2003)

As the gap between the CPU and memory speeds increases, there has been an increasingly important need to study the memory-hierarchy designs. Investigations of memory performance have typically been conducted using trace-driven simulation, which could take tremendous resources (e.g. long simulation time, large storage requirements for traces, and high overall cost). Recent works have proposed the use of hardware for performing cache simulations. Such approach is advantageous as it can be done in real-time, which eliminates the need or large storage for traces, reduces the simulation time, and improves the accuracy of the results. This paper discusses our preliminary work with theProgrammable Hardware-Assisted Cache Emulator (PHA$E), a system for emulating cache in real-time. We discuss the design and implementation of our system. Furthermore, the results of simulating varying sizes of off-chip L3 caches on various workloads (SPECcpu2000, SPECjbb2000, SPECjAppServer2002, and a large vocabulary continuous speech recognition system are presented and analyzed. Lastly, future research directions are elaborated on.
Mozart′s Requiem–Liver Transplantation in 1988 (1990)

Liver transplantation is one of the most spectacular of surgical achievements. It is a demanding and expensive procedure, requiring great surgical skill and a great depth of supporting services. Precisely because it is a procedure at the leading edge of medicine, more and more units in developed countries are pressing to be allowed to carry it out. But there are many moral and ethical problems, some of which can be usefully examined using a "Mozart model" as proposed by Starzl.
A novel functional cell surface dimer (kp43) serves as accessory molecule for the activation of a subset of human gamma delta T cells. (1993)

Kp43 is a cell surface molecule expressed by NK cells, gamma delta T lymphocytes, and a small subset of CD56+ alpha beta T cells. In the present study the distribution and function of Kp43 on gamma delta T cells is described. The expression of Kp43 on freshly isolated gamma delta T-cell populations derived from fetal and adult tissues was biased toward memory V gamma 2+/V delta 2+ T lymphocytes and appeared to be up-regulated after activation. Several gamma delta T-cell clones were derived from different sources. Adult V gamma 2+/V delta 2+ T-cell clones expressed the highest levels of Kp43, V delta 1 T-cell clones derived from periphery expressed moderate levels, whereas some thymus V delta 1 T cells and fetal gamma delta T-cell clones displayed low or undetectable levels of Kp43 molecule. Based on the effect of a specific mAb, this dimer appears to be fully functional as previously shown for NK cells. The stimulation of Kp43+ gamma delta T-cell clones with a combination of anti-CD3 and anti-Kp43 co-immobilized on a solid substratum enhanced both the expression of cell surface CD25 and the secretion of TNF-alpha. The restricted expression and functional activity of the Kp43 dimer suggests that it may play an important regulatory role in activation, selection, Ag recognition, and responsiveness of a subset of gamma delta T cells.
Ovarian Cancer Pathogenesis: A Model in Evolution (2009)

Ovarian cancer is a deadly disease for which there is no effective means of early detection. Ovarian carcinomas comprise a diverse group of neoplasms, exhibiting a wide range of morphological characteristics, clinical manifestations, genetic alterations, and tumor behaviors. This high degree of heterogeneity presents a major clinical challenge in both diagnosing and treating ovarian cancer. Furthermore, the early events leading to ovarian carcinoma development are poorly understood, thus complicating efforts to develop screening modalities for this disease. Here, we provide an overview of the current models of ovarian cancer pathogenesis, highlighting recent findings implicating the fallopian tube fimbria as a possible site of origin of ovarian carcinomas. The ovarian cancer model will continue to evolve as we learn more about the genetics and etiology of this disease.
Combined nested RT-PCR assay for prostate-specific antigen and prostate-specific membrane antigen in prostate cancer patients: correlation with pathological stage. (1998)

Nested reverse transcription (RT)-PCR for prostate-specific antigen (PSA) and prostate-specific membrane antigen (PSM) can detect circulating prostatic cells in patients with prostate cancer. We evaluated the role of a combined screening approach for PSA and PSM in prostate cancer staging. We examined the peripheral blood samples from 136 patients with adenocarcinoma of the prostate (PCA), 15 patients with benign prostatic hyperplasia, 15 normal male subjects, and 5 female subjects. The controls (benign prostatic hyperplasias, normal males, and normal females) were negative for both PSA and PSM. In patients with metastatic PCA (n = 11), 100% were positive by combined PSA/PSM (64% by PSA and 91% by PSM). In biochemical failure PCA patients (n = 18), 39% were positive by PSM, compared to only 6% by PSA. In patients with clinically localized PCA (n = 107), 48% were positive by combined PSA/PSM approach (43% by PSM and 14% by PSA). These results show that PSM is a more sensitive marker than PSA in detecting circulating prostatic cells (P < 0.0001). We correlated preoperative RT-PCR results with final pathological stages in 67 prostatectomy patients. RT-PCR positivity was 81.5% in patients with non-organ-confined disease versus 37.5% in organ-confined disease (P = 0.001). PSA/PSM RT-PCR had an odds ratio of 7.3 (95% confidence interval, 2.3-23.4; P = 0.001) in predicting tumor extracapsular extension. PSA/PSM RT-PCR was a better predictor of tumor extracapsular extension than initial serum PSA, clinical stage, and biopsy Gleason score. Our data show that PSA/PSM nested RT-PCR may provide the staging information unavailable from the current modalities. The ultimate impact of this technique in the management of patients with prostate cancer will require continued investigation.
A Randomized Controlled Double-Masked Trial of Albuterol Add-on Therapy in Patients With Multiple Sclerosis (2010)

clinicaltrials.gov Identifier: NCT00039988.
Immunoglobulin gene ‘fingerprinting’: an approach to analysis of B lymphoid clonality in lymphoproliferative disorders (1991)

Rearrangement of the immunoglobulin heavy chain (IgH) gene is widely exploited as a marker of B cell lineage and clonality in the pathology of lymphoproliferative disorders. We have developed a simple, polymerase chain reaction (PCR) based method for detecting IgH gene rearrangement which relies on the observation that by using a panel of PCR amplimers specific for each of the six heavy chain variable region families in conjunction with a common joining region amplimer, clonal rearrangement can be detected in over 90% of cases of B lymphoid malignancy. By using radiolabelled amplimers and exploiting the size heterogeneity resulting from independent IgH rearrangement events, we show that high resolution gel electrophoresis can be used to generate a 'fingerprint' representing the spectrum of B cell clonality in complex populations of B lymphocytes. The method effectively scans the entire IgH gene rearrangement repertoire and is capable of detecting rare clonal or oligoclonal B lymphoid cell populations. In normal bone marrow mononuclear cells, clonal IgH rearrangement could be readily detected at a sensitivity of 10(-3). We illustrate the application of the method in assessing the spectrum of B cell clonality occurring in an autoimmune condition. Hashimoto's thyroiditis, and in a malignant B cell disorder, chronic lymphocytic leukaemia. In addition, we explore the potential application of the technique in tracking minimal residual disease and for monitoring clonal evolution in acute lymphoblastic leukaemia.
The Effect of Rigidity, Shape, Unsaturation, and Length on the Anesthetic Potency of Hydrocarbons (2001)

We previously hypothesized that anesthesia results from an action on two sites separated by 5 A. The hypothesis relied on the finding that fluorinated alkanes having active anesthetic sites at each end of the molecule produce anesthesia as long as the total number of carbon atoms in their structure does not exceed five (i.e., approximately 5 A), and on the sustaining of the 5-A separation by the rigidity produced by fluorination. In this study, we tested an alternative hypothesis: that the site of action cannot accommodate a rigid compound, particularly a rectilinear compound, having more than five carbon atoms, and that rigidity itself might limit the anesthetic potency of larger compounds. We tested the anesthetic potency of 11 hydrocarbons in which rigidity was increased by unsaturation. In 72 rats exposed to such compounds, we found that unsaturation, rigidity, or both produced by unsaturation either did not change (double bonds) or increased (triple bonds) potency for a given number of carbon atoms. For example, we found that the rectilinear, rigid 2,4-trans-trans-hexadiene was no less potent (minimum alveolar anesthetic concentration [MAC] 0.042 +/- 0.002 atm; mean +/- SD) than the flexible 1,5-hexadiene (0.047 +/- 0.005 atm) or n-hexane (0.0467 +/- 0.0055 atm) and that 3-hexyne was more potent (MAC 0.0146 +/- 0.0014 atm) than n-hexane (MAC 0.0467 +/- 0.0055 atm). We conclude that the site of anesthetic action can accommodate straight rigid structures of up to six carbons in length.
Procedure for detection of and response to Distributed Denial of Service cyber attacks on complex enterprise systems (2012)

The increasing frequency, rising costs, and growing sophistication of cyber attacks on DoD, agency and commercial enterprise systems are dramatically reducing the quality of end-user services and compromising mission effectiveness. Of those attacks, one of the more severe is Distributed Denial-of-Service (DDoS) through which an attacker can disrupt, and possibly shutdown, local network enclaves and global net-centric enterprise systems. Previous attempts to overcome this threat include intrusion detection and prevention systems (IDS/IPS), firewalls, and packet scanning software. However, none of these approaches individually achieves prevention or provides sufficient countermeasures to overcome and resolve DDoS threats. This paper presents a detailed procedure for identifying both the on-set of DDoS attacks and corresponding countermeasures to prevent or limit their effects. This procedure applies a hybrid approach that adapts to changing DDoS attack scenarios. Concrete examples provided for each step of the procedure identify the key tools to proactively prevent or respond to DDoS events. Simulated results demonstrate the effectiveness of the procedure for a representative DDoS attack scenario.