gebhart/patrepeval huggingface dataset:
Construction and Evaluation of Plasmid Vectors Optimized for Constitutive and Regulated Gene Expression in Burkholderia cepacia Complex Isolates (2002)

Genetic studies with Burkholderia cepacia complex isolates are hampered by the limited availability of cloning vectors and by the inherent resistance of these isolates to the most common antibiotics used for genetic selection. Also, some of the promoters widely employed for gene expression in Escherichia coli are inefficient in B. cepacia. In this study, we have utilized the backbone of the vector pME6000, a derivative of the pBBR1 plasmid that was originally isolated from Bordetella bronchiseptica, to construct a set of vectors useful for gene expression in B. cepacia. These vectors contain either the constitutive promoter of the S7 ribosomal protein gene from Burkholderia sp. strain LB400 or the arabinose-inducible P(BAD) promoter from E. coli. Promoter sequences were placed immediately upstream of multiple cloning sites in combination with the minimal sequence of pME6000 required for plasmid maintenance and mobilization. The functionality of both vectors was assessed by cloning the enhanced green fluorescent protein gene (e-gfp) and determining the levels of enhanced green fluorescent protein expression and fluorescence emission for a variety of clinical and environmental isolates of the B. cepacia complex. We also demonstrate that B. cepacia carrying these constructs can readily be detected intracellularly by fluorescence microscopy following the infection of Acanthamoeba polyphaga.
Integrated analytic spatial and temporal anti-aliasing for polyhedra in 4-space (1985)

A visible surface algorithm with integrated analytic spatial and temporal anti-aliasing is presented. This algorithm models moving polygons as four dimensional (X,Y,Z,T) image space polyhedra, where time (T) is treated as an additional spatial dimension. The linearity of these primitives allows simplification of the analytic algorithms. The algorithm is exact for non-intersecting primitives, and exact for the class of intersecting primitives generated by translation and scaling of 3-d (X,Y,Z) polygons in image space. This algorithm is an extension of Catmull's analytic visible surface algorithm for independent pixel processing, based on the outline of integrated spatial and temporal anti-aliasing given by Korien and Badler. An analytic solution requires that the visible surface calculations produce a continuous representation of visible primitives in the time and space dimensions. Visible surface algorithm, graphical primitives, and filtering algorithm, (by Feibush, Levoy and Cook) are extended to include continuous representation of the additional dimension of time. A performance analysis of the algorithm contrasted with a non-temporally anti-aliased version is given.
High Levels of a Major Histocompatibility Complex II–Self Peptide Complex on Dendritic Cells from the T Cell Areas of Lymph Nodes (1997)

T lymphocytes recirculate continually through the T cell areas of peripheral lymph nodes. During each passage, the T cells survey the surface of large dendritic cells (DCs), also known as interdigitating cells. However, these DCs have been difficult to release from the lymph node. By emphasizing the use of calcium-free media, as shown by Vremec et al. (Vremec, D., M. Zorbas, R. Scollay, D.J. Saunders, C.F. Ardavin, L. Wu, and K. Shortman. 1992. J. Exp. Med. 176:47-58.), we have been able to release and enrich DCs from the T cell areas. The DCs express the CD11c leukocyte integrin, the DEC-205 multilectin receptor for antigen presentation, the intracellular granule antigens which are recognized by monoclonal antibodies M342, 2A1, and MIDC-8, very high levels of MHC I and MHC II, and abundant accessory molecules such as CD40, CD54, and CD86. When examined with the Y-Ae monoclonal which recognizes complexes formed between I-Ab and a peptide derived from I-Ealpha, the T cell area DCs expressed the highest levels. The enriched DCs also stimulated a T-T hybridoma specific for this MHC II-peptide complex, and the hybridoma underwent apoptosis. Therefore DCs within the T cell areas can be isolated. Because they present very high levels of self peptides, these DCs should be considered in the regulation of self reactivity in the periphery.
Systemic Delivery of Tumor Suppressor microRNA Mimics Using a Neutral Lipid Emulsion Inhibits Lung Tumors in Mice (2011)

MicroRNAs (miRNAs) are emerging as potential cancer therapeutics, but effective delivery mechanisms to tumor sites are a roadblock to utility. Here we show that systemically delivered, synthetic miRNA mimics in complex with a novel neutral lipid emulsion are preferentially targeted to lung tumors and show therapeutic benefit in mouse models of lung cancer. Therapeutic delivery was demonstrated using mimics of the tumor suppressors, microRNA-34a (miR-34a) and let-7, both of which are often down regulated or lost in lung cancer. Systemic treatment of a Kras-activated autochthonous mouse model of non-small cell lung cancer (NSCLC) led to a significant decrease in tumor burden. Specifically, mice treated with miR-34a displayed a 60% reduction in tumor area compared to mice treated with a miRNA control. Similar results were obtained with the let-7 mimic. These findings provide direct evidence that synthetic miRNA mimics can be systemically delivered to the mammalian lung and support the promise of miRNAs as a future targeted therapy for lung cancer.
Dual reality : an emerging medium (2007)

Thesis (Ph. D.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2007.
Alteration of Stimulus-Specific Guard Cell Calcium Oscillations and Stomatal Closing in Arabidopsis det3 Mutant (2000)

Cytosolic calcium oscillations control signaling in animal cells, whereas in plants their importance remains largely unknown. In wild-type Arabidopsis guard cells abscisic acid, oxidative stress, cold, and external calcium elicited cytosolic calcium oscillations of differing amplitudes and frequencies and induced stomatal closure. In guard cells of the V-ATPase mutant det3, external calcium and oxidative stress elicited prolonged calcium increases, which did not oscillate, and stomatal closure was abolished. Conversely, cold and abscisic acid elicited calcium oscillations in det3, and stomatal closure occurred normally. Moreover, in det3 guard cells, experimentally imposing external calcium-induced oscillations rescued stomatal closure. These data provide genetic evidence that stimulus-specific calcium oscillations are necessary for stomatal closure.
A Natural Human IgM Antibody that Neutralizes Botulinum Neurotoxin in vivo (2008)

Affinity-matured human antibodies have demonstrated efficacy as countermeasures for exposure to botulinum neurotoxin (BoNT), which is the cause of the disease botulism category A select bioterror agent. Little is known, however, about the potential role of natural (un-mutated) antibodies in the protective immune response to BoNT. Here we describe the cloning of two human IgM antibodies that bind serotype A BoNT. Both are un-mutated IgM antibodies, consistent with an origin in naive B cells. One of the antibodies is able to fully neutralize a lethal dose of serotype A BoNT in vivo. These results suggest that the natural human antibody repertoire may play a role in protection from exposure to biological toxins.
The application of input shaping to a system with varying parameters (1991)

The original input shaping technique, that was developed in earlier work, is summarized, and a different definition for residual vibration is proposed. The new definition gives better insight into the ability of the input shaping method to reduce vibration. The extension of input shaping to a system with varying parameters, e.g., natural frequency, is discussed, and the effect of these variations is shown to induce vibration. A modified command shaping technique is developed to eliminate this unwanted motion.
Concepts for Distributed Systems Design (1983)

This book is written for computer programmers, analysts and scientists, as well as computer science students, as an intro duction to the principles of distributed system design. The emphasis is placed
Cloning and mutagenesis of a herpesvirus genome as an infectious bacterial artificial chromosome (1997)

A strategy for cloning and mutagenesis of an infectious herpesvirus genome is described. The mouse cytomegalovirus genome was cloned and maintained as a 230 kb bacterial artificial chromosome (BAC) in E. coli. Transfection of the BAC plasmid into eukaryotic cells led to a productive virus infection. The feasibility to introduce targeted mutations into the BAC cloned virus genome was shown by mutation of the immediate-early 1 gene and generation of a mutant virus. Thus, the complete construction of a mutant herpesvirus genome can now be carried out in a controlled manner prior to the reconstitution of infectious progeny. The described approach should be generally applicable to the mutagenesis of genomes of other large DNA viruses.
Music and mirror neurons: from motion to ’e’motion (2006)

The ability to create and enjoy music is a universal human trait and plays an important role in the daily life of most cultures. Music has a unique ability to trigger memories, awaken emotions and to intensify our social experiences. We do not need to be trained in music performance or appreciation to be able to reap its benefits-already as infants, we relate to it spontaneously and effortlessly. There has been a recent surge in neuroimaging investigations of the neural basis of musical experience, but the way in which the abstract shapes and patterns of musical sound can have such profound meaning to us remains elusive. Here we review recent neuroimaging evidence and suggest that music, like language, involves an intimate coupling between the perception and production of hierarchically organized sequential information, the structure of which has the ability to communicate meaning and emotion. We propose that these aspects of musical experience may be mediated by the human mirror neuron system.
A Recommendation System for Semantic Mashup Design (2010)

Techniques and tools for semantic description of mashup components are gaining more and more interest as an opportunity for a (semi-) automatic support of mashup design. We propose a recommendation system to design mashup applications, relying on the semantic description of mashup components for their proactive suggestion to the designer. A semantic organization of components is defined to propose ranked components, according to their similarity with designer's requirements and their mutual coupling.
Some Notes on— (1971)

Journal Article Some Notes on— Get access Crow by Ted Hughes. Faber and Faber, £1.00. J. M. Newton J. M. Newton Search for other works by this author on: Oxford Academic Google Scholar The Cambridge Quarterly, Volume V, Issue 4, Summer-Autumn 1971, Pages 376–384, https://doi.org/10.1093/camqtly/V.4.376 Published: 01 July 1971
From IPTV services to shared experiences: Challenges in architecture design (2010)

This paper discusses the architectural challenges of transitioning from services to experiences. In particular, it focuses on evolution from traditional IPTV services to more social scenarios, in which groups of people in different locations watch synchronized multimedia content together. In addition to the multimedia content, the shared experiences envisioned in this article provide a real-time communication channel between the participants. Based on an implemented architecture, this paper identifies a number of challenges and analyze them. The most important challenges highlighted in this article include: shared experience modeling, universal session handling, synchronization, and quality of service. This article is the first stone paving the way for a truly interoperable ecosystem, which can offer cross-domain experiences to the users.
Treatment of Thalamic Pain by Chronic Motor Cortex Stimulation (1991)

All forms of therapy, including chronic stimulation of the thalamic relay nucleus, can provide satisfactory pain control in only 20%-30% of cases of thalamic pain syndrome. In order to develop a more effective treatment for thalamic pain syndrome, we investigated the effects of stimulation of various brain regions on the burst hyperactivity of thalamic neurons recorded in cats after deafferentiation of the spinothalamic pathway. Complete, long-term inhibition of the burst hyperactivity was induced by stimulation of the motor cortex. Based on this experimental finding, we treated seven cases of thalamic pain syndrome by chronic motor cortex stimulation employing epidural plate electrodes. Excellent or good pain control was obtained in all cases without any complications or side effects. During the stimulation, an increase in regional blood flow of the cerebral cortex and thalamus, a marked rise in temperature of the painful skin regions, and improved movements of the painful limbs were observed. These results suggest that thalamic pain syndrome can be most effectively treated by chronic motor cortex stimulation.
Lymphocyte Activation Antigen CD70 Expressed by Renal Cell Carcinoma Is a Potential Therapeutic Target for Anti-CD70 Antibody-Drug Conjugates (2006)

Metastatic renal cell carcinoma (RCC) is an aggressive disease refractory to most existing therapeutic modalities. Identifying new markers for disease progression and drug targets for RCC will benefit this unmet medical need. We report a subset of clear cell and papillary cell RCC aberrantly expressing the lymphocyte activation marker CD70, a member of the tumor necrosis factor superfamily. Importantly, CD70 expression was found to be maintained at the metastatic sites of RCC. Anti-CD70 antibody-drug conjugates (ADC) consisting of auristatin phenylalanine phenylenediamine (AFP) or monomethyl auristatin phenylalanine (MMAF), two novel derivatives of the anti-tubulin agent auristatin, mediated potent antigen-dependent cytotoxicity in CD70-expressing RCC cells. Cytotoxic activity of these anti-CD70 ADCs was associated with their internalization and subcellular trafficking through the endosomal-lysosomal pathway, disruption of cellular microtubule network, and G2-M phase cell cycle arrest. The efficiency of drug delivery using anti-CD70 as vehicle was illustrated by the much enhanced cytotoxicity of antibody-conjugated MMAF compared with free MMAF. Hence, ADCs targeted to CD70 can selectively recognize RCC, internalize, and reach the appropriate subcellular compartment(s) for drug release and tumor cell killing. In vitro cytotoxicity of these ADCs was confirmed in xenograft models using RCC cell lines. Our findings provide evidence that CD70 is an attractive target for antibody-based therapeutics against metastatic RCC and suggest that anti-CD70 ADCs can provide a new treatment approach for advanced RCC patients who currently have no chemotherapeutic options.
Construction and characterization of a Vi-positive variant of the Salmonella typhi live oral vaccine strain Ty21a (1989)

The viaB locus coding for the Vi antigen of Salmonella typhi Ty2 was cloned on a 40.6-kilobase fragment into the cosmid vector pHC79. The live, oral, attenuated Vi-negative S. typhi Ty21a vaccine strain was transformed with the recombinant cosmid encoding the viaB locus. Homologous recombination of the viaB locus into the chromosome of S. typhi Ty21a was induced by UV irradiation, and Vi-positive recombinants were selected in the presence of D-cycloserine. One such isolate, termed WR4103, contained no plasmids or the attendant antibiotic resistance markers and expressed the Vi antigen stably. Vi antigen extracted from WR4103 was immunologically indistinguishable from Vi antigen purified from S. typhi Ty2. The only detectable difference between Ty21a and WR4103 was in the production of Vi antigen. The mean lethal doses of Ty21a and WR4103 for mice were nearly identical. Immunization of mice with WR4103 engendered a Vi antibody response and afforded complete protection against fatal infection with virulent S. typhi Ty2. Thus, S. typhi WR4103 may serve as an improved oral vaccine for protection against typhoid fever.
Zwitteration: Coating Surfaces with Zwitterionic Functionality to Reduce Nonspecific Adsorption (2014)

Coating surfaces with thin or thick films of zwitterionic material is an effective way to reduce or eliminate nonspecific adsorption to the solid/liquid interface. This review tracks the various approaches to zwitteration, such as monolayer assemblies and polymeric brush coatings, on micro- to macroscopic surfaces. A critical summary of the mechanisms responsible for antifouling shows how zwitterions are ideally suited to this task.
A New Trick of an Old Molecule: Androgen Receptor Splice Variants Taking the Stage?! (2011)

Prostate cancer is the second leading cause of cancer-related death in American men. Although most prostate cancers are initially androgen-dependent and respond to androgen ablation therapy, majority of them eventually relapse and progress into incurable castration-resistant (or hormone refractory) prostate cancer. The underlying mechanisms are the focus of intensive investigation for development of more effective treatment. Mounting evidence from both clinical and basic research has demonstrated that the activity of the androgen receptor (AR) is still required for castration-resistant prostate cancer. Multiple mechanisms by which AR is re-activated under androgen-depleted conditions may be involved in the development of castration resistance. The recent identification of AR splicing variants may add another layer of complexity in AR biology. The present review summarizes recent progress in study of AR splicing variants in prostate cancer.
Developmental expression of the α receptor for platelet-derived growth factor, which is deleted in the embryonic lethal Patch mutation (1992)

The alpha receptor of PDGF (Pdgfra) is expressed in primitive endoderm and mesoderm derivatives throughout embryogenesis. In the early primitive streak stage the gene is transcribed in the visceral and parietal endoderm. Later it is expressed in the presomitic mesoderm, yolk sac and amnion. During somitogenesis its transcription localizes to the heart and the somites. Subsequently, it is transcribed in the dermatome, the sclerotome, the developing limb and in various mesenchymal tissues of visceral organs. Its wild-type expression pattern correlates well with the phenotype of homozygous mutant Patch (Ph) embryos, where the Pdgfra gene is deleted. The Ph phenotype is first detectable at the primitive streak stage with convoluted and hypertrophic visceral yolk sac, deformed neural plate and disorganized or missing mesoderm. Most Ph/Ph embryos die before the 11th day of gestation. Those that survive till early organogenesis are very small, have hypertrophic yolk sacs, small and undifferentiated somites, convoluted neural tubes, large heart and pericardium, rudimentary limb buds and branchial arches. Our observations together suggest that the alpha PDGF receptor may be required for the normal development of visceral endoderm and mesoderm derivatives.
Translation elongation factor-1 alpha interacts with the 3' stem-loop region of West Nile virus genomic RNA (1997)

The conserved 3'-terminal stem-loop (3' SL) of the West Nile virus (WNV) genomic RNA was previously used to probe for cellular proteins that may be involved in flavivirus replication and three cellular proteins were detected that specifically interact with the WNV 3' SL RNA (J. L. Blackwell and M. A. Brinton, J. Virol. 69:5650-5658, 1995). In this study, one of these cellular proteins was purified to apparent homogeneity by ammonium sulfate precipitation and liquid chromatography. Amino acid sequence Western blotting, and supershift analyses identified the cellular protein as translation elongation factor-1 alpha (EF-1 alpha). Competition gel mobility shift assays demonstrated that the interaction between EF-1 alpha and WNV 3' SL RNA was specific. Dephosphorylation of EF-1 alpha by calf intestinal alkaline phosphatase inhibited its binding to WNV 3' SL RNA. The apparent equilibrium dissociation constant for the interaction between EF-1 alpha and WNV 3' SL RNA was calculated to be 1.1 x 10(-9) M. Calculation of the stoichiometry of the interaction indicated that one molecule of EF-1 alpha binds to each molecule of WNV 3' SL RNA. Using RNase footprinting and nitrocellulose filter binding assays, we detected a high-activity binding site on the main stem of the WNV 3' SL RNA. Interaction with EF-1 alpha at the high-activity binding site was sequence specific, since nucleotide substitution in this region reduced the binding activity of the WNV 3' SL RNA for EF-1 alpha by approximately 60%. Two low-activity binding sites were also detected, and each accounted for approximately 15 to 20% of the binding activity. Intracellular association between the host protein and the viral RNA was suggested by coimmunoprecipitation of WNV genomic RNA and EF-1 alpha, using an anti-EF-1 alpha antibody.
Remote polarization control for fiber-optic interferometers (1987)

A simple method has been developed for control and prevention of polarization fade on a single output lead from a remotely located fiber-optic interferometer. The method has been demonstrated using a fiber-optic Michelson interferometer. In contrast to a previously suggested method, only a single detector is required. The technique has application for passive, remotely located sensors. Extension to balanced homodyne detection schemes and coherent communications is discussed.
Differentiating and Managing Common Psychiatric Comorbidities Seen in Chronic Pain Patients (2010)

Pain patients often have comorbid psychiatric disorders that can complicate their management. Failure to recognize and address psychological comorbidities often limits pain treatment success. This paper describes some of the more commonly seen psychiatric comorbidities in pain patients, briefly discusses how the diagnoses are made, and provides some initial treatment guidelines. The multiaxial diagnostic system of the Diagnostic and Statistical Manual of Mental Disorders (DSM) is described. Three common psychiatric issues seen in pain patients: anxiety, depression, and adjustment disorder, are discussed. A brief history of the DSM is also discussed.
Far-UVC light (222 nm) efficiently and safely inactivates airborne human coronaviruses (2020)

A direct approach to limit airborne viral transmissions is to inactivate them within a short time of their production. Germicidal ultraviolet light, typically at 254 nm, is effective in this context but, used directly, can be a health hazard to skin and eyes. By contrast, far-UVC light (207-222 nm) efficiently kills pathogens potentially without harm to exposed human tissues. We previously demonstrated that 222-nm far-UVC light efficiently kills airborne influenza virus and we extend those studies to explore far-UVC efficacy against airborne human coronaviruses alpha HCoV-229E and beta HCoV-OC43. Low doses of 1.7 and 1.2 mJ/cm<sup>2</sup> inactivated 99.9% of aerosolized coronavirus 229E and OC43, respectively. As all human coronaviruses have similar genomic sizes, far-UVC light would be expected to show similar inactivation efficiency against other human coronaviruses including SARS-CoV-2. Based on the beta-HCoV-OC43 results, continuous far-UVC exposure in occupied public locations at the current regulatory exposure limit (~3 mJ/cm<sup>2</sup>/hour) would result in ~90% viral inactivation in ~8 minutes, 95% in ~11 minutes, 99% in ~16 minutes and 99.9% inactivation in ~25 minutes. Thus while staying within current regulatory dose limits, low-dose-rate far-UVC exposure can potentially safely provide a major reduction in the ambient level of airborne coronaviruses in occupied public locations.