gebhart/patrepeval huggingface dataset:
Protoplast transformation of glutamate-producing bacteria with plasmid DNA (1984)

A method for polyethylene glycol-induced protoplast transformation of glutamate-producing bacteria with plasmid DNA was established. Protoplasts were prepared from cells grown in the presence of penicillin by treatment with lysozyme in a hypertonic medium. The concentration of penicillin during growth affected the efficiency of formation, regeneration, and polyethylene glycol-induced DNA uptake of protoplasts. Regeneration of protoplasts was accomplished on a hypertonic agar medium containing sodium succinate and yeast extract. The spectinomycin and streptomycin resistance plasmid pCG4, originally from Corynebacterium glutamicum T250, could transform various glutamate-producing bacteria such as C. glutamicum, Corynebacterium herculis, Brevibacterium flavum, and Microbacterium ammoniaphilum. The plasmid was structurally unchanged and stably maintained in new hosts. The transformation frequency of most competent protoplasts with pCG4 DNA isolated from primary transformants was high (ca. 10(6) transformants per microgram of covalently closed circular DNA) but was still two orders of magnitude below the frequency of transfection with modified DNA of the bacteriophage phi CGI. The difference was ascribed to the involvement of regeneration in transformation.
The Specificity and Flexibility of L1 Reverse Transcription Priming at Imperfect T-Tracts (2013)

L1 retrotransposons have a prominent role in reshaping mammalian genomes. To replicate, the L1 ribonucleoprotein particle (RNP) first uses its endonuclease (EN) to nick the genomic DNA. The newly generated DNA end is subsequently used as a primer to initiate reverse transcription within the L1 RNA poly(A) tail, a process known as target-primed reverse transcription (TPRT). Prior studies demonstrated that most L1 insertions occur into sequences related to the L1 EN consensus sequence (degenerate 5'-TTTT/A-3' sites) and frequently preceded by imperfect T-tracts. However, it is currently unclear whether--and to which degree--the liberated 3'-hydroxyl extremity on the genomic DNA needs to be accessible and complementary to the poly(A) tail of the L1 RNA for efficient priming of reverse transcription. Here, we employed a direct assay for the initiation of L1 reverse transcription to define the molecular rules that guide this process. First, efficient priming is detected with as few as 4 matching nucleotides at the primer 3' end. Second, L1 RNP can tolerate terminal mismatches if they are compensated within the 10 last bases of the primer by an increased number of matching nucleotides. All terminal mismatches are not equally detrimental to DNA extension, a C being extended at higher levels than an A or a G. Third, efficient priming in the context of duplex DNA requires a 3' overhang. This suggests the possible existence of additional DNA processing steps, which generate a single-stranded 3' end to allow L1 reverse transcription. Based on these data we propose that the specificity of L1 reverse transcription initiation contributes, together with the specificity of the initial EN cleavage, to the distribution of new L1 insertions within the human genome.
Synthesis and Biological Evaluation of a Potent E-Selectin Antagonist (1999)

An early step of the inflammatory response-the rolling of leukocytes on activated endothelial cells-is mediated by selectin/carbohydrate interactions. The tetrasaccharide sialyl Lewis(x) (sLe(x)) 1 is a ligand for E-, P-, and L-selectin and, therefore, serves as a lead structure to develop analogues which allow the control of acute and chronic inflammation. Here we describe the efficient synthesis (10 linear steps) of the potent sLe(x) mimetic 2. Compared to sLe(x), compound 2 showed a 30-fold improved affinity in a static, cell-free E-selectin-ligand binding assay (IC(50) = 36 microM). These data were confirmed by a marked inhibition in an in vitro cell-cell rolling assay which simulates in vivo conditions (IC(50) approximately 40 microM). The assays are predictive for the in vivo efficacy of test compounds as indicated by a marked inhibitory effect of 2 in a thioglycollate induced peritonitis model of acute inflammation in mice (ED(50) approximately 15 mg/kg).
Water−Silica Force Field for Simulating Nanodevices (2006)

Amorphous silica is an inorganic material that is central for many nanotechnology applications, such as nanoelectronics, microfluidics, and nanopore sensors. To use molecular dynamics (MD) simulations to study the behavior of biomolecules interacting with silica, we developed a force field for amorphous silica surfaces based on their macroscopic wetting properties that is compatible with the CHARMM force field and TIP3P water model. The contact angle of a water droplet on a silica surface served as a criterion to tune the intermolecular interactions. The resulting force field was used to study the permeation of water through silica nanopores, illustrating the influence of the surface topography and the intermolecular parameters on permeation kinetics. We find that minute modeling of the amorphous surface is critical for MD studies, since the particular arrangement of surface atoms controls sensitively electrostatic interactions between silica and water.
New Developments in the Virus Therapy of Cancer: A Historical Review (1993)

Since the 1920s, viruses had been used for oncolysis. Natural human viral infections can rarely induce remissions of leukemias or lymphomas. Inoculation of tumor-bearing patients with live viruses very seldom resulted in durable complete remissions. Genetically engineered or tumor-adapted virus strains may perform better. Virally modified tumor cell membrane vaccines can induce in the host rejection strength antitumor immunity. Modern technology and much more work is needed before the optimal procedures for viral oncolysis or active antitumor immunization with virally modified tumor cell vaccines are learned and can be implemented in the clinical practice. Laboratory monitoring of the host's immunological reactions accompanying failure and success of tumor rejection is essential for the recognition and duplication of the successful and for the avoidance of the unsuccessful interventions.
HoloDesk (2012)

HoloDesk is an interactive system combining an optical see through display and Kinect camera to create the illusion that users are directly interacting with 3D graphics. A virtual image of a 3D scene is rendered through a half silvered mirror and spatially aligned with the real-world for the viewer. Users easily reach into an interaction volume displaying the virtual image. This allows the user to literally get their hands into the virtual display and to directly interact with an spatially aligned 3D virtual world, without the need for any specialized head-worn hardware or input device. We introduce a new technique for interpreting raw Kinect data to approximate and track rigid (e.g., books, cups) and non-rigid (e.g., hands, paper) physical objects and support a variety of physics-inspired interactions between virtual and real. In particular the algorithm models natural human grasping of virtual objects with more fidelity than previously demonstrated. A qualitative study highlights rich emergent 3D interactions, using hands and real-world objects. The implementation of HoloDesk is described in full, and example application scenarios explored. Finally, HoloDesk is quantitatively evaluated in a 3D target acquisition task, comparing the system with indirect and glasses-based variants.
βIV spectrin is recruited to axon initial segments and nodes of Ranvier by ankyrinG (2007)

High densities of ion channels at axon initial segments (AISs) and nodes of Ranvier are required for initiation, propagation, and modulation of action potentials in axons. The organization of these membrane domains depends on a specialized cytoskeleton consisting of two submembranous cytoskeletal and scaffolding proteins, ankyrinG (ankG) and betaIV spectrin. However, it is not known which of these proteins is the principal organizer, or if the mechanisms governing formation of the cytoskeleton at the AIS also apply to nodes. We identify a distinct protein domain in betaIV spectrin required for its localization to the AIS, and show that this domain mediates betaIV spectrin's interaction with ankG. Dominant-negative ankG disrupts betaIV spectrin localization, but does not alter endogenous ankG or Na(+) channel clustering at the AIS. Finally, using adenovirus for transgene delivery into myelinated neurons, we demonstrate that betaIV spectrin recruitment to nodes of Ranvier also depends on binding to ankG.
Reduced T Helper 1 Responses in IL-12 p40 Transgenic Mice (1998)

To investigate the antagonistic effect of IL-12 p40 on IL-12 activity in vivo, we generated transgenic (Tg) mice in which p40 gene was regulated by a liver-specific promoter. Three Tg mouse lines were generated, and they expressed the p40 transgene predominantly in liver. Serum p40 level was extremely high, and it consisted of mainly monomer and homodimer and also of higher m.w. complexes. These Tg mice did not show any apparent phenotypic difference from control littermates in lymphoid cells. Enhancement of NK cell lytic activity in spleen by administration of rIL-12 to these mice was greatly diminished. Ag induced cytokine production was impaired: decreased production of IFN-gamma and increased production of IL-4 and IL-10. Delayed-type hypersensitivity response was also significantly reduced. Moreover, these Tg mice showed increased susceptibility to the infection with an intracellular pathogen, blood-stage Plasmodium berghei XAT, which is an irradiation-induced attenuated substrain of P. berghei NK65, presumably due to the decreased IFN-gamma production. These results suggest that p40 functions as an IL-12 antagonist in vivo, and that Th1 responses in p40 Tg mice are significantly reduced. Thus, these Tg mice could be a useful model to evaluate the inhibitory effect of p40 on IL-12-mediated various immune responses in vivo.
Single-PA-feedback digital predistortion for beamforming MIMO transmitter (2016)

In this paper, a simplified method of digital predistortion (DPD) based on the feedback for single power amplifier (PA) is proposed to linearize beamforming Multiple-Input Multiple-Output (MIMO) transmitter. In MIMO beamforming transmitter, a couple of radio frequency (RF) channels are paralleled to transmit signals simultaneously, it is almost impractical to perform linearization for each channel individually. The proposed method can not only achieve good linearization effect, but also greatly simplifies the system structure. A simple MIMO system with 2×4 beamformer is constructed to evaluate the proposed method. The experiment is based on two Long Term Evolution (LTE) signals with different bandwidth and peak-to-average power ratio (PAPR) operating at 2.12 GHz and 2.18 GHz, respectively. With a two dimensional memory polynomials (2-D-MP) model, the nonlinearity of the transmitter is compensated, and the adjacent channels power ratio (ACPR) can reach lower than -45dBc, which has been compressed 9-21 dB in the results.
A modified random perturbation method for database security (1994)

The random data perturbation (RDP) method of preserving the privacy of individual records in a statistical database is discussed. In particular, it is shown that if confidential attributes are allowed as query-defining variables, severe biases may result in responses to queries. It is also shown that even if query definition through confidential variables is not allowed, biases can still occur in responses to queries such as those involving proportions or counts. In either case, serious distortions may occur in user statistical analyses. A modified version of RDP is presented, in the form of a query adjustment procedure and specialized perturbation structure which will produce unbiased results.
Time-kill curve analysis and pharmacodynamic modelling for in vitro evaluation of antimicrobials against Neisseria gonorrhoeae (2016)

N. gonorrhoeae time-kill curve experiments analysed with a pharmacodynamic model have potential for in vitro evaluation of new and existing antimicrobials. The pharmacodynamic parameters based on a wide range of concentrations below and above the MIC provide information that could support improving future dosing strategies to treat gonorrhoea.
General-purpose harmonic balance analysis of nonlinear microwave circuits under multitone excitation (1988)

A powerful software tools for the simulation of nonlinear microwave circuits under single- or multiple-frequency excitation is described. The program operates in a truly general-purpose fashion, both circuit topology and active-device equivalent circuits being arbitrarily established by the user at the data entry level. Built-in facilities based on the multidimensional Fourier transform allow a straightforward and unrestricted treatment of mixer and intermodulation problems. The capabilities of the program are illustrated by a number of practical examples.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Materials Characterization in the Vacuum Ultraviolet with Variable Angle Spectroscopic Ellipsometry (2001)

The shift towards shorter wavelengths in the lithographic process has been the driving force for development of a commercial spectroscopic ellipsometer covering the vacuum ultraviolet (VUV) spectrum. Understanding the optical properties of thin films and substrate materials at short wavelengths (193 nm, 157 nm, and shorter) is necessary to develop the lithographic process. Lithography applications include optical coatings, photoresists, AR films, and masks. We present results for both single and multi-layer structures important to this industry. A complete description of the thin film optical properties can be used to track process changes or variations in sample structure. As an example, we compare the measured index for three oxynitrides that were subjected to different process conditions. In addition to lithography applications, VUV ellipsometry has many other potential applications. A variety of other materials have been characterized, often incorporating generalized ellipsometry to investigate anisotropic optical properties. The ordinary and extraordinary dielectric functions for bulk 4H SiC were measured over the wide spectral range from 0.73 to 8.5 eV.
Regulation of Adhesion to ICAM-1 by the Cytoplasmic Domain of LFA-1 Integrin β Subunit (1991)

Interactions between cytotoxic lymphocytes and their targets require the T cell antigen receptor (TCR) and the integrin lymphocyte function-associated molecule-1 (LFA-1, CD11a/CD18). LFA-1 is not constitutively avid for its counter-receptors, intercellular adhesion molecules (ICAMs)-1 and -2. Cross-linking of the TCR transiently converts LFA-1 to a high avidity state and thus provides a mechanism for regulating cellular adhesion and de-adhesion in an antigen-specific manner. Truncation of the cytoplasmic domain of the beta, but not the alpha, subunit of LFA-1 eliminated binding to ICAM-1 and sensitivity to phorbol esters. Thus, LFA-1 binding to ICAM-1 was found to be regulated by the cytoplasmic domain of the beta subunit of LFA-1.
[Prophylaxis of venous thromboembolic complications in patients with hematological diseases after laparoscopic splenectomy]. (2001)

In 8 patients, to whom laparoscopic splenectomy was performed, the measures for venous thromboembolic complications (VTHEC) prophylaxis were done. The expediency of application of low molecular weight heparin clecsan was substantiated, its advantages over non-fractionized heparin were depicted. Laparoscopic splenectomy permits to minimize the risk of the VTHEC occurrence in hematological practice.
Atomic Layer Deposition of Oxide Thin Films with Metal Alkoxides as Oxygen Sources (2000)

A chemical approach to atomic layer deposition (ALD) of oxide thin films is reported here. Instead of using water or other compounds for an oxygen source, oxygen is obtained from a metal alkoxide, which serves as both an oxygen and a metal source when it reacts with another metal compound such as a metal chloride or a metal alkyl. These reactions generally enable deposition of oxides of many metals. With this approach, an alumina film has been deposited on silicon without creating an interfacial silicon oxide layer that otherwise forms easily. This finding adds to the other benefits of the ALD method, especially the atomic-level thickness control and excellent uniformity, and takes a major step toward the scientifically challenging and technologically important task of replacing silica as the gate dielectric in the future generations of metal oxide semiconductor field effect transistors.
IgG Fc engineering to modulate antibody effector functions (2017)

Therapeutic monoclonal antibodies are among the most effective biotherapeutics to date. An important aspect of antibodies is their ability to bind antigen while at the same time recruit immune effector functions. The majority of approved recombinant monoclonal antibody therapies are of the human IgG1 subclass, which can engage both humoral and cellular components of the immune system. The wealth of information generated about antibodies has afforded investigators the ability to molecularly engineer antibodies to modulate effector functions. Here, we review various antibody engineering efforts intended to improve efficacy and safety relative to the human IgG isotype. Further, we will discuss proposed mechanisms by which engineering approaches led to modified interactions with immune components and provide examples of clinical studies using next generation antibodies.
Acoustic analysis of snoring sound in patients with simple snoring and obstructive sleep apnoea (1996)

Snoring, a symptom which may indicate the presence of the obstructive sleep apnoea syndrome (OSA), is also common in the general population. Recent studies have suggested that the acoustic characteristics of snoring sound may differ between simple snorers and OSA patients. We have studied a small number of patients with simple snoring and OSA, analysing the acoustic characteristics of the snoring sound. Seventeen male patients, 10 with OSA (apnoea/hypopnoea index (AHI) 26.2 events x h(-1)) and seven simple snorers (AHI 3.8 events x h(-1)), were studied. Full night polysomnography was performed and the snoring sound power spectrum was analysed. Spectral analysis of snoring sound showed the existence of two different patterns. The first pattern was characterized by the presence of a fundamental frequency and several harmonics. The second pattern was characterized by a low frequency peak with the sound energy scattered on a narrower band of frequencies, but without clearly identified harmonics. The seven simple snorers and two of the 10 patients with OSA (AIH 13 and 14 events x h(-1), respectively) showed the first pattern. The rest of the OSA patients showed the second pattern. The peak frequency of snoring was significantly lower in OSA patients, with all but one OSA patient and only one simple snorer showing a peak frequency below 150 Hz. A significant negative correlation was found between AHI and peak and mean frequencies of the snoring power spectrum (p<0.0016 and p<0.0089, respectively). In conclusion, this study demonstrates significant differences in the sound power spectrum of snoring sound between subjects with simple snoring and obstructive sleep apnoea patients.
Salt‐inducible kinase‐1 represses cAMP response element‐binding protein activity both in the nucleus and in the cytoplasm (2004)

Salt-inducible kinase-1 (SIK1) is phosphorylated at Ser577 by protein kinase A in adrenocorticotropic hormone-stimulated Y1 cells, and the phospho-SIK1 translocates from the nucleus to the cytoplasm. The phospho-SIK1 is dephosphorylated in the cytoplasm and re-enters the nucleus several hours later. By using green-fluorescent protein-tagged SIK1 fragments, we found that a peptide region (586-612) was responsible for the nuclear localization of SIK1. The region was named the 'RK-rich region' because of its Arg- and Lys-rich nature. SIK1s mutated in the RK-rich region were localized mainly in the cytoplasm. Because SIK1 represses cAMP-response element (CRE)-mediated transcription of steroidogenic genes, the mutants were examined for their effect on transcription. To our surprise, the cytoplasmic mutants strongly repressed the CRE-binding protein (CREB) activity, the extent of repression being similar to that of SIK1(S577A), a mutant localized exclusively in the nucleus. Several chimeras were constructed from SIK1 and from its isoform SIK2, which was localized mainly in the cytoplasm, and they were examined for intracellular localization as well as CREB-repression activity. A SIK1-derived chimera, where the RK-rich region had been replaced with the corresponding region of SIK2, was found in the cytoplasm, its CREB-modulating activity being similar to that of wild-type SIK1. On the other hand, a SIK2-derived chimera with the RK-rich region of SIK1 was localized in both the nucleus and the cytoplasm, and had a CREB-repressing activity similar to that of the wild-type SIK2. Green fluorescent protein-fused transducer of regulated CREB activity 2 (TORC2), a CREB-specific co-activator, was localized in the cytoplasm and nucleus of Y1 cells, and, after treatment with adrenocorticotropic hormone, cytoplasmic TORC2 entered the nucleus, activating CREB. The SIK1 mutants, having a strong CRE-repressing activity, completely inhibited the adrenocorticotropic hormone-induced nuclear entry of green fluorescent protein-fused TORC2. This suggests that SIK1 may regulate the intracellular movement of TORC2, and as a result modulates the CREB-dependent transcription activity. Together, these results indicate that the RK-rich region of SIK1 is important for determining the nuclear localization and attenuating CREB-repressing activity, but the degree of the nuclear localization of SIK1 itself does not necessarily reflect the degree of SIK1-mediated CREB repression.
The Supernatural in the Naturalists (2021)

“Supernatural” is used in contemporary liberal, radical, and revisionist theological discourse with invariably pejorative connotations. The term designates what no reasonable, contemporary person would affirm. Paul Tillich changes the spelling to “supranatural” and uses it in several contexts with these meanings: revealed truths alien to actual human existence; a rationalistic theory of miracles which interprets them as interruptions of the natural law; the Roman Catholic ontology of grace wherein grace becomes a substance; a theory opposed by naturalism, which involves a divine world alongside the natural world; and the attribution of individual substance to the divine. The naturalists have formulated their basic position with clarity and without falling into the more egregious blunders of either Hume or Kant. The naturalists justifiably pride themselves on attention to experience. A work of art elicits and accentuates the quality of being a whole and belonging to the larger, all-inclusive, whole which is the universe in which people live.