gebhart/patrepeval huggingface dataset:
Interaction of the taxilin family with the nascent polypeptide‐associated complex that is involved in the transcriptional and translational processes (2005)

alpha-Taxilin is a novel binding partner of the syntaxin family, which is implicated in intracellular vesicle traffic. We have here found that alpha-taxilin interacts with the nascent polypeptide-associated complex (NAC), which is involved in transferring growing nascent polypeptide chains to appropriate co-translationally acting factors. NAC is composed of two subunits, alpha- and betaNACs. Both these subunits bound to alpha-taxilin through its C-terminal coiled-coil region in dose-dependent and saturable manners. The interactions of alpha-taxilin with alphaNAC and NAC but not with betaNAC were inhibited by syntaxin-4, indicating that alpha-taxilin binds to NAC mainly through its interaction with alphaNAC. When alphaNAC was over-expressed in COS-7 cells, alphaNAC was distributed in the cytosol and nucleus. However, co-expression of the alpha-taxilin fragment containing the alphaNAC-binding region eliminated the nuclear distribution of over-expressed alphaNAC. Moreover, other taxilin family members, beta- and gamma-taxilins, also bound to alphaNAC and thereby affected the nuclear distribution of over-expressed alphaNAC. Taken together with the evidence that alphaNAC functions in the nucleus as a transcriptional coactivator, our results raise the possibility that the taxilin family is involved not only in the translational process through its interaction with NAC but also in the transcriptional process through its interaction with alphaNAC alone.
Cross-Reactive HIV-1-Neutralizing Human Monoclonal Antibodies Identified from a Patient with 2F5-Like Antibodies (2011)

The genes encoding broadly HIV-1-neutralizing human monoclonal antibodies (MAbs) are highly divergent from their germ line counterparts. We have hypothesized that such high levels of somatic hypermutation could pose a challenge for elicitation of the broadly neutralizing (bn) Abs and that identification of less somatically mutated bn Abs may help in the design of effective vaccine immunogens. In a quest for such bn Abs, phage- and yeast-displayed antibody libraries, constructed using peripheral blood mononuclear cells (PBMCs) from a patient with bn serum containing Abs targeting the epitope of the bn MAb 2F5, were panned against peptides containing the 2F5 epitope and against the HIV-1 gp140(JR-FL). Two MAbs (m66 and m66.6) were identified; the more mutated variant (m66.6) exhibited higher HIV-1-neutralizing activity than m66, although it was weaker than 2F5 in a TZM-bl cell assay. Binding of both MAbs to gp41 alanine substitution mutant peptides required the DKW(664-666) core of the 2F5 epitope and two additional upstream residues (L(660,663)). The MAbs have long (21-residue) heavy-chain third complementarity-determining regions (CDR-H3s), and m66.6 (but not m66) exhibited polyspecific reactivity to self- and non-self-antigens. Both m66 and m66.6 are significantly less divergent from their germ line Ab counterparts than 2F5--they have a total of 11 and 18 amino acid changes, respectively, from the closest VH and Vκ germ line gene products compared to 25 for 2F5. These new MAbs could help explore the complex maturation pathways involved in broad neutralization and its relationship with auto- and polyreactivity and may aid design of vaccine immunogens and development of therapeutics against HIV-1 infection.
Studies on antitumor agents. VII. Antitumor activities of O-alkoxyalkyl derivatives of 2'-deoxy-5-trifluoromethyluridine. (1987)

Various O-alkoxyalkyl derivatives of 2'-deoxy-5-trifluoromethyluridine (F3Thd) were synthesized, and the antitumor activities of the compounds against sarcoma 180 were examined by oral administration to mice. Among the formal-type derivatives, 3', 5'-di-O-ethoxymethyl (3), 3', 5'-di-O-benzyloxymethyl (12), 5'-O-benzyloxymethyl (13) and 3'-O-benzyloxymethyl (14) compounds showed high activities, which were six-fold higher than that of F3Thd itself. Since acetal-type derivatives were unstable under acidic conditions, antitumor testing of the compounds was also carried out with co-administration of sodium bicarbonate. 5'-O- (1-Ethoxypropyl) -F3Thd (25) and 5'-O- (1-benzyloxypropyl) -F3Thd (37) showed the highest activities among the acetal-type derivatives, but the ED50 values of the compounds were not lower than those of effective formal-type compounds.These O-alkoxyalkyl derivatives of F3Thd are resistant to degradation by thymidine phosphorylase and are activated by microsomal drug-metabolizing enzymes after absorption.
Software for a cascade/parallel formant synthesizer (1980)

A software formant synthesizer is described that can generate synthetic speech using a laboratory digital computer. A flexible synthesizer configuration permits the synthesis of sonorants by either a cascade or parallel connection of digital resonators, but frication spectra must be synthesized by a set of resonators connected in parallel. A control program lets the user specify variable control parameter data, such as formant frequencies as a function of time, as a sequence of 〈time, value〉 points. The synthesizer design is described and motivated in Secs. I–III, and fortran listings for the synthesizer and control program are provided in an appendix. Computer requirements and necessary support software are described in Sec. IV. Strategies for the imitation of any speech utterance are described in Sec. V, and suggested values of control parameters for the synthesis of many English sounds are presented in tabular form.
chpA and chpB, Escherichia coli chromosomal homologs of the pem locus responsible for stable maintenance of plasmid R100 (1993)

The pem locus is responsible for stable maintenance of plasmid R100 and consists of two genes, pemI and pemK. The pemK gene product is a growth inhibitor, while the pemI gene product is a suppressor of this inhibitory function. We found that the PemI amino acid sequence is homologous to two open reading frames from Escherichia coli called mazE and orf-83, which are located at 60 and 100 min on the chromosome, respectively. We cloned and sequenced these loci and found additional open reading frames, one downstream of each pemI homolog, both of which encode proteins homologous to PemK. The pem locus homolog at 60 min was named chpA and consists of two genes, chpAI and chpAK; the other, at 100 min, was named chpB and consists of two genes, chpBI and chpBK. The distal portion of chpBK was found to be adjacent to the ppa gene that encodes pyrophosphatase, whose map position had not been previously determined. We then demonstrated that the chpAK and chpBK genes encode growth inhibitors, while the chpAI and chpBI genes encode suppressors for the inhibitory function of the ChpAK and ChpBK proteins, respectively. These E. coli pem locus homologs may be involved in regulation of cell growth.
GaN/AlGaN Terahertz Quantum Cascade Laser (2005)

The quantum-cascade laser (QCL) has, since its first realization, demonstrated an impressive and rapid development, extending the emission wavelengths from midinfrared to terahertz spectral range. However, QCLs based on GaAs/AlGaAs and AlInAs/GaInAs are not capable of emitting in the energy range around the LO-phonon energies (ELO~36 meV in GaAs and ELO~34 meV in InGaAs), leaving a gap in the spectral scale between 30 and 40 &amp;#956;m. This can be overcome by using GaN/AlGaN material. The GaN based QCL has many advantages over the GaAs QCL. These include larger LO-phonon energy (ELO~90 meV), very fast carrier dynamics, far infrared emission wavelengths (&gt; 40 &amp;#956;m), and room temperature operation capability. Therefore it has been considered the most desirable candidate for far infrared intersubband emission laser.
The International Workshop on Meibomian Gland Dysfunction: Report of the Subcommittee on Anatomy, Physiology, and Pathophysiology of the Meibomian Gland (2011)

T he tarsal glands of Meibom (glandulae tarsales) are large sebaceous glands located in the eyelids and, unlike those of the skin, are unassociated with hairs. According to Duke-Elder and Wyler, 1 they were first mentioned by Galenus in 200 AD and later, in 1666, they were described in more detail by the German physician and anatomist Heinrich Meibom, after whom they are named.
Automated Registration for Enhanced Reality Visualization in Surgery (1994)

There is a need for frameless guidance systems to aid neurosurgeons in planning the exact lo- cation of a craniotomy, to define the margins of tumors and to precisely locate neighboring criti- cal structures. We have developed an automatic technique for registering clinical data, such as segmented MRI or CT reconstructions, with the actual head of the patient on the operating ts- ble. A second method calibrates the position of a video camera relative to the patient. The combi- nation allows a visual mix of live video of the pa- tient with the segmented 3D MR/or CT model. This registration enables us to employ enhanced reality techniques for planning and guiding nell- rosurgical procedures by merging live video im- ages with the 3D reconstructions, and to inter- actively view extracranial or intracraniai struc- tures in a non-intrusive manner.
Peptomer Aluminum Oxide Nanoparticle Conjugates as Systemic and Mucosal Vaccine Candidates:  Synthesis and Characterization of a Conjugate Derived from the C4 Domain of HIV-1MNGp120 (1997)

Peptomers are polymers composed of peptides that are specifically cross-linked in a head-to-tail fashion. Recently, a peptomer composed of an amphipathic peptide from the C4 domain of HIV-1MN gp120 was shown to display a prominent alpha-helical conformation that, as an immunogen, elicited rabbit antibodies recognizing native and recombinant gp120 [Robey et al. (1995) J. Biol. Chem. 270, 23918-23921]. For the present study, we synthesized a conjugate composed of the C4 peptomer covalently linked to calcinated aluminum oxide nanoparticles. The nanoparticles were first reacted with (3-aminopropy])-triethoxysilane to provide an amine load of 15.9 mmol of R-NH2/g of solid. The amine-modified aluminum oxide nanoparticles then were reacted with N-acetylhomocysteine thiolactone at pH 10 to place a reactive thiol on the nanoparticles. A bromoacetylated C4 peptomer, modified at the epsilon-amines of lysine residues, then was reacted with the thiolated nanoparticles to give the peptomer covalently linked to aluminum oxide via a thioether bond. The peptomer load was determined to be 16 mg of peptomer/g of particles, a 55% theoretical yield. Particle shape and size of the peptomer-conjugated alumina were analyzed by electron microscopy and displayed a mean maximum diameter of 355 nm and a mean minimum diameter of 113 nm, well within the desired size range of 300 nm believed to be optimal for mucosal immunization purposes. Experimentally determined values of mean particle diameters, specific surface area, and specific peptomer load provided the information necessary to calculate the mean antigen load, which was determined to be 53000 +/- 42000 peptomer epitopes per particle. Peptomer-alumina conjugates, such as that described here, could form the basis of a new class of biomaterial that combines a chemically defined organic immunogen with a nontoxic chemically defined inorganic adjuvant.
Isolation of a novel class of bZIP transcription factors that interact with ABA‐responsive and embryo‐specification elements in the Dc3 promoter using a modified yeast one‐hybrid system (1997)

Dc3 is a carrot lea class gene that is abundantly expressed during somatic and zygotic embryogenesis. Its expression is normally embryo-specific and also can be induced by abscisic acid. The regulatory elements mediating the embryo-specific expression of Dc3 reside within the proximal promoter region (-117 to +26), which is also essential for ABA-induced expression. In this study, an optimized version of the yeast one-hybrid system has been used to clone factors that bind to the promoter region of the Dc3 gene. Twenty-five million yeast transformants were screened in a single experiment, and nine independent cDNA clones were isolated from a sunflower library that encode proteins that specifically bind to functional cis-regulatory elements in the Dc3 promoter. Analysis of these clones showed that they are derived from three different mRNA species that encode two basic leucine zipper proteins. The basic regions of these proteins, named DPBF-1 and 2 (Dc3 Promoter-Binding Factor-1 and 2), respectively, are nearly identical to each other and are similar to the plant G-box binding factor GBF-4. Outside the basic region, however, DPBF-1 and 2 diverge significantly from each other and from other known factors. Both factors have transcriptional activity in yeast, and bind to DNA as dimers. Unlike other plant bZIP factors, DPBF-1 and 2 recognize sequences containing the ACACNNG core. Cloning of these factors demonstrates the power of the one-hybrid approach when optimally applied.
Dendrimer-RNA nanoparticles generate protective immunity against lethal Ebola, H1N1 influenza, and Toxoplasma gondii challenges with a single dose (2016)

Vaccines have had broad medical impact, but existing vaccine technologies and production methods are limited in their ability to respond rapidly to evolving and emerging pathogens, or sudden outbreaks. Here, we develop a rapid-response, fully synthetic, single-dose, adjuvant-free dendrimer nanoparticle vaccine platform wherein antigens are encoded by encapsulated mRNA replicons. To our knowledge, this system is the first capable of generating protective immunity against a broad spectrum of lethal pathogen challenges, including H1N1 influenza, Toxoplasma gondii, and Ebola virus. The vaccine can be formed with multiple antigen-expressing replicons, and is capable of eliciting both CD8(+) T-cell and antibody responses. The ability to generate viable, contaminant-free vaccines within days, to single or multiple antigens, may have broad utility for a range of diseases.
Secretion Management in the Mechanically Ventilated Patient (2007)

Secretion management in the mechanically ventilated patient includes routine methods for maintaining mucociliary function, as well as techniques for secretion removal. Humidification, mobilization of the patient, and airway suctioning are all routine procedures for managing secretions in the ventilated patient. Early ambulation of the post-surgical patient and routine turning of the ventilated patient are common secretion-management techniques that have little supporting evidence of efficacy. Humidification is a standard of care and a requisite for secretion management. Both active and passive humidification can be used. The humidifier selected and the level of humidification required depend on the patient's condition and the expected duration of intubation. In patients with thick, copious secretions, heated humidification is superior to a heat and moisture exchanger. Airway suctioning is the most important secretion removal technique. Open-circuit and closed-circuit suctioning have similar efficacy. Instilling saline prior to suctioning, to thin the secretions or stimulate a cough, is not supported by the literature. Adequate humidification and as-needed suctioning are the foundation of secretion management in the mechanically ventilated patient. Intermittent therapy for secretion removal includes techniques either to simulate a cough, to mechanically loosen secretions, or both. Patient positioning for secretion drainage is also widely used. Percussion and postural drainage have been widely employed for mechanically ventilated patients but have not been shown to reduce ventilator-associated pneumonia or atelectasis. Manual hyperinflation and insufflation-exsufflation, which attempt to improve secretion removal by simulating a cough, have been described in mechanically ventilated patients, but neither has been studied sufficiently to support routine use. Continuous lateral rotation with a specialized bed reduces atelectasis in some patients, but has not been shown to improve secretion removal. Intrapulmonary percussive ventilation combines percussion with hyperinflation and a simulated cough, but the evidence for intrapulmonary percussive ventilation in mechanically ventilated patients is insufficient to support routine use. Secretion management in the mechanically ventilated patient consists of appropriate humidification and as-needed airway suctioning. Intermittent techniques may play a role when secretion retention persists despite adequate humidification and suctioning. The technique selected should remedy the suspected etiology of the secretion retention (eg, insufflation-exsufflation for impaired cough). Further research into secretion management in the mechanically ventilated patient is needed.
An Algebraic Theory of 3D Sound Synthesis with Loudspeakers (2002)

The problem of reproducing signals with loudspeakers is considered. A algebraic, time-domain synthesis approach is developed that extends the multi-input multi-output inverse theorem (MINT) of Miyoshi and Kaneda. The approach is general and can encompass joint surround sound synthesis and loudspeaker/room correction. First, a discrete timedomain matrix description is developed that captures the effects of amplifiers, loudspeakers, and room acoustics. Based on this model, it is shown that exact synthesis is possible with practical reproduction apparatus only if . Sufficient conditions are also presented. The results are specialized to the case of zero-crosstalk transaural sound reproduction, and the theoretical importance of loudspeaker time alignment is illustrated. Finally, minimum-power exact synthesis is briefly described.
A timer-actuated immunoassay cassette for detecting molecular markers in oral fluids (2008)

An inexpensive, hand-held, point-of-care, disposable, self-contained immunoassay cassette comprised of air pouches for pumping, a metering chamber, reagents storage chambers, a mixer, and a lateral flow strip was designed, constructed, and tested. The assay was carried out in a consecutive flow format. The detection was facilitated with up-converting phosphor (UCP) reporter particles. The automated, timely pumping of the various reagents was driven by a spring-loaded timer. The utility of the cassette was demonstrated by detecting antibodies to HIV in saliva samples and further evaluated with a non-contagious, haptenized DNA assay. The cassette has several advantages over dip sticks such as sample preprocessing, integrated storage of reagents, and automated operation that reduces operator errors and training. The cassette and actuator described herein can readily be extended to detect biomarkers of other diseases in body fluids and other fluids at the point of care. The system is particularly suitable for resource-poor countries, where funds and trained personnel are in short supply.
Two novel SOD1 mutations in patients with familial amyotrophic lateral sclerosis (1995)

Journal Article Two novel SOD1 mutations in patients with familial amyotrophic lateral sclerosis Get access Han-Xiang Deng, Han-Xiang Deng Search for other works by this author on: Oxford Academic PubMed Google Scholar John A. Tainer, John A. Tainer 1Department of Molecular Biology, The Scripps Research InstituteLa Jolla, CA 92037 Search for other works by this author on: Oxford Academic PubMed Google Scholar Hiroshi Mitsumoto, Hiroshi Mitsumoto 2Department of Neurology, The Cleveland Clinic Foundation9500 Euclid Avenue, Cleveland, OH 44195, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Akio Ohnishi, Akio Ohnishi 3Department of Neurology, University of Occupational and Enviromental Health School of MedicineYahata-nishi-ku, Kitakyushu 807, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Xiaoxuan He, Xiaoxuan He Search for other works by this author on: Oxford Academic PubMed Google Scholar Wu-Yen Hung, Wu-Yen Hung Search for other works by this author on: Oxford Academic PubMed Google Scholar Yaliang Zhao, Yaliang Zhao Search for other works by this author on: Oxford Academic PubMed Google Scholar Tony Juneja, Tony Juneja Search for other works by this author on: Oxford Academic PubMed Google Scholar Afif Hentati, Afif Hentati Search for other works by this author on: Oxford Academic PubMed Google Scholar Teepu Siddique Teepu Siddique * *To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Human Molecular Genetics, Volume 4, Issue 6, June 1995, Pages 1113–1116, https://doi.org/10.1093/hmg/4.6.1113 Published: 01 June 1995 Article history Received: 10 March 1995 Revision received: 17 March 1995 Accepted: 17 March 1995 Published: 01 June 1995
Evolution of Organic–Inorganic Lead Halide Perovskite from Solid-State Iodoplumbate Complexes (2015)

The optoelectronic properties of hybrid perovskites are a strong function of their physical structure, and understanding the fundamental steps involved in the formation of these films can aid in the optimization and rational design of devices with tailored properties. Here we investigate the structural and optical characteristics of CH3NH3PbI3 films prepared from solutions composed of stoichiometric and nonstoichiometric quantities of lead iodide and methylammonium iodide precursors. In the presence of excess organohalide salt, a precursor phase composed of various iodoplumbate complexes is stabilized. The complexes dominate the optical properties of as-deposited films. Upon thermal treatment, the iodoplumbate precursor phase gradually evolves into the final tetragonal perovskite structure. Employing transient absorption spectroscopy, we have succeeded in tracking this transformation and gain insight into the interplay between the solid-state precursor and perovskite phases at various stages of formation. Correlation between time-resolved spectroscopic data and structural character can aid in better defining the structure–property relationship of hybrid perovskite thin films.
Physical and functional interaction between WT1 and p53 proteins. (1993)

WT1 is a tumor-suppressor gene expressed in the developing kidney, whose inactivation leads to the development of Wilms tumor, a pediatric kidney cancer. WT1 encodes a transcription factor which binds to the EGR1 consensus sequence, mediating transcriptional repression. We now demonstrate that p53, the product of a tumor-suppressor gene with ubiquitous expression, physically associates with WT1 in transfected cells. The interaction between WT1 and p53 modulates their ability to transactivate their respective targets. In the absence of p53, WT1 acts as a potent transcriptional activator of the early growth response gene 1 (EGR1) site, rather than a transcriptional repressor. In contrast, WT1 exerts a cooperative effect on p53, enhancing its ability to transactivate the muscle creatine kinase promoter.