gebhart/patrepeval huggingface dataset:
Membrane Dipeptidase Is the Receptor for a Lung-targeting Peptide Identified by in Vivo Phage Display (1999)

In vivo phage display is a powerful method to study organ- and tissue-specific vascular addresses. Using this approach, peptides capable of tissue-specific homing can be identified by performing a selection for that trait in vivo. We recently showed that the CGFECVRQCPERC (termed GFE-1) peptide can selectively bind to mouse lung vasculature after an intravenous injection. Our aim in the present study was to identify the receptor for this lung-homing peptide. By using affinity chromatography, we isolated a 55-kDa lung cell-surface protein that selectively binds to the GFE-1 peptide. Protein sequencing established the identity of the receptor as membrane dipeptidase (MDP), a cell-surface zinc metalloprotease involved in the metabolism of glutathione, leukotriene D4, and certain beta-lactam antibiotics. Phage particles displaying the GFE-1 peptide selectively bind to COS-1 cells transfected with the murine MDP cDNA. Moreover, the synthetic GFE-1 peptide could inhibit MDP activity. By establishing MDP as the receptor for the GFE-1 peptide, our results suggest potential applications for both MDP and the GFE-1 peptide in delivery of compounds to the lungs. This work also demonstrates that cell-surface proteases can be involved in tissue-specific homing.
Structure of initiation factor eIF‐3 from rat liver (1986)

On the basis of hydrodynamic, electron microscopic and biochemical investigations a new model of the structure of initiation factor eIF-3 is proposed. From sedimentation and diffusion coefficients of 16.35 S and 2.13 X 10(-7) cm2/s, respectively, as well as from sedimentation equilibrium measurements, a molecular mass of about 650 kDa was determined for isolated eIF-3. This is in agreement with molecular mass estimations by sodium dodecyl sulphate gel electrophoresis. A partial specific volume of 0.723 cm3/g was determined by means of the amino acid composition and the specific volume increments of the amino acids. From this value and from the molecular mass, a volume of 780 nm3 was calculated for eIF-3. In electron micrographs of isolated eIF-3, images with triangular profiles and side lengths of 14 nm, 16 nm, and 17 nm have been observed. Taking into account the calculated volume and considering the triangular image as one face of the particle, it is suggested that eIF-3 has the shape of a flat triangular prism with a height of about 7 nm and the above-mentioned side-lengths. This model is in agreement with results of electron microscopic investigations of eIF-3 in native small ribosomal subunits [Lutsch, G., Benndorf, R., Westermann, P., Bommer, U.-A. & Bielka, H. (1986) Eur. J. Cell Biol. 40/2, in press]. The high frictional ratio of about 1.7 also supports eIF-3 to be rather of a flat than of a globular shape.
Synthesizing Samples for Zero-shot Learning (2017)

Zero-shot learning (ZSL) is to construct recognition models for unseen target classes that have no labeled samples for training. It utilizes the class attributes or semantic vectors as side information and transfers supervision information from related source classes with abundant labeled samples. Existing ZSL approaches adopt an intermediary embedding space to measure the similarity between a sample and the attributes of a target class to perform zero-shot classification. However, this way may suffer from the information loss caused by the embedding process and the similarity measure cannot fully make use of the data distribution. In this paper, we propose a novel approach which turns the ZSL problem into a conventional supervised learning problem by synthesizing samples for the unseen classes. Firstly, the probability distribution of an unseen class is estimated by using the knowledge from seen classes and the class attributes. Secondly, the samples are synthesized based on the distribution for the unseen class. Finally, we can train any supervised classifiers based on the synthesized samples. Extensive experiments on benchmarks demonstrate the superiority of the proposed approach to the state-of-the-art ZSL approaches.
Oncogenic Raf-1 Activates p70 S6 Kinase via a Mitogen-activated Protein Kinase-independent Pathway (1996)

Cell proliferation requires the co-ordinate triggering of several protein kinases of Ser/Thr specificity such as p70 S6 kinase (S6K), which phosphorylates the ribosomal S6 protein and thus increases translation of mRNAs with polypyrimidine tracts. The multiplicity of signaling pathways leading to p70 S6K activation are not fully elucidated. However, several reports have indicated that the activation of p70 S6K is independent of mitogen-activated protein kinase (MAPK) activation. Interestingly, we and others have shown that constitutive activation of the MAPK pathway promotes cell proliferation, suggesting that this cascade is able to activate p70 S6K, a key step to trigger cell cycle entry. In this report we demonstrate that transfection of constitutively active mitogen-activated protein kinase kinase 1 in CCL 39 cells leads to activation of p70 S6K. Furthermore, we have established a cell line that stably expresses DeltaRaf-1:ER, an estradiol-regulated form of oncogenic Raf-1. The addition of estradiol to these cells was sufficient to elicit rapid activation of mitogen-activated protein kinase kinase 1, MAPK, and p70 S6K. Surprisingly, the activation of p70 S6K is not mediated by MAPK because blocking MAPK activation by expression of the phosphatase MKP-1 did not prevent p70 S6K activation by DeltaRaf-1:ER. In conclusion, we have demonstrated that activation of p70 S6K by DeltaRaf-1:ER is mediated by a new MAPK-independent pathway. This pathway is resistant to low nanomolar concentrations of wortmannin, indicating that it does not involve membrane-bound phosphatidylinositol-trisphosphate kinase activation.
Generation of diffraction-free beams for applications in optical microlithography (1997)

A new concept based on a Fabry–Pérot interferometer for the generation of nondiffracting Bessel beams is described and proposed for potential applications in microlithography such as the fabrication of small isolated patterns. It was experimentally demonstrated that the depth of focus can be increased by a factor of about 2, and simultaneously the transverse resolution improved by a factor of 1.6, when using this technique to image contact holes. The properties of simultaneous imaging of two contact holes were also investigated. It was shown experimentally that, even in the most critical case (when the first diffraction rings overlap), undesirable interference effects between the adjacent contact holes can be eliminated by means of a phase shifting technique.
Peptide antisense nanoparticles (2008)

We have designed a heterofunctionalized nanoparticle conjugate consisting of a 13-nm gold nanoparticle (Au NP) containing both antisense oligonucleotides and synthetic peptides. The synthesis of this conjugate is accomplished by mixing thiolated oligonucleotides and cysteine-terminated peptides with gold nanoparticles in the presence of salt, which screens interactions between biomolecules, yielding a densely functionalized nanomaterial. By controlling the stoichiometry of the components in solution, we can control the surface loading of each biomolecule. The conjugates are prepared easily and show perinuclear localization and an enhanced gene regulation activity when tested in a cellular model. This heterofunctionalized structure represents a new strategy for preparing nanomaterials with potential therapeutic applications.
A federated architecture for information management (1985)

An approach to the coordinated sharing and interchange of computerized information is described emphasizing partial, controlled sharing among autonomous databases. Office information systems provide a particularly appropriate context for this type of information sharing and exchange. A federated database architecture is described in which a collection of independent database systems are united into a loosely coupled federation in order to share and exchange information. A federation consists of components (of which there may be any number) and a single federal dictionary. The components represent individual users, applications, workstations, or other components in an office information system. The federal dictionary is a specialized component that maintains the topology of the federation and oversees the entry of new components. Each component in the federation controls its interactions with other components by means of an export schema and an import schema. The export schema specifies the information that a component will share with other components, while the import schema specifies the nonlocal information that a component wishes to manipulate. The federated architecture provides mechanisms for sharing data, for sharing transactions (via message types) for combining information from several components, and for coordinating activities among autonomous components (via negotiation). A prototype implementation of the federated database mechanism is currently operational on an experimental basis.
Designer DNA-Binding Drugs: The Crystal Structure of a Meta-Hydroxy Analogue of Hoechst 33258 Bound to d(CGCGAATTCGCG)2 (1996)

An analogue of the DNA binding compound Hoechst 33258, which has the para hydroxyl group altered to be at the meta position, together with the replacement of one benzimidazole group by pyridylimidazole, has been cocrystallized with the dodecanucleotide sequence d(CGCGAATTCGCG)2. The X-ray structure has been determined at 2.2 A resolution and refined to an R factor of 20.1%. The ligand binds in the minor groove at the sequence 5'-AATTC with the bulky piperazine group extending over the CxG base pair. This binding is stabilised by hydrogen bonding and numerous close van der Waals contacts to the surface of the groove walls. The meta-hydroxyl group was found in two distinct orientations, neither of which participates in direct hydrogen bonds to the exocyclic amino group of a guanine base. The conformation of the drug differs from that found previously in other X-ray structures of Hoechst 33258-DNA complexes. There is significant variation between the minor groove widths in the complexes of Hoechst 33258 and the meta-hydroxyl derivative as a result of these conformational differences. Reasons are discussed for the inability of this derivative to actively recognise guanine.
Multimedia streaming via TCP (2008)

TCP is widely used in commercial multimedia streaming systems, with recent measurement studies indicating that a significant fraction of Internet streaming media is currently delivered over HTTP/TCP. These observations motivate us to develop analytic performance models to systematically investigate the performance of TCP for both live and stored-media streaming. We validate our models via ns simulations and experiments conducted over the Internet. Our models provide guidelines indicating the circumstances under which TCP streaming leads to satisfactory performance, showing, for example, that TCP generally provides good streaming performance when the achievable TCP throughput is roughly twice the media bitrate, with only a few seconds of startup delay.
A Knockout Mouse Approach Reveals that TCTP Functions as an Essential Factor for Cell Proliferation and Survival in a Tissue- or Cell Type–specific Manner (2007)

Translationally controlled Tumor Protein (TCTP) is an evolutionally highly conserved protein which has been implicated in many cellular functions that are related to cell growth, death, and even the allergic response of the host. To address the physiological roles of TCTP, we generated TCTP knockout mice by targeted gene disruption. Heterozygous mutants appeared to be developmentally normal. However, homozygous mutants (TCTP(-/-)) were embryonic lethal. TCTP(-/-) embryos were smaller in size than the control littermates at all postimplantation stages examined. Although TCTP is widely expressed in both extraembryonic and embryonic tissues, the most prominent defect of the TCTP(-/-) embryo at embryonic stage day 5.5 (E5.5) was in its epiblast, which had a reduced number of cells compared with wild-type controls. The knockout embryos also suffered a higher incidence of apoptosis in epiblast starting about E6.5 and subsequently died around E9.5-10.5 with a severely disorganized structure. Last, we demonstrated that TCTP(-/-) and control mouse embryonic fibroblasts manifested similar proliferation activities and apoptotic sensitivities to various death stimuli. Taken together, our results suggest that despite that TCTP is widely expressed in many tissues or cell types, it appears to regulate cell proliferation and survival in a tissue- or cell type-specific manner.
Chronic low back pain: evaluation and management. (2009)

Chronic low back pain is a common problem in primary care. A history and physical examination should place patients into one of several categories: (1) nonspecific low back pain; (2) back pain associated with radiculopathy or spinal stenosis; (3) back pain referred from a nonspinal source; or (4) back pain associated with another specific spinal cause. For patients who have back pain associated with radiculopathy, spinal stenosis, or another specific spinal cause, magnetic resonance imaging or computed tomography may establish the diagnosis and guide management. Because evidence of improved outcomes is lacking, lumbar spine radiography should be delayed for at least one to two months in patients with nonspecific pain. Acetaminophen and nonsteroidal anti-inflammatory drugs are first-line medications for chronic low back pain. Tramadol, opioids, and other adjunctive medications may benefit some patients who do not respond to nonsteroidal anti-inflammatory drugs. Acupuncture, exercise therapy, multidisciplinary rehabilitation programs, massage, behavior therapy, and spinal manipulation are effective in certain clinical situations. Patients with radicular symptoms may benefit from epidural steroid injections, but studies have produced mixed results. Most patients with chronic low back pain will not benefit from surgery. A surgical evaluation may be considered for select patients with functional disabilities or refractory pain despite multiple nonsurgical treatments.
Quantum annealing of the random-field Ising model by transverse ferromagnetic interactions (2007)

We introduce transverse ferromagnetic interactions, in addition to a simple transverse field, to accelerate the convergence of quantum annealing of the random-field Ising model. The conventional approach using only the transverse-field term is known to be plagued by slow convergence when the true ground state has strong ferromagnetic characteristics for the random-field Ising model. The transverse ferromagnetic interactions are shown to improve the performance significantly in such cases. This conclusion is drawn from the analyses of the energy eigenvalues of instantaneous stationary states as well as by the very fast algorithm of Bethe-type mean-field annealing adopted to quantum systems. The present study highlights the importance of a flexible choice of the type of quantum fluctuations to achieve the best possible performance in quantum annealing. The existence of such flexibility is an outstanding advantage of quantum annealing over simulated annealing.
Developmental regulation of transcription of a novel prespore-specific gene (Dp87) in Dictyostelium discoideum (1993)

The Dp87 is a novel prespore specific gene of Dictyostelium discoideum which has a long open reading frame of 555 amino acids. The entire amino acid sequence had low but significant homology to the spore coat proteins, SP96 and SP70, of this organism. When a chimeric gene, containing a 1380 bp of the 5' upstream region of this gene fused with CAT gene, as reporter, was introduced into cells of this organism, it was expressed only in prespore cells of the slug. Transformation experiments, using chimeric genes, containing a series of 5' deletions of the upstream region, showed that -447 bp to -357 bp is an important cis-acting regulatory region for transcription. A nuclear factor(s) that specifically bind to this cis-acting region were detected from slug cell nuclei. Transformation experiments using a chimeric gene consisting of the 5' region between -666 bp and +149 bp of this gene, a beta-galactosidase reporter and an actin 8 terminator, showed that the reporter gene was expressed as early as in aggregation streams, indicating that Dp87 become transcribed a few hours earlier than the other prespore-specific genes so far reported. This was confirmed by northern hybridization detected using an image plate analyzer. The fact that cells expressing Dp87 appeared at random in aggregation streams gives solid support to the idea that position-independent differentiation of prespore and prestalk cells, followed by their sorting, brings about pattern formation in this organism.
Morphology, growth, chromosomal pattern and fibrinolytic activity of two new human neuroblastoma cell lines. (1977)

Neuroblastoma cell lines LA-N-1 and LA-N-2 were extablished from neuroblastoma cells in the bone marrow and in the primary tumor, respectively, of two children with metastatic neuroblastoma. Morphology, growth in vitro and in athymic nude mice, chromosomal patter, and fibrinolytic activity of these cell lines and of previously extablished human neuroblastoma cell lines IMR-32, SK-N-MC, and SK-N-SH were compared. Most LA-N-1 cells were tear-drop shaped, small cells with processes; they tended to grow in clusters. LA-N-2 was comprised of elongated cells and small round cells, the latter growing in dense clumps on the former. Electron microscopy revealed numerous cytoplasmic dense cores in many LA-N-1 cells but none in LA-N-2 CELLS. During logarithmic growth in vitro, doubling times for LA-N-1, LA-N-2, SK-N-MC, SK-N-SH, and IMR-32 cells were 32,56, 23, 36, and 26 hr, respectively. Cells of all lines formed colonies in soft agar, and, after variable latency periods, LA-N-1, LA-N-2, SK-N-MC, and IMR-32 cells formed tumors in athymic nude mice. The marker chromosome(s) characteristic of each cell line was present in more than 90% of cells of given line. Significant plasminogen-dependent fibrinolytic activity was present in cells of all lines. These studies indicate that LA-N-1 and LA-N-2 cells arose from single but different aberrant progenitor cells and that they have properties of neuroblastoma cells. They also demonstrate that cell lines derived from human neuroblastomas are heterogenous as are the tumors in children.
Narrow line semiconductor laser using fibre grating (1991)

A narrow linewidth, low chirp, wavelength selectable, packaged alternative to current DFB structures has been developed which employs a fibre reflection grating incorporated in the fibre pigtail. The wavelength of the packaged device can be determined by the appropriate choice of fibre grating coupled to the antireflection coated facet of a 1.55μm BH laser. Linewidths of less than 50 kHz, sidemode suppression of more than 30 dB and chirp when modulated at 1.2 Gbit/s of &lt;0.5 MHz have been demonstrated.
Molecular Cloning and Characterization of EndoGlyx-1, an EMILIN-like Multisubunit Glycoprotein of Vascular Endothelium (2001)

EndoGlyx-1, the antigen identified with the monoclonal antibody H572, is a pan-endothelial human cell surface glycoprotein complex composed of four different disulfide-bonded protein species with an apparent molecular mass of approximately 500 kDa. Here, we report the purification and peptide analysis of two EndoGlyx-1 subunits, p125 and p140, and the identification of a common, full-length cDNA with an open reading frame of 2847 base pairs. The EndoGlyx-1 cDNA encodes a protein of 949 amino acids with a predicted molecular mass of 105 kDa, found as an entry for an unnamed protein with unknown function in public data bases. A short sequence tag matching the cDNA of this gene was independently discovered by serial analysis of gene expression profiling as a pan-endothelial marker, PEM87. Bioinformatic evaluation classifies EndoGlyx-1 as an EMILIN-like protein composed of a signal sequence, an N-terminal EMI domain, and a C-terminal C1q-like domain, separated from each other by a central coiled-coil-rich region. Biochemical and carbohydrate analysis revealed that p125, p140, and the two additional EndoGlyx-1 subunits, p110 and p200, are exposed on the cell surface. The three smaller subunits show a similar pattern of N-linked and O-linked carbohydrates, as shown by enzyme digestion. Because the two globular domains of EndoGlyx-1 p125/p140 show structural features shared by EMILIN-1 and Multimerin, two oligomerizing glycoproteins implicated in cell-matrix adhesion and hemostasis, it will be of interest to explore similar functions for EndoGlyx-1 in human vascular endothelium.
MicroRNA profiling in ischemic injury of the gracilis muscle in rats (2010)

This study revealed 3 upregulated miRNAs in the gracilis muscle following ischemic injury and identified 4 potential target genes of miR-21 by examining miRNAs and mRNAs expression patterns in a time-course fashion using a combined approach with prediction algorithms and a whole genome expression array experiment.
Process Variation Aware Timing Optimization through Transistor Sizing in Dynamic CMOS Logic (2008)

A major challenge in the design of microprocessor circuits is transistor sizing in dynamic CMOS logic due to increased number of channel-connected transistors on various paths of the design, and increased magnitude of process variations in the nanometer process. This paper proposes a process variation aware transistor sizing algorithm for dynamic CMOS logic. The efficiency of this algorithm is illustrated first by a 2-b weighted binary-to-thermometric converter, of which the critical path delay was optimized from 355 to 157 ps which accounts for a 55.77% delay improvement, and the delay uncertainty due to process variation was optimized by 60.75%. A 4-b unity weight binary-to-thermometric converter was also optimized, of which the critical path delay was reduced from 152 to 103 ps which accounts for a 32.23% delay improvement, and delay uncertainty was optimized by 63.6%. Applying the proposed timing optimization algorithm to a mixed-dynamic-static CMOS 64-bit adder, the critical path delay and the power-delay-product were optimized to 632 ps and 84.17 pJ, respectively.
Randomized trial of three chemotherapy regimens and two radiotherapy regimens in postoperative treatment of malignant glioma (1989)

Within 3 weeks of definitive surgery, 571 adult patients with histologically confirmed, supratentorial malignant gliomas were randomly assigned to receive one of three chemotherapy regimens: BCNU (1,3-bis(2-chloroethyl)-1-nitrosourea) alone, alternating courses (every 8 weeks) of BCNU and procarbazine, or BCNU plus hydroxyurea alternating with procarbazine plus VM-26 (epipodophyllotoxin). Patients accrued in 1980 and 1981 were to receive 6020 rads of whole-brain radiotherapy concurrent with the first course of chemotherapy. Patients accrued in 1982 and 1983 were randomly assigned to receive either whole-brain irradiation as above, or 4300 rads of whole-brain radiotherapy plus 1720 rads coned down to to the tumor volume. The data were analyzed for the total randomized population and separately for the 510 patients, termed the "Valid Study Group (VSG)," who met protocol eligibility specifications (including central pathology review), 80% of whom had glioblastoma multiforme. The median survival times from time of randomization for the three chemotherapy groups of the VSG ranged from 11.3 to 13.8 months, and 29% to 37% of the patients survived for 18 months (life-table estimate); the differences between these groups were not statistically significant. Survival differences between the radiotherapy groups were small and not statistically significant. It is concluded that, for malignant glioma, giving part of the radiotherapy by coned-down boost is as effective as full whole-brain irradiation, and that multiple-drug chemotherapy as outlined in this protocol conferred no significant survival advantage over BCNU alone.