gebhart/patrepeval huggingface dataset:
The GRB family of SH2 domain proteins (1994)

The cloning of SH2 domain proteins based on their binding to growth factor receptors is a powerful technique to elucidate new signaling pathways. In some cases the function of these proteins has been quickly ascertained while in others the answers still elude us. However the major power of the technique is its ability to identify novel signaling cascades that can emanate from tyrosine kinases. The challenge is to define the nature of these signaling cascades.
Assembly and movement of a plant virus carrying a green fluorescent protein overcoat. (1996)

Potato virus X (PVX) is a filamentous plant virus infecting many members of the family Solanaceae. A modified form of PVX, PVX.GFP-CP which expressed a chimeric gene encoding a fusion between the 27-kDa Aequorea victoria green fluorescent protein and the amino terminus of the 25-kDa PVX coat protein, assembled into virions and moved both locally and systemically. The PVX.GFP-CP virions were over twice the diameter of wild-type PVX virions. Assembly of PVX.GFP-CP virions required the presence of free coat protein subunits in addition to the fusion protein subunits. PVX.GFP-CP virions accumulated as paracrystalline arrays in infected cells similar to those seen in cells infected with wild-type PVX The formation of virions carrying large superficial fusions illustrates a novel approach for production of high levels of foreign proteins in plants. Aggregates of PVX.GFP-CP particles were fluorescent, emitting green light when excited with ultraviolet light and could be imaged using confocal laser scanning microscopy. The detection of virus particles in infected tissue demonstrates the potential of fusions between the green fluorescent protein and virus coat protein for the non-invasive study of virus multiplication and spread.
A Generalized Memory Polynomial Model for Digital Predistortion of RF Power Amplifiers (2006)

Conventional radio-frequency (RF) power amplifiers operating with wideband signals, such as wideband code-division multiple access (WCDMA) in the Universal Mobile Telecommunications System (UMTS) must be backed off considerably from their peak power level in order to control out-of-band spurious emissions, also known as “spectral regrowth.” Adapting these amplifiers to wideband operation therefore entails larger size and higher cost than would otherwise be required for the same power output. An alternative solution, which is gaining widespread popularity, is to employ digital baseband predistortion ahead of the amplifier to compensate for the nonlinearity effects, hence allowing it to run closer to its maximum output power while maintaining low spectral regrowth. Recent improvements to the technique have included memory effects in the predistortion model, which are essential as the bandwidth increases. In this paper, we relate the general Volterra representation to the classical Wiener, Hammerstein, Wiener–Hammerstein, and parallel Wiener structures, and go on to describe some state-of-the-art predistortion models based on memory polynomials. We then propose a new generalized memory polynomial that achieves the best performance to date, as demonstrated herein with experimental results obtained from a testbed using an actual 30-W, 2-GHz power amplifier.
Alternative pathway complement activation induces proinflammatory activity in human proximal tubular epithelial cells (1997)

In vitro complement activation on the proximal tubular cell surface triggers the generation of proinflammatory mediators, which may potentially contribute to the pathogenesis of tubulointerstitial injury.
Tumor Imaging Using a Picomolar Affinity HER2 Binding Affibody Molecule (2006)

The detection of cell-bound proteins that are produced due to aberrant gene expression in malignant tumors can provide important diagnostic information influencing patient management. The use of small radiolabeled targeting proteins would enable high-contrast radionuclide imaging of cancers expressing such antigens if adequate binding affinity and specificity could be provided. Here, we describe a HER2-specific 6 kDa Affibody molecule (hereinafter denoted Affibody molecule) with 22 pmol/L affinity that can be used for the visualization of HER2 expression in tumors in vivo using gamma camera. A library for affinity maturation was constructed by re-randomization of relevant positions identified after the alignment of first-generation variants of nanomolar affinity (50 nmol/L). One selected Affibody molecule, Z(HER2:342) showed a >2,200-fold increase in affinity achieved through a single-library affinity maturation step. When radioiodinated, the affinity-matured Affibody molecule showed clear, high-contrast visualization of HER2-expressing xenografts in mice as early as 6 hours post-injection. The tumor uptake at 4 hours post-injection was improved 4-fold (due to increased affinity) with 9% of the injected dose per gram of tissue in the tumor. Affibody molecules represent a new class of affinity molecules that can provide small sized, high affinity cancer-specific ligands, which may be well suited for tumor imaging.
Ultrafast laser-scanning time-stretch imaging at visible wavelengths (2016)

Optical time-stretch imaging enables the continuous capture of non-repetitive events in real time at a line-scan rate of tens of MHz-a distinct advantage for the ultrafast dynamics monitoring and high-throughput screening that are widely needed in biological microscopy. However, its potential is limited by the technical challenge of achieving significant pulse stretching (that is, high temporal dispersion) and low optical loss, which are the critical factors influencing imaging quality, in the visible spectrum demanded in many of these applications. We present a new pulse-stretching technique, termed free-space angular-chirp-enhanced delay (FACED), with three distinguishing features absent in the prevailing dispersive-fiber-based implementations: (1) it generates substantial, reconfigurable temporal dispersion in free space (>1 ns nm<sup>-1</sup>) with low intrinsic loss (<6 dB) at visible wavelengths; (2) its wavelength-invariant pulse-stretching operation introduces a new paradigm in time-stretch imaging, which can now be implemented both with and without spectral encoding; and (3) pulse stretching in FACED inherently provides an ultrafast all-optical laser-beam scanning mechanism at a line-scan rate of tens of MHz. Using FACED, we demonstrate not only ultrafast laser-scanning time-stretch imaging with superior bright-field image quality compared with previous work but also, for the first time, MHz fluorescence and colorized time-stretch microscopy. Our results show that this technique could enable a wider scope of applications in high-speed and high-throughput biological microscopy that were once out of reach.
How Should Remission From Depression Be Defined? The Depressed Patient’s Perspective (2006)

Patients aspire to a range of outcomes from the treatment of their depression.
MD-2 Mediates the Ability of Tetra-Acylated and Penta-Acylated Lipopolysaccharides to Antagonize Escherichia coli Lipopolysaccharide at the TLR4 Signaling Complex (2005)

We have demonstrated previously that tetra-acylated LPS derived from the oral bacterium, Porphyromonas gingivalis, and penta-acylated msbB LPS derived from a mutant strain of Escherichia coli can antagonize the ability of canonical hexa-acylated E. coli LPS to signal through the TLR4 signaling complex in human endothelial cells. Activation of the TLR4 signaling complex requires the coordinated function of LPS binding protein (LBP), CD14, MD-2, and TLR4. To elucidate the specific molecular components that mediate antagonism, we developed a recombinant human TLR4 signaling complex that displayed efficient LPS-dependent antagonism of E. coli LPS in HEK293 cells. Notably, changes in the expression levels of TLR4 in HEK293 cells modulated the efficiency of antagonism by P. gingivalis LPS. Both soluble (s) CD14 and membrane (m) CD14 supported efficient P. gingivalis LPS-dependent and msbB LPS-dependent antagonism of E. coli LPS in the recombinant TLR4 system. When cells expressing TLR4, MD-2, and mCD14 were exposed to LPS in the absence of serum-derived LBP, efficient LPS-dependent antagonism of E. coli LPS was still observed indicating that LPS-dependent antagonism occurs downstream of LBP. Experiments using immunoprecipitates of sCD14 or sMD-2 that had been pre-exposed to agonist and antagonist indicated that LPS-dependent antagonism occurs partially at sCD14 and potently at sMD-2. This study provides novel evidence that expression levels of TLR4 can modulate the efficiency of LPS-dependent antagonism. However, MD-2 represents the principal molecular component that tetra-acylated P. gingivalis LPS and penta-acylated msbB LPS use to antagonize hexa-acylated E. coli LPS at the TLR4 signaling complex.
Fibroblast Cell Behavior on Bound and Adsorbed Fibronectin onto Hyaluronan and Sulfated Hyaluronan Substrates (2005)

The effect of fibronectin protein (Fn) coating onto polysaccharide layers of hyaluronic acid (Hyal) and its sulfated derivative (HyalS) on fibroblast cell adhesion was analyzed. The Hyal or HyalS were coated and grafted on the glass substrate by a photolithographic method. The Fn coating was achieved by two different routes: the immobilization of Fn by covalent bond to the polysaccharide layers and the simple adsorption of Fn onto Hyal and HyalS surfaces. AFM, SEM, and ATR-FTIR techniques were used for the chemical and topographical characterization of the surfaces. According to AFM and SEM data, the surface topography was dependent on the method used to cover the polysaccharide layers with the protein. ATR-FTIR analysis supplied information about the rearrangement of Fn after the interaction (adsorption or binding) with the Hyal and the HyalS. The conformational changes of the Fn were minimal when it was simply adsorbed on HyalS surfaces and larger once bound, whereas on the Hyal layer the protein underwent a bigger conformational change once adsorbed and covalently grafted. Then, the biological characterization was carried out by analyzing the human diploid skin fibroblasts adhesion on these surfaces. The morphology of fibroblasts was evaluated by SEM, whereas the dynamics of fibroblasts movement were recorded by a time-lapse system. Cell variations in area, perimeter, and length were analyzed at 2, 4, and 6 h. It was found that the addition of Fn (covalently bound or merely adsorbed) was fundamental in the promotion of fibroblasts adhesion and spreading. The greatest adhesion occurred onto HyalS layers covered by the adsorbed Fn.
A vision based onboard approach for landing and position control of an autonomous multirotor UAV in GPS-denied environments (2009)

We describe our work on multirotor UAVs and focus on our method for autonomous landing and position control. The paper describes the design of our landing pad and the vision based detection algorithm that estimates the 3D-position of the UAV relative to the landing pad. A cascaded controller structure stabilizes velocity and position in the absence of GPS signals by using a dedicated optical flow sensor. Practical experiments prove the quality of our approach.
Purification and properties of dihydrothymine dehydrogenase from rat liver. (1981)

Rat liver dihydrothymine dehydrogenase, the rate-limiting enzyme of thymidine and uridine degradation, was purified to homogeneity as judged by polyacrylamide disc gel electrophoresis, sedimentation velocity, and Ultrogel ACA-34 elution profile. The enzyme has a molecular weight of 220,000 +/- 5,000 as determined by Ultrogel ACA-34 and sedimentation equilibrium The s20,w value of the enzyme was 9.2 S. The isoelectric point was at pH 5.25. The enzyme is composed of two identical subunits of an approximate molecular weight of 110,000 +/- 3,000 as determined by sodium dodecyl sulfate disc gel electrophoresis. The enzyme contains 4 mol of FAD and 3 mol of iron per mol of enzyme. Flavin released from the enzyme by boiling was identified as FAD by absorption spectra and thin layer chromatography, indicating that the enzyme is a flavometal protein. During dialysis, the enzyme was stabilized by 2-mercaptoethanol, but neither NADPH nor thymine was effective. The relative rates of reduction of pyrimidine analogues substituted at position 5 were 5-fluorouracil > 5-bromouracil > 5-diazouracil > 5-iodouracil > 5-nitrouracil, with 5-fluorouracil and 5-diazouracil 70% faster than thymine. Uracil was reduced 25% faster than thymine. The pH optimum for the forward and reverse reactions was 7.4. In the presence of NADPH, the apparent Km was 2.6 microM for thymine and 1.8 microM for uracil. Apparent Km for NADPH was 15 microM with thymine as substrate and 11 microM with uracil. In the reverse reaction, apparent Km values were 43 microM for dihydrothymine and 193 microM for dihydrouracil; apparent Km for NADP+ was 3.8 microM with dihydrothymine as substrate and 2.9 microM with dihydrouracil.
Flyways To De-Congest Data Center Networks. (2009)

Abstract – Astudyofapplicationdemandsfromaproductiondatacenterof1500serversshowsthatexceptforafewoutliers, application demandscan begenerally metbyanetwork that isslightly oversubscribed. Eliminating over-subscription is hence a needless overkill. In a significant departure from recent proposals that do so, we advocate a hybrid architecture. The base network is provisioned for the average case, is oversubscribed, and canbebuiltwith any ofthe existing networkdesigns. Totacklethehotspotsthatremain,weaddextra links on an on-demand basis. Theselinks called flywaysprovideadditional capacity whereandwhenneeded. Ourresults showthatevenafewadditional flywayssubstantially improve performance (by over 50%), as long as they are added at the right place in the network. We consider two design alternatives foradding flywaysatnegligibleadditional cost: onethat useswirelesslinks (60GHzor802.11n) andanother thatuses commodityswitchestoaddcapacityinarandomizedmanner. 1.
Palladium-catalyzed synthesis of alkynylamino nucleosides. A universal linker for nucleic acids (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPalladium-catalyzed synthesis of alkynylamino nucleosides. A universal linker for nucleic acidsFrank W. Hobbs Jr.Cite this: J. Org. Chem. 1989, 54, 14, 3420–3422Publication Date (Print):July 1, 1989Publication History Published online1 May 2002Published inissue 1 July 1989https://pubs.acs.org/doi/10.1021/jo00275a030https://doi.org/10.1021/jo00275a030research-articleACS PublicationsRequest reuse permissionsArticle Views1079Altmetric-Citations156LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
The Effects of Time Delay Spread on Portable Radio Communications Channels with Digital Modulation (1987)

Frequency-selective fading caused by multipath time delay spread degrades digital communication channels by causing intersymbol interference, thus resulting in an irreducible BER and imposing a upper limit on the data symbol rate. In this paper, a frequencyselective, slowly fading channel is studied by computer simulation. The unfiltered BPSK, QPSK, OQPSK, and MSK modulations are considered first to illustrate the physical insights and the error mechanisms. Two classes of modulation with spectral-shaping filtering are studied next to assess the tradeoff between spectral occupancy and the performance under the influence of time delay spread. The simulation is very flexible so that different channel parameters can be studied and optimized either individually or collectively. The irreducible BER averaged over fading samples with a given delay profile is used to compare different modulation/detection methods, while the cumulative distribution of short-term BER is employed to show allowable data symbol rates for given values of delay spread. It is found that both GMSK and QPSK with a raised-cosine Nyquist pulse are suitable for a TDM/TDMA digital portable communications channel.
Differential expression of S100 calcium‐binding proteins characterizes distinct clinical entities in both WHO grade II and III astrocytic tumours (2000)

The computer-assisted microscopic analysis of Feulgen-stained nuclei enabled us to identify two subgroups of astrocytomas (WHO grade II) and two subgroups of anaplastic astrocytomas (WHO grade III) with significantly distinct clinical outcomes (Decaestecker et al. Brain Pathol 1998; 8: 29-38). The astrocytomas labelled in the present study as typical (TYP-ASTs) behaved clinically like real astrocytomas while atypical astrocytomas (ATYP-ASTs) behaved similarly to anaplastic astrocytomas. The anaplastic astrocytomas that we labelled as typical (TYP-ANAs) behaved clinically like anaplastic astrocytomas while atypical ones (ATYP-ANAs) behaved like glioblastomas. In the present study, we investigate whether some biological characteristics could be evidenced across these four groups of TYP- and ATYP-ASTs and TYP- and ATYP-ANAs. The data show that the levels of expression (immunohistochemically assayed and quantitatively determined by means of computer-assisted microscopy) of vimentin, the glial fibrillary acidic protein and the platelet-derived growth factor-alpha did not differ significantly across these four groups of astrocytic tumours. The level of cell proliferation (determined by means of both the anti-proliferating cell nuclear antigen and the anti-MIB-1 antibodies; P < 0.001 to P < 0.0001) differed very significantly between the astrocytomas and anaplastic astrocytomas, but not between the typical and atypical variants identified in each group. In sharp contrast, the levels of expression of the S100A3 and S100A5 proteins differed markedly in the solid tumour tissue in relation to the astrocytic tumour types and grades. In addition, while the levels of expression of S100A6 did not change in the astrocytic tumour tissue in relation to histopathological grade, the levels of expression of this S100 protein (but not those of S100A3 and S100A5) differed markedly in the blood vessel walls according to whether these vessels originated from low- or high-grade astrocytic tumours.
TIBFIT: Trust Index Based Fault Tolerance for Arbitrary Data Faults in Sensor Networks (2005)

Since sensor data gathering is the primary functionality of sensor networks, it is important to provide a fault tolerant method for reasoning about sensed events in the face of arbitrary failures of nodes sending in the event reports. In this paper, we propose a protocol called TIBFIT to diagnose and mask arbitrary node failures in an event-driven wireless sensor network. In our system model, sensor nodes are organized into clusters with rotating cluster heads. The nodes, including the cluster head, can fail in an arbitrary manner generating missed event reports, false reports, or wrong location reports. Correct nodes are also allowed to make occasional natural errors. Each node is assigned a trust index to indicate its track record in reporting past events correctly. The cluster head analyzes the event reports using the trust index and makes event decisions. TIBFIT is analyzed and simulated using the network simulator ns-2 and its coverage evaluated with a varying number and varying intelligence of the malicious nodes. We show that once TIBFIT gathers enough system state, accurate event detection is possible even if more than 50% of the network nodes are compromised.
Convection-Enhanced Delivery of Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand with Systemic Administration of Temozolomide Prolongs Survival in an Intracranial Glioblastoma Xenograft Model (2004)

Although tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a potent activator of cell death, preferentially killing neoplastic cells over normal cells, the efficacy of TRAIL for the treatment of glioma might be limited due to cellular resistance and, importantly, poor distribution after systemic administration. TRAIL and temozolomide (TMZ) were recently shown to have a synergistic antitumor effect against U87MG glioma cells in vitro. Convection-enhanced delivery (CED) can effectively distribute TRAIL protein throughout a brain tumor mass. In this study, we evaluated CED of TRAIL, alone and in conjunction with systemic TMZ administration, for antitumor efficacy. CED of TRAIL demonstrated safe and effective distribution in both normal brain and a U87MG intracranial xenograft model. Individually, both CED of TRAIL and systemic TMZ administration prolonged survival in tumor-bearing rats. However, the combination of these two treatments was significantly more effective than either treatment alone. CED of TRAIL in conjunction with systemic TMZ treatment is a promising strategy for the treatment of malignant gliomas.
Cytomegalovirus infection in patients with solid-organ transplant. Recently reviewed immunologic response and pathogenicity mechanisms. (2007)

Cytomegalovirus (CMV) infection in immunocompromised host is an important cause of morbidity and mortality. The protective immunity against the virus is both humoral and cellular. Immunologic mechanisms in rejection as in the immune response against CMV infection are similar but there is difficult to separe as histologic and clinically independent events. At least eight different genes of CMV are homologous to human proteins related to the immune response. The potential role of these genes with homology to human genes can be at different levels. The relevance that immunodominant antigens have on the natural control of CMV infection, suggests that the future design of a vaccine directed to protecting from disease those susceptible to primary infection, in an immunocompromised state, should involve a combination of antigens that include pp65, IE1-exon 4 and gB as a recombinant proteins.
Demonstration of the longitudinal modes and aberration-correction properties of a continuous-wave dye laser with a phase-conjugate mirror (1981)

We have experimentally demonstrated a cw dye laser incorporating a phase-conjugate mirror (PCM). The mirror was generated by using four-wave mixing in sodium. The unique bandwidth and pump-probe detuning properties of such a PCM permitted the first reported demonstration of the c/4L spaced paired half-axial modes. In addition, the aberration correction ability is demonstrated.