gebhart/patrepeval huggingface dataset:
In vitro read-through polysome/ribosome display of full-length protein ORF and it's applications (2005)

Combination of nonsense suppression and protein-ribosome-mRNA (PRM) complexation techniques leads to a new strategy "read-through polysome/ribosome display", which is designed to display full-length open reading frame (ORF) domain of the protein on the natural mRNA templates. The optimised conditions are to use the anticodon-adjusted tRNA for Leu as a nonsense suppressor in a reconstituted translation system containing diminished amounts of release factors (RFs). When applied to pseudo-natural mRNAs of Escherichia coli dihydrofolate reductase (E. coli DHFR), the input mRNA was recovered as a polysome complex displaying full-length DHFR.
A cold electron bolometer using a two-dimensional electron gas absorber (2005)

We describe a new type of Terahertz (THz) detector using a two-dimensional electron gas (2DEG) hot electron bolometer where the temperature of the electrons read out using superconducting tunnel junctions connected to the 2DEG (similar to a SINIS detector). We present measurements of the electron-phonon thermal conductivity in a high-mobility GaAs/AlGaAs 2DEG sample at 4.2 K as a function of electron temperature and magnetic field. From these measurements we estimate the sensitivity of an element in a filled array of S-2DEG-S detectors at 4.2 K to be approximately 10-14 W/[square root]Hz with a response time of 1 ns. Using measured parameters for the normal resistance of the S-2DEG-S contacts, we calculate the effect of using a voltage bias to cool the electrons in the absorber significantly from a 300 mK base temperature. In this configuration, these detectors can achieve sufficient sensitivity to detect individual THz photons.
High-quality nonalloyed rhodium-based ohmic contacts to p-type GaN (2003)

We report on a promising Rh-based scheme for high-quality ohmic contacts to surface-treated p-GaN:Mg (4×1017 cm−3). It is shown that the two-step surface-treated Rh contacts (10 nm) produce a specific contact resistance of 1.7×10−5 Ω cm2. It is also shown that the two-step treated Rh/Ni (5/5 nm) and Rh/Au (5/5 nm) contacts yield 6.0×10−5 and 9.3×10−6 Ω cm2, respectively. Based on the current–voltage measurement, x-ray photoemission spectroscopy, and Auger electron spectroscopy results, the mechanisms for the formation of the nonalloyed Rh-based ohmic contacts is described and discussed.
Parthenogenetic dopamine neurons from primate embryonic stem cells restore function in experimental Parkinson's disease (2008)

The identity and functional potential of dopamine neurons derived in vitro from embryonic stem cells are critical for the development of a stem cell-based replacement therapy for Parkinson's disease. Using a parthenogenetic primate embryonic stem cell line, we have generated dopamine neurons that display persistent expression of midbrain regional and cell-specific transcription factors, which establish their proper identity and allow for their survival. We show here that transplantation of parthenogenetic dopamine neurons restores motor function in hemi-parkinsonian, 6-hydroxy-dopamine-lesioned rats. Exposure to Wnt5a and fibroblast growth factors (FGF) 20 and 2 at the final stage of in vitro differentiation enhanced the survival of dopamine neurons and, correspondingly, the extent of motor recovery of transplanted animals. Importantly for future development of clinical applications, dopamine neurons were post-mitotic at the time of transplantation and there was no tumour formation. These data provide proof for the concept that parthenogenetic stem cells are a suitable source of functional neurons for therapeutic applications.
A theoretical study of the Curtius rearrangement. The electronic structures and interconversions of the CHNO species (1977)

The thermal and photochemical decomposition of formyl azide in the Curtius rearrangement has been studied by means of RHF–LCAO–MO–SCF calculations augmented by CI. The lower electronic states of carbonyl azides, carbonyl nitrenes, isocyanates, cyanates, oxazirenes, nitrile oxides (fulminates), and isofulminates are discussed on the basis of the results for formyl azide and the corresponding isomers of formula CHNO. The discovery of two nearly degenerate states of A′′ symmetry for formyl azide which may channel decomposition products directly to both isocyanates and carbonyl nitrenes explains some puzzling features of the photolytic Curtius rearrangement. The interconvertibility of the CHNO isomers (and the RCNO isomers) is discussed in terms of the energetics and intended correlations of the accessible electronic states of these species.
Wasserlösliche Metall‐Komplexe des sulfonierten Triphenylphosphans TPPTS: Reindarstellung und Verwendung für Katalysen (1990)

Durch Gel‐Permeations‐Chromatographie gelang nun die Isolierung von reinem TPPTS 1 und daraus hergestellten Komplexen [L x M y (TPPTS) z ·(H 2 O) 3z ], die für die Homogenkatalyse von großer Bedeutung sind, da sie aufgrund ihrer Wasserlöslichkeit leicht von den hydrophoben organischen Produkten abgetrennt werden können. Die Ladungsanhäufung in der Molekülperipherie dürfte Ursache dafür sein, daß TPPTS‐Komplexe, z. B. 2 , häufig eine niedrigere Koordinationszahl aufweisen als ihre Triphenylphosphan‐Analoga. magnified image
Reservoir Prediction Utilising AVO Walkaway VSP Data to Calibrate Surface Seismic Gathers, a Case Study in Indonesia (1993)

In prediction of reservoir properties using seismic data, use is frequently made of AVO techniques. However, such techniques may not always be successful. Hence a new technique has been devised — based on recording a subsurface AVO response in the well. Recording is achieved from five triaxial geophone shuttles at 15 m intervals — ideally one wavelength (of the predicted dominant source frequency) above the target. The source (two 150 cubic-inch Sleeve Guns) was deployed from the marine vessel’s boom and moving in a line such that shot spacing is as close as possible to the surface seismic offsets. The line might extend 3 km to each side the well. Processing of the AVO walkaway data takes place in three steps: data orientation; separation of the down and up P-wavefields; and deconvolution (using the downgoing P-wavefield to deconvolve the upgoing P-wavefield) to remove propagation effects. The surface seismic data (in this case a 3-D data set) are processed (gathered) and put through a rigorous 12-stage signal processing sequence. The AVOWSP and the surface gathers are then carefully tied to the zero-offset VSP. After application of the Offset Dependent Gain Function the data are solved for P-wave reflection amplitude (at angle 0°) and the gradient. Those results can then be mapped and contoured — to identify anomalous areas, at known sites (wells) and elsewhere. Additional refinement is continuously being sought, and is welcome.
ChemInform Abstract: A Combinatorial Polymer Library Approach Yields Insight into Nonviral Gene Delivery (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Targeted Capture of Chinese Hamster Ovary Host Cell Proteins: Peptide Ligand Discovery (2019)

The growing integration of quality-by-design (QbD) concepts in biomanufacturing calls for a detailed and quantitative knowledge of the profile of impurities and their impact on the product safety and efficacy. Particularly valuable is the determination of the residual level of host cell proteins (HCPs) secreted, together with the product of interest, by the recombinant cells utilized for production. Though often referred to as a single impurity, HCPs comprise a variety of species with diverse abundance, size, function, and composition. The clearance of these impurities is a complex issue due to their cell line to cell line, product-to-product, and batch-to-batch variations. Improvements in HCP monitoring through proteomic-based methods have led to identification of a subset of "problematic" HCPs that are particularly challenging to remove, both at the product capture and product polishing steps, and compromise product stability and safety even at trace concentrations. This paper describes the development of synthetic peptide ligands capable of capturing a broad spectrum of Chinese hamster ovary (CHO) HCPs with a combination of peptide species that allow for advanced mixed-mode binding. Solid phase peptide libraries were screened for identification and characterization of peptides that capture CHO HCPs while showing minimal binding of human IgG, utilized here as a model product. Tetrameric and hexameric ligands featuring either multipolar or hydrophobic/positive amino acid compositions were found to be the most effective. Tetrameric multipolar ligands exhibited the highest targeted binding ratio (ratio of HCP clearance over IgG loss), more than double that of commercial mixed-mode and anion exchange resins utilized by industry for IgG polishing. All peptide resins tested showed preferential binding to HCPs compared to IgG, indicating potential uses in flow-through mode or weak-partitioning-mode chromatography.
Design and Synthesis of Potent and Selective BACE-1 Inhibitors (2010)

Highly potent BACE-1 protease inhibitors have been developed from an inhibitors containing a hydroxyethylene (HE) core displaying aryloxymethyl or benzyloxymethyl P1 side chain and a methoxy P1' side chain. The target molecules were synthesized in good overall yields from chiral carbohydrate starting materials. The inhibitors show high BACE-1 potency and good selectivity against cathepsin D, where the most potent inhibitor furnishes BACE-1 K(i) << 1 nM and displays >1000-fold selectivity over cathepsin D.
Single-cell mechanical analysis and tension quantification via electrodeformation relaxation (2021)

The mechanical behavior and cortical tension of single cells are analyzed using electrodeformation relaxation. Four types of cells, namely, MCF-10A, MCF-7, MDA-MB-231, and GBM, are studied, with pulse durations ranging from 0.01 to 10 s. Mechanical response in the long-pulse regime is characterized by a power-law behavior, consistent with soft glassy rheology resulting from unbinding events within the cortex network. In the subsecond short-pulse regime, a single timescale well describes the process and indicates the naive tensioned (prestressed) state of the cortex with minimal force-induced alteration. A mathematical model is employed and the simple ellipsoidal geometry allows for use of an analytical solution to extract the cortical tension. At the shortest pulse of 0.01 s, tensions for all four cell types are on the order of 10^{-2} N/m.
Lowering the error floors of irregular high-rate LDPC codes by graph conditioning (2005)

This paper applies a graph conditioning algorithm, called the approximate cycle extrinsic message degree (ACE) algorithm, to design high-rate (R/spl ges/1/2) irregular LDPC codes. The algorithm was shown to be an effective tool to lower the error floors of lower-rate (R/spl les/1/2) LDPC codes. However, for high-rate LDPC codes, due to the large number of degree-2 variable nodes in the optimal degree distribution, the error floor is high and it is more difficult to condition the graph. By constraining the number of degree-2 nodes, we found that the ACE algorithm can dramatically lower the error floor with little compromise of the threshold. A rate-3/4, length-10688 LDPC code is proposed whose AWGN channel performance is within 0.67 dB of the Shannon limit at BER=10/sup -5/ and its error floor is lower than 10/sup -7/. Compared to existing semi-regular codes which lower the floor by adopting non-optimal degree distributions, our graph-conditioned codes provides 0.38 dB of performance improvement at BER=10/sup -5/. The same design criteria also apply well to medium-length LDPC code design and are suitable for rate-compatible applications using the information-nulling technique. The rate-compatible scheme has consistently good thresholds and low error floors for 1/2/spl les/ R/spl les/ 8/9.
Multi-phase magnetic component and method of forming (2023)

A magnetic component including first and second regions, and a method of varying the magnetization values in different regions of the magnetic component are disclosed. The first and the second regions are characterized by a nitrogen content that is different from each other. At least one of the first region and the second region is partially-magnetic and has a nitrogen content in a range from about 0.1 weight % to about 0.4 weight % of that region. A concentration of carbon, if present, of both the first and second regions is less than about 0.05 weight % of the respective regions.
Supplementary Figure 3 from Combination Epigenetic Therapy in Advanced Breast Cancer with 5-Azacitidine and Entinostat: A Phase II National Cancer Institute/Stand Up to Cancer Study (2023)

&lt;p&gt;Gene list and biological pathways of significant differentially expressed genes in hormone-resistant breast cancer volcano plot.&lt;/p&gt;
Recent advances in the chemistry of aromatic cyclic oligomers (1992)

Abstract Development of an efficient and convenient means for preparation of aromatic cyclic oligomeric carbonates has made these materials available for a wide range of polymerization and processing studies. Building on the workbased on bisphenol A cyclics, recent efforts have concentrated on the preparation of new cyclics which afford polymers with properties substantially different from bisphenol A polycarbonate. Cyclic systems have been developed which lead to polycarbonates with improved solvent resistance, either through cross‐linking or via crystallization. Polycarbonates with both high or low glass transition temperatures have also been achieved.
Thick Silicon Double-Sided Strip Detectors for Low-Energy Small-Animal SPECT (2009)

This work presents characterization studies of thick silicon double-sided strip detectors for a high-resolution small-animal SPECT. The dimension of these detectors is 60.4 mm × 60.4 mm × 1 mm. There are 1024 strips on each side that give the coordinates of the photon interaction, with each strip processed by a separate ASIC channel. Our measurement shows that intrinsic spatial resolution equivalent to the 59 μm strip pitch is attainable. Good trigger uniformity can be achieved by proper setting of a 4-bit DAC in each ASIC channel to remove trigger threshold variations. This is particularly important for triggering at low energies. The thick silicon DSSD (Double-sided strip detector) shows high potential for small-animal SPECT.
Arrayed microcolumns for high throughput lithography (2005)

The small size of the microcolumn opens the possibility for arrayed operation on a scale commensurate. An arrayed microcolumn test-bed system has been developed for high throughput applications. The arrayed microcolumns based on of Single Column Module (SCM), and Wafer-Scale Column Module (WCM) concepts have been fabricated and successfully demonstrated. Low energy microcolumn lithography has been operated in the energy range from 100 eV to 1 keV for the generation of nano patterns. Probe beam current at the sample was measured about 2 nA at a total beam current of ~0.4 mA. The magnitude of probe beam current is strong enough for the low energy lithography. The thin layers of PMMA resist have been employed. The results of nano-patterning by low energy microcolumn lithography will be discussed.
ChemInform Abstract: (Dipropylphenoxy)phenylacetic Acids: A New Generation of Nonpeptide Angiotensin II Receptor Antagonists. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Supplementary Tables S1-S3 and Supplementary Figures S1-S6 from Selective Inhibition of HDAC1 and HDAC2 as a Potential Therapeutic Option for B-ALL (2023)

&lt;p&gt;Supplementary Tables S1-S3 and Supplementary Figures S1-S6. Table S1 - EC50 values for B-cell malignancies treated with HDAC inhibitors of varying isoform selectivity Table S2 - EC50 values for B-ALL cell line treated with a panel of HDAC inhibitors Table S3 - statistics for cell growth assay in Figure 3 Figure S1 - In vitro survival and PD for B-ALL cells treated with LAQ824 Figure S2 - Western analyses of B-ALL cells treated with MS275 Figure S3 - Western blots, cell growth and cell cycle analysis for B-ALL cells transduced with HDAC1,2, or 3 specific shRNA Figure S4 - Western analyses, cell growth and survival of B-ALL cell treated with Merck60 Figure S5 - Survival and western blots for B-ALL cells treated with HDACi with an apoptosis inhibitor. Figure S6 - Western blots to show DNA damage caused by HDACi or doxorubicin in Merck60 insensitive multiple myeloma cell lines.&lt;/p&gt;
Enantioselective Formal Synthesis of Uleine Alkaloids from Phenylglycinol‐Derived Bicyclic Lactams. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Prehospital Emergency Inguinal Clamp Controls Hemorrhage in Cadaver Model (2013)

Background: The Combat Ready Clamp is indicated to stop difficult inguinal bleeding on the battlefield, the most common type of junctional bleeding and now the most common cause of preventable battlefield death. The purpose of the present study is to report the data of clamp development to help appliers use it correctly. Methods: Wake Forest University investigators used a cadaver model to test the clamp's ability to control hemorrhage. Ten fresh cadavers were made to simulate inguinal and popliteal wound bleeding. Blood simulant was pumped to quantify device effectiveness in testing. Points of application included proximal pressure point control of popliteal, inguinal, and bilateral bleeding. Results: Clamp use promptly controlled pulsing arterial hemorrhages from inguinal, popliteal, and bilateral wounds. The device, when placed on the common iliac artery, stopped all ipsilateral distal bleeding. Conclusions: The evidence of how the clamp works in the cadaver model showed that clamp use can plausibly be tailored to control inguinal hemorrhage from one wound, control two ipsilateral wounds with hemorrhage from one artery (e.g., common iliac artery), and control bilateral inguinal wounds (compression of the origins of bilateral common iliac arteries).
Contact sensitivity responses in mice infected with Trypanosoma cruzi (1978)

Mechanisms of depression of contact sensitivity responses in C57BL/10 mice infected with Trypanosoma cruzi were studied. Cellular involvement during sensitization with oxazolone was investigated in mice acutely infected with T. cruzi. Contact sensitivity was not expressed in mice during the latter stages of the acute infection. Spleen cells from sensitized, infected mice which were unable to respond to oxazolone could confer contact sensitivity upon normal syngenic mice as effectively as spleen cells from uninfected, sensitized donors. The ability of mice infected with T. cruzi to respond to an eliciting dose of oxazolone was significantly improved when macrophages from normal syngenic donors were administered to them at the time of skin test. When either normal or infected mice were used as recipients of lymphocytes from sensitized donors, the normal mice responded significantly better than did infected mice after administration of an eliciting dose of oxazolone. An increase in pyroninophilic cells was observed in draining lymph nodes after application of a sensitizing dose of oxaxolone to the ears of either normal or acutely infected mice. These results indicate that suppression of contact sensitivity during acute T. cruzi infection is directed toward the efferent arm rather than the afferent arm of the response.
Brachytherapy with Intratumoral Injections of Radiometal-Labeled Polymers That Thermoresponsively Self-Aggregate in Tumor Tissues (2017)

Brachytherapy is a type of radiotherapy wherein titanium capsules containing therapeutic radioisotopes are implanted within tumor tissues, enabling high-dose radioirradiation to tumor tissues around the seeds. Although marked therapeutic effects have been demonstrated, brachytherapy needs a complicated implantation technique under general anesthesia and the seeds could migrate to other organs. The aim of this study was to establish a novel brachytherapy using biocompatible, injectable thermoresponsive polymers (polyoxazoline [POZ]) labeled with <sup>90</sup>Y, which can self-aggregate above a specific transition temperature (Tt), resulting in long-term intratumoral retention of radioactivity and therapeutic effect. Therefore, we evaluated the tumor retention of radiolabeled POZ derivatives and their therapeutic effects. <b>Methods:</b> Using oxazoline derivatives with ethyl (Et), isopropyl (Isp), and propyl (Pr) side chains, we synthesized EtPOZ, IspPOZ, Isp-PrPOZ (heteropolymer), and PrPOZ and measured their characteristic Tts. The intratumoral retention of <sup>111</sup>In-labeled POZ was evaluated until 7 d after injection in nude mice bearing PC-3 human prostate cancer. The intratumoral localization of <sup>111</sup>In-labeled POZ derivatives was investigated by an autoradiographic study. Furthermore, a therapeutic study using <sup>90</sup>Y-labeled Isp-PrPOZ was performed, and tumor growth and survival rate were evaluated. <b>Results:</b> The Tts of EtPOZ, IspPOZ, Isp-PrPOZ, and PrPOZ (∼20 kDa) were greater than 70°C, 34°C, 25°C, and 19°C, respectively. In the intratumoral injection study, Isp-PrPOZ and PrPOZ (2,000 μM) with Tts lower than tumor temperature (33.5°C under anesthesia) showed a significantly higher retention of radioactivity at 1 d after injection (73.6% and 73.9%, respectively) than EtPOZ (5.6%) and IspPOZ (15.8%). Even at low injected dose (100 μM), Isp-PrPOZ exhibited high retention (68.3% at 1 d). The high level of radioactivity of Isp-PrPOZ was retained in the tumor 7 d after injection (69.5%). The autoradiographic study demonstrated that the radioactivity of <sup>111</sup>In-labeled Isp-PrPOZ and PrPOZ was localized in a small area. In the therapeutic study using <sup>90</sup>Y-labeled Isp-PrPOZ, significant suppression of tumor growth and prolonged survival rate were achieved in an injection dose-dependent manner compared with that observed for the vehicle-injected group and nonradioactive Isp-PrPOZ-injected group. <b>Conclusion:</b> The injectable <sup>90</sup>Y-labeled Isp-PrPOZ was retained for a prolonged period within tumor tissues via self-aggregation and exhibited marked therapeutic effect, suggesting its usefulness for brachytherapy.
TIM3 Mediates T Cell Exhaustion during Mycobacterium tuberculosis Infection (2016)

While T cell immunity initially limits Mycobacterium tuberculosis infection, why T cell immunity fails to sterilize the infection and allows recrudescence is not clear. One hypothesis is that T cell exhaustion impairs immunity and is detrimental to the outcome of M. tuberculosis infection. Here we provide functional evidence for the development T cell exhaustion during chronic TB. Second, we evaluate the role of the inhibitory receptor T cell immunoglobulin and mucin domain-containing-3 (TIM3) during chronic M. tuberculosis infection. We find that TIM3 expressing T cells accumulate during chronic infection, co-express other inhibitory receptors including PD1, produce less IL-2 and TNF but more IL-10, and are functionally exhausted. Finally, we show that TIM3 blockade restores T cell function and improves bacterial control, particularly in chronically infected susceptible mice. These data show that T cell immunity is suboptimal during chronic M. tuberculosis infection due to T cell exhaustion. Moreover, in chronically infected mice, treatment with anti-TIM3 mAb is an effective therapeutic strategy against tuberculosis.