gebhart/patrepeval huggingface dataset:
Immunity to murine breast cancer cells modified to express MUC-1, a human breast cancer antigen, in transgenic mice tolerant to human MUC-1. (2000)

The high incidence of breast cancer in women and the severity of the disease have stimulated a need for improved and novel forms of therapy. The product of the MUC-1 gene has been identified as a breast cancer-associated antigen in breast cancer patients. The gene has been cloned and sequenced. Transgenic mice were prepared that express human mucin and are naturally tolerant to the molecule, providing a unique opportunity to investigate immunotherapeutic strategies in experimental animals that might eventually be applied to breast cancer patients. A cell line (410.4) derived from a mouse mammary adenocarcinoma that arose in a BALB/c mouse was transduced with a retroviral vector (R1-MUC1-pEMSVscribe) that encoded MUC-1. After confirmation of the expression of human mucin, the cells (E3) were further modified by transduction with retroviral vectors encoding interleukin (IL)-2, IL-4, IL-12, or IFN-gamma to evaluate the effect of cytokine-secretion on the immunogenic properties of the cells in the MUC-1 transgenic mice. The results indicated that modification of the breast cancer cells to secrete IL-12 reduced and at times eliminated the tumorigenic growth properties of the cells. Under similar circumstances, progressively growing tumors formed in MUC-1 transgenic mice that received injections of unmodified E3 cells or with E3 cells modified to secrete IL-2, IL-4, or IFN-gamma. Immunity to breast cancer developed in MUC-1 transgenic mice that had rejected IL-12-secreting E3 cells because the animals were resistant to challenge with (non-cytokine-secreting) E3 cells. In vitro analyses confirmed the presence of T cell-mediated cytotoxicity toward the breast cancer cells in MUC-1 transgenic mice immunized with the IL-12-secreting cells. Our data obtained in a unique animal model system point toward an analogous form of therapy for breast cancer patients.
De-interleaved direct down-conversion receiver for SDR applications (2009)

This paper proposes a low complexity subsampling based direct down-conversion architecture suitable for software defined radio (SDR) receivers. The proposed topology only needs a single branch to down-convert and extract the in-phase (I) and quadrature (Q) baseband signals. Using a single branch down-conversion eliminates the I/Q mismatch issue of the traditional direct down-conversion receivers. Furthermore, the proposed receiver requires only simple circuit components compared to the well-known subsampling low-IF receiver architectures, especially in designing the RF band-pass filter. The simplicity of the proposed receiver architecture makes it appropriate for low-cost low-power applications. Moreover, the potential use over a wide range of frequencies makes the proposed receiver a suitable solution for multi-standard and multi-band applications.
Dynamic Proteomics of Human Protein Level and Localization across the Cell Cycle (2012)

Regulation of proteins across the cell cycle is a basic process in cell biology. It has been difficult to study this globally in human cells due to lack of methods to accurately follow protein levels and localizations over time. Estimates based on global mRNA measurements suggest that only a few percent of human genes have cell-cycle dependent mRNA levels. Here, we used dynamic proteomics to study the cell-cycle dependence of proteins. We used 495 clones of a human cell line, each with a different protein tagged fluorescently at its endogenous locus. Protein level and localization was quantified in individual cells over 24h of growth using time-lapse microscopy. Instead of standard chemical or mechanical methods for cell synchronization, we employed in-silico synchronization to place protein levels and localization on a time axis between two cell divisions. This non-perturbative synchronization approach, together with the high accuracy of the measurements, allowed a sensitive assay of cell-cycle dependence. We further developed a computational approach that uses texture features to evaluate changes in protein localizations. We find that 40% of the proteins showed cell cycle dependence, of which 11% showed changes in protein level and 35% in localization. This suggests that a broader range of cell-cycle dependent proteins exists in human cells than was previously appreciated. Most of the cell-cycle dependent proteins exhibit changes in cellular localization. Such changes can be a useful tool in the regulation of the cell-cycle being fast and efficient.
Abstract PL07-04: Engineered T cell transfer for cancer immunotherapy in the era of synthetic biology: Challenges and opportunities. (2013)

Abstract Adoptive T cell transfer for cancer and chronic infection is an emerging field that shows promise in recent trials. Synthetic-biology-based engineering of T lymphocytes to express high-affinity antigen receptors can overcome immune tolerance, which has been a major limitation of previous immunotherapy-based strategies. Advances in cell engineering and culture approaches to enable efficient gene transfer and ex vivo cell expansion have facilitated broader evaluation of this technology, moving adoptive transfer from a "boutique"’ application to the cusp of a mainstream technology. Recent observations from ongoing clinical trials in patients with leukemia and carcinomas will be discussed. The major scientific challenge currently facing the field is identification of cancer specific targets to avoid on-target, off-tissue toxicity. As the field of adoptive transfer technology matures, the major engineering challenge is the development of automated cell culture systems, so that the approach can extend beyond specialized academic centers and become widely available. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):PL07-04. Citation Format: Carl H. June. Engineered T cell transfer for cancer immunotherapy in the era of synthetic biology: Challenges and opportunities. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr PL07-04.
Suppression of human psychophysiological and biochemical stress responses using high-frequency pulse-modulated transdermal electrical neurosignaling (2015)

We have developed a neuromodulation approach that targets peripheral nerves and utilizes their afferents as signaling conduits to influence brain function. We investigated the effects of this transdermal electrical neurosignaling (TEN) approach on physiological responses to acute stress induction. TEN was targeted to the ophthalmic and maxillary divisions of the right trigeminal nerve and cervical spinal nerve afferents (C2/C3) using high-frequency, pulse-modulated electrical currents. Compared to active sham stimulation, TEN significantly suppressed sympathetic activity in response to acute stress without impeding cognitive performance. This sympatholytic action of TEN was indicated by significant suppression of heart rate variability changes, galvanic skin responses, and salivary α-amylase levels in response to stress. These observations are consistent with the hypothesis that TEN acted partially by modulating activity in the locus coeruleus and subsequent noradrenergic signaling. Dampening sympathetic tone using TEN in such a manner represents a promising approach to managing daily stress and improving brain health.
Semiconductor quantum dot nanostructures and their roles in the future of photonics (2004)

This paper discusses the growth and the properties of semiconductor nanostructures based on self-assembled quantum dots (QDs). These QDs confine electrons or excitons in zero-dimension (0D), similar to an artificial atom or to an artificial molecule in the case of coupled QDs with vertical alignment. They are obtained in a simple step during the epitaxy of strained III-V semiconductors such as InAs on GaAs, or InAs on InP. We will elaborate on the unique optical properties and the physics of self-assembled QDs and their applications, including QD lasers.
Mechanism for epigenetic variegation of gene expression at yeast telomeric heterochromatin (2012)

Yeast contains heterochromatin at telomeres and the silent mating-type loci (HML/HMR). Genes positioned within the telomeric heterochromatin of Saccharomyces cerevisiae switch stochastically between epigenetically bistable ON and OFF expression states. Important aspects of the mechanism of variegated gene expression, including the chromatin structure of the natural ON state and the mechanism by which it is maintained, are unknown. To address this issue, we developed approaches to select cells in the ON and OFF states. We found by chromatin immunoprecipitation (ChIP) that natural ON telomeres are associated with Rap1 binding and, surprisingly, also contain known characteristics of OFF telomeres, including significant amounts of Sir3 and H4K16 deacetylated nucleosomes. Moreover, we found that H3K79 methylation (H3K79me), H3K4me, and H3K36me, which are depleted from OFF telomeres, are enriched at ON telomeres. We demonstrate in vitro that H3K79me, but not H3K4me or H3K36me, disrupts transcriptional silencing. Importantly, H3K79me does not significantly reduce Sir complex binding in vivo or in vitro. Finally, we show that maintenance of H3K79me at ON telomeres is dependent on transcription. Therefore, although Sir proteins are required for silencing, we propose that epigenetic variegation of telomeric gene expression is due to the bistable enrichment/depletion of H3K79me and not the fluctuation in the amount of Sir protein binding to nucleosomes.
O processo de latenciação no planejamento de fármacos (1999)

Short review about the main aspects of prodrug design, as its objectives, applicability and importance, showing the new trends in the research for selective latent forms, namely targeted drugs.
Dual Dopable Poly(phenylacetylene) with Nitronyl Nitroxide Pendants for Reversible Ambipolar Charging and Discharging (2011)

Abstract An electrode-attached layer of poly(phenylacetylene) bearing a pendant nitronyl nitroxide group per repeating unit, obtained by the Rh-catalyzed polymerization of 2-(4-ethynylphenyl)-4,4,5,5-tetramethylimidazoline-l-oxyl 3-oxide, underwent oxidation and reduction at 0.80 and −0.84 V vs. Ag/AgCl, respectively. The magnetically determined unpaired electron density of 92% was coulometrically reproduced, which supported the presumption that the radical survived during the course of the polymerization to allow both positive and negative charging of the pristine neutral polymer substantially per repeating unit. Galvanostatic Coulomb titration revealed the charge storage capability of the polymer, which demonstrated usefulness as organic electrode-active material with unprecedented ambipolar chargeability.
Automatenbasierte Entscheidungsverfahren für Teilsysteme der Arithmetik. (2004)

Vor ungefahr vierzig Jahren wurde entdeckt, dass Automaten ein nutzliches mathematisches Werkzeug sind, um die Entscheidbarkeit bestimmter Teilsysteme der Arithmetik zu verstehen. Heutzutage werden Automaten auch als Werkzeug eingesetzt, um Entscheidungsverfahren fur eben solche logischen Theorien umzusetzen. Meine Dissertation behandelt Fragestellungen aus eben diesem Bereich zwischen Automatentheorie und Logik. Ziel dieses Artikels ist es, Einblicke in diesen Themenbereich zu geben und die Beitrage meiner Dissertation zu beschreiben.
Method of heavy reforma te conversion into btx over metal-impregnated ZSM-5+SSZ-33 zeolite composite catalyst (2019)

Methods of making BTX compounds including benzene, toluene, and xylene include feeding heavy reformate to a reactor containing a composite zeolite catalyst. The composite zeolite catalyst includes a mixture of SSZ-33 and ZSM-5. The SSZ-33, the ZSM-5, or both comprise one or more impregnated metals. The method further includes producing the BTX compounds by simultaneously performing transalkylation and dealkylation of the heavy reformate in the reactor. The composite zeolite catalyst is able to simultaneously catalyze both the transalkylation and dealkylation reactions
Stability of Self-Configuring Large Multiport Interferometers (2021)

Realistic multiport interferometers (beamsplitter meshes) are sensitive to component imperfections, and this sensitivity increases with size. Self-configuration techniques can be employed to correct these imperfections, but not all techniques are equal. This paper highlights the importance of algorithmic stability in self-configuration. Naive approaches based on sequentially setting matrix elements are unstable and perform poorly for large meshes, while techniques based on power ratios perform well in all cases, even in the presence of large errors. Based on this insight, we propose a self-configuration scheme for triangular meshes that requires only external detectors and works without prior knowledge of the component imperfections. This scheme extends to the rectangular mesh by adding a single array of detectors along the diagonal.
SELF-ASSEMBLED POLYPEPTIDESURFACTANT BASED AEROSOL NANO- PARTICLES FOR CONTROLLED DRUG DELIVERY (2008)

Nanoparticles of PLL-DBS were prepared by the aerosol flow reactor method [2]. For drug release experiments, PLL-DBS formulations containing ketoprofen, budesonide, or 1,8-ANS fluorescence probes were also prepared. The complexes, with the additional drug or fluorescent molecules, were dissolved in an organic solvent. The solution was then atomized into nanodroplets, which converted into solid aerosol nanoparticles in a heated reactor. The structure of the self-assembled PLL-DBS nanoparticles were analyzed by TEM revealing a few lamellar layers on the surface with wormlike cylinders in the core at room temperature with increasing lamellar content as the reactor temperature was incremented from 20 °C up to 240 °C. FTIR analysis on the nanoparticles indicated that PLL conformation depended on the solvent used. With 1-propanol PLL adopted β-sheet conformation at each temperature, while using CHCl3 or DMF the conversion from α-helix to β-sheet took place at 100 °C and 240 °C, respectively. Figure 1. PLL-DBS nanoparticles prepared from DMF as a solvent with 240 °C annealing temperature showing a) lamellar structure in a TEM micrograph and b) nanoparticle clusters in a SEM micrograph.
Acne Treatment Cases with Hwangryeonhaedok-tang (2009)

Objectives : Acne, one of the most common disorders in dermatology clinic, is a chronic inflammatory disease which has the symptoms of comedones, papules, pustules, cysts, nodules and scars mainly on the face. Although some of pathologic findings are suggested, but the exact causes and mechanisms are not yet known in Western Medicine. Hwangryeonhaedok-Tang(HRHDT) is an antiinflammatory, antipyretic and detoxifying herb decoction. In this report, we would like to share our experience of acne treatment with HRHDT. Methods : We had treated several patients with acne, facial flushing and uprising febrile sensation on face using oral administration and external application of HRHDT. HRHDT is basically made up with Scutellariae Radix, Coptidis Rhizoma, Phellodendri Cortex and Gardeniae Fructus. In this trial, several other herbs were added according to the individual patient's accompanying symptoms. After the decoction of herbs in amount for 10 days, Kefir Starter 10 g was added to the herbal solution that was then fermented in an incubator at for 72 hours, and divided into 30 doses. Results : Photographies were taken before and after the treatment. The severities of acne were evaluated with these photos according to the Korean Acne Grading System(KAGS). As results, we observed dramatic clinical improvements and the decreases of KAGS grades after the average treatment period of 8 weeks. The medication was orally administered 3 times a day and the external treatment was applied average twice a week during the whole treatment period. Conclusions : From these results, HRHDT may be considered as a good prescription for the febrile and toxic type of acne patients.
Application of Ovine Luteinizing Hormone (LH) Radioimmunoassay in the Quantitation of LH in Different Mammalian Species (1977)

A sensitive double antibody radioimmunoassay has been developed for measuring luteinizing hormone (LH) in various African mammalian species, using rabbit anti-ovine LH serum (GDN 15) and radioiodinated rat LH or ovine LH. Serum and pituitary homogenates from some African mammals (hyrax, reedbuck, sable, impala, tsessebe, thar, spring-hare, ground squirrel and cheetah, as well as the domestic sheep, cow and horse and laboratory rat and hamster) produced displacement curves parallel to that of the ovine LH standards. The specificity of the assay was examined in detail for one species, the rock hyrax. Radioimmunoassay and bioassay estimates of LH in hyrax pituitaries containing widely differing quantities of pituitary hormones were similar. In sexually active male hyrax mean plasma LH was 12.1 ng/ml and pituitary LH 194 microgram/gland, but in sexually quiescent hyrax mean plasma LH was 2.4 ng/ml and mean pituitary LH 76 microgram/gland. Intravenous injection of 10 microgram of luteinizing hormone releasing hormone increased mean LH levels in hyrax from 0.9 ng/ml to 23.2 ng/ml by 30 min. Conversely, im injection of 250 microgram testosterone induced a fall in LH levels in male hyrax from 1.7 ng/ml to 0.7 ng/ml 6 h after administration. Although the specificity of the assay for quantitating plasma LH in other species was not categorically established, there was a good correlation between plasma LH concentration and reproductive state in the bontebok, impala, spring-hare, thar, cheetah, domestic horse and laboratory rat, suggesting the potential use of the antiserum in quantitating LH in a variety of mammalian species.
Leukocyte depletion attenuates vascular injury in postischemic skeletal muscle (1988)

To determine whether leukocytes play an important role in the pathogenesis of the vascular injury (increased vascular permeability and resistance) associated with ischemia-reperfusion, isolated canine gracilis muscles were perfused with autologous whole blood or with whole blood that had been depleted of leukocytes (primarily granulocytes) using Leukopak filters. The osmotic reflection coefficient for total plasma proteins, isogravimetric capillary pressure, and total vascular resistance was determined for the following conditions: control, ischemia (4 h inflow occlusion) plus reperfusion with whole blood, and ischemia plus reperfusion with granulocyte-depleted whole blood. Reperfusion with whole blood was associated with a reduction in the osmotic reflection coefficient from 0.96 to 0.61, whereas isogravimetric capillary pressure was reduced by 40%, indicating a dramatic increase in vascular permeability. Total vascular resistance was increased approximately twofold. Reperfusion with leukocyte-depleted blood largely prevented the increases in vascular permeability and resistance. These data suggest that leukocytes play a major role in the pathogenesis of ischemia-reperfusion injury in skeletal muscle.
“Longitudinal Fecal Microbiome Study of Total Body Irradiated Mice Treated With Radiation Mitigators Identifies Bacterial Associations With Survival” (2021)

Total body irradiation (TBI) has been demonstrated to alter the intestinal microbiome, but the effects of successful small molecule ionizing radiation mitigators on the intestinal microbiome are not well-known. Our survival experiments examined the effects of anti-cell death radiation mitigators on and in conjunction with the host's microbiota. Mice received 9.25 Gy TBI and then were administered radiation mitigators 24 hours later. Passed stool were collected pre-irradiation, then on days 1, 3, 5, 7, 10, 14, 21, and 30 post-irradiation for 16S rRNA gene (V4 region) sequencing. The Cox proportional hazards (CPH) model was fit with taxonomic composition (time varying covariates) and treatment as predictors. In the first experiment, mice were administered drugs for "granulocyte stimulation and anti-apoptosis" in four protocol combinations: JP4-039 (anti-apoptosis), granulocyte colony-stimulating factor (G-CSF, granulopoietic precursor cell stimulator), both mitigators, and control. Survival improved relative to control (30.0%) for G-CSF (80%, p-value = 0.025), G-CSF/JP4-039 (70%, p-value = 0.084), but not for JP4-039 (50.0%). In the second experiment, mice were administered mitigation drugs "inhibiting programmed cell death" pathways: JP4-039 (anti-apoptosis), necrostatin-1 (anti-necroptosis), and baicalein (anti-ferroptosis), in eight combinations. The survival of JP4-039/baicalein (60.0%, p-value = 0.010) and JP4-039/baicalein/necrostatin-1 (60.0%, p-value = 0.06) treatment combinations were significantly different from the control (26.7%). The JP4-039/necrostatin-1 (46.7%) and baicalein/necrostatin-1 (40.0%) and singlet treatment combinations (26.7%) were not significantly different from the control. Despite differences between the baseline microbiota compositions of the two experiments, consistent changes in composition after irradiation were found: <i>Lactobacillus</i> decreased post-irradiation, relative to baseline. By day 7, microbiota perturbations had incompletely reversed, and no drug-specific differences were identifiable. The CPH model identified <i>Lactobacillus</i> and members of <i>Ruminococcaceae</i>, including <i>Ruminococcus</i>, as protective and <i>Akkermansia</i> as deleterious. By day 30, the microbiota of surviving mice had not returned to baseline, but the differences between experiments suggest the resultant microbiota composition of the survivors are stochastic or batch specific in nature, rather than a requirement for survival. In conclusion, the study determined that key taxa identified in fecal samples, when applied towards the prediction of TBI survival, improves the survival model relative to treatment information alone.
Resolution and polarization distribution in cryogenic DNP/MAS experiments (2010)

This contribution addresses four potential misconceptions associated with high-resolution dynamic nuclear polarization/magic angle spinning (DNP/MAS) experiments. First, spectral resolution is not generally compromised at the cryogenic temperatures at which DNP experiments are performed. As we demonstrate at a modest field of 9 T (380 MHz (1)H), 1 ppm linewidths are observed in DNP/MAS spectra of a membrane protein in its native lipid bilayer, and <0.4 ppm linewidths are reported in a crystalline peptide at 85 K. Second, we address the concerns about paramagnetic broadening in DNP/MAS spectra of proteins by demonstrating that the exogenous radical polarizing agents utilized for DNP are distributed in the sample in such a manner as to avoid paramagnetic broadening and thus maintain full spectral resolution. Third, the enhanced polarization is not localized around the polarizing agent, but rather is effectively and uniformly dispersed throughout the sample, even in the case of membrane proteins. Fourth, the distribution of polarization from the electron spins mediated via spin diffusion between (1)H-(1)H strongly dipolar coupled spins is so rapid that shorter magnetization recovery periods between signal averaging transients can be utilized in DNP/MAS experiments than in typical experiments performed at ambient temperature.