gebhart/patrepeval huggingface dataset:
Triplet–triplet annihilation upconversion followed by FRET for the red light activation of a photodissociative ruthenium complex in liposomes (2015)

Upconversion is a promising way to trigger high-energy photochemistry with low-energy photons. However, combining upconversion schemes with non-radiative energy transfer is challenging because bringing several photochemically active components in close proximity results in complex multi-component systems where quenching processes may deactivate the whole assembly. In this work, PEGylated liposomes were prepared that contained three photoactive components: a porphyrin dye absorbing red light, a perylene moiety emitting in the blue, and a light-activatable ruthenium prodrug sensitive to blue light. Time-dependent spectroscopic studies demonstrate that singlet perylene excited states are non-radiatively transferred to the nearby ruthenium complex by Förster resonance energy transfer (FRET). Under red-light irradiation of the three-component membranes, triplet-triplet annihilation upconversion (TTA-UC) occurs followed by FRET, which results in a more efficient activation of the ruthenium prodrug compared to a physical mixture of two-component upconverting liposomes and liposomes containing only the ruthenium complex. This work represents a rare example where TTA-UC and Förster resonance energy transfer are combined to achieve prodrug activation in the phototherapeutic window.
The Class I HLA Repertoire of Pancreatic Islets Comprises the Nonclassical Class Ib Antigen HLA-G (2006)

Selective expression of the human class Ib HLA molecule HLA-G in immunologically protected sites and its function in the inhibition of NK and T-cell effector functions support an important role of this molecule in immunoregulation. Here, we demonstrate that HLA-G is constitutively expressed in the endocrine compartment of the human pancreas. Surface expression of this HLA determinant in endocrine cells is regulated in response to growth and inflammatory stimuli. Furthermore, we provide evidence that HLA-G expressed in this tissue may associate with a subset of insulin-containing granules and may be shuttled to the cell surface in response to secretory stimuli. Thus, HLA-G presentation by endocrine cells may be regulated in concert with their secretory activity. These results identify the expression of a major histocompatibility complex locus with putative regulatory functions in human pancreatic islets, a finding with potentially important implications for the progression of autoimmunity as well as for the establishment of transplant tolerance to this tissue.
Hyaluronan Modulation Impacts Staphylococcus aureus Biofilm Infection (2016)

Staphylococcus aureus is a leading cause of chronic biofilm infections. Hyaluronic acid (HA) is a large glycosaminoglycan abundant in mammalian tissues that has been shown to enhance biofilm formation in multiple Gram-positive pathogens. We observed that HA accumulated in an S. aureus biofilm infection using a murine implant-associated infection model and that HA levels increased in a mutant strain lacking hyaluronidase (HysA). S. aureus secretes HysA in order to cleave HA during infection. Through in vitro biofilm studies with HA, the hysA mutant was found to accumulate increased biofilm biomass compared to the wild type, and confocal microscopy showed that HA is incorporated into the biofilm matrix. Exogenous addition of purified HysA enzyme dispersed HA-containing biofilms, while catalytically inactive enzyme had no impact. Additionally, induction of hysA expression prevented biofilm formation and also dispersed an established biofilm in the presence of HA. These observations were corroborated in the implant model, where there was decreased dissemination from an hysA mutant biofilm infection compared to the S. aureus wild type. Histopathology demonstrated that infection with an hysA mutant caused significantly reduced distribution of tissue inflammation compared to wild-type infection. To extend these studies, the impact of HA and S. aureus HysA on biofilm-like aggregates found in joint infections was examined. We found that HA contributes to the formation of synovial fluid aggregates, and HysA can disrupt aggregate formation. Taken together, these studies demonstrate that HA is a relevant component of the S. aureus biofilm matrix and HysA is important for dissemination from a biofilm infection.
Mitofusin 1 and 2 play distinct roles in mitochondrial fusion reactions via GTPase activity (2004)

The mammalian homologues of yeast and Drosophila Fzo, mitofusin (Mfn) 1 and 2, are both essential for mitochondrial fusion and maintenance of mitochondrial morphology. Though the GTPase domain is required for Mfn protein function, the molecular mechanisms of the GTPase-dependent reaction as well as the functional division of the two Mfn proteins are unknown. To examine the function of Mfn proteins, tethering of mitochondrial membranes was measured in vitro by fluorescence microscopy using green fluorescence protein- or red fluorescent protein-tagged and Mfn1-expressing mitochondria, or by immunoprecipitation using mitochondria harboring HA- or FLAG-tagged Mfn proteins. These experiments revealed that Mfn1-harboring mitochondria were efficiently tethered in a GTP-dependent manner, whereas Mfn2-harboring mitochondria were tethered with only low efficiency. Sucrose density gradient centrifugation followed by co-immunoprecipitation revealed that Mfn1 produced oligomerized approximately 250 kDa and approximately 450 kDa complexes in a GTP-dependent manner. The approximately 450 kDa complex contained oligomerized Mfn1 from distinct apposing membranes (docking complex), whereas the approximately 250 kDa complex was composed of Mfn1 present on the same membrane or in the membrane-solubilized state (cis complex). These results were also confirmed using blue-native PAGE. Mfn1 exhibited higher activity for this reaction than Mfn2. Purified recombinant Mfn1 exhibited approximately eightfold higher GTPase activity than Mfn2. These findings indicate that the two Mfn proteins have distinct activities, and suggest that Mfn1 is mainly responsible for GTP-dependent membrane tethering.
FlexiMine - a flexible platform for KDD research and application construction (1998)

* FlexiMine is a KDD system designed as a testbed for data-mining research, as well as a generic knowledge discovery tool for varied database domains. Flexibility is achieved by an open-ended design for extensibility, enabling integration of existing data-mining algorithms, new locally developed algorithms, and support functions, such as visualization and preprocessing. Support for new databases is simple- currently via SQL queries to an INFORMIX database server. With a view of serving remote, as well as local, users, internet availability was a design goal. By implementing the system in Java, minor modifications allow us to run the user-end of the system either as a Java applications or as a Java Applet.
Time-dependent expression and processing of a hypothetical protein of possible importance for regulation of theChlamydia pneumoniae developmental cycle (2001)

Chlamydia pneumoniae is an obligate intracellular human pathogen infecting epithelial cells of the upper respiratory tract. It is a Gram-negative bacteria and has a unique biphasic developmental cycle. In this study, we use two-dimensional gel electrophoresis in combination with radioactive labeling to investigate time-dependent expression and processing of C. pneumoniae proteins. We report on (i) the identification of a hypothetical protein which is expressed late in the developmental cycle and subsequently processed; we speculate that this protein may be of importance for the developmental cycle of Chlamydia; (ii) the identification of the major outer membrane protein in three different variants, which may all be present in vivo.
Alkalinity Between Masonry Blocks of a Segmental Retaining Wall (SRW) (2005)

The technology of SRWs using geosynthetic reinforcement is arguably the fastest growing segment of geosynthetics. Due to their good aesthetics, costs, constructability and performance, these structures are seen throughout the world. However, some of these systems are being challenged for having very high alkalinity which is unsuitable for some PET geosynthetics. The focus of this paper is to share preliminary data from a SRW at GSI which was built with three different block types. The wall was built as a test wall, but it is full size and serves a dual purpose of replacing a failed timber wall. Alkalinity (as measured by pH) measurements are being taken directly between the block surfaces at the contact of the geogrids to the SRW block units. Data for the first year of monitoring is presented.
Metabolic changes during gonadotropin‐releasing hormone agonist therapy for prostate cancer (2008)

The term metabolic syndrome does not appear to adequately describe the effects of GnRH agonists in men with prostate cancer. In contrast to the metabolic syndrome, GnRH agonists increase subcutaneous fat mass, HDL cholesterol, and adiponectin, and do not alter the waist-to-hip ratio, blood pressure, or C-reactive protein level.
Efficient and sustained transgene expression in mature rat oligodendrocytes in primary culture (1996)

In order to evaluate the characteristics and efficiency of gene transfer in primary cultures of oligodendrocytes, four different techniques including particle bombardment (Accell gene gun), cationic liposome-mediated transfection (lipofection), calcium phosphate co-precipitation and retroviral infection were compared using the LacZ and luciferase reporter genes. Highly purified postnatal adult rat oligodendrocytes were obtained by sequential immunopanning, plated in culture, and transfected using various reporter and promoter genes. The most efficient expression of LacZ and luciferase genes was found with particle mediated gene delivery. The transgene expression level obtained with gene gun delivery was at least two- to 100-fold greater than three other tested gene transfer methods. Comparison of the relative strength of four viral and two cellular promoters in these primary oligodendrocytes cultures demonstrated that the CMV promoter was the strongest. Using a human growth hormone (hGH) reporter gene, a long-term transgene expression pattern in primary oligodendrocytes was demonstrated to be sustained in culture for the entire experimental period (4 weeks) after particle-mediated gene transfer. These results demonstrate that expression of a foreign gene can be effectively achieved in primary cultures of adult oligodendrocytes, especially by using the particle bombardment method. The results also suggest that the current ex vivo gene transfer system may be used to manipulate oligodendrocytes for future application in gene therapy studies.
Size-dependent flame retardancy of black phosphorus nanosheets (2022)

Two-dimensional black phosphorus (BP) nanosheets are potential flame-retardant nano-additives. Herein, the effects of the size of BP nanosheets embedded in epoxy resin (EP) on flame retardancy are studied. BP nanosheets with four different sizes are synthesized from bulk BP by different exfoliation methods including solid ball milling, liquid ball milling, ultrasonic liquid exfoliation, and electrochemical exfoliation (samples are designated as sb-BP, lb-BP, us-BP, and ec-BP, respectively). lb-BP exhibits the best dispersion in the EP matrix, and the lb-BP/EP composite shows the best flame-retardancy properties among the four BP/EP composites. Compared to bare EP, lb-BP/EP shows obvious improvements including the reduction in the heat release peak rate by 34.4%, total heat release by 27.0%, peak of smoke production rate by 69.2%, and total production of carbon monoxide by 50.8%. The mechanistic study reveals that lb-BP serves as a barrier and carbonization catalyst to delay combustion. These results confirm the size dependence of flame-retardancy properties of BP nanosheets and the new knowledge provides insights into the size dependent effects of other two-dimensional materials.
A 79 GHz Millimeter-Wave Receiver Frontend with High Linearity for Civil-Automotive Radars in a 22-nm FD-SOI CMOS Technology (2022)

This paper investigates a concept for a 79 GHz millimeter-wave receiver (Rx) frontend optimized for highly linear frequency-modulated continuous-wave civil-automotive radars. It consists of a double-balanced passive ring mixer for the frequency down-conversion, and two highly-linear differential amplifiers as low-noise amplifier and driver for the local-oscillator (LO) signal. To prove the concept, the circuit is implemented in a 22nm FDSOI CMOS technology. It is also studied how the control of the threshold voltage by the back-gate (BG) biasing can increase the circuit performance. Leveraging this feature, no dc biasing is required for the passive mixer and the trade-off between gain and linearity of the amplifiers can be easily tuned with the BG voltage. To characterize the Rx, the chip is mounted on a print circuit board with external resistive loads. Measurements of the fabricated chip show a maximum differential voltage conversion gain (CG) of 10.8 dB at a <tex>$1 \mathrm{k}\Omega$</tex> load and the minimum double side-band NF <tex>$\boldsymbol{(\text{NF}_{\text{dsb},\min})}$</tex> of 9.7 dB with a 50Ω-load. The simulation shows that the <tex>$\boldsymbol{\text{NF}_{\text{dsb},\min}}$</tex> can be further improved, while the Rx drives a higher resistive load. With a 1 kΩ load, the simulated NF<inf>dsb,min</inf> is 7.5 dB. In the measured RF signal range from -30 dBm to -5 dBm, the CG is nearly linear, and the simulated input-referred 1dB-compression-point is between -4 dBm to -2 dBm depending on the LO frequency. To the best knowledge of the authors, this is the highest reported.
Brain tumor segmentation using cascaded deep convolutional neural network (2017)

Gliomas are the most common and threatening brain tumors with little to no survival rate. Accurate detection of such tumors is crucial for survival of the subject. Naturally, tumors have irregular shape and can be spatially located anywhere in the brain, which makes it a challenging task to segment them accurately enough for clinical purposes. In this paper, an automated segmentation algorithm for brain tumor using deep convolutional neural networks (DCNN) is proposed. Deep networks tend to have a lot of parameters thus over-fitting is almost always an issue especially when data are sparse. Max-out and drop-out layers are used to reduce the chances of over-fitting since data are scant. Patch based training method is used for the model where two types of patches sized 37×37 and 19×19 with same center pixel are selected. The proposed algorithm includes preprocessing in which images are normalized and bias field corrected, and post processing where small false positives are removed using morphological operators. BRATS 2013 dataset is used for evaluation of the proposed method, where it outperforms state-of-the-art methods with similar settings in key performance indicators.
Evidence for biological nitrification inhibition inBrachiariapastures (2009)

Nitrification, a key process in the global nitrogen cycle that generates nitrate through microbial activity, may enhance losses of fertilizer nitrogen by leaching and denitrification. Certain plants can suppress soil-nitrification by releasing inhibitors from roots, a phenomenon termed biological nitrification inhibition (BNI). Here, we report the discovery of an effective nitrification inhibitor in the root-exudates of the tropical forage grass Brachiaria humidicola (Rendle) Schweick. Named "brachialactone," this inhibitor is a recently discovered cyclic diterpene with a unique 5-8-5-membered ring system and a gamma-lactone ring. It contributed 60-90% of the inhibitory activity released from the roots of this tropical grass. Unlike nitrapyrin (a synthetic nitrification inhibitor), which affects only the ammonia monooxygenase (AMO) pathway, brachialactone appears to block both AMO and hydroxylamine oxidoreductase enzymatic pathways in Nitrosomonas. Release of this inhibitor is a regulated plant function, triggered and sustained by the availability of ammonium (NH(4)(+)) in the root environment. Brachialactone release is restricted to those roots that are directly exposed to NH(4)(+). Within 3 years of establishment, Brachiaria pastures have suppressed soil nitrifier populations (determined as amoA genes; ammonia-oxidizing bacteria and ammonia-oxidizing archaea), along with nitrification and nitrous oxide emissions. These findings provide direct evidence for the existence and active regulation of a nitrification inhibitor (or inhibitors) release from tropical pasture root systems. Exploiting the BNI function could become a powerful strategy toward the development of low-nitrifying agronomic systems, benefiting both agriculture and the environment.
Investigation of longitudinal proton acceleration in exploded targets irradiated by intense short-pulse laser (2014)

It was recently shown that a promising way to accelerate protons in the forward direction to high energies is to use under-dense or near-critical density targets instead of solids. Simulations have revealed that the acceleration process depends on the density gradients of the plasma target. Indeed, under certain conditions, the most energetic protons are predicted to be accelerated by a collisionless shock mechanism that significantly increases their energy. We report here the results of a recent experiment dedicated to the study of longitudinal ion acceleration in partially exploded foils using a high intensity (∼5 × 1018 W/cm2) picosecond laser pulse. We show that protons accelerated using targets having moderate front and rear plasma gradients (up to ∼8 μm gradient length) exhibit similar maximum proton energy and number compared to proton beams that are produced, in similar laser conditions, from solid targets, in the well-known target normal sheath acceleration regime. Particle-In-Cell simulations, performed in the same conditions as the experiment and consistent with the measurements, allow laying a path for further improvement of this acceleration scheme.
Intraparenchymal Striatal Transplants Required for Maintenance of Behavioral Recovery in an Animal Model of Huntington′s Disease (1989)

Rats which receive injections of kainic acid (KA) into the striatum show many of the anatomical, biochemical and behavioral abnormalities seen in patients with Huntington's disease. Recently, it has been reported that fetal striatal transplants into the lesioned striatum could normalize the neurological and behavioral abnormalities produced by the KA lesion. The present study examined the issue of transplant integration in producing behavioral recovery. In one experiment, lesioned animals with transplants located within the lateral ventricle were compared against parenchymally transplanted rats. It was found that unless the ventricular transplant grew into the lesioned striatum there was no recovery. The second experiment demonstrated that electrolytic destruction of a successful fetal striatal transplant could reverse the transplant-induced behavioral recovery. These results suggest that the integrity of the transplant is important in maintaining behavioral recovery. A continuing functional interaction between the host brain and transplanted tissue may be a vital element in the success of the fetal striatal transplant.
Kissing Stents for Superior Vena Cava Syndrome Due to Mediastinal Fibrosis (2018)

Extensive endovascular venous reconstruction is an effective treatment for SVCS due to mediastinal fibrosis.
A Phase 2 Study of Tramiprosate for Cerebral Amyloid Angiopathy (2006)

These data suggest that tramiprosate can be given safely to subjects with suspected CAA and support future efficacy trials.
DiffusionRank (2007)

While the PageRank algorithm has proven to be very effective for ranking Web pages, the rank scores of Web pages can be manipulated. To handle the manipulation problem and to cast a new insight on the Web structure, we propose a ranking algorithm called DiffusionRank. DiffusionRank is motivated by the heat diffusion phenomena, which can be connected to Web ranking because the activities flow on the Web can be imagined as heat flow, the link from a page to another can be treated as the pipe of an air-conditioner, and heat flow can embody the structure of the underlying Web graph. Theoretically we show that DiffusionRank can serve as a generalization of PageRank when the heat diffusion co-efficient γ tends to infinity. In such a case 1=γ= 0, DiffusionRank (PageRank) has low ability of anti-manipulation. When γ = 0, DiffusionRank obtains the highest ability of anti-manipulation, but in such a case, the web structure is completely ignored. Consequently, γ is an interesting factor that can control the balance between the ability of preserving the original Web and the ability of reducing the effect of manipulation. It is found empirically that, when γ = 1, DiffusionRank has a Penicillin-like effect on the link manipulation. Moreover, DiffusionRank can be employed to find group-to-group relations on the Web, to divide the Web graph into several parts, and to find link communities. Experimental results show that the DiffusionRank algorithm achieves the above mentioned advantages as expected.
Racial Differences in Association of Serum Calcium with Mortality and Incident Cardio- and Cerebrovascular Events (2016)

Race modified the U-shaped association between calcium and all-cause mortality. Serum calcium is not associated with incident stroke or CHD in either AA or white patients. The race-specific difference in the association of calcium levels with mortality warrants further examination.
The virology–RNA biology connection (2015)

My goal in writing this article is to offer my personal reflections on RNA research, focusing on the last 20 years, to be published in a special issue marking the 20th anniversary of RNA, the premier journal in the then-emerging but now well established field of RNA biology. While I have published a number of papers relevant to RNA research, my main focus has always been on virology and I will therefore take this opportunity to remind especially younger readers that RNA research actually initially grew out of virology and that these two subjects continue to be highly interconnected.
Early-Onset Scoliosis: A Review of History, Current Treatment, and Future Directions (2015)

Early-onset scoliosis (EOS) is defined as curvature of the spine in children >10° with onset before age 10 years. Young children with EOS are at risk for impaired pulmonary function because of the high risk of progressive spinal deformity and thoracic constraints during a critical time of lung development. The treatment of EOS is very challenging because the population is inhomogeneous, often medically complex, and often needs multiple surgeries. In the past, early spinal fusion was performed in children with severe progressive EOS, which corrected scoliosis but limited spine and thoracic growth and resulted in poor pulmonary outcomes. The current goal in treatment of EOS is to maximize growth of the spine and thorax by controlling the spinal deformity, with the aim of promoting normal lung development and pulmonary function. Bracing and casting may improve on the natural history of progression of spinal deformity and are often used to delay surgical intervention or in some cases obviate surgery. Recent advances in surgical implants and techniques have led to the development of growth-friendly implants, which have replaced early spine fusion as the surgical treatment of choice. Treatment with growth-friendly implants usually requires multiple surgeries and is associated with frequent complications. However, growth-friendly spine surgery has been shown to correct spinal deformity while allowing growth of the spine and subsequently lung growth.