gebhart/patrepeval huggingface dataset:
Emergence of complex cell properties by decomposition of natural images into independent feature subspaces (1999)

Olshausen and Field (1996) applied the principle of independence maximization by sparse coding to extract features from natural images. This leads to the emergence of oriented linear filters that have simultaneous localization in space and in frequency, thus resembling Gabor functions and simple cell receptive fields. In this paper, we show that the same principle of independence maximization can explain the emergence of phase and shift invariant features, similar to those found in complex cells. This new kind of emergence is obtained by maximizing the independence between norms of projections on linear (instead of the independence of simple linear filter outputs). The norms of the projections on such independent feature subspaces then indicate the values of invariant features.
Achieving Non-Inclusive Cache Performance with Inclusive Caches: Temporal Locality Aware (TLA) Cache Management Policies (2010)

Inclusive caches are commonly used by processors to simplify cache coherence. However, the trade-off has been lower performance compared to non-inclusive and exclusive caches. Contrary to conventional wisdom, we show that the limited performance of inclusive caches is mostly due to inclusion victims—lines that are evicted from the core caches to satisfy the inclusion property—and not the reduced cache capacity of the hierarchy due to the duplication of data. These inclusion victims are incorrectly chosen for replacement because the last-level cache (LLC) is unaware of the temporal locality of lines in the core caches. We propose Temporal Locality Aware (TLA) cache management policies to allow an inclusive LLC to be aware of the temporal locality of lines in the core caches. We propose three TLA policies: Temporal Locality Hints (TLH), Early Core Invalidation (ECI), and Query Based Selection (QBS). All three policies improve inclusive cache performance without requiring any additional hardware structures. In fact, QBS performs similar to a non-inclusive cache hierarchy.
Design and Applications of Biodegradable Polyester Tissue Scaffolds Based on Endogenous Monomers Found in Human Metabolism (2009)

Synthetic polyesters have deeply impacted various biomedical and engineering fields, such as tissue scaffolding and therapeutic delivery. Currently, many applications involving polyesters are being explored with polymers derived from monomers that are endogenous to the human metabolism. Examples of these monomers include glycerol, xylitol, sorbitol, and lactic, sebacic, citric, succinic, alpha-ketoglutaric, and fumaric acids. In terms of mechanical versatility, crystallinity, hydrophobicity, and biocompatibility, polyesters synthesized partially or completely from these monomers can display a wide range of properties. The flexibility in these macromolecular properties allows for materials to be tailored according to the needs of a particular application. Along with the presence of natural monomers that allows for a high probability of biocompatibility, there is also an added benefit that this class of polyesters is more environmentally friendly than many other materials used in biomedical engineering. While the selection of monomers may be limited by nature, these polymers have produced or have the potential to produce an enormous number of successes in vitro and in vivo.
Parylene Coatings in Medical Devices and Implants: A Review (2015)

This paper reviews various aspects of parylene coatings in medical devices and industry and summarises the fabrication methods of parylene coatings and their potential medical applications. In medical industry, two major beneficial properties of parylene include excellent barrier qualities and inherent bio-compatibility and bio-stability. The need for a bio-compatible material with good surface characteristics is of paramount importance. The recent findings indicate the application of parylene coatings in several areas of medical industry such as surgical instruments, implants, medical devices, mandrels, and medical electronics. Parylene has been slowly introduced into the research market, and has found to be competitive for available materials in the market. A review of the literature was undertaken to identify the prospective use to determine whether parylene coatings can survive the needs in medical industry.
Relationship between stearoyl-CoA desaturase activity and plasma triglycerides in human and mouse hypertriglyceridemia (2002)

Stearoyl-CoA desaturase (SCD) is expressed at high levels in several human tissues and is required for the biosynthesis of oleate (18:1) and palmitoleate (16:1). These monounsaturated fatty acids are the major components of phospholipids, triglycerides, wax esters, and cholesterol esters. Mice with a targeted disruption of the SCD1 gene have very low levels of VLDL and impaired triglyceride and cholesterol ester biosynthesis. In the HYPLIP mouse, a model of hyperlipidemia, there was a 4-fold increase in hepatic SCD activity, a 1.8-fold increase in the desaturation index, and a 2-fold increase in plasma triglycerides. We used the plasma ratio of 18:1/18:0 (the "desaturation index") as an in vivo measure of SCD activity in human subjects. In human subjects with triglycerides ranging from 0.3 to 20 mM, the desaturation ratio accounted for one-third of the variance in plasma triglyceride levels. A 2-fold increase in the desaturation index was associated with a 4-fold increase in plasma triglycerides. In human subjects exposed to a high carbohydrate diet, the desaturation index explained 44% of the variance in triglycerides. We propose that many of the factors that influence plasma triglyceride levels do so by converging upon the regulation of SCD activity.
Pseudolinearization of the acrobot using spline functions (2005)

The authors present an algorithm for the construction of approximation to both the nonlinear control and coordinate transformation under which a single-input nonlinear system has a linear tangent model independent of its operating point. Substituting spline approximations for functions that can be difficult to compute yields a stable closed-loop system with an arbitrarily small deterioration in performance. The approximate pseudolinearization control law is easy to calculate and inexpensive to implement, regardless of the complexity of the nonlinear model. Experimental results obtained by implementing the approximate pseudolinearization control law on a remotely driven acrobot verify the controller's ease of design and computational efficiency.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Quantitative Profile of the Uropathogenic Escherichia coli Outer Membrane Proteome during Growth in Human Urine (2007)

Outer membrane proteins (OMPs) of microbial pathogens are critical components that mediate direct interactions between microbes and their surrounding environment. Consequently, the study of OMPs is integral to furthering the understanding of host-pathogen interactions and to identifying key targets for development of improved antimicrobial agents and vaccines. In this study, we used two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and tandem mass spectrometry to characterize the uropathogenic Escherichia coli (UPEC) outer membrane subproteome; 30 individual OMPs present on the bacterial surface during growth in human urine were identified. Fluorescence difference gel electrophoresis was used to identify quantitative changes in levels of UPEC strain CFT073 OMPs during growth in urine; six known receptors for iron compounds were induced in this environment, i.e., ChuA, IutA, FhuA, IroN, IreA, and Iha. A seventh putative iron compound receptor, encoded by CFT073 open reading frame (ORF) c2482, was also identified and found to be induced in urine. Further, the induction of these seven iron receptors in human urine and during defined iron limitation was verified by using quantitative real-time PCR (qPCR). An eighth iron receptor, fepA, displayed similar induction levels under these conditions as measured by qPCR but was not identified by 2D-PAGE. Addition of 10 microM FeCl(2) to human urine repressed the transcription of all eight iron receptor genes. A number of fecal-commensal, intestinal pathogenic, and uropathogenic E. coli strains all displayed similar growth rates in human urine, showing that the ability to grow in urine per se is not a urovirulence trait. Thus, human urine is an iron-limiting environment and UPEC enriches its outer membrane with iron receptors to contend with this iron limitation.
52. Gorilla Adenovirus Vectors for Molecular Therapeutics and Vaccines (2015)

Adenovirus vectors built from gorilla adenovirus are showing superior performance characteristics for molecular vaccines. These new adenovectors (GC Ads) are built from virus isolated from gorilla, and have been cloned and engineered to be replication-defective. GC Ads grow efficiently to high titer on cell lines GenVec has characterized, banked and filed with regulatory agencies for scalable manufacturing. They can be deleted of multiple regions (e.g., E1, E3, and E4) to provide space for multiple transgene cassettes, provide multiple blocks to eliminate replication competent virus and to ensure safer transgene delivery. These new adenovectors have been shown to not be recognized by human sera from either the United States or from Africa. A single intramuscular injection of these GC Ads can induce durable immune responses to encoded antigen. For example, intramuscular injection of GC Ads expressing RSV fusion (F0) glycoprotein induced neutralizing antibody titers that were durable > 24weeks, and protected the lung and nose against RSV challenge at even low doses of immunization in cotton rats. A single intramuscular administration of GC Ads expressing the malaria antigen CSP generated CD8 T cell and antibody responses to CSP that were greater than those generated with Ad5 in mice. In a mouse malaria challenge model the GC Ad regimen was more protective than Ad5. A single intramuscular administration of GC Ads expressing two HSV antigens, UL19 and UL47, resulted in high level cellular responses that were protective against intravaginal HSV2 challenge in mice and the CD8 T cell responses were shown to be durable, 26 weeks. Moreover, repeat administration of the same GC Ad resulted in a boost of antigen-specific immune response. Unlike other adenoviral vectors, homologous prime boost regimens with these GC Ads resulted in a boost of the CD8 T cell responses at all doses and intervals tested. These new GC Ads based on gorilla adenoviruses show generation of strong, durable T cell and neutralizing antibody responses to multiple antigens from a single administration that can be further enhanced by repeat administration. Based on these data, the platform shows great promise for development of a broad array of immunotherapeutic and molecular vaccine product candidates.
Resources for linkage of primary health care and substance abuse services (1993)

Abstract Most practitioners would agree that substance abusing clients benefit from a comprehensive and coordinated approach to their medical and psychosocial problems. For practitioners in private practice, it is not always clear how to manage alcohol and drug cases in a way that achieves the level of intensity that is appropriate for each client and maintains continuity of care across settings and treatment providers. The purpose of this article is to suggest a range of strategies that have been used to enhance communication among practitioners and the agencies and organizations with whom they interact, both formally and informally. The article will describe strategies in the following four areas: (1) coordination of services, (2) interagency agreement, (3) community resources, and (4) public‐private cooperation. Some of the strategies apply directly to the practitioners' activities, while others are included to improve practitioners' understanding of how to deal more effectively with bureaucratic struc...
Early enteral supplementation with key pharmaconutrients improves Sequential Organ Failure Assessment score in critically ill patients with sepsis: Outcome of a randomized, controlled, double-blind trial* (2008)

In medical patients with sepsis, early enteral pharmaconutrition with glutamine dipeptides, vitamin C and E, beta-carotene, selenium, zinc, and butyrate in combination with an immunonutrition formula results in significantly faster recovery of organ function compared with control.
Severity of symptoms and demyelination in MOG-induced EAE depends on TNFR1 (1999)

The individual role of tumor necrosis factor receptor 1 (TNFR1) and TNFR2 signaling in experimental autoimmune encephalomeylitis (EAE) was investigated using mice lacking TNFR1 (TNFR1-/-), TNFR2 (TNFR2-/-) as well as double receptor (TNFR1/2-/-) and double ligand (TNF/LT alpha-/-) knockout mice. In wild-type (wt) mice immunized with myelin oligodendrocyte glycoprotein (MOG) peptide 35-55 the clinical course is characterized by an acute disease onset with peak disease scores and a consecutive chronic phase lasting up to 60 days. Compared to control mice, TNF/LT alpha-deficient mice showed a significant delay in disease onset and a remarkable reduction in demyelination which was, however, associated with increased inflammation. In TNFR1-/- and TNFR1/2-/- mice, the disease course was comparable to TNF/LT alpha-deficient mice but rather monophasic and less severe at late time points. Likewise only minimal spinal cord demyelination became apparent. In contrast, the course of EAE in TNFR2-/- mice was severe and associated with remarkable demyelination. Taken together these findings define TNFR1 as crucial mediator in MOG-induced EAE and suggest a protective role for TNFR2 signaling in the clinical course of EAE.
Myocarditis and Abortion Associated with Intrauterine Infection of Sows with Porcine Circovirus 2 (1999)

Porcine circovirus 2 (PCV2) is a recently identified agent that has been associated with postweaning multisystemic wasting syndrome (PMWS) in swine populations. In this report, the potential spectrum of disease associated with PCV2 is expanded by evidence of vertical transmission and associated reproductive failure. PCV2 was isolated from a litter of aborted piglets from a farm experiencing late-term abortions and stillbirths. Severe, diffuse myocarditis was present in 1 piglet associated with extensive immunohistochemical staining for PCV2 antigen. Variable amounts of PCV2 antigen were also present in liver, lung, and kidney of multiple fetuses. The presence of other agents that have been associated with fetal lesions and abortion in swine, including porcine parvovirus, porcine reproductive respiratory syndrome virus, encephalomyocarditis virus, and enterovirus, could not be established.
Synapse elimination from the mouse neuromuscular junction in vitro: A non‐hebbian activity‐dependent process (1993)

The effect of action potentials on elimination of mouse neuromuscular junctions (NMJ) was studied in a three-compartment cell culture preparation. Axons from superior cervical ganglion or ventral spinal cord neurons in two lateral compartments formed multiple neuromuscular junctions with muscle cells in a central compartment. The loss of synapses over a 2-7-day period was determined by serial electrophysiological recording and a functional assay. Electrical stimulation of axons from one side compartment during this period, using 30-Hz bursts of 2-s duration, repeated at 10-s intervals, caused a significant increase in synapse elimination compared to unstimulated cultures (p < 0.001). The extent of homosynaptic and heterosynaptic elimination was comparable, i.e., of the 226 functional synapses of each type studied, 111 (49%) of the synapses that had been stimulated were eliminated, and 87 (39%) of unstimulated synapses on the same muscle cells were eliminated. Also, simultaneous bilateral stimulation caused significantly greater elimination of synapses than unilateral stimulation (p < 0.005). These observations are contrary to the Hebbian hypothesis of synaptic plasticity. A spatial effect of stimulus-induced synapse elimination was also evident following simultaneous bilateral stimulation. Prior to stimulation, most muscle cells were innervated by axons from both side compartments, but after bilateral stimulation, muscle cells were predominantly unilaterally innervated by axons from the closer compartment. These experiments suggest that synapse elimination at the NMJ is an activity-dependent process, but it does not follow Hebbian or anti-Hebbian rules of synaptic plasticity. Rather, elimination is a consequence of postsynaptic activation and a function of location of the muscle cell relative to the neuron. An interaction between spatial and activity-dependent effects on synapse elimination could help produce optimal refinement of synaptic connections during postnatal development.
OCCURRENCE OF SECTORAL CHOROIDAL OCCLUSIVE VASCULOPATHY AND RETINAL ARTERIOLAR EMBOLIZATION AFTER SUPERSELECTIVE OPHTHALMIC ARTERY CHEMOTHERAPY FOR ADVANCED INTRAOCULAR RETINOBLASTOMA (2011)

Superselective ophthalmic artery chemotherapy (SOAC) has recently been proposed as an alternative to intravenous chemoreduction for advanced intraocular retinoblastoma. Preliminary results appear promising in terms of tumor control and eye conservation, but little is known regarding ocular toxicity and visual prognosis. In this study, we report on the vascular adverse effects observed in our initial cohort of 13 patients. The charts of 13 consecutive patients with retinoblastoma who received a total of 30 injections (up to 3 injections of a single agent per patient at 3-week interval) of melphalan (0.35 mg/kg) in the ophthalmic artery between November 2008 and June 2010 were retrospectively reviewed. RetCam fundus photography and fluorescein angiography were performed at presentation and before each injection. Vision was assessed at the latest visit. Enucleation and external beam radiotherapy could be avoided in all cases but one, with a mean follow-up of 7 months. Sectoral choroidal occlusive vasculopathy leading to chorioretinal atrophy was observed temporally in 2 eyes (15%) 3 weeks to 6 weeks after the beginning of SOAC and retinal arteriolar emboli in 1 eye 2 weeks after injection. There was no stroke or other clinically significant systemic side effects except a perioperative transient spasm of the internal carotid artery in one patient. Vision ranged between 20/1600 and 20/32 depending on the status of the macula. Superselective ophthalmic artery chemotherapy was effective in all patients with no stroke or other systemic vascular complications. Unlike intravenous chemoreduction, SOAC is associated with potentially sight-threatening adverse effects, such as severe chorioretinal atrophy secondary to subacute choroidal occlusive vasculopathy or central retinal artery embolism, not to mention the risk of ophthalmic artery obstruction, which was not observed in this series. Further analysis of the risks and benefits of SOAC will define its role within the therapeutic arsenal. Meanwhile, we suggest that SOAC should be given in one eye only and restricted to advanced cases of retinoblastoma, as an alternative to enucleation and/or external beam radiotherapy.
The major non-integrin laminin binding protein of macrophages is identical to carbohydrate binding protein 35 (Mac-2). (1990)

Current data indicate that cell adhesion to laminin, the major basement membrane glycoprotein, is mediated by specific integrins, a family of adhesion receptors. In addition, most cell types express a complement of high affinity non-integrin laminin binding proteins (LBPs). Despite considerable effort, the function of these LBPs has not been elucidated. We report here that the major non-integrin LBP of murine macrophages exhibits an Mr of 35,000 and is expressed on the cell surface. Protein microsequencing data revealed that this protein is identical to carbohydrate binding protein 35. This murine galactose-specific lectin is the macrophage antigen Mac-2. Thus, these data suggest that the non-integrin LBPs may contribute to laminin adhesion by a mechanism involving protein-carbohydrate interactions.
Aryl hydrocarbon receptor-mediated antiestrogenic and antitumorigenic activity of diindolylmethane (1998)

Phytochemicals such as indole-3-carbinol (I3C) and sulforaphane are components of cruciferous vegetables which exhibit antitumorigenic activity associated with altered carcinogen metabolism and detoxification. Diindolylmethane (DIM) is a major acid-catalyzed metabolite of I3C formed in the gut that binds to the aryl hydrocarbon receptor (AhR) and treatment of MCF-7 human breast cancer cells with 10-50 microM DIM resulted in rapid formation of the nuclear AhR complex and induction of CYP1A1 gene expression was observed at concentrations >50 microM. Previous studies have demonstrated that 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a high affinity AhR ligand, inhibits 17beta-estradiol (E2)-induced responses in MCF-7 cells and growth of E2-dependent 7,12-dimethylbenzanthracene (DMBA)-induced mammary tumors in female Sprague-Dawley rats. Results of this study show that like TCDD, DIM inhibits E2-induced proliferation of MCF-7 cells, reporter gene activity in cells transiently transfected with an E2-responsive plasmid (containing a frog vitellogenin A2 gene promoter insert) and down-regulates the nuclear estrogen receptor. Moreover, DIM (5 mg/kg every other day) also inhibits DMBA-induced mammary tumor growth in Sprague-Dawley rats and this was not accompanied by induction of hepatic CYP1A1-dependent activity. Thus, DIM represents a new class of relatively non-toxic AhR-based antiestrogens that inhibit E2-dependent tumor growth in rodents and current studies are focused on development of analogs for clinical treatment of breast cancer.
Transcripts encoding an oleosin and a dormancy‐related protein are present in both the aleurone layer and the embryo of developing barley (Hordeum vulgare L.) seeds (1994)

In cereal seeds, the aleurone layer and the embryo share several characteristics, including synthesis and accumulation of lipid bodies, desiccation tolerance and dormancy. A number of Balem transcripts present in both the barley aleurone layer and the embryo have been cloned by differential screening of a cDNA library from aleurone layers of immature barley grains. The Balem clones constitute two subgroups, one for which the transcripts are detectable in aleurone layers and embryos of developing seeds only (B23D and B15C), and another for which transcripts are present also in germinating embryos and in maternal tissues (B12D, B14E and B31E). Sequence analysis identified B23D and B15C as the barley homologues of the 18 kDa oleosin of maize embryos (72% amino acid identity) and the dormancy-associated transcript pBS128 from Bromus secalinus (95% identity), respectively. In situ hybridization experiments demonstrate that in the embryo, the B23D transcript is mainly present in the scutellum, whereas the B15C transcript is predominantly present in shoot and root apices. Using anther-derived embryos and embryogenic cell suspensions, it is demonstrated that the B23D and B15C transcripts can be used as molecular markers for somatic embryogenesis. The functions of the transcripts in the second Balem subgroup remain unknown. Further studies on the Balem transcripts may shed light on the molecular basis for the extensive similarities between the embryo and the aleurone layer of the endosperm in the grass family.