gebhart/patrepeval huggingface dataset:
Autonomic innervation of immune organs and neuroimmune modulation (2003)

1. Increasing evidence indicates the occurrence of functional interconnections between immune and nervous systems, although data available on the mechanisms of this bi-directional cross-talking are frequently incomplete and not always focussed on their relevance for neuroimmune modulation. 2. Primary (bone marrow and thymus) and secondary (spleen and lymph nodes) lymphoid organs are supplied with an autonomic (mainly sympathetic) efferent innervation and with an afferent sensory innervation. Anatomical studies have revealed origin, pattern of distribution and targets of nerve fibre populations supplying lymphoid organs. 3. Classic (catecholamines and acetylcholine) and peptide transmitters of neural and non-neural origin are released in the lymphoid microenvironment and contribute to neuroimmune modulation. Neuropeptide Y, substance P, calcitonin gene-related peptide, and vasoactive intestinal peptide represent the neuropeptides most involved in neuroimmune modulation. 4. Immune cells and immune organs express specific receptors for (neuro)transmitters. These receptors have been shown to respond in vivo and/or in vitro to the neural substances and their manipulation can alter immune responses. Changes in immune function can also influence the distribution of nerves and the expression of neural receptors in lymphoid organs. 5. Data on different populations of nerve fibres supplying immune organs and their role in providing a link between nervous and immune systems are reviewed. Anatomical connections between nervous and immune systems represent the structural support of the complex network of immune responses. A detailed knowledge of interactions between nervous and immune systems may represent an important basis for the development of strategies for treating pathologies in which altered neuroimmune cross-talking may be involved.
Machine Learning in Basecalling ¿ Decoding Trace Peak Behaviour (2006)

DNA sequence basecalling is commonly regarded as a solved problem, despite significant error rates being reflected in inaccuracies in databases and genome annotations. These errors commonly arise from an inability to sequence through peak height variations in DNA sequencing traces from the Sanger sequencing method. Recent efforts toward improving basecalling accuracy have taken the form of more sophisticated digital filters and feature detectors. We demonstrate that the variation in peak heights itself encodes novel information which can be used for basecalling. To isolate this information for a clear demonstration, we perform a peculiar blind basecalling experiment using ABI processed output. Using classifiers responding to measurements in the context of the basecalling position, we call bases without reference to the peak heights at the basecalling position itself. Tree classifiers indicate which features are pertinent, and the application of neural nets to these features results in a startlingly high initial success rate of 78%. Our analysis indicates that we can make viable basecalls using information that has never been accessed before
Analysis of integrated boost-flyback step-up converter (2005)

The operating principles, theoretical analysis, and design methodology of a high-efficiency step-up converter are presented. The integrated boost-flyback converter (IBFC) uses coupled-inductor techniques to achieve high step-up voltage with low duty ratio, and thus the slope compensation circuit is disregarded. The voltage gain and efficiency at steady state are derived using the principles of inductor volt–second balance, capacitor charge balance and the small-ripple approximation for continuous-conduction mode. Finally, a 35 W, 12 V DC input, 48 V DC output, fsw=40 kHz IBFC has been implemented in the laboratory to validate the theoretical analysis. A design procedure is expounded, and design guidelines for selecting critical components are also presented. It is shown that high voltage gain with high efficiency can be achieved by the IBFC system.
Bioengineering of Therapeutic Aerosols (2002)

The new field of therapeutic aerosol bioengineering (TAB), driven primarily by the medical need for inhaled insulin, is now expanding to address medical needs ranging from respiratory to systemic diseases, including asthma, growth deficiency, and pain. Bioengineering of therapeutic aerosols involves a level of aerosol particle design absent in traditional therapeutic aerosols, which are created by conventionally spraying a liquid solution or suspension of drug or milling and mixing a dry drug form into respirable particles. Bioengineered particles may be created in liquid form from devices specially designed to create an unusually fine size distribution, possibly with special purity properties, or solid particles that possess a mixture of drug and excipient, with designed shape, size, porosity, and drug release characteristics. Such aerosols have enabled several high-visibility clinical programs of inhaled insulin, as well as earlier-stage programs involving inhaled morphine, growth hormone, beta-interferon, alpha-1-antitrypsin, and several asthma drugs. The design of these aerosols, limited by partial knowledge of the lungs' physiological environment, and driven largely at this stage by market forces, relies on a mixture of new and old science, pharmaceutical science intuition, and a degree of biological-impact empiricism that speaks to the importance of an increased level of academic involvement.
OPG and PTH-(1–34) Have Additive Effects on Bone Density and Mechanical Strength in Osteopenic Ovariectomized Rats (2001)

PTH is a potent bone anabolic factor, and its combination with antiresorptive agents has been proposed as a therapy for osteoporosis. We tested the effects of PTH, alone and in combination with the novel antiresorptive agent OPG, in a rat model of severe osteopenia. Sprague Dawley rats were sham-operated or ovariectomized at 3 months of age. Rats were untreated for 15 months, at which time ovariectomy had caused significant decreases in bone mineral density in the lumbar vertebrae and femur. Rats were then treated for 5.5 months with vehicle (PBS), human PTH-(1-34) (80 microg/kg), rat OPG (10 mg/kg), or OPG plus PTH (all three times per wk, sc). Treatment of ovariectomized rats with OPG or PTH alone increased bone mineral density in the lumbar vertebrae and femur, whereas PTH plus OPG caused significantly greater and more rapid increases than either therapy alone (P < 0.05). OPG significantly reduced osteoclast surface in the lumbar vertebrae and femur (P < 0.05 vs. sham or ovariectomized), but had no effect on osteoblast surface at either site. Ovariectomy significantly decreased the mechanical strength of the lumbar vertebrae and femur. In the lumbar vertebrae, OPG plus PTH was significantly more effective than PTH alone at reversing ovariectomy-induced deficits in stiffness and elastic modulus. These data suggest that OPG plus PTH represent a potentially useful therapeutic option for patients with severe osteoporosis.
Heat flow analysis of long-wavelength VCSELs with various DBR materials (2002)

The paper utilizes finite element analysis to systematically investigate heat flux and thermal resistance of lasers with different combinations of a bottom DBR (InGaAsP/InP, AlAs/GaAs, or SiO/sub 2//Si) and a top DBR. The latter consists of pairs of a low index material (SiO/sub 2/, Al/sub 2/O/sub 3/, CaF/sub 2/, Si/sub 3/N/sub 4/, MgO, or BeO) and a high index material (Si, TiO/sub 2/, ZnSe, or SiC). 1.55 /spl mu/m VCSELs with polyimide or InP insulating regrowth in top-up or top-down mounting are considered.
[Expression and clinical significance of COX-2, p-Stat3, and p-Stat5 in esophageal carcinoma]. (2007)

The up-regulation of COX-2, p-Stat3, and p-Stat5 may be correlated to the carcinogenesis of ESCC. The activation of Stat3 is correlated to the aggressive behavior of ESCC.
Proteolytic activity in leg ulcer exudate (1993)

Twenty-five leg ulcer exudate samples from 17 patients with chronic non-healing venous leg ulcer were analyzed for proteolytic activity using radial caseinolysis procedures and zymographic analysis, and for fibronectin fragmentation using immunoblotting technology. Caseinolytic activity was detected in 21 of the 25 samples. A minority of them were inhibited (3 were totally, 6 partially inhibited) by aprotinin, a serine proteinase inhibitor, suggesting that proteinase(s) other than plasmin were also responsible for the caseinolysis. In zymographic analysis, 23 of the 25 samples showed positive reactions for enzyme activities comigrating with plasmin and urokinase-type plasminogen activator. Fibronectin fragmentation, another sign of proteolytic activity, was seen in all but 2 ulcers. No correlation was seen between bacterial infection or inflammatory cells and the above parameters in the wound fluid. Acute wound fluid collected from the donor sites of patients undergoing split skin grafting was used as a control. In the control specimens no proteolytic activity was found during the days following operation. These results show that there is proteolytic activity in the chronic ulcer exudate and support the possibility that the proteolytic activity and consequent fibronectin fragmentation may be related to the retarded epithelization and ulcer healing.
Alignment of carbon nanotubes in a polymer matrix by mechanical stretching (1998)

We report a method to fabricate polymer-based composites with aligned carbon nanotubes, and a procedure to determine the nanotube orientation and the degree of alignment. The composites were fabricated by casting a suspension of carbon nanotubes in a solution of a thermoplastic polymer and chloroform. They were uniaxially stretched at 100 °C and were found to remain elongated after removal of the load at room temperature. The orientation and the degree of alignment were determined by x-ray diffraction. The dispersion and the alignment of the nanotubes were also studied by transmission electron microscopy.
LightSaber: Efficient Window Aggregation on Multi-core Processors (2020)

Window aggregation queries are a core part of streaming applications. To support window aggregation efficiently, stream processing engines face a trade-off between exploiting parallelism (at the instruction/multi-core levels) and incremental computation (across overlapping windows and queries). Existing engines implement ad-hoc aggregation and parallelization strategies. As a result, they only achieve high performance for specific queries depending on the window definition and the type of aggregation function. We describe a general model for the design space of window aggregation strategies. Based on this, we introduce LightSaber, a new stream processing engine that balances parallelism and incremental processing when executing window aggregation queries on multi-core CPUs. Its design generalizes existing approaches: (i) for parallel processing, LightSaber constructs a parallel aggregation tree (PAT) that exploits the parallelism of modern processors. The PAT divides window aggregation into intermediate steps that enable the efficient use of both instruction-level (i.e., SIMD) and task-level (i.e., multi-core) parallelism; and (ii) to generate efficient incremental code from the PAT, LightSaber uses a generalized aggregation graph (GAG), which encodes the low-level data dependencies required to produce aggregates over the stream. A GAG thus generalizes state-of-the-art approaches for incremental window aggregation and supports work-sharing between overlapping windows. LightSaber achieves up to an order of magnitude higher throughput compared to existing systems-on a 16-core server, it processes 470 million records/s with 132 ?s average latency.
Common DNS Implementation Errors and Suggested Fixes (1993)

This memo describes common errors seen in DNS implementations and suggests some fixes. Where applicable, violations of recommendations from STD 13, RFC 1034 and STD 13, RFC 1035 are mentioned. The memo also describes, where relevant, the algorithms followed in BIND (versions 4.8.3 and 4.9 which the authors referred to) to serve as an example.
Angiotensin-(1–7) Attenuates the Development of Heart Failure After Myocardial Infarction in Rats (2002)

Angiotensin-(1-7) preserved cardiac function, coronary perfusion, and aortic endothelial function in a rat model for heart failure.
Quantification and monitoring of visual disturbances for patients with cataracts using Halo v1.0 software (2013)

We objectively measured optical quality and quantified such night- vision disturbances as glare, starbursts, and halos perceived by patients diagnosed with cataracts. For this purpose, retinal-image quality was measured with a double-pass device (OQAS, Visiometrics SL). Visual-discrimination capacity was quantified by the disturbance index under low illumination (Halo v1.0 software, Laboratory of Vision Sciences and Applications). We took data for 15 normal subjects and 15 subjects affected by cataracts. Cataract patients had worse optical quality, and also showed a more extended double-pass image due to a higher contribution of ocular scattering and aberrations. Furthermore, results from the Halo test reflected a higher disturbance index for pathological subjects and, consequently, a deterioration in visual performance. Halo v1.0 software could be useful in daily clinical practice for characterizing the time course of visual disturbances shown by subjects with increased lens opacity, after ocular surgery or secondary to other ocular pathologies.
A Controlled Trial of HA-1A in a Canine Model of Gram-negative Septic Shock (1993)

In a canine model of E coli sepsis, HA-1A did not alter levels of bacteremia or endotoxemia and actually decreased survival. If these data are relevant to human septic shock, HA-1A therapy should be limited until the conditions under which this monoclonal antibody has beneficial or deleterious effects are more completely defined.
Interleukin-2 after autologous bone marrow transplantation as consolidative immunotherapy against minimal residual disease. (1990)

Recipients of autologous BMT demonstrate clinically significant immune deficiency, particularly involving the T lymphocytes. While quantitatively the immune system generally returns to normal during the first 3 months, there is a prolonged delay in the recovery of qualitative immune functions. T cell proliferation is impaired immediately after transplantation and slowly recovers over a period of more than 1 year. In addition, a defect has been documented in IL-2 producing cells and may be of major importance in the pathophysiology of this immunodeficiency. However, post-ABMT, PHA-stimulated T cells are TAC+ and are able to respond to exogenous IL-2 in vitro. Very early after ABMT, NK and LAK activities of PBMC normalize but are significantly increased in vitro by IL-2. On this basis, a clinical assessment of rIL-2 administration on the immunological reconstitution of ABMT patients and as consolidation immunotherapy against minimal disease has been initiated in a phase I/II study.
Production of interleukin‐6 in contracting human skeletal muscles can account for the exercise‐induced increase in plasma interleukin‐6 (2000)

1. Plasma interleukin (IL)-6 concentration is increased with exercise and it has been demonstrated that contracting muscles can produce IL-The question addressed in the present study was whether the IL-6 production by contracting skeletal muscle is of such a magnitude that it can account for the IL-6 accumulating in the blood. 2. This was studied in six healthy males, who performed one-legged dynamic knee extensor exercise for 5 h at 25 W, which represented 40% of peak power output (Wmax). Arterial-femoral venous (a-fv) differences over the exercising and the resting leg were obtained before and every hour during the exercise. Leg blood flow was measured in parallel by the ultrasound Doppler technique. IL-6 was measured by enzyme-linked immunosorbent assay (ELISA). 3. Arterial plasma concentrations for IL-6 increased 19-fold compared to rest. The a-fv difference for IL-6 over the exercising leg followed the same pattern as did the net IL-6 release. Over the resting leg, there was no significant a-fv difference or net IL-6 release. The work was produced by 2.5 kg of active muscle, which means that during the last 2 h of exercise, the median IL-6 production was 6.8 ng min-1 (kg active muscle)-1 (range, 3.96-9.69 ng min-1 kg-1). 4. The net IL-6 release from the muscle over the last 2 h of exercise was 17-fold higher than the elevation in arterial IL-6 concentration and at 5 h of exercise the net release during 1 min was half of the IL-6 content in the plasma. This indicates a very high turnover of IL-6 during muscular exercise. We suggest that IL-6 produced by skeletal contracting muscle contributes to the maintenance of glucose homeostasis during prolonged exercise.
Are Tau Aggregates Toxic or Protective in Tauopathies? (2013)

Aggregation of highly phosphorylated tau into aggregated forms such as filaments and neurofibrillary tangles is one of the defining pathological hallmarks of Alzheimer's disease and other tauopathies. Hence therapeutic strategies have focused on inhibition of tau phosphorylation or disruption of aggregation. However, animal models imply that tau-mediated dysfunction and toxicity do not require aggregation but instead are caused by soluble hyper-phosphorylated tau. Over the years, our findings from a Drosophila model of tauopathy have reinforced this. We have shown that highly phosphorylated wild-type human tau causes behavioral deficits resulting from synaptic dysfunction, axonal transport disruption, and cytoskeletal destabilization in vivo. These deficits are evident in the absence of neuronal death or filament/tangle formation. Unsurprisingly, both pharmacological and genetic inhibition of GSK-3β rescue these tau phenotypes. However, GSK-3β inhibition also unexpectedly increases tau protein levels, and produces insoluble granular tau oligomers. As well as underlining the growing consensus that tau toxicity is mediated by a highly phosphorylated soluble tau species, our findings further show that not all insoluble tau aggregates are toxic. Some tau aggregates, in particular tau oligomers, are non-toxic, and may even be protective against tau toxicity in vivo. This has serious implications for emerging therapeutic strategies to dissolve tau aggregates, which might be ineffective or even counter-productive. In light of this, it is imperative to identify the key toxic tau species and to understand how it mediates dysfunction and degeneration so that the effective disease-modifying therapies can be developed.
Neuroblast mitosis in dissociated culture: regulation and relationship to differentiation. (1990)

Although neuron generation is precisely regulated during ontogeny, little is known about underlying mechanisms. In addition, relationships between precursor proliferation and the apparent sequence of developmental processes, including cell migration, neurite elaboration, transmitter expression and synaptogenesis remain unknown. To address these issues, we used a fully defined neuronal cell culture system derived from embryonic rat sympathetic ganglia (DiCicco-Bloom, E., and I. B. Black. 1988. Proc. Natl. Acad. Sci. USA. 85:4066-4070) in which precursors enter the mitotic cycle. We now find that, in addition to synthesizing DNA, neuroblasts also underwent division in culture, allowing analysis of developmental relationships and mitotic regulation. Our observations indicate that mitotic neuroblasts expressed a wide array of neuron-specific characteristics including extension of neuritic processes with growth cones, elaboration of neurotransmitter enzyme, synthesis and transport of transmitter vesicles and organization of transmitter release sites. These data suggest that neuroblasts in the cell cycle may simultaneously differentiate. Consequently, the apparent sequence of ontogenetic processes is not an immutable, intrinsic neuronal program. How, then, are diverse developmental events coordinated? Our observations indicate that neuroblast mitosis is regulated by a small number of epigenetic factors, including insulin and EGF. Since these signals also influence other processes in developing neurons, epigenetic regulation normally may synchronize diverse ontogenetic events.
Type Less, Find More: Fast Autocompletion Search with a Succinct Index (2006)

We consider the following full-text search autocompletion feature. Imagine a \nuser of a search engine typing a query. Then with every letter being typed, we \nwould like an instant display of completions of the last query word which would \nlead to good hits. At the same time, the best hits for any of these completions \nshould be displayed. Known indexing data structures that apply to this problem \neither incur large processing times for a substantial class of queries, or they \nuse a lot of space. We present a new indexing data structure that uses no more \nspace than a state-of-the-art compressed inverted index, but with 10 times \nfaster query processing times. Even on the large TREC Terabyte collection, \nwhich comprises over 25 million documents, we achieve, on a single machine and \nwith the index on disk, average response times of one tenth of a second. We \nhave built a full-fledged, interactive search engine that realizes the proposed \nautocompletion feature combined with support for proximity search, \nsemi-structured (XML) text, subword and phrase completion, and semantic tags.
Direct detection of dystrophin gene rearrangements by analysis of dystrophin mRNA in peripheral blood lymphocytes. (1991)

Using 10 overlapping nested sets of primers and using peripheral blood lymphocyte (PBL) total RNA as template, we have developed a system, based on PCR, which allows the rapid production of double-stranded cDNA corresponding to the entire coding sequence of the dystrophin gene. The product can be visualized on native minigels by ethidium staining and directly sequenced after gel purification. We have used this system to analyze the structures of PBL dystrophin mRNA in 26 Duchenne, Becker, or intermediate muscular dystrophy patients who have gross rearrangements of the dystrophin gene. In each case, the effect that the genomic rearrangement has on the structure of the transcript--and, by inference, on the dystrophin protein--has been determined, and the results confirm the frameshift hypothesis. The study also identifies a series of alternatively spliced transcripts which are specific to the rearranged genotypes and which seem therefore to arise following the alteration in the context of the splice signal. The system has been used for unambiguous identification of carrier females. Furthermore, the rapid production of microgram quantities of dystrophin cDNA from a readily accessible tissue makes point-mutation screening a practical proposition.