gebhart/patrepeval huggingface dataset:
Cholinergic and Purinergic Neurohumoral Signalling in the Inner Ear: A Molecular Physiological Analysis (1997)

The ability to identify the expression of the protein subunits which assemble to form ionotropic receptors for acetylcholine and extracellular adenosine 5'-triphosphate (ATP) in individual cells of the inner ear provides examples of the high resolution and exquisite sensitivity which molecular biology brings to the study of hearing and balance. The data from these studies provide both fine detail with respect to the classification of the elements involved and an overview of the sites of potential interaction of both extracellular and intracellular signalling pathways. The high sensitivity necessitates a molecular physiological approach when using these techniques so that these data on the site and extent of expression can be balanced against functional significance. With the demonstration of expression of the alpha 9 subunit of the nicotinic acetylcholine receptor in cochlear outer hair cells, molecular biology has provided an explanation for the unusual cholinergic receptor pharmacology of the olivocochlear efferent innervation which has confounded investigators for decades. In addition, a role for extracellular ATP as a signalling molecule regulating electrochemical gradients and neurotransmission within the inner ear is supported by the extent of P2 receptor expression in this tissue, data which beg for intense functional study.
Evidence of proteoglycan/proteoglycan interactions within aggregates (1991)

Nonaggregated proteoglycan monomers, digested fragments of the monomers, as well as link proteins have been shown to self-associate. These associations have not been shown to occur on the aggregate. However, previous reports, using the Kleinschmidt technique of monolayer electron microscopy, have noted proteoglycan subunits on the aggregate that appear to interact, either as branched proteoglycans or as proteoglycan subunits that appear to share the same attachment site on the hyaluronic acid chain. Branching and shared attachments were noted in all aggregates analyzed in this study. Increasing the average space between proteoglycan subunits on the reconstituted aggregate resulted in a significant decrease in branched proteoglycans, indicating either a weak association occurring on the aggregate, or an artifact created by a three-dimensional structure being reduced to a two-dimensional monolayer image. The shared attachments were independent of both the presence of link proteins and changes in spacing between proteoglycans, suggesting a proteoglycan-proteoglycan interaction occurring before aggregation. The interactions were not influenced by proteoglycan concentration at the time of aggregation. Link proteins, however, did increase the number of proteoglycans on the aggregate that could be cross-linked with a bifunctional reagent, suggesting that link proteins facilitate proteoglycan-proteoglycan interactions.
Accelerating the Development of Software-Defined Network Optimization Applications Using SOL (2015)

Software-defined networking (SDN) can enable diverse network management applications such as traffic engineering, service chaining, network function outsourcing, and topology reconfiguration. Realizing the benefits of SDN for these applications, however, entails addressing complex network optimizations that are central to these problems. Unfortunately, such optimization problems require significant manual effort and expertise to express and non-trivial computation and/or carefully crafted heuristics to solve. Our vision is to simplify the deployment of SDN applications using general high-level abstractions for capturing optimization requirements from which we can efficiently generate optimal solutions. To this end, we present SOL, a framework that demonstrates that it is indeed possible to simultaneously achieve generality and efficiency. The insight underlying SOL is that SDN applications can be recast within a unifying path-based optimization abstraction, from which it efficiently generates near-optimal solutions, and device configurations to implement those solutions. We illustrate the generality of SOL by prototyping diverse and new applications. We show that SOL simplifies the development of SDN-based network optimization applications and provides comparable or better scalability than custom optimization solutions.
Perspectives on Sharing Models and Related Resources in Computational Biomechanics Research (2017)

The role of computational modeling for biomechanics research and related clinical care will be increasingly prominent. The biomechanics community has been developing computational models routinely for exploration of the mechanics and mechanobiology of diverse biological structures. As a result, a large array of models, data, and discipline-specific simulation software has emerged to support endeavors in computational biomechanics. Sharing computational models and related data and simulation software has first become a utilitarian interest, and now, it is a necessity. Exchange of models, in support of knowledge exchange provided by scholarly publishing, has important implications. Specifically, model sharing can facilitate assessment of reproducibility in computational biomechanics and can provide an opportunity for repurposing and reuse, and a venue for medical training. The community's desire to investigate biological and biomechanical phenomena crossing multiple systems, scales, and physical domains, also motivates sharing of modeling resources as blending of models developed by domain experts will be a required step for comprehensive simulation studies as well as the enhancement of their rigor and reproducibility. The goal of this paper is to understand current perspectives in the biomechanics community for the sharing of computational models and related resources. Opinions on opportunities, challenges, and pathways to model sharing, particularly as part of the scholarly publishing workflow, were sought. A group of journal editors and a handful of investigators active in computational biomechanics were approached to collect short opinion pieces as a part of a larger effort of the IEEE EMBS Computational Biology and the Physiome Technical Committee to address model reproducibility through publications. A synthesis of these opinion pieces indicates that the community recognizes the necessity and usefulness of model sharing. There is a strong will to facilitate model sharing, and there are corresponding initiatives by the scientific journals. Outside the publishing enterprise, infrastructure to facilitate model sharing in biomechanics exists, and simulation software developers are interested in accommodating the community's needs for sharing of modeling resources. Encouragement for the use of standardized markups, concerns related to quality assurance, acknowledgement of increased burden, and importance of stewardship of resources are noted. In the short-term, it is advisable that the community builds upon recent strategies and experiments with new pathways for continued demonstration of model sharing, its promotion, and its utility. Nonetheless, the need for a long-term strategy to unify approaches in sharing computational models and related resources is acknowledged. Development of a sustainable platform supported by a culture of open model sharing will likely evolve through continued and inclusive discussions bringing all stakeholders at the table, e.g., by possibly establishing a consortium.
Methylenetriphenylphosphorane, Polystyrene-supported (2004)

[3487-44-3] (a cross-linked polystyrene, 1% or 2% divinylbenzene, used as a reagent in Wittig reactions) Alternate Name: methylenetriphenylphosphorane, polymer- supported. Physical Data: the ylide on solid support is usually highly colored. Solubility: this is an insoluble polymer-bound reagent that is incompatible with solvents that do not swell gel-type polystyrene (for example, H2O, ethanol, isopropanol). The phosphorous ylide is usually prepared in THF and the subsequent reactions are run in the same solvent. However, the reagent is compatible with DMF, THF, DCM, benzene, and other non-acidic solvents that swell gel-type polystyrene. Form Supplied in: not commercially available but the precursor polystyrene-supported triphenylphosphine is commercially available in various loadings (1–3 mmol/g). Analysis of Reagent Purity: combustion analysis, Fourier transform infrared spectroscopy. Although the ylide has not been directly analyzed, it is possible to quantify the amount of phosphonium salt by ion-exchange analysis.2 Preparative Methods: the reagent is prepared in two steps from commercially available polystyrene-supported triphenylphosphine.2-4 Alkylation of the phosphine followed by deprotonation of the corresponding phosphonium salt provides the ylide which is usually used directly in a subsequent reaction. Handling, Storage, and Precautions: the reagent is prepared in situ from polystyrene-supported methyl triphenylphosphonium halide which is stable at room temperature; the ylide should be used immediately after its formation.
Genesis of the round window rupture syndrome; some experimental observations (1978)

Abstract Clinical and experimental evidence has revealed that rupture of the round window membrane, by itself, is not a major cause of sensorineural hearing loss. Eighteen guinea pigs underwent removal of the round window. The status of cochlear function was determined by recording the cochlear microphonic. An average loss of only about 6 db was observed after surgery. It is felt that there must commonly be more cochlear damage concurrent with window rupture to explain the significant and often relatively immediate hearing losses seen in clinical practice. The site(s) of this primary trauma has not yet been discovered, but it would seem reasonable in the light of recent reports that the perilymphatic vessels, the vas spirale, the stria vascularis and/or the integrity of the cochlear duct might be involved in the genesis of this hearing loss. We propose that the term “round window rupture syndrome” be used as a more accurate description of this entity. The round window damage provides evidence of more devastating trauma within the cochlea. Thus, the clinician, being alerted, should not stop his therapeutic efforts with surgical closure of the RW. Better prognosis for the patient, as well as leading into new avenues for the investigation of cochlear function, would be the result.
Zeolite Catalysts for Green Production of Caprolactam (2022)

Caprolactam is an important petrochemical platform molecule that has been widely used to prepare nylon-6 and other polyamide engineering plastics. Compared with traditional routes in caprolactam synthesis with environmentally unfriendly wastes, a recent green route involves benzene semihydrogenation, cyclohexene hydration, cyclohexanol dehydrogenation, cyclohexanone ammoximation, and Beckmann rearrangement. In most of these reactions, zeolite catalysts have displayed crucial roles, for example, ZSM-5 zeolite for hydration, TS-1 zeolite for ammoximation, and S-1 zeolite for Beckmann rearrangement. In this Review, these processes and the catalytic performances of different zeolite catalysts are summarized, and the significant advantages of zeolites compared with the previous homogeneous catalysts and general supported catalysts are mentioned. In addition, the structure–performance interplay of these zeolites was particularly discussed, which is expected to guide the development of more efficient zeolite catalysts with optimized structures in the future.
Enhancement of Neuroplastic P2 and N1c Auditory Evoked Potentials in Musicians (2003)

P2 and N1c components of the auditory evoked potential (AEP) have been shown to be sensitive to remodeling of the auditory cortex by training at pitch discrimination in nonmusician subjects. Here, we investigated whether these neuroplastic components of the AEP are enhanced in musicians in accordance with their musical training histories. Highly skilled violinists and pianists and nonmusician controls listened under conditions of passive attention to violin tones, piano tones, and pure tones matched in fundamental frequency to the musical tones. Compared with nonmusician controls, both musician groups evidenced larger N1c (latency, 138 msec) and P2 (latency, 185 msec) responses to the three types of tonal stimuli. As in training studies with nonmusicians, N1c enhancement was expressed preferentially in the right hemisphere, where auditory neurons may be specialized for processing of spectral pitch. Equivalent current dipoles fitted to the N1c and P2 field patterns localized to spatially differentiable regions of the secondary auditory cortex, in agreement with previous findings. These results suggest that the tuning properties of neurons are modified in distributed regions of the auditory cortex in accordance with the acoustic training history (musical- or laboratory-based) of the subject. Enhanced P2 and N1c responses in musicians need not be considered genetic or prenatal markers for musical skill.
Liver Angiotensinogen Is the Primary Source of Renal Angiotensin II (2012)

Angiotensin II content in the kidney is much higher than in the plasma, and it increases more in kidney diseases through an uncertain mechanism. Because the kidney abundantly expresses angiotensinogen mRNA, transcriptional dysregulation of angiotensinogen within the kidney is one potential cause of increased renal angiotensin II in the setting of disease. Here, we observed that kidney-specific angiotensinogen knockout mice had levels of renal angiotensinogen protein and angiotensin II that were similar to those levels of control mice. In contrast, liver-specific knockout of angiotensinogen nearly abolished plasma and renal angiotensinogen protein and renal tissue angiotensin II. Immunohistochemical analysis in mosaic proximal tubules of megalin knockout mice revealed that angiotensinogen protein was incorporated selectively in megalin-intact cells of the proximal tubule, indicating that the proximal tubule reabsorbs filtered angiotensinogen through megalin. Disruption of the filtration barrier in a transgenic mouse model of podocyte-selective injury increased renal angiotensin II content and markedly increased both tubular and urinary angiotensinogen protein without an increase in renal renin activity, supporting the dependency of renal angiotensin II generation on filtered angiotensinogen. Taken together, these data suggest that liver-derived angiotensinogen is the primary source of renal angiotensinogen protein and angiotensin II. Furthermore, an abnormal increase in the permeability of the glomerular capillary wall to angiotensinogen, which characterizes proteinuric kidney diseases, enhances the synthesis of renal angiotensin II.
Importance of margin width in breast‐conserving treatment of early breast cancer (2016)

An overall low rate of IBTR was observed. A final positive margin was associated with a more than twofold risk of IBTR. There was no evidence for better local control with wider margins, but the data were insufficient to show whether narrow margins were as good as wider negative margins in terms of local control. J. Surg. Oncol. 2016;113:609-615. © 2016 Wiley Periodicals, Inc.
Digital Imaging of Black and White Photomicrographs (1998)

The publication of black and white photomicrographs has a long tradition in pathology. High-resolution film and quality objectives have been the backbone of generating quality photomicrographs suitable for publication. However, the digital imaging revolution has changed the way we view and capture images. As the quality of image capture devices increases and as their price decreases, more and more investigators are using digital imaging, and the use of color digital imaging for teleconferencing, telediagnosis, and reproduction is now well established. The purpose of this study was to determine the file sizes needed to obtain publication-quality black and white images using digital imaging technology. In this study, four experts in renal pathology reviewed 70 black and white images of various file sizes obtained from specimens representing a variety of renal histopathology. Without knowledge of the file size, the four renal pathologists graded the degree of pixelation, and the overall diagnostic and publication quality of the images. In all cases, digital imaging was capable of obtaining publication quality images equal to those achieved using film. The file size needed to achieve publication quality black and white images depended on magnification, with lower magnification images requiring larger file sizes.
Study of the dependence of human monocytes and macrophages antitumoral properties upon TNF-alpha expression or release. (1990)

This study compares the antitumoral properties of isolated circulating human blood monocytes (Mo) and of mature macrophages (MO) obtained by 7 days differentiation of Mo or isolated from alveolar washing. These cells were activated to cytotoxicity in the presence of recombinant human interferon-gamma (rHuIFN-gamma). This antitumoral effect was measured at a low (1/1) effector/target ratio without pretreatment of the tumor cells. Activated Mo released tumor necrosis factor-alpha (TNF-alpha) in the culture medium where their antitumoral activity could be totally neutralized by specific anti-rHuTNF-alpha antibodies. In contrast, blood monocytes derived macrophages differentiated and activated in vitro expressed TNF-alpha on their membrane where it could be labelled and partially neutralized by anti-rHuTNF-alpha antibodies. Direct effector/target contact was required for the activity of macrophages differentiated in culture or collected from the lung cavity of healthy subjects. When these macrophages were obtained from infected patients or subjected to LPS treatment, they directly released cytotoxic amounts of TNF in the extracellular fluid after activation with IFN-gamma. Monocytes act mainly by soluble mediators (TNF-alpha being a key factor), while differentiated macrophages in the absence of endotoxin act by close cell to cell contact involving the lytic action of membranous TNF-alpha as well as some release of soluble TNF-alpha. We also present evidences (based on the use of various protease inhibitors) that the role of proteases is much less crucial in the cytotoxic action of monocytes and macrophages.
The Genome Sequence of the Eastern Woodchuck (Marmota monax) – A Preclinical Animal Model for Chronic Hepatitis B (2019)

The Eastern woodchuck (<i>Marmota monax</i>) has been extensively used in research of chronic hepatitis B and liver cancer because its infection with the woodchuck hepatitis virus closely resembles a human hepatitis B virus infection. Development of novel immunotherapeutic approaches requires genetic information on immune pathway genes in this animal model. The woodchuck genome was assembled with a combination of high-coverage whole-genome shotgun sequencing of Illumina paired-end, mate-pair libraries and fosmid pool sequencing. The result is a 2.63 Gigabase (Gb) assembly with a contig N50 of 74.5 kilobases (kb), scaffold N50 of 892 kb, and genome completeness of 99.2%. RNA sequencing (RNA-seq) from seven different tissues aided in the annotation of 30,873 protein-coding genes, which in turn encode 41,826 unique protein products. More than 90% of the genes have been functionally annotated, with 82% of them containing open reading frames. This genome sequence and its annotation will enable further research in chronic hepatitis B and hepatocellular carcinoma and contribute to the understanding of immunological responses in the woodchuck.
VCSEL to VCSEL Injection Locking for Uncompensated 40-km Transmission at 10 Gb/s (2009)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text P. Boffi, A. Boletti, A. Gatto, and M. Martinelli, "VCSEL to VCSEL Injection Locking for Uncompensated 40-km Transmission at 10 Gb/s," in Optical Fiber Communication Conference and National Fiber Optic Engineers Conference, OSA Technical Digest (CD) (Optica Publishing Group, 2009), paper JThA32. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Molecular biology of demosponge axial filaments and their roles in biosilicification (2003)

For hundreds of years, the skeletal elements of marine and freshwater sponges have intrigued investigators with a diverse array of remarkably complex morphologies. Early studies of demosponge monaxonal megascleres revealed the presence of a central organic axial filament running their entire length. Until recently, however, the precise function of these axial filaments was largely unknown. The spicules from the temperate Eastern Pacific demosponge, Tethya aurantia, comprise approximately 75% of the dry weight of this species, facilitating the large-scale isolation and purification of the biosilica-associated proteins. Silicateins, the most abundant proteins comprising the axial filaments of these spicules, prove to be members of a well-known superfamily of proteolytic and hydrolytic enzymes and can be easily collected after silica demineralization with hydrofluoric acid. Consistent with these findings, the intact filaments are more than simple, passive templates; in vitro, they actively catalyze and spatially direct the hydrolysis and polycondensation of silicon alkoxides to yield silica at neutral pH and low temperature. Catalytic activity also is exhibited by the monomeric subunits obtained by disaggregation of the protein filaments and those produced from recombinant DNA templates cloned in bacteria. These proteins also can be used to direct the polymerization of organosilicon polymers (silicones) from the corresponding organically functionalized silicon alkoxides. Based on these observations, the silicateins are currently being used as models for the design of biomimetic agents with unique catalytic and structure-directing properties. The presence of axial filaments in a diversity of spicule types and the evolutionary implications of these findings are also discussed.
Supplementary Figure S3 from Tumor Cell–Autonomous SHP2 Contributes to Immune Suppression in Metastatic Breast Cancer (2023)

&lt;p&gt;Corresponding representative dot plots for the quantification in figure 2A and additional T cell composition analysis in the study of D2.A1 model.&lt;/p&gt;
Recombinant human tumour necrosis factor (rTNF)2 enhances leukotriene biosynthesis in neutrophils and eosinophils stimulated with the Ca2+ ionophore A23187. (1987)

Recombinant human tumour necrosis factor alpha (rTNF) did not cause the release of leukotrienes (LT) by human neutrophils and eosinophils. It did, however, prepare neutrophils and eosinophils for enhanced production of LT after activation with the calcium ionophore A23187. The effect was observed with 10(2) to 10(4) units/ml of rTNF which enhanced LTB4 production by ionophore-stimulated neutrophils, by 40 to 400%, while 10(3) to 10(4) units/ml of rTNF increased LTC4 production by ionophore-stimulated eosinophils by 30 to 120%. The enhancement was observed when granulocytes were incubated for 5 to 10 min with rTNF before stimulation with the ionophore. Increased leukotriene production was attributed to the induction of fatty acid hydrolase and/or 5-lipoxygenase activities on the basis of the increment in the total counts released after 3H-arachidonic acid labelling of neutrophils pretreated with rTNF as compared to control medium.
Risk factors for the recurrence of cervical cancer using MR-based T1 mapping: A pilot study (2023)

Quantitative T1 mapping could help identify CC patients with a high risk of recurrence, supplementing information on tumor prognosis other than clinicopathological features and providing the basis for individualized treatment and follow-up schemes.