gebhart/patrepeval huggingface dataset:
Upregulation of osmo-mechanosensitive TRPV4 channel facilitates chronic hypoxia-induced myogenic tone and pulmonary hypertension (2011)

Chronic hypoxia causes pulmonary hypertension with vascular remodeling, increase in vascular tone, and altered reactivity to agonists. These changes involve alterations in multiple Ca(2+) pathways in pulmonary arterial smooth muscle cells (PASMCs). We have previously shown that vanilloid (TRPV)- and melastatin-related transient receptor potential (TRPM) channels are expressed in pulmonary arteries (PAs). Here we found that TRPV4 was the only member of the TRPV and TRPM subfamilies upregulated in PAs of chronic hypoxic rats. The increase in TRPV4 expression occurred within 1 day of hypoxia exposure, indicative of an early hypoxic response. TRPV4 in PASMCs were found to be mechanosensitive. Osmo-mechanical stress imposed by hypotonic solution activated Ca(2+) transients; they were inhibited by TRPV4 specific short interfering RNA, the TRPV blocker ruthenium red, and the cytochrome P450 epoxygenase inhibitor N-(methylsulfonyl)-2-(2-propynyloxy)-benzenehexanamide. Consistent with TRPV4 upregulation, the Ca(2+) response induced by the TRPV4 agonist 4α-phorbol 12,13-didecanoate and hypotonicity was potentiated in hypoxic PASMCs. Moreover, a significant myogenic tone, sensitive to ruthenium red, was observed in pressurized endothelium denuded small PAs of hypoxic but not normoxic rats. The elevated basal intracellular Ca(2+) concentration in hypoxic PASMCs was also reduced by ruthenium red. In extension of these results, the development of pulmonary hypertension, right heart hypertrophy, and vascular remodeling was significantly delayed and suppressed in hypoxic trpv4(-/-) mice. These results suggest the novel concept that TRPV4 serves as a signal pathway crucial for the development of hypoxia-induced pulmonary hypertension. Its upregulation may provide a pathogenic feed-forward mechanism that promotes pulmonary hypertension via facilitated Ca(2+) influx, subsequently enhanced myogenic tone and vascular remodeling.
Ceramide turnover in GtoPdb v.2023.1 (2023)

Ceramides are a family of sphingophospholipids synthesized in the endoplasmic reticulum, which mediate cell stress responses, including apoptosis, autophagy and senescence, Serine palmitoyltransferase generates 3-ketosphinganine, which is reduced to dihydrosphingosine. N-Acylation allows the formation of dihydroceramides, which are subsequently reduced to form ceramides. Once synthesized, ceramides are trafficked from the ER to the Golgi bound to the ceramide transfer protein, CERT (COL4A3BP, Q9Y5P4). Ceramide can be metabolized via multiple routes, ensuring tight regulation of its cellular levels. Addition of phosphocholine generates sphingomyelin while carbohydrate is added to form glucosyl- or galactosylceramides. Ceramidase re-forms sphingosine or sphinganine from ceramide or dihydroceramide. Phosphorylation of ceramide generates ceramide phosphate. The determination of accurate kinetic parameters for many of the enzymes in the sphingolipid metabolic pathway is complicated by the lipophilic nature of the substrates.
Complex Coacervate Core Micelles Containing Poly(vinyl alcohol) Inhibit Ice Recrystallization (2018)

Complex coacervate core micelles (C3Ms) form upon complexation of oppositely charged copolymers. These co-assembled structures are widely investigated as promising building blocks for encapsulation, nanoparticle synthesis, multimodal imaging, and coating technology. Here, the impact on ice growth is investigated of C3Ms containing poly(vinyl alcohol), PVA, which is well known for its high ice recrystallization inhibition (IRI) activity. The PVA-based C3Ms are prepared upon co-assembly of poly(4-vinyl-N-methyl-pyridinium iodide) and poly(vinyl alcohol)-block-poly(acrylic acid). Their formation conditions, size, and performance as ice recrystallization inhibitors are studied. It is found that the C3Ms exhibit IRI activity at PVA monomer concentrations as low as 1 × 10<sup>-3</sup> m. The IRI efficacy of PVA-C3Ms is similar to that of linear PVA and PVA graft polymers, underlining the influence of vinyl alcohol monomer concentration rather than polymer architecture.
Development of a smart mass flow sensor based on adaptive notch filtering and frequency domain identification (2002)

A popular method for measuring mass flows of granular materials is to register the induced force on a circular chute. When properly designed, an accurate, friction independent and linear flow measurement is achieved, ready to install in agricultural machinery or process lines. Since this type of sensor is strongly subject to wear and is installed in inaccessible places, it is important to know when it provides wrong measurements without interrupting the process. In this study, an off-line frequency domain procedure is designed to estimate wear on the chute suspension based on normal grain flow variations without extra excitation devices. The uncertainty bounds on the dynamic parameters are iteratively estimated based on a non-linear transformation between the parameter and pole/zero space. As an alternative, a robust and stable method is presented to track the resonance frequency of the mechanical sensor and paddle rate of a feeding elevator on-line.
Prediction of anaerobic biodegradability and bioaccessibility of municipal sludge by coupling sequential extractions with fluorescence spectroscopy: towards ADM1 implementation (2013)

International audience
<i>In Vivo</i> Expression of a GST-Fusion Protein Mediates the Rapid Generation of Affinity Matured Monoclonal Antibodies Using DNA-Based Immunizations (2002)

Previously we demonstrated the rapid generation of affinity matured monoclonal antibody (MAb) producing cell lines following gene gun delivery of DNA using a mammalian expression vector (pAlpha/hFc), which enables the expression of human Fc-chimera proteins in vivo. Here we compare the pAlpha/hFc vector to modified vectors that replace human IgG(1) with either a Glutathione-S-Transferase (GST) fusion protein or a mouse IgG(2c) (mFc) fusion protein. We report that in vivo expression of a GST-chimera results in the rapid generation of affinity matured MAbs, comparable with antibodies raised using the pAlpha/hFc vector, that were reactive with annexin V. The mFc vector failed to induce early antigen-specific B-cell responses suitable for MAb development.
Active navigation landmarks for a service robot in a home environment (2010)

This paper proposes a physical user interface for a user to teach a robot to navigate a home environment. The user places small devices containing infrared based communication functionality as landmarks in the environment. The robot follows these landmarks to navigate to a goal landmark. Active landmarks communicate with each other to map their spatial relationships. Our method allows the user to start using the system immediately after placing the landmarks without installing any global position sensing system or prior mapping by the robot.
Conditional pre-charge techniques for power-efficient dual-edge clocking (2002)

A new dual edge-triggered flip-flop that saves power by inhibiting transitions of the nodes that are not used to change the state is presented. The proposed flip-flop is 12% faster with 10% lower Energy-Delay Product for 50% data activity, as compared to the previously published dual edge-triggered storage elements. This was confirmed by simulation using 0.18um process, 1.8V power supply, and clock frequency of 250MHz. This flip-flop is particularly suitable for low-power applications.
System level performance of cellular networks utilizing ASA/LSA mechanisms (2014)

Flexible and efficient spectrum usage in cellular communication systems is a key to meet the service demand of forthcoming 4G and 5G networks by 2020. Recent wide-band power measurements in an urban environment show that spectrum below 6 GHz is still under-utilized. Licensed shared access (LSA) is one technique which can be deployed to make use of these valuable resources. In this paper we highlight cell-planning aspects for the implementation of licensed shared access (LSA) in LTE cellular networks. Different cellular deployments are evaluated by means of system-level simulations. Numerical results show that transmit power, antenna type and orientation, as well as antenna downtilt should be carefully evaluated during the planning of spectrum sharing deployments using LSA in cellular wireless.
Negative expression of N-acetylglucosaminyltransferase V in oral squamous cell carcinoma correlates with poor prognosis (2013)

N-acetylglucosaminyltransferase V (GnT-V), an enzyme with a key role in the branching of asparagine-linked oligosaccharides, is strongly linked to tumor invasion and metastasis of many solid tumors. Here we searched for correlations between the clinical features of patients with oral squamous cell carcinoma (OSCC) and GnT-V expression in the tumor, and we studied the feasibility of using GnT-V as a marker for oral cancer prognosis. Samples from 68 patients with OSCC were examined by immunohistochemistry using antibodies against GnT-V. Correlations between the expression level of GnT-V in the tumor and patient clinical features were statistically analyzed. Positive GnT-V expression was found in 48 cases (70.6%), and negative GnT-V expression was found in 20 cases (29.4%). Negative GnT-V expression was associated with mode of invasion by multiple logistic regression analysis (OR: 3.605; P = 0.048). Biological characteristics of tumors and the Ki-67 labeling index were higher in tumors with negative GnT-V expression than in those with positive GnT-V expression, although the difference was not significant (P = 0.176). Patients with negative GnT-V expression had significantly shorter survival than those with tumors having positive GnT-V expression (5-year survival rate, 58.2% and 86.5%, respectively; P = 0.025). Negative GnT-V expression was a significant unfavorable prognostic factor for OSCC (hazard ratio, 4.246; P = 0.045). The loss of GnT-V expression is a likely indicator of tumors with high potential of tumor invasion and poor prognosis in OSCC patients.
Supplementary Information from Activated ALK Cooperates with N-Myc via Wnt/β-Catenin Signaling to Induce Neuroendocrine Prostate Cancer (2023)

&lt;p&gt;Supplementary Information&lt;/p&gt;
Two homologous <i>LHY</i> pairs negatively control soybean drought tolerance by repressing the abscisic acid responses (2020)

The circadian clock plays essential roles in diverse plant biological processes, such as flowering, phytohormone biosynthesis and abiotic stress responses. The manner in which circadian clock genes regulate drought stress responses in model plants has been well established, but comparatively little is known in crop species, such as soybean, a major global crop. This paper reports that the core clock components GmLHYs, the orthologues of CCA1/LHY in Arabidopsis, negatively control drought tolerance in soybean. The expressions of four GmLHYs were all induced by drought, and the quadruple mutants of GmLHYs demonstrated significantly improved drought tolerance. Transcriptome profiling suggested that the abscisic acid (ABA) signaling pathway is regulated by GmLHYs to respond to drought tolerance. Genetic dissections showed that two homologous pairs of LHY1a and LHY1b redundantly control the drought response. Functional characterization of LHY1a and LHY1b in Arabidopsis and soybean further supported the notion that GmLHYs can maintain cellular homeostasis through the ABA signaling pathway under drought stress. This study improves our understanding of the underlying molecular mechanisms on soybean drought tolerance. Furthermore, the two homologues of LHY1a and LHY1b provide alternative targets for genome editing to rapidly generate mutant alleles in elite soybean cultivars to enhance their drought tolerance.
Sonographic diagnosis of pancreatic islet cell tumor: Value of intermittent harmonic imaging (2001)

We describe a case of nonfunctioning islet cell tumor of the pancreas diagnosed preoperatively by intermittent harmonic power Doppler imaging and digital subtraction gray-scale harmonic imaging and the use of the contrast agent SH U 508A (Levovist). Hypervascularity and tumor perfusion were clearly demonstrated with both harmonic imaging techniques in the early arterial phase. Sonographic findings were confirmed by other modalities and by histopathologic examination.
Microfabrication of Black Acrylic Resin Using Pulse-Width-Variable Picosecond Fiber Laser (2020)

In this study, fine grooves were processed on the surfaces of acrylic resins using a variable-pulse-width-picosecond laser. The near-infrared radiation range objectives for bright-field observation is introduced near the laser beam exit. This objective lens has a high focusing ability. (the beam diameter is approximately 46 μm when using a 5× lens and approximately 2.4 μm when using a 100× lens.) We derived the optimum processing conditions based on the relationships between the surface properties and XY stage scanning speed. As previous studies, we found that the groove shapes can be controlled by adjusting the XY stage scanning speed and duty cycle. The groove shapes were compared and the differences in the fabricated shapes from the previous research were quantitatively shown. The slope of XY stage or the roughness of workpieces before laser processing were evaluated because some groove shapes had low quality. It was suggested that measuring the roughness and waviness of workpieces prior to laser processing and adopting the low-frequency processing conditions could help solve problems during laser processing.
Experimental selection of hypoxia-tolerant <i>Drosophila melanogaster</i> (2011)

Through long-term laboratory selection (over 200 generations), we have generated Drosophila melanogaster populations that tolerate severe, normally lethal, levels of hypoxia. Because of initial experiments suspecting genetic mechanisms underlying this adaptation, we compared the genomes of the hypoxia-selected flies with those of controls using deep resequencing. By applying unique computing and analytical methods we identified a number of DNA regions under selection, mostly on the X chromosome. Several of the hypoxia-selected regions contained genes encoding or regulating the Notch pathway. In addition, previous expression profiling revealed an activation of the Notch pathway in the hypoxia-selected flies. We confirmed the contribution of Notch activation to hypoxia tolerance using a specific γ-secretase inhibitor, N-[N-(3,5-Difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT), which significantly reduced adult survival and life span in the hypoxia-selected flies. We also demonstrated that flies with loss-of-function Notch mutations or RNAi-mediated Notch knockdown had a significant reduction in hypoxia tolerance, but those with a gain-of-function had a dramatic opposite effect. Using the UAS-Gal4 system, we also showed that specific overexpression of the Notch intracellular domain in glial cells was critical for conferring hypoxia tolerance. Unique analytical tools and genetic and bioinformatic strategies allowed us to discover that Notch activation plays a major role in this hypoxia tolerance in Drosophila melanogaster.
Distal Ulna Allograft for Proximal Humerus Fractures (2016)

Treatment of displaced proximal humerus fractures can be challenging, particularly in patients with osteopenia. Although large strides have been made with the advent of locking plate technology in the treatment of these fractures, severe fracture comminution and thin cortices can lead to loss of fixation and varus collapse. The use of an allograft strut, usually a fibular allograft, has been advocated in these fractures to help increase stability of the construct. In this report, we describe the use of a distal ulna allograft for reconstruction of proximal humerus fractures. Because of its anatomic curve, the distal ulna may aid in reduction and help prevent varus collapse. Surgical technique, procedure pearls, and results are described.
Three-Dimensional Printing of Proteinaceous Structures by Aqueous Solvent-Directed Molecular Assembly (2019)

&lt;p&gt;Hierarchical molecular assembly directed by cell-regulated aqueous solvent is a fundamental strategy for manufacturing various proteinaceous structures that are of intense interest for nanotechnology, sustainable manufacturing and regenerative medicine. However, to translate the natural strategy into advanced digital manufacturing like three-dimensional (3D) printing remains a tremendous technical and theoretical challenge. This work presents a 3D printing technique of a particular protein, silk fibroin, by rationally designing an&lt;i&gt; de novo &lt;/i&gt;aqueous salt bath capable of directing the hierarchical assembly of the protein molecules. This technique, conducted under aqueous and ambient conditions, results in 3D proteinaceous architectures characterized by intrinsic biocompatibility/biodegradability and remarkable mechanical performance. The versatility of this method is shown in a diversity of 3D shapes and a range of functional components integrated into the 3D prints. Exceptional manufacturing capability and one promising application is exemplified by the single-step construction of perfusable microfluidic chips, also an analogy of small-diameter vascular grafts, which eliminates the use of supporting or sacrificial materials owing to optimized crosslinking dynamics and compartmentalized printing parameters. The 3D shaping capability of the protein material can benefit a multitude of biomedical devices, from drug delivery to surgical implants to tissue scaffolds.&lt;/p&gt;
EDITORIAL (2001)

The completion of the human genome product, as well as the isolation and characterization of growth factors, represents a significant opportunity to provide solutions to hand and upper extremity problems previously treated by surgical intervention. The treatments that hand surgeons have developed over the past 50 years may be looked upon by our peers 50 years from now as being extremely archaic. An excellent introduction to the molecular control of upper extremity development recently appeared article in the Journal of Hand Surgery.1 I have asked Dr. Aaron Daluiski, the author, to write a guest editorial on the future impact of these techniques in hand and upper extremity surgery. Andrew J. Weiland, M.D. Editor-in-Chief Hospital for Special Surgery Cornell University Medical Center New York, New York, U.S.A. As a final draft of the human genome is being assembled it seems appropriate to address how this information will impact the future of hand surgery. New data is flowing at a remarkable rate. Most of the genes are known, but their functions and potential clinical benefit will likely not be discovered for years. The isolation and characterization of growth factors will probably be the most clinically useful of these discoveries. Induction of osteogenesis by bone morphogenetic protein (BMP) is well characterized, but other tissue-specific growth factors exist. Currently, there are factors that are involved with indication of growth of tendon, nerve, vessel, and cartilage tissues. Complex tissues are formed by complex molecular interactions. Understanding of normal developmental processes is vital to determining which factor(s) are necessary, and in which order, for tissue regeneration. This knowledge can then be pirated for regeneration of complex tissues either in vivo or in vitro. Growth factors with potential clinical use will have to be delivered in appropriate doses within appropriate carriers. Even more important is the bed in which they are placed. Appropriate target cells must be present and responsive to the applied growth factor. Anatomy doesn't change, nor will the need for mechanical solutions to surgical problems. The tools and techniques for solving these problems will, however, continue to evolve as we understand more about the biology of regenerating tissues. Basic scientific research will give us the information regarding the biology of these novel growth factors. It will be we as surgeons who will need to develop the mechanism for application and clinical use of these new biological tools. As we have learned from free microvascular transfer, biologic solutions are often better than their synthetic or allograft counterparts. The use of growth factors in hand surgery will undoubtedly become an increasing part of surgical treatments. It will be interesting to see how the Journal and its readers adapt and the resultant modifications in surgical techniques. Aaron Daluiski, M.D. Hospital for Special Surgery Cornell University Medical Center New York, New York, U.S.A.
Distance-Sensitive Bloom Filters (2006)

A Bloom filter is a space-efficient data structure that answers set membership queries with some chance of a false positive. We introduce the problem of designing generalizations of Bloom filters designed to answer queries of the form, “Is x close to an element of S?” where closeness is measured under a suitable metric. Such a data structure would have several natural applications in networking and database applications. We demonstrate how appropriate data structures can be designed using locality-sensitive hash functions as a building block, and we specifically analyze the performance of a natural scheme under the Hamming metric.
Breeding progress and preparedness for mass‐scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar (2018)

Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output-input energy ratios: namely <i>Panicum virgatum</i> (switchgrass), species of the genera <i>Miscanthus</i> (miscanthus), <i>Salix</i> (willow) and <i>Populus</i> (poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed-based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5 years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass-scale deployment of PBCs.