gebhart/patrepeval huggingface dataset:
Recent advances in cutaneous angiogenesis (2002)

An understanding of the molecular basis of angiogenesis is key to the appreciation of many of the advances made in the field of neovascularization over the past two decades. The sequence of events involved in angiogenesis includes: (i) increased vascular permeability and leakage; (ii) degradation of basement membrane; (iii) endothelial cell proliferation and migration through the surrounding extracellular matrix; and (iv) maturation and stabilization of the newly formed vessel bed. This review provides an update on the molecular basis of such pathways in the skin, with particular emphasis on the endothelial cell-specific vascular endothelial growth factor and angiopoietins as modulators of angiogenesis that can be targeted in therapy of cutaneous disease.
An Evaluation of Landmarking Variants (2001)

. Landmarking is a novel technique for data characterization in metalearning. While conventional approaches typically describe a database with its statistical measurements and properties, landmarking proposes to enrich such a description with quick and easy-to-obtain performance measures of simple learning algorithms. In this paper, we will discuss two novel aspects of landmarking. First, we investigate relative landmarking, which tries to exploit the relative order of the landmark measures instead of their absolute value. Second, we propose to use subsampling estimates as a different way for efficiently obtaining landmarks. In general, our results are mostly negative. The most interesting result is a surprisingly simple rule that predicts quite accurately when it is worth to boost decision trees. 1
Adaptive Hot-Spot Cooling of Integrated Circuits Using Digital Microfluidics (2005)

Thermal management is becoming an increasingly important issue in integrated circuit (IC) design. The ability to cool ICs is quickly reaching a limit with today’s package-level solutions. While a number of novel cooling methods have been introduced, many of which are microfluidic approaches, these methods are unable to adaptively address the uneven thermal profiles and hot-spots generated in high performance ICs. In this paper, we present a droplet-based digital microfluidic cooling system for ICs that can adaptively cool hot-spots through real-time reprogrammable flow. This paper characterizes the effectiveness of microliter-sized droplets for cooling by determining the heat transfer coefficient of a droplet shuttling back and forth in an open system over a hot-spot at various speeds. Cooling is found to be significantly enhanced at higher flow rates of droplets. In order to further enhance cooling, the effect of varying droplet aspect ratio (width/height) in a confined system was also studied.
Towards Practical Verification of Machine Learning: The Case of Computer Vision Systems (2017)

Due to the increasing usage of machine learning (ML) techniques in security- and safety-critical domains, such as autonomous systems and medical diagnosis, ensuring correct behavior of ML systems, especially for different corner cases, is of growing importance. In this paper, we propose a generic framework for evaluating security and robustness of ML systems using different real-world safety properties. We further design, implement and evaluate VeriVis, a scalable methodology that can verify a diverse set of safety properties for state-of-the-art computer vision systems with only blackbox access. VeriVis leverage different input space reduction techniques for efficient verification of different safety properties. VeriVis is able to find thousands of safety violations in fifteen state-of-the-art computer vision systems including ten Deep Neural Networks (DNNs) such as Inception-v3 and Nvidia's Dave self-driving system with thousands of neurons as well as five commercial third-party vision APIs including Google vision and Clarifai for twelve different safety properties. Furthermore, VeriVis can successfully verify local safety properties, on average, for around 31.7% of the test images. VeriVis finds up to 64.8x more violations than existing gradient-based methods that, unlike VeriVis, cannot ensure non-existence of any violations. Finally, we show that retraining using the safety violations detected by VeriVis can reduce the average number of violations up to 60.2%.
CBS' New-Technology Station, WBBM-TV: Station Design using Media Room, ENG, and other Advanced Technology (1978)

WBBM-TV, the CBS station in Chicago, has recently been rebuilt utilizing new technologies and modern system techniques. The major features of the station are: installation of a Media Room; complete conversion to ENG; a News Control Room; an automated program-continuity system; and a remotely controlled transmitter system. The decision to provide these new facilities for WBBM-TV was made in order to take advantage of new technology and system concepts to improve the quality and flexibility of the station while reducing overall operating costs. Combining these technologies results in beneficial interrelations so that the whole is greater than the sum of the parts. As a consequence, WBBM-TV can be described as an advanced, synergistic, new-technology station.
Comparison of transformation to low-resistivity phase and agglomeration of TiSi/sub 2/ and CoSi/sub 2/ (1991)

The phase transformation and stability of TiSi/sub 2/ on n/sup +/ diffusions are investigated. Narrower n/sup +/ diffusions require higher anneal temperatures, or longer anneal times, than wider diffusions for complete transitions from the high-resistivity C49 phase to the low-resistivity C54 phase. A model is presented which explains this in terms of the probability of forming C54 nuclei on narrow diffusions and the influence of diffusion width on C54 grain size. The results are that more C49 and C54 nucleation events are required to completely transform narrow lines. For thin TiSi/sub 2/ (40 nm), there is a narrow process window for achieving complete transformation without causing agglomeration of the TiSi/sub 2/. The process window decreases with decreasing silicide thickness. A significantly larger process window is achieved with short-time rapid annealing. Similar studies are performed for CoSi/sub 2/ on n/sup +/ and p/sup +/ diffusions. No linewidth dependence is observed for the transformation from CoSi/sub x/ to CoSi/sub 2/. There is a broad process window from 575 degrees C to 850 degrees C using furnace annealing, for which the low-resistivity phase is obtained without causing agglomeration.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A new approach to construction of artificial monolayer assemblies (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA new approach to construction of artificial monolayer assembliesLucy Netzer and Jacob SagivCite this: J. Am. Chem. Soc. 1983, 105, 3, 674–676Publication Date (Print):February 1, 1983Publication History Published online1 May 2002Published inissue 1 February 1983https://pubs.acs.org/doi/10.1021/ja00341a087https://doi.org/10.1021/ja00341a087research-articleACS PublicationsRequest reuse permissionsArticle Views1556Altmetric-Citations312LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Epidermal Growth Factor and Hypoxia-induced Expression of CXC Chemokine Receptor 4 on Non-small Cell Lung Cancer Cells Is Regulated by the Phosphatidylinositol 3-Kinase/PTEN/AKT/Mammalian Target of Rapamycin Signaling Pathway and Activation of Hypoxia Inducible Factor-1α (2005)

Non-small cell lung cancer (NSCLC) expresses a particularly aggressive metastatic phenotype, and patients with this disease have a poor prognosis. CXC chemokine receptor 4 (CXCR4) is a cell surface receptor that has been shown to mediate the metastasis of many solid tumors including lung, breast, kidney, and prostate. In addition, overexpression of the epidermal growth factor receptor (EGFR) is associated with the majority of NSCLC and has been implicated in the process of malignant transformation by promoting cell proliferation, cell survival, and motility. Here we show for the first time that activation of the EGFR by EGF increases CXCR4 expression and the migratory capacity of NSCLC cells. Furthermore, many solid tumors are associated with low oxygen tension, and when NSCLC cells were cultured with EGF under hypoxic conditions, CXCR4 expression was dramatically enhanced. A molecular analysis of these events indicated that augmented CXCR4 expression was regulated by the phosphatidylinositol 3-kinase/PTEN/AKT/mammalian target of rapamycin signal transduction pathway, activation of hypoxia inducible factor (HIF) 1alpha, and ultimately HIF-1-dependent transcription of the CXCR4 gene. Thus, a combination of low oxygen tension and overexpression of EGFR within the primary tumor of NSCLC may provide the microenvironmental signals necessary to upregulate CXCR4 expression and promote metastasis.
Rad18/Rad5/Mms2‐mediated polyubiquitination of PCNA is implicated in replication completion during replication stress (2004)

Ubiquitination of proteins was previously shown to modulate various processes of DNA metabolism. PCNA, a processivity factor with essential functions in replication and repair, is modified with ubiquitin at K164. In addition, PCNA is sumoylated at K127 and K164. We found that the rad18delta mutation suppresses the temperature sensitivity of the polymerase delta mutants hys2-1 and cdc2-1 as well as the synthetic lethality of cdc2-1 pol32delta mutants, suggesting a role for Rad18 in modulating DNA replication. As Rad18 mediates ubiquitination of PCNA, we examined whether PCNA modifications affected its function in replication. Multicopy PCNA alleviated the replication defects of rfc5-1 strains, but not those of poldelta mutants. In contrast, multicopy PCNA-K164R had reduced ability to suppress the replication defects of rfc5-1, but alleviated those of poldelta mutants. The roles of sumoylated and ubiquitinated PCNA in rfc5-1 and hys2-1 mutants were addressed by using mutant backgrounds that selectively affected sumoylation (siz1delta), ubiquitination (rad18delta), polyubiquitination (rad5delta, mms2delta), or the ability of cells to perform translesion synthesis (polzetadelta, poletadelta). Our results are consistent with the idea that the Rad18/Rad5/Mms2 polyubiquitination pathway is important for replication completion, perhaps by promoting a template switch type of DNA synthesis.
Heparan Sulfate Oligosaccharides Require 6-O-Sulfation for Promotion of Basic Fibroblast Growth Factor Mitogenic Activity (1998)

The interaction of heparan sulfate (HS) with basic fibroblast growth factor (bFGF) is influential in enabling the growth factor to bind to its cell surface tyrosine kinase receptor. In this study, we have investigated further the structural properties of HS required to mediate the activity of bFGF in a mitogenic assay. We have prepared a library of heparinase III-generated HS oligosaccharides fractionated by both their size (dp6-dp12) and sulfate content. The ability of these oligosaccharides to activate bFGF in a mitogenic assay was then correlated with their length and disaccharide composition. All octa- and hexasaccharide fractions tested were unable to activate bFGF. Dodeca- and decasaccharide fractions were found to contain both activating and non-activating oligosaccharides, and showed a clear correlation between total sulfate content and the level of activatory activity. Disaccharide analysis of a range of dodeca- and decasaccharide fractions showed that both activating and non-activating oligosaccharides were composed mainly of N-sulfated and IdoA(2S)-containing disaccharides. The only significant difference between activating and non-activating oligosaccharides was the content of 6-O-sulfated disaccharides, in particular the disaccharide IdoA(2S)alpha1,4GlcNSO3(6S). These results show that there is a requirement for 6-O-sulfation of N-sulfated glucosamine residues, in addition to the 2-O-sulfation of IdoA, for the promotion of bFGF mitogenic activity by naturally occurring HS oligosaccharides. Analysis of the structure-activity relationships in the dodecasaccharide fractions in particular, suggests that a minimum bFGF activation sequence exists which is dependent on the positioning of at least one 6-O-sulfate group.
Genetic Relations between Varicella-Zoster Virus and Epstein-Barr Virus (1987)

Varicella-zoster virus (VZV) and Epstein-Barr virus (EBV) are important human pathogens which belong to different subfamilies of the herpesviruses: the Alpha- and Gammaherpesvirinae, respectively. Computer comparisons of the amino acid sequences of proteins predicted from the published complete VZV and EBV DNA sequences resulted in the detection of EBV counterparts to 29 of the 67 unique VZV genes. Conserved genes were detected only in the UL component of each genome, and are located in three major regions, within which conserved genes are generally colinear. However, the three regions are arranged differently in the two genomes. These results make it possible in principle to propose the functions of EBV genes on the basis of the functions of their VZV counterparts. The data also allow identification of the types of events which may have occurred during divergence of VZV and EBV, as representatives of the Alpha- and Gammaherpesvirinae, from a common ancestor.
Evidence to Challenge the “2% Rule” for Biotelemetry (1999)

Swimming performance was compared among groups of juvenile rainbow trout Oncorhynchus mykiss (5–10 g) with and without intraperitoneally implanted radio transmitters. The generally accepted rule of 2% body weight : transmitter weight was extended to a 6–12% ratio, and swimming performance was not altered by the presence of the transmitter or effects of the operation. Also, no relationship was found between the weight of the fish and its swimming performance among the groups examined. Although we found swimming performance was not affected by implantation of transmitters weighing up to 12% of the body weight, changes in behavior were not evaluated. We suggest further research be done so that the “2% rule” can be replaced by an index with a more scientific basis. Instead of using a scale based on percentage of transmitter to body weight in air, preferred indices could be weight in water, volume of the tag, or both.
Targeting myeloid-derived suppressor cells using all-trans retinoic acid in melanoma patients treated with Ipilimumab (2018)

These results illustrate the importance of MDSCs in immunotherapy resistance and provide evidence that targeting MDSCs in cancer patients may augment immunotherapeutic approaches.
Photocurable surgical tissue adhesive glues composed of photoreactive gelatin and poly(ethylene glycol) diacrylate (1999)

This article presents a novel photochemically driven surgical tissue adhesive technology using photoreactive gelatins and a water-soluble difunctional macromer (poly(ethylene glycol) diacrylate: PEGDA).The gelatins were partially derivatized with photoreactive groups, such as ultraviolet light (UV)-reactive benzophenone and visible light-reactive xanthene dye (e.g., fluorescein sodium salt, eosin Y, and rose bengal). A series of the prepared photocurable tissue adhesive glues, consisting of the photoreactive gelatin, PEGDA, and a saline solution with or without ascorbic acid as a reducing agent, were viscous solutions under warming, and their effectiveness was evaluated as hemostasis- and anastomosis-aid in cardiovascular surgery. Regardless of the type of photoreactive groups, the irradiation of the photocurable tissue adhesive glues by UV or visible light within 1 min produced water-swollen gels, which had a high adhesive strength to wet collagen film. These were due to the synergistic action of photoreactive group-initiated photo-cross-linking and photograft polymerization. An increase in the irradiation time resulted in increased gel yield and reduced water swellability. A decrease in the molecular weight of PEGDA and an increase in concentration of both gelatin and PEGDA resulted in reduced water swellability and increased tensile and burst strengths of the resultant gels. In rats whose livers were injured with a trephine in laparotomy, the bleeding spots were coated with the photocurable adhesive glue and irradiated through an optical fiber. The coated solution was immediately converted to a swollen gel. The gel was tightly adhered to the liver tissue presumably by interpenetration, and concomitantly hemostasis was completed. The anastomosis treatment with the photocurable glue in the canine abdominal or thoracic aortas incised with a knife resulted in little bleeding under pulsatile flow after declamping. Histological examination showed that the glues photocured on rat liver surfaces were gradually degraded with time in vivo with infiltration of inflammatory cells and connective tissues without necrotic sign in surrounding tissue. In addition, in the laparoscopic surgery, percutaneous delivery of the glue and its in situ photogelation on rat liver surfaces were demonstrated using a specially designed fiberscope. These results indicate that the photocurable glues developed here may serve as a biodegradable tissue adhesive glue usable in cardiovascular surgery and endoscopic surgery.
Introduction to phasing (2010)

When collecting X-ray diffraction data from a crystal, we measure the intensities of the diffracted waves scattered from a series of planes that we can imagine slicing through the crystal in all directions. From these intensities we derive the amplitudes of the scattered waves, but in the experiment we lose the phase information; that is, how we offset these waves when we add them together to reconstruct an image of our molecule. This is generally known as the 'phase problem'. We can only derive the phases from some knowledge of the molecular structure. In small-molecule crystallography, some basic assumptions about atomicity give rise to relationships between the amplitudes from which phase information can be extracted. In protein crystallography, these ab initio methods can only be used in the rare cases in which there are data to at least 1.2 A resolution. For the majority of cases in protein crystallography phases are derived either by using the atomic coordinates of a structurally similar protein (molecular replacement) or by finding the positions of heavy atoms that are intrinsic to the protein or that have been added (methods such as MIR, MIRAS, SIR, SIRAS, MAD, SAD or combinations of these). The pioneering work of Perutz, Kendrew, Blow, Crick and others developed the methods of isomorphous replacement: adding electron-dense atoms to the protein without disturbing the protein structure. Nowadays, methods from small-molecule crystallography can be used to find the heavy-atom substructure and the phases for the whole protein can be bootstrapped from this prior knowledge. More recently, improved X-ray sources, detectors and software have led to the routine use of anomalous scattering to obtain phase information from either incorporated selenium or intrinsic sulfurs. In the best cases, only a single set of X-ray data (SAD) is required to provide the positions of the anomalous scatters, which together with density-modification procedures can reveal the structure of the complete protein.
Helicase‐Dependent Isothermal Amplification of DNA and RNA by Using Self‐Avoiding Molecular Recognition Systems (2015)

Assays that detect DNA or RNA (xNA) are highly sensitive, as small amounts of xNA can be amplified by PCR. Unfortunately, PCR is inconvenient in low-resource environments, and requires equipment and power that might not be available in these environments. Isothermal procedures, which avoid thermal cycling, are often confounded by primer dimers, off-target priming, and other artifacts. Here, we show how a "self avoiding molecular recognition system" (SAMRS) eliminates these artifacts and gives clean amplicons in a helicase-dependent isothermal amplification (SAMRS-HDA). We also show that incorporating SAMRS into the 3'-ends of primers facilitates the design and screening of primers for HDA assays. Finally, we show that SAMRS-HDA can be twofold multiplexed, difficult to achieve with HDA using standard primers. Thus, SAMRS-HDA is a more versatile approach than standard HDA, with a broader applicability for xNA-targeted diagnostics and research.
Bone marrow is a major site of long-term antibody production after acute viral infection (1995)

Antiviral antibody production is often sustained for long periods after resolution of an acute viral infection. Despite extensive documentation of this phenomenon, the mechanisms involved in maintaining long-term antibody production remain poorly defined. As a first step towards understanding the nature of long-term humoral immunity, we examined the anatomical location of antibody-producing cells during acute viral infection. Using the lymphocytic choriomeningitis virus (LCMV) model, we found that after resolution of the acute infection, when antiviral plasma cells in the spleen decline, a population of virus-specific plasma cells appears in the bone marrow and constitutes the major source of long-term antibody production. Following infection of adult mice, LCMV-specific antibody-secreting cells (ASC) peaked in the spleen at 8 days postinfection but were undetectable in the bone marrow at that time. The infection was essentially cleared by 15 days, and the ASC numbers in the spleen rapidly declined while an increasing population of LCMV-specific ASC began to appear in the bone marrow. Compared with the peak response at 8 days postinfection, time points from 30 days to more than 1 year later demonstrated greater-than-10-fold reductions in splenic ASC. In contrast, LCMV-specific plasma cell numbers in the bone marrow remained high and correlated with the high levels of antiviral serum antibody. The presence of LCMV-specific plasma cells in the bone marrow was not due to persistent infection at this site, since the virus was cleared from both the spleen and bone marrow with similar kinetics as determined by infectivity and PCR assays. The immunoglobulin G subclass profile of antibody-secreting cells derived from bone marrow and the spleen correlated with the immunoglobulin G subclass distribution of LCMV-specific antibody in the serum. Upon rechallenge with LCMV, the spleen exhibited a substantial increase in virus-specific plasma cell numbers during the early phase of the secondary response, followed by an equally sharp decline. Bone marrow ASC populations and LCMV-specific antibody levels in the serum did not change during the early phase of the reinfection, but both increased about two-fold by 15 days postchallenge. After both primary and secondary viral infections, LCMV-specific plasma cells were maintained in the bone marrow, showing that the bone marrow is a major site of long-term antibody production after acute viral infection. These results documenting long-term persistence of plasma cells in the bone marrow suggest a reexamination of our current notions regarding the half-life of plasma cells.