gebhart/patrepeval huggingface dataset:
Radiolabeled Antibodies for Cancer Imaging and Therapy (2012)

Radiolabeled antibodies were studied first for tumor detection by single-photon imaging, but FDG PET stopped these developments. In the meantime, radiolabeled antibodies were shown to be effective in the treatment of lymphoma. Radiolabeling techniques are well established and radiolabeled antibodies are a clinical and commercial reality that deserves further studies to advance their application in earlier phase of the diseases and to test combination and adjuvant therapies including radiolabeled antibodies in hematological diseases. In solid tumors, more resistant to radiations and less accessible to large molecules such as antibodies, clinical efficacy remains limited. However, radiolabeled antibodies used in minimal or small-size metastatic disease have shown promising clinical efficacy. In the adjuvant setting, ongoing clinical trials show impressive increase in survival in otherwise unmanageable tumors. New technologies are being developed over the years: recombinant antibodies and pretargeting approaches have shown potential in increasing the therapeutic index of radiolabeled antibodies. In several cases, clinical trials have confirmed preclinical studies. Finally, new radionuclides, such as lutetium-177, with better physical properties will further improve the safety of radioimmunotherapy. Alpha particle and Auger electron emitters offer the theoretical possibility to kill isolated tumor cells and microscopic clusters of tumor cells, opening the perspective of killing the last tumor cell, which is the ultimate challenge in cancer therapy. Preliminary preclinical and preliminary clinical results confirm the feasibility of this approach.
Distributed ray tracing (1984)

Ray tracing is one of the most elegant techniques in computer graphics. Many phenomena that are difficult or impossible with other techniques are simple with ray tracing, including shadows, reflections, and refracted light. Ray directions, however, have been determined precisely, and this has limited the capabilities of ray tracing. By distributing the directions of the rays according to the analytic function they sample, ray tracing can incorporate fuzzy phenomena. This provides correct and easy solutions to some previously unsolved or partially solved problems, including motion blur, depth of field, penumbras, translucency, and fuzzy reflections. Motion blur and depth of field calculations can be integrated with the visible surface calculations, avoiding the problems found in previous methods.
Efficient and Robust Detection of Duplicate Videos in a Large Database (2010)

We present an efficient and accurate method for duplicate video detection in a large database using video fingerprints. We have empirically chosen the color layout descriptor, a compact and robust frame-based descriptor, to create fingerprints which are further encoded by vector quantization (VQ). We propose a new nonmetric distance measure to find the similarity between the query and a database video fingerprint and experimentally show its superior performance over other distance measures for accurate duplicate detection. Efficient search cannot be performed for high-dimensional data using a nonmetric distance measure with existing indexing techniques. Therefore, we develop novel search algorithms based on precomputed distances and new dataset pruning techniques yielding practical retrieval times. We perform experiments with a database of 38 000 videos, worth 1600 h of content. For individual queries with an average duration of 60 s (about 50% of the average database video length), the duplicate video is retrieved in 0.032 s, on Intel Xeon with CPU 2.33 GHz, with a very high accuracy of 97.5%.
Silver staining of DNA in polyacrylamide gels: Linearity and effect of fragment size (1982)

Abstract A simplified, inexpensive silver stain for proteins in polyacrylamide gels also stains DNA with a sensitivity of 1 ng (&lt; 0.03 ng/mm 2 ). Sensitivity of detection is superior to ethidium bromide and, for 11 double‐stranded fragments of ϕX174 DNA, staining is linear with respect to concentration. Surprisingly, the slope of staining is similar for pieces of DNA larger than 300 base pairs, but is greater for fragments of smaller size. Staining of DNA with silver is a practical alternative to visualization with ethidium bromide and may serve as a tool for elucidating the basis of silver staining.
Prevention of immunotoxin-mediated vascular leak syndrome in rats with retention of antitumor activity. (1994)

Immunotoxins are hybrid molecules composed of a cell-surface binding domain and a protein toxin moiety that together target specific cell populations for elimination. These agents represent a promising approach for the treatment of many human diseases, most notably cancer. However, it has recently become clear that many immunotoxins when used in human clinical trials induce vascular leak syndrome (VLS), restricting the administration of doses necessary to achieve good therapeutic responses. The lack of an appropriate animal model has hindered efforts to understand and prevent immunotoxin-induced VLS. We have found that in rats, intravenous administration of the single-chain immunotoxin BR96 sFv-PE40 results in symptoms that closely resemble VLS seen in human immunotoxin trials. A large fluid accumulation in the thoracic cavity was observed, along with an increase in hematocrit and body weight and a decrease in serum albumin. The VLS was apparent within 24 hr after administration of immunotoxin and was seen in both immunocompetent and athymic rats. Similar symptoms were not found in mice even at lethal doses. Prophylactic administration of the corticosteroid dexamethasone resulted in prevention of VLS and survival of rats injected with what would otherwise be lethal doses of BR96 sFv-PE40. Prophylactic treatment with dexamethasone in rats xenografted with human tumors either did not inhibit or minimally inhibited the antitumor activity of BR96 sFv-PE40. The use of prophylactic corticosteroids should be considered for immunotoxin clinical trials, since it may improve therapeutic efficacy by decreasing the dose-limiting toxicity of VLS.
Sugar Crystallization, X-Ray Diffractometer and Microscopic Investigation of Crystallization of Amorphous Sucrose (1956)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSugar Crystallization, X-Ray Diffractometer and Microscopic Investigation of Crystallization of Amorphous SucroseK. J. Palmer, W. B. Dye, and Dale BlackCite this: J. Agric. Food Chem. 1956, 4, 1, 77–81Publication Date (Print):January 1, 1956Publication History Published online1 May 2002Published inissue 1 January 1956https://pubs.acs.org/doi/10.1021/jf60059a011https://doi.org/10.1021/jf60059a011research-articleACS PublicationsRequest reuse permissionsArticle Views529Altmetric-Citations36LEARN 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
Characterization of pseudorabies virus glycoprotein C attachment to heparan sulfate proteoglycans (2002)

Pseudorabies virus first attaches to cells through an interaction between the envelope glycoprotein C (gC) and the cell surface heparan sulfate (HS) that is linked to proteoglycans (HSPGs). The HS-binding domain of gC is composed of three discrete heparin-binding domains (HBDs), designated HBD1, -2 and -3 for their proximity to the amino terminus of gC. Each HBD can independently mediate virus attachment to HS, yet each also exhibits a distinct binding preference for differentially sulfated derivatives of heparin. To demonstrate this, affinity columns composed of wild-type gC or mutant gC retaining a single HBD to capture several HSPGs from cultured pig and bovine kidney cells were used. The wild-type gC column bound all of the HSPGs well and, overall, bound more than 90% of the total sample applied to the column. Columns composed of either HBD2 or -3 bound intermediate amounts (40%) of the total sample applied, while the HBD1 column bound low amounts of HSPGs. HBD2 and -3 columns did not uniformly bind all of the HSPGs from bovine kidney cells, but the same HSPGs were bound with equal efficiency on each column. Thus, despite their different preferences for sulfation patterns on HS side-chains, HBD2 and -3 appear to bind the same proteoglycan cores. These results established a hierarchy of HBD2=HBD3>HBD1 in importance for HSPG binding. These in vitro-binding results correlated with the attachment phenotype of virus strains expressing gC with a single HBD in their envelopes.
MRI of the lung (1/3): methods (2012)

Proton magnetic resonance imaging (MRI) has recently emerged as a clinical tool to image the lungs. This paper outlines the current technical aspects of MRI pulse sequences, radiofrequency (RF) coils and MRI system requirements needed for imaging the pulmonary parenchyma and vasculature. Lung MRI techniques are presented as a "technical toolkit", from which MR protocols will be composed in the subsequent papers for comprehensive imaging of lung disease and function (parts 2 and 3). This paper is pitched at MR scientists, technicians and radiologists who are interested in understanding and establishing lung MRI methods. Images from a 1.5 T scanner are used for illustration of the sequences and methods that are highlighted. Main Messages • Outline of the hardware and pulse sequence requirements for proton lung MRI • Overview of pulse sequences for lung parenchyma, vascular and functional imaging with protons • Demonstration of the pulse-sequence building blocks for clinical lung MRI protocols.
Frequency response of a focused SAW device based on concentric wave surfaces: simulation and experiment (2005)

Focused interdigital transducers (FIDTs) based on concentric wave surfaces can excite surface acoustic wave (SAW) with high intensity, high beamwidth compression ratio and small localized area. In this paper, we developed a model to analyse the frequency response of a SAW device with FIDTs based on concentric wave surfaces. First, we constructed a focused SAW device by adopting a pair of FIDTs shaped as the concentric wave surface. To calculate its frequency response, a simulation model was established based on the 2D SAW filter model, effective permittivity approach and perturbation theory. Further, the focused SAW devices were designed and fabricated via the microelectromechanical system process technique. A good agreement between the simulated and measured results was found. Finally, the frequency responses of focused SAW devices based on concentric wave surfaces were discussed and some attractive features were found, such as less ripples of pass-band and high stop-band rejection. In addition, in comparison with the conventional SAW devices with uniform interdigital transducers, the focused SAW devices are more sensitive to variations in the focal area, instead of the whole delayline region. Accordingly, they are suitable to be applied to detect or manipulate some localized variations, such as acousto-optic or acousto-electric effects.
The Role of C3 as an Opsonin in the Early Stages of Infection (1975)

In order to investigate the role of C3 in host defense in vivo, normal AKR/J mice, genetically deficient in C5, were depleted of serum C3 by the injection of purified cobra venom factor (CoVF). Concurrent with their C3 depletion, their serum opsonizing activity decreased to a level less than 20% of normal. When these mice were challenged with an intraperitoneal injection of pneumococci 2 hr after the CoVF treatment, the LD50 was from 30 to 80 times lower than the LD50 in saline-treated control animals. When the CoVF was given only 6 hr after the pneumococcal challenge, the LD50 was the same as in the control mice. If the pneumococci were first preopsonized in vitro and then injected into CoVF-treated animals, the LD50 was the same as that in control animals. These experiments demonstrate that C3 plays a significant role in vivo in the host's defense against infection and that a major part of that role is through its action as an opsonin. Furthermore, these experiments demonstrate that the role of C3 is most significant during the early stages of bacterial invasion.
High Frequency, Spontaneous motA Mutations in Campylobacter jejuni Strain 81-176 (2014)

Campylobacter jejuni is an important cause of bacterial diarrhea worldwide. The pathogenesis of C. jejuni is poorly understood and complicated by phase variation of multiple surface structures including lipooligosaccharide, capsule, and flagellum. When C. jejuni strain 81-176 was plated on blood agar for single colonies, the presence of translucent, non-motile colonial variants was noted among the majority of opaque, motile colonies. High-throughput genomic sequencing of two flagellated translucent and two opaque variants as well as the parent strain revealed multiple genetic changes compared to the published genome. However, the only mutated open reading frame common between the two translucent variants and absent from the opaque variants and the parent was motA, encoding a flagellar motor protein. A total of 18 spontaneous motA mutations were found that mapped to four distinct sites in the gene, with only one class of mutation present in a phase variable region. This study exemplifies the mutative/adaptive properties of C. jejuni and demonstrates additional variability in C. jejuni beyond phase variation.
Sweet's syndrome associated with myelodysplasia: possible role of cytokines in the pathogenesis of the disease (1993)

The clinical course of a 56-year-old female patient with Sweet's syndrome (SS) preceded by a myelodysplastic syndrome (MDS) is described. During the acute phase of the disease with high remittent fever, painful skin lesions and maximal leucocytosis IL-6 and G-CSF serum levels were extremely high, while TNF-alpha was only slightly elevated and gamma-interferon and IL1-beta were not increased. On clinical improvement IL-6 serum levels rapidly fell, whereas G-CSF values already slightly elevated before the manifestation of the disease slowly declined. High G-CSF levels triggered by a yet unknown factor could explain the leucocytosis, neutrophilic dermatosis and skin lesions in SS, while IL-6 probably induced the associated clinical symptoms of fever and pain.
Allele-specific copy number analysis of tumors (2010)

We present an allele-specific copy number analysis of the in vivo breast cancer genome. We describe a unique bioinformatics approach, ASCAT (allele-specific copy number analysis of tumors), to accurately dissect the allele-specific copy number of solid tumors, simultaneously estimating and adjusting for both tumor ploidy and nonaberrant cell admixture. This allows calculation of "ASCAT profiles" (genome-wide allele-specific copy-number profiles) from which gains, losses, copy number-neutral events, and loss of heterozygosity (LOH) can accurately be determined. In an early-stage breast carcinoma series, we observe aneuploidy (>2.7n) in 45% of the cases and an average nonaberrant cell admixture of 49%. By aggregation of ASCAT profiles across our series, we obtain genomic frequency distributions of gains and losses, as well as genome-wide views of LOH and copy number-neutral events in breast cancer. In addition, the ASCAT profiles reveal differences in aberrant tumor cell fraction, ploidy, gains, losses, LOH, and copy number-neutral events between the five previously identified molecular breast cancer subtypes. Basal-like breast carcinomas have a significantly higher frequency of LOH compared with other subtypes, and their ASCAT profiles show large-scale loss of genomic material during tumor development, followed by a whole-genome duplication, resulting in near-triploid genomes. Finally, from the ASCAT profiles, we construct a genome-wide map of allelic skewness in breast cancer, indicating loci where one allele is preferentially lost, whereas the other allele is preferentially gained. We hypothesize that these alternative alleles have a different influence on breast carcinoma development.
Identification of Biofilm Matrix-Associated Proteins from an Acid Mine Drainage Microbial Community (2011)

In microbial communities, extracellular polymeric substances (EPS), also called the extracellular matrix, provide the spatial organization and structural stability during biofilm development. One of the major components of EPS is protein, but it is not clear what specific functions these proteins contribute to the extracellular matrix or to microbial physiology. To investigate this in biofilms from an extremely acidic environment, we used shotgun proteomics analyses to identify proteins associated with EPS in biofilms at two developmental stages, designated DS1 and DS2. The proteome composition of the EPS was significantly different from that of the cell fraction, with more than 80% of the cellular proteins underrepresented or undetectable in EPS. In contrast, predicted periplasmic, outer membrane, and extracellular proteins were overrepresented by 3- to 7-fold in EPS. Also, EPS proteins were more basic by ∼2 pH units on average and about half the length. When categorized by predicted function, proteins involved in motility, defense, cell envelope, and unknown functions were enriched in EPS. Chaperones, such as histone-like DNA binding protein and cold shock protein, were overrepresented in EPS. Enzymes, such as protein peptidases, disulfide-isomerases, and those associated with cell wall and polysaccharide metabolism, were also detected. Two of these enzymes, identified as β-N-acetylhexosaminidase and cellulase, were confirmed in the EPS fraction by enzymatic activity assays. Compared to the differences between EPS and cellular fractions, the relative differences in the EPS proteomes between DS1 and DS2 were smaller and consistent with expected physiological changes during biofilm development.
A Parallel Quadruplex DNA Is Bound Tightly but Unfolded Slowly by Pif1 Helicase (2015)

DNA sequences that can form intramolecular quadruplex structures are found in promoters of proto-oncogenes. Many of these sequences readily fold into parallel quadruplexes. Here we characterize the ability of yeast Pif1 to bind and unfold a parallel quadruplex DNA substrate. We found that Pif1 binds more tightly to the parallel quadruplex DNA than single-stranded DNA or tailed duplexes. However, Pif1 unwinding of duplexes occurs at a much faster rate than unfolding of a parallel intramolecular quadruplex. Pif1 readily unfolds a parallel quadruplex DNA substrate in a multiturnover reaction and also generates some product under single cycle conditions. The rate of ATP hydrolysis by Pif1 is reduced when bound to a parallel quadruplex compared with single-stranded DNA. ATP hydrolysis occurs at a faster rate than quadruplex unfolding, indicating that some ATP hydrolysis events are non-productive during unfolding of intramolecular parallel quadruplex DNA. However, product eventually accumulates at a slow rate.
EDITOR’S COMMENTS (2012)

There is a time in the development of new orthoses and prostheses, when it can suddenly all come together—when researchers surpass what they hope might be, and achieve what they dream about. I was reminded of this today when a patient, colleague, and friend looked at me profoundly and said, “This is the best my prosthesis has ever felt to me.” It was the ultimate reward in our latest work.Thinking about how one gets to that point of success, I think back on a very long timeline. Edison spoke of inspiration and considerably more perspiration being required for invention. In almost every case, there are years and years of separate, unconnected thoughts that slowly coalesce into new ideas. We ponder what could be and more importantly, what should be. Collegial contacts prompt us and challenge our assumptions. And then, if we have the doggedness to see it through, there are hundreds of ways we test those ideas until failure and observation form solid concepts to build on. Yet, finishing is still far from certain. Usually it is the help of many colleagues that will make possible the actual creation of something wonderful. For prosthetists and orthotists, I think the driving force to see us through is helping our patients achieve that experience of feeling better now than anytime since before their physical challenges. We measure success not by the object we make or how much it costs but rather by the simple human experience of how it helps someone feel better than they thought they could. As a profession, we are incredibly fortunate when we get to share that. Thinking about it now makes me smile. I was just that fortunate today. David A. Boone, CP, MPH, PhD Editor-in-Chief Journal of Prosthetics and Orthotics
Profile of JTE-522 as a Human Cyclooxygenase-2 Inhibitor (1998)

Inhibitory activity and the mechanism of action of JTE-522 (4-(4-cyclohexyl-2-methyloxazol-5-yl)-2-fluorobenzenesulfonamid e), a novel selective cyclooxygenase (COX)-2 inhibitor, on human COX-1 and COX-2 were investigated and compared with those of reference compounds. In an enzyme assay, JTE-522 inhibited yeast-expressed human recombinant COX-2 with an IC50 value of 0.085 microM. In contrast, JTE-522 did not inhibit human COX-1 prepared from human platelets at concentrations up to 100 microM. In a cell-based assay, JTE-522 diminished lipopolysaccharide-induced prostaglandin E2 production in human peripheral blood mononuclear cells (COX-2) (IC50 value = 15.1 nM). On the other hand, JTE-522 was less potent at inhibiting calcium ionophore-induced thromboxane B2 production in washed human platelets (COX-1) (IC50 value = 6210 nM). JTE-522 showed highly selective inhibition of human COX-2, and its activity was more selective than that of other COX-2 inhibitors (NS-398 and SC-58635). Human recombinant COX-2 activity was attenuated by JTE-522 in a dose-dependent and time-dependent manner. In contrast, the inhibitory activity of JTE-522 on human COX-1 was not affected by preincubation time. COX-2 inhibition by JTE-522 could not be recovered by gel filtration. These results indicate that JTE-522 is a highly selective, time-dependent and irreversible inhibitor of human COX-2.