gebhart/patrepeval huggingface dataset:
Homologous Recombination Deficiency and Platinum-Based Therapy Outcomes in Advanced Breast Cancer (2017)

<b>Purpose:</b> Recent studies have identified mutation signatures of homologous recombination deficiency (HRD) in over 20% of breast cancers, as well as pancreatic, ovarian, and gastric cancers. There is an urgent need to understand the clinical implications of HRD signatures. Whereas <i>BRCA1/2</i> mutations confer sensitivity to platinum-based chemotherapies, it is not yet clear whether mutation signatures can independently predict platinum response.<b>Experimental Design:</b> In this observational study, we sequenced tumor whole genomes (100× depth) and matched normals (60×) of 93 advanced-stage breast cancers (33 platinum-treated). We computed a published metric called HRDetect, independently trained to predict <i>BRCA1/2</i> status, and assessed its capacity to predict outcomes on platinum-based chemotherapies. Clinical endpoints were overall survival (OS), total duration on platinum-based therapy (TDT), and radiographic evidence of clinical improvement (CI).<b>Results:</b> HRDetect predicted <i>BRCA1/2</i> status with an area under the curve (AUC) of 0.94 and optimal threshold of 0.7. Elevated HRDetect was also significantly associated with CI on platinum-based therapy (AUC = 0.89; <i>P</i> = 0.006) with the same optimal threshold, even after adjusting for <i>BRCA1/2</i> mutation status and treatment timing. HRDetect scores over 0.7 were associated with a 3-month extended median TDT (<i>P</i> = 0.0003) and 1.3-year extended median OS (<i>P</i> = 0.04).<b>Conclusions:</b> Our findings not only independently validate HRDetect, but also provide the first evidence of its association with platinum response in advanced breast cancer. We demonstrate that HRD mutation signatures may offer clinically relevant information independently of <i>BRCA1/2</i> mutation status and hope this work will guide the development of clinical trials. <i>Clin Cancer Res; 23(24); 7521-30. ©2017 AACR</i>.
A fast poly-energetic iterative FBP algorithm (2014)

The beam hardening (BH) effect can influence medical interpretations in two notable ways. First, high attenuation materials, such as bones, can induce strong artifacts, which severely deteriorate the image quality. Second, voxel values can significantly deviate from the real values, which can lead to unreliable quantitative evaluation results. Some iterative methods have been proposed to eliminate the BH effect, but they cannot be widely applied for clinical practice because of the slow computational speed. The purpose of this study was to develop a new fast and practical poly-energetic iterative filtered backward projection algorithm (piFBP). The piFBP is composed of a novel poly-energetic forward projection process and a robust FBP-type backward updating process. In the forward projection process, an adaptive base material decomposition method is presented, based on which diverse body tissues (e.g., lung, fat, breast, soft tissue, and bone) and metal implants can be incorporated to accurately evaluate poly-energetic forward projections. In the backward updating process, one robust and fast FBP-type backward updating equation with a smoothing kernel is introduced to avoid the noise accumulation in the iteration process and to improve the convergence properties. Two phantoms were designed to quantitatively validate our piFBP algorithm in terms of the beam hardening index (BIdx) and the noise index (NIdx). The simulation results showed that piFBP possessed fast convergence speed, as the images could be reconstructed within four iterations. The variation range of the BIdx's of various tissues across phantom size and spectrum were reduced from [-7.5, 17.5] for FBP to [-0.1, 0.1] for piFBP while the NIdx's were maintained in the same low level (about [0.3, 1.7]). When a metal implant presented in a complex phantom, piFBP still had excellent reconstruction performance, as the variation range of the BIdx's of body tissues were reduced from [-2.9, 15.9] for FBP to [-0.3, 0.3] for piFBP and the magnitude of the BIdx of the metal implant was reduced from 23.3 to 1.3. The proposed algorithm piFBP can effectively eliminate beam hardening artifacts caused by bones, greatly reduce metal artifacts caused by metal implants, and quantitatively reconstruct accurate images with poly-energetic spectrum. Its fast reconstruction speed and excellent performance make it ready for clinical applications on the current single spectrum CT scanners.
Determination of Immunoglobulin A against <i>Gardnerella vaginalis</i> Hemolysin, Sialidase, and Prolidase Activities in Vaginal Fluid: Implications for Adverse Pregnancy Outcomes (2003)

A nested case-control study of low birth weight and preterm delivery was performed with singleton women. Immunoglobulin A (IgA) against the Gardnerella vaginalis hemolysin (anti-Gvh IgA) and sialidase and prolidase activities were determined in vaginal fluid at 17 weeks of gestation. Sialidase positivity and bacterial vaginosis with high prolidase activity were associated with 2- and 11-fold increased risks for low birth weight, respectively. No woman with bacterial vaginosis plus a strong anti-Gvh IgA response had an adverse outcome.
NMDA receptor-dependent GABA <sub>B</sub> receptor internalization via CaMKII phosphorylation of serine 867 in GABA <sub>B1</sub> (2010)

GABAB receptors are the G-protein-coupled receptors for GABA, the main inhibitory neurotransmitter in the brain. GABAB receptors are abundant on dendritic spines, where they dampen postsynaptic excitability and inhibit Ca2+ influx through NMDA receptors when activated by spillover of GABA from neighboring GABAergic terminals. Here, we show that an excitatory signaling cascade enables spines to counteract this GABAB-mediated inhibition. We found that NMDA application to cultured hippocampal neurons promotes dynamin-dependent endocytosis of GABAB receptors. NMDA-dependent internalization of GABAB receptors requires activation of Ca2+/Calmodulin-dependent protein kinase II (CaMKII), which associates with GABAB receptors in vivo and phosphorylates serine 867 (S867) in the intracellular C terminus of the GABAB1 subunit. Blockade of either CaMKII or phosphorylation of S867 renders GABAB receptors refractory to NMDA-mediated internalization. Time-lapse two-photon imaging of organotypic hippocampal slices reveals that activation of NMDA receptors removes GABAB receptors within minutes from the surface of dendritic spines and shafts. NMDA-dependent S867 phosphorylation and internalization is predominantly detectable with the GABAB1b subunit isoform, which is the isoform that clusters with inhibitory effector K+ channels in the spines. Consistent with this, NMDA receptor activation in neurons impairs the ability of GABAB receptors to activate K+ channels. Thus, our data support that NMDA receptor activity endocytoses postsynaptic GABAB receptors through CaMKII-mediated phosphorylation of S867. This provides a means to spare NMDA receptors at individual glutamatergic synapses from reciprocal inhibition through GABAB receptors.
The Role of Immune Escape and Immune Cell Infiltration in Breast Cancer (2018)

While detailed analysis of aberrant cancer cell signaling pathways and changes in cancer cell DNA has dominated the field of breast cancer biology for years, there now exists increasing evidence that the tumor microenvironment (TME) including tumor-infiltrating immune cells support the growth and development of breast cancer and further facilitate invasion and metastasis formation as well as sensitivity to drug therapy. Furthermore, breast cancer cells have developed different strategies to escape surveillance from the adaptive and innate immune system. These include loss of expression of immunostimulatory molecules, gain of expression of immunoinhibitory molecules such as PD-L1 and HLA-G, and altered expression of components involved in apoptosis. Furthermore, the composition of the TME plays a key role in breast cancer development and treatment response. In this review we will focus on i) the different immune evasion mechanisms used by breast cancer cells, ii) the role of immune cell infiltration in this disease, and (iii) implication for breast cancer-based immunotherapies.
Biodiversity in helminths and nematodes as a field of study: an overview (2001)

Abstract Despite their potential negative effects, parasites may be used as targets for biological conservation and studies on the evolutionary and ecological impact of parasitism. These purposes serve to increase our knowledge on the species diversity of parasites. In the present paper we try to precisely define the composite zoological group currently designated as 'helminths' and to address the question of how many known species there are in the different clades of parasitic worms, as compared with the other major groups described in the Animalia. The relationships between helminthology and nematology are discussed. Finally, the question of how to improve the organisation of research in these different fields of study is briefly considered. The Nematoda seems to be the group which needs the greatest effort in the future. This supposes that specialists in nematode taxonomy are numerous enough to maintain a substantial effort. The necessary taxonomical effort is weakened by the distribution of the fields of study between helminthology and nematology, something which is inadequate from a zoological, as well as from a logical, point of view. The study of nematode zoology would certainly improve if nematology could emerge as an undivided speciality. One of the prior goals in such a unified field of study would be an exhaustive inventory of the nominal living species. A cooperative effort will also be needed to found the basis of a general classification of the phylum Nematoda. Finally, a clarification and a standardisation of the terminology is also needed.
Repair of ruptured spinal nerve roots in a brachial plexus lesion (1995)

A 22-year-old woman sustained a brachial plexus injury with supraganglionic rupture of the C-8 and T-1 nerve roots as a result of a traffic accident. She was operated on approximately 1 week following the accident. After a hemilaminectomy, the intradural defects in the ruptured roots were bridged with sural nerve grafts. Within 3 years she recovered function in all muscles supplied from the lower roots in the plexus except for the intrinsic hand muscles, but she had a persisting, complete sensory loss in the ulnar nerve distribution. The possibility for functional gain after repair of spinal root lesions in brachial plexus patients is discussed.
Stereoisomeric Flavor Compounds. 79. Simultaneous Enantio- selective Analysis of 3-Butylphthalide and 3-Butylhexahydro- phthalide Stereoisomers in Celery, Celeriac, and Fennel (1997)

Using enantioselective multidimensional gas chromatography with heptakis[2,3-di-O-acetyl-6-O-(tert-butyldimethylsilyl)]-β-cyclodextrin as the chiral stationary phase, the simultaneous analysis of the 3-butylphthalide enantiomers and all eight 3-butylhexahydrophthalide stereoisomers was achieved. Enantiomeric distributions of compounds in celery, celeriac, celery seed, and fennel extracts were elucidated. Keywords: Enantioselective multidimensional gas chromatography (enantio-MDGC); 3-butyl(hexahydro)phthalide stereoisomers; celery; celeriac; fennel
Magnetic Resonance Imaging in Stroke (2003)

Magnetic resonance imaging provides non-invasive information about the brain's blood flow, water movement and biochemical abnormalities following stroke, and advances in magnetic resonance imaging (MRI) are transforming the investigation and treatment of cerebrovascular disease. Echoplanar techniques with diffusion and perfusion weighted imaging, together with developments in magnetic resonance spectroscopy and angiography, are replacing CT scanning as the diagnostic modality of choice. In this profusely illustrated book world leaders in these technologies review the scientific basis and clinical applications of MRI in stroke. It will appeal to a broad readership including stroke physicians, neurologists, neurosurgeons, rehabilitation specialists, and others with a clinical or research interest in cerebrovascular disease.
Crystal chemistry of the rare earth sesquisulfides (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCrystal chemistry of the rare earth sesquisulfidesArthur W. Sleight and Charles T. PrewittCite this: Inorg. Chem. 1968, 7, 11, 2282–2288Publication Date (Print):November 1, 1968Publication History Published online1 May 2002Published inissue 1 November 1968https://pubs.acs.org/doi/10.1021/ic50069a022https://doi.org/10.1021/ic50069a022research-articleACS PublicationsRequest reuse permissionsArticle Views447Altmetric-Citations101LEARN 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
High Density Ozone Monitoring Using Gas Sensitive Semi-Conductor Sensors in the Lower Fraser Valley, British Columbia (2014)

A cost-efficient technology for accurate surface ozone monitoring using gas-sensitive semiconducting oxide (GSS) technology, solar power, and automated cell-phone communications was deployed and validated in a 50 sensor test-bed in the Lower Fraser Valley of British Columbia, over 3 months from May-September 2012. Before field deployment, the entire set of instruments was colocated with reference instruments for at least 48 h, comparing hourly averaged data. The standard error of estimate over a typical range 0-50 ppb for the set was 3 ± 2 ppb. Long-term accuracy was assessed over several months by colocation of a subset of ten instruments each at a different reference site. The differences (GSS-reference) of hourly average ozone concentration were normally distributed with mean -1 ppb and standard deviation 6 ppb (6000 measurement pairs). Instrument failures in the field were detected using network correlations and consistency checks on the raw sensor resistance data. Comparisons with modeled spatial O3 fields demonstrate the enhanced monitoring capability of a network that was a hybrid of low-cost and reference instruments, in which GSS sensors are used both to increase station density within a network as well as to extend monitoring into remote areas. This ambitious deployment exposed a number of challenges and lessons, including the logistical effort required to deploy and maintain sites over a summer period, and deficiencies in cell phone communications and battery life. Instrument failures at remote sites suggested that redundancy should be built into the network (especially at critical sites) as well as the possible addition of a "sleep-mode" for GSS monitors. At the network design phase, a more objective approach to optimize interstation distances, and the "information" content of the network is recommended. This study has demonstrated the utility and affordability of the GSS technology for a variety of applications, and the effectiveness of this technology as a means substantially and economically to extend the coverage of an air quality monitoring network. Low-cost, neighborhood-scale networks that produce reliable data can be envisaged.
Computing in Civil Engineering (2011) (2011)

Proceedings of the 2011 ASCE International Workshop on Computing in Civil Engineering, held in Miami, Florida, June 19-22, 2011. Sponsored by Technical Council on Computing and Information Technology of ASCE. This collection contains 112 peer-reviewed papers that offer the best and latest in contemporary research on the practical challenges, along with the areas of technological growth and development, of computing in civil engineering. Contributors from around the world examine such topics as: novel engineering, construction, and management technologies; design, engineering, and analysis; sustainable and resilient infrastructure; and cutting-edge developments.
Toll-like receptor 4-mediated activation of murine mast cells (2001)

Toll-like receptors (TLRs) are a family of pattern recognition receptors that are critical for cellular responses to a variety of bacterial, viral, and fungal products. Mast cells are important to host survival in a number of models of bacterial infection and might act as sentinel cells in host defense. We therefore examined the expression of TLRs and associated molecules by murine bone marrow-derived mast cells (BMMCs). BMMCs and the murine mast cell line MC/9 expressed mRNA for TLR2, TLR4, and TLR6 but not TLR5 and for both adapter molecule MD-2 and signaling molecule MyD88 but lacked surface CD14. After activation with the TLR2- and TLR4-dependent stimuli Staphylococcus aureus-derived peptidoglycan and Escherichia coli-derived lipopolysaccharide (LPS), respectively, mast cells produced significant levels of interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-alpha). To determine whether mast cells require TLR4 for cellular responses to LPS, mast cells were derived from the bone marrow cells of C3H/HeJ and C57Bl/10ScNCr mice containing a point mutation and a null mutation, respectively, in TLR4. Using these models, we demonstrated that the BMMC IL-6 and TNF-alpha responses to LPS were completely dependent on functional TLR4 with no significant LPS response observed in its absence. These findings have important implications for the mechanism of mast cell responses to pathogens and their products and suggest that different TLR4-expressing cells might have different thresholds for activation with LPS.
A Regulator and Filter for Tracking Aerodynamic Force (2006)

A closed-loop control system has been developed and tested for tracking prescribed values of aerodynamic force on a NACA 4412 airfoil. The system includes a measurement-based estimator - utilizing a low-dimensional model of the perturbation flow based on the method of proper orthogonal decomposition - and a stochastic correlation between the measurement and the state estimate. The system employs a nonlinear approximation of the performance output, defined as unsteady oscillations in the lift coefficient, and an extended Kalman filter, based on the nonlinear estimators. The control objective is to reduce or eliminate lift oscillations by tracking a prescribed, constant value. Using a proportional-integral regulator, control-in-the-loop computational fluid dynamics (CFD) simulations demonstrate that lift oscillations are reduced by a factor of approximately six - with and without the extended Kalman filter in the loop. The filter reduces noise in the output approximation and state estimates that result from measurement noise with some improvement in tracking
INFERENCE FOR SEMIPARAMETRIC MODELS: SOME QUESTIONS AND AN ANSWER (2001)

Non-and semi-parametric models have flourished during the last twenty five years. They have been applied widely and their theoretical properties have been studied extensively. We briefly review some of their development and list a few questions that we would like to see addressed. We develop an answer to one of these questions by formulating a 'calculus' similar to that of the i.i.d. case that enables us to analyze the efficiency of procedures in general semiparametric models when a nonparametric model has been defined. Our approach is illustrated by applying it to regression models, counting process models in survival analysis and submodels of Markov chains, which traditionally require elaborate special arguments. In the examples, the calculus lets us easily read off the structure of efficient estimators and check if a candidate estimator is efficient.
Efektifitas larutan kumur serbuk kayu manis konsentrasi 45% terhadap penurunan gingivitis (2006)

Telah diketahui kayu manis berfungsi dalam mencegah pembentukan plak gigi, obat sariawan dan mencegah bau mulut. Kandungan kimia yang dimiliki kayu manis diantaranya adalah tannin, eugenol dan kumarin yang mempunyai manfaat bagi kesehatan, khususnya kesehatan gigi dan mulut dalam hubungannya dengan gingivitis. Penelitian ini bertujuan untuk mengetahui efektifitas larutan serbuk kayu manis konsentrasi 45% dalam menurunkan gingivitis. Jenis penelitian Penelitian eksperimental semu di SMP Negeri 34 Makassar. Jumlah sampel sebanyak 50 orang dengan kriteria menderita gingivitis, semua gigi indeks masih ada dan tidak memakai gigi tiruan lepas atau alat ortodontik menggunakan metode Accidental sampling. Analisis data dengan uji t-berpasangan dan uji t-independent dengan program SPSS versi windows 11,5. Hasil uji tberpasangan pada perbedaan rata-rata skor gingivitis sebelum dan sesudah berkumur larutan serbuk kayu manis konsentrasi 45% pada kelompok uji dengan nilai p
The Action of Lithium on an Optically Active Aliphatic Chloride (1939)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Action of Lithium on an Optically Active Aliphatic ChlorideD. S. Tarbell and Marvin. WeissCite this: J. Am. Chem. Soc. 1939, 61, 5, 1203–1205Publication Date (Print):May 1, 1939Publication History Published online1 May 2002Published inissue 1 May 1939https://pubs.acs.org/doi/10.1021/ja01874a055https://doi.org/10.1021/ja01874a055research-articleACS PublicationsRequest reuse permissionsArticle Views40Altmetric-Citations9LEARN 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
Improved Video Mosaic Construction by Selecting a Suitable Subset of Video Images. (2004)

By stitching together adjacent images from a video sequence surveying a scene, a video mosaic of the entire panorama can be formed. Since a video survey consists of a sequence of images having small relative displacements with respect to each other, there is redundant overlapping information in consecutive images so that not all consecutive video images are required to create a mosaic, and only a subset of suitable images needs to be chosen. Images that are misaligned due to subpixel translation, rotation or shear are difficult to perfectly re-align and stitching of such images can result in a mosaic where discontinuities are noticeable. We propose a new technique for the construction of a seamless mosaic to minimise discontinuities. Our technique partitions an image into four quadrants to register with those of successive images. These registration values are used to form a misalignment index for selecting the best images for stitching.