gebhart/patrepeval huggingface dataset:
Incorporating demographics into a skin cancer diagnosis algorithm for Raman spectroscopy improves diagnostic specificity (Conference Presentation) (2019)

Background & objective: Skin cancer is a very common malignancy that occurs more frequently in fair skin and older individuals. Raman spectroscopy is a non-invasive optical technique that can be used as an adjunct for skin cancer diagnosis. The objective of this study is to evaluate whether incorporating patient demographics can improve skin cancer diagnosis based on Raman spectroscopy. Patients & Methods: Raman spectra of 731 lesions and their respective adjacent normal skin were measured in vivo using a real-time Raman spectrometer. The lesions were divided into skin cancers (including malignant melanoma, basal cell carcinoma, squamous cell carcinoma and precancerous lesion - actinic keratosis, n = 340) and benign skin lesions (including pigmented nevi and seborrheic keratosis, n = 391). Patient age, gender, skin type and location of the lesion were incorporated into the analysis. Multivariate statistical analysis including principal component and general discriminant analysis (PC-GDA) and partial least squares (PLS) are used for skin cancer discrimination based on leave-one-out cross-validation. Results: The posterior probability of being a cancer is significantly dependent on gender, age and location of the lesion (p<0.05) but independent of skin type (p>0.05). The area under the receiver operating characteristic curve (ROC) is increased from 0.905 (95%CI: 0.884-0.927) to 0.932 (95%CI: 0.919-0.945) after taking into account demographics. Correspondingly, the specificity is increased from 43.2% to 50.1% at sensitivity of 99%; and from 73.4% to 77.5% at sensitivity of 90%. Conclusions: The specificity is increased after incorporating demographics into the algorithm for skin cancer diagnosis based on Raman spectroscopy.
Triple Contrast CT Method Enables Simultaneous Evaluation of Articular Cartilage Composition and Segmentation (2019)

Early degenerative changes of articular cartilage are detected using contrast-enhanced computed tomography (CT) with a cationic contrast agent (CA). However, cationic CA diffusion into degenerated cartilage decreases with proteoglycan depletion and increases with elevated water content, thus hampering tissue evaluation at early diffusion time points. Furthermore, the contrast at synovial fluid-cartilage interface diminishes as a function of diffusion time hindering accurate cartilage segmentation. For the first time, we employ quantitative dual-energy CT (QDECT) imaging utilizing a mixture of three CAs (cationic CA4+ and non-ionic gadoteridol which are sensitive to proteoglycan and water contents, respectively, and bismuth nanoparticles which highlight the cartilage surface) to simultaneously segment the articulating surfaces and determine of the cartilage condition. Intact healthy, proteoglycan-depleted, and mechanically injured bovine cartilage samples (n = 27) were halved and imaged with synchrotron microCT 2-h post immersion in triple CA or in dual CA (CA4+ and gadoteridol). CA4+ and gadoteridol partitions were determined using QDECT, and pairwise evaluation of these partitions was conducted for samples immersed in dual and triple CAs. In conclusion, the triple CA method is sensitive to proteoglycan depletion while maintaining sufficient contrast at the articular surface to enable detection of cartilage lesions caused by mechanical impact.
Evaluation of Nicked Human Chorionic Gonadotropin Content in Clinical Specimens by a Specific Immunometric Assay (1999)

We report the development and characterization of an IRMA for the direct measurement of nicked human chorionic gonadotropin (hCGn) in blood and urine. hCGn derived from a reference preparation of hCG used as an immunogen elicits monoclonal antibodies (mAbs) with enhanced recognition of human luteinizing hormone epitopes. The most specific assay for pregnancy hCGn is an IRMA composed of one mAb to choriocarcinoma-derived hCGn (C5) and a second mAb developed from immunization with normal-pregnancy hCGn. This assay was used to evaluate hCGn profiles in normal, in vitro fertilization, Down syndrome, and ectopic pregnancies. In all pregnancies, hCGn was usually present in much lower concentrations than the non-nicked hCG isoform. Our results suggest that some form of physical separation from the overwhelming quantities of non-nicked hCG present in clinical specimens will be required before accurate immunochemical estimations of hCGn can be made.
Development of A Combined Optical and Fluorescence Imaging System in Frequency-Domain for Breast Cancer Detection (2000)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text N. Iftimia, S. Liao, and H. Jiang, "Development of A Combined Optical and Fluorescence Imaging System in Frequency-Domain for Breast Cancer Detection," in Biomedical Optical Spectroscopy and Diagnostics, T. Li, ed., Vol. 38 of OSA Trends in Optics and Photonics (Optical Society of America, 2000), paper TuE2. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Evaluation of Grain‐Boundary Conduction of Dense AlN–SiC Solid Solution by Scanning Nonlinear Dielectric Microscopy (2010)

Dense and elemental homogeneous 2H AlN–SiC solid solution doped with Al and C was fabricated by using spark plasma sintering. The p ‐type electrical conduction of the sample was confirmed by measurements of electrical conductivities and Seebeck coefficient. Dopant profiling of the sample by scanning nonlinear dielectric microscopy showed that the AlN–SiC grains respond to p ‐type electrical conduction. These results indicated that added Al and C were dissolved to the grains and acted as p ‐type dopants. In contrast, the grain boundaries did not show any response, suggesting the presence of depletion layer in the boundary.
Sensitivity of Osteosarcoma Cells to Concentration-Dependent Bioactivities of Lipid Peroxidation Product 4-Hydroxynonenal Depend on Their Level of Differentiation (2021)

4-Hydroxynonenal (HNE) is a major aldehydic product of lipid peroxidation known to exert several biological effects. Normal and malignant cells of the same origin express different sensitivity to HNE. We used human osteosarcoma cells (HOS) in different stages of differentiation in vitro, showing differences in mitosis, DNA synthesis, and alkaline phosphatase (ALP) staining. Differentiated HOS cells showed decreased proliferation (<sup>3</sup>H-thymidine incorporation), decreased viability (thiazolyl blue tetrazolium bromide-MTT), and increased apoptosis and necrosis (nuclear morphology by staining with 4',6-diamidino-2-phenylindole-DAPI). Differentiated HOS also had less expressed c-MYC, but the same amount of c-FOS (immunocytochemistry). When exposed to HNE, differentiated HOS produced more reactive oxygen species (ROS) in comparison with undifferentiated HOS. To clarify this, we measured HNE metabolism by an HPLC method, total glutathione (GSH), oxidized GSH (ox GSH), glutathione transferase activity (GST), proteasomal activity by enzymatic methods, HNE-protein adducts by genuine ELISA and fatty acid composition by GC-MS in these cell cultures. Differentiated HOS cells had less GSH, lower HNE metabolism, increased formation of HNE-protein adducts, and lower proteasomal activity, in comparison to undifferentiated counterpart cells, while GST and oxGSH were the same. Fatty acids analyzed by GC-MS showed that there is an increase in C20:3 in differentiated HOS while the amount of C20:4 remained the same. The results showed that the cellular machinery responsible for protection against toxicity of HNE was less efficient in differentiated HOS cells. Moreover, differentiated HOS cells contained more C20:3 fatty acid, which might make them more sensitive to free radical-initiated oxidative chain reactions and more vulnerable to the effects of reactive aldehydes such as HNE. We propose that HNE might act as natural promotor of decay of malignant (osteosarcoma) cells in case of their differentiation associated with alteration of the lipid metabolism.
Task-based quantization with application to MIMO receivers (2020)

Multiple-input multiple-output (MIMO) systems are required to communicate reliably at high spectral bands using a large number of antennas, while operating under strict power and cost constraints. In order to meet these constraints, future MIMO receivers are expected to operate with low resolution quantizers, namely, utilize a limited number of bits for representing their observed measurements, inherently distorting the digital representation of the acquired signals. The fact that MIMO receivers use their measurements for some task, such as symbol detection and channel estimation, other than recovering the underlying analog signal, indicates that the distortion induced by bit-constrained quantization can be reduced by designing the acquisition scheme in light of the system task, i.e., by {\em task-based quantization}. In this work we survey the theory and design approaches to task-based quantization, presenting model-aware designs as well as data-driven implementations. Then, we show how one can implement a task-based bit-constrained MIMO receiver, presenting approaches ranging from conventional hybrid receiver architectures to structures exploiting the dynamic nature of metasurface antennas. This survey narrows the gap between theoretical task-based quantization and its implementation in practice, providing concrete algorithmic and hardware design principles for realizing task-based MIMO receivers.
The promising alliance of anti-cancer electrochemotherapy with immunotherapy (2016)

Anti-tumor electrochemotherapy, which consists in increasing anti-cancer drug uptake by means of electroporation, is now implanted in about 140 cancer treatment centers in Europe. Its use is supported by the English National Institute for Health and Care Excellence for the palliative treatment of skin metastases, and about 13,000 cancer patients were treated by this technology by the end of 2015. Efforts are now focused on turning this local anti-tumor treatment into a systemic one. Electrogenetherapy, that is the electroporation-mediated transfer of therapeutic genes, is currently under clinical evaluation and has brought excitement to enlarge the anti-cancer armamentarium. Among the promising electrogenetherapy strategies, DNA vaccination and cytokine-based immunotherapy aim at stimulating anti-tumor immunity. We review here the interests and state of development of both electrochemotherapy and electrogenetherapy. We then emphasize the potent beneficial outcome of the combination of electrochemotherapy with immunotherapy, such as immune checkpoint inhibitors or strategies based on electrogenetherapy, to simultaneously achieve excellent local debulking anti-tumor responses and systemic anti-metastatic effects.
Temporary Electrostatic Impairment of DNA Recognition: Light‐Driven DNA Binding of Peptide Dimers (2012)

Negativ geladene Anhängsel – zum Beispiel Glu8-Sequenzen – an einem Peptiddimer, das sich vom GCN4-Transkriptionsfaktor ableitet, verhindern dessen Bindung an DNA. Die spezifische DNA-Erkennung lässt sich aber durch Bestrahlung mit UV-Licht wiederherstellen, wenn eine photolabile Brücke zwischen dem aciden Anhängsel und dem DNA bindenden Peptid eingebaut wird. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Inhibition of protein kinase C and calmodulin by the geometric isomers <i>cis</i>‐ and <i>trans</i>‐tamoxifen (1990)

The triphenylethylene antiestrogen trans-tamoxifen is an effective antitumor agent used in the treatment of human breast cancer. While the antiestrogenic activity of trans-tamoxifen clearly plays an important role in its tumoricidal action, some of the biological effects of trans-tamoxifen are independent of estrogen. Therapeutic concentrations of trans-tamoxifen inhibit protein kinase C (PKC) and calmodulin-dependent enzymes. PKC and calmodulin play critical roles in growth regulation, and there is evidence that inhibition of PKC and calmodulin by trans-tamoxifen may contribute to the antitumor activity of the drug in vivo. The geometric isomers cis- and trans-tamoxifen have a number of opposing biological activities that have been attributed to their interactions with the estrogen receptor. Cis-tamoxifen is generally estrogenic, whereas trans-tamoxifen is generally antiestrogenic. In this report, we compared the effects of cis- and trans-tamoxifen on PKC activity and on calmodulin-dependent cAMP phosphodiesterase activity. Cis- and trans-tamoxifen inhibited the Ca2(+)- and phosphatidylserine- (PS-) dependent activity of purified rat brain PKC with indistinguishable potencies, but cis-tamoxifen was somewhat more potent than the trans isomer in the inhibition of the Ca2(+)- and PS-independent activity of PKC. In addition, cis-tamoxifen was the more potent isomer in the inhibition of T lymphocyte activation, an event that entails a PKC-requiring signal transduction pathway. A modest preference for the cis isomer was also observed in the inhibition of a calmodulin-dependent cAMP phosphodiesterase. These results suggest a congruence between triphenylethylene binding sites on PKC and on the activated calmodulin-cAMP phosphodiesterase complex.(ABSTRACT TRUNCATED AT 250 WORDS)
Serotonin-based pharmacotherapy for acute neuroleptic-induced akathisia: A new approach to an old problem (2001)

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PATHOLOGICAL AND ENZYMATIC FEATURES OF 1,2-DIMETHYLHYDRAZINE INDUCED COLORECTAL CARCINOMAS IN RATS (1995)

Well- and moderately well-differentiated colorectal adenocarcinomas accounted for 86% of all tumors induced by 1,2-dimethylhydrazine in rats, and were distributed throughout the colorectal tract. Poorly differentiated carcinomas, 14% of all tumors, were markedly restricted to the proximal half of colon, i.e., 94% of the poorly differentiated type was found in the proximal colon and caecum. Thymidylate synthetase and thymidine kinase, key enzymes in the de novo and salvage pathways, respectively, for pyrimidine nucleotide synthesis were found to be reduced and elevated, respectively, with increasing cellular differentiation. These results suggest that biochemical differences in colorectal tumors may be associated with differences in tumor frequency, distribution, and histological type.
Combination of FTIRspectral imaging and chemometrics for tumour detection from paraffin-embedded biopsies (2007)

FTIR spectral imaging was applied on formalin-fixed paraffin-embedded biopsies from colon and skin cancerous lesions. These samples were deposited onto different substrates (zinc selenide and calcium fluoride respectively) and embedded using two types of paraffin. Formalin fixation followed by paraffin embedding is the gold standard in tissue storage. It can preserve molecular structures and it is compatible with immunohistochemistry. However, paraffin absorption bands are significant in the mid-infrared region and can mask some molecular vibrations of the tissue. Direct data processing was applied on spectral images without any chemical dewaxing of the tissues. Extended Multiplicative Signal Correction was used to correct the spectral contribution from paraffin. For this purpose, the signal of paraffin was modelled using Principal Component Analysis and paraffin spectra were removed from the raw images based on an outlier detection. Then, pseudo-colour images were computed by K-means clustering in order to highlight histological structures of interest. This robust chemometrics methodology was applied on the two samples. Tumour areas were successfully demarcated from the rest of the tissue in both colon and skin independently of the embedding material and of the substrate.
OmniGuide photonic bandgap fibers for flexible delivery of CO 2 laser energy for laryngeal and airway surgery (2005)

The CO<sub>2</sub> laser is the most widely used laser in laryngology, offering very precise cutting, predictable depth of penetration, and minimal collateral damage due to the efficient absorption of CO<sub>2</sub> laser by water. Surgical applications of CO<sub>2</sub> laser in microlaryngoscopy include removal of benign lesions and early-stage laryngeal cancer. A Transoral Laser Microsurgery (TLM) approach is routinely employed for treatment of laryngeal cancer; however, the role of TLM in advanced malignant lesions remains controversial. The main limiting factor of TLM is the restrictive exposure of the endoscopes combined with the limited cutting ability offered by the existing micromanipulator, enabling cutting only along the straight line-of-sight axis. A flexible fiber delivery system offering a very high quality output beam can offer tangential cutting and can therefore significantly enhance the existing surgical capabilities. Moreover, a flexible fiber for CO<sub>2</sub> laser delivery can be used for treatment of benign conditions through flexible endoscopy in an office setting using local anesthesia. OmniGuide Communications Inc. (OGCI) has fabricated a photonic bandgap fiber capable of flexibly guiding CO<sub>2</sub> laser energy. Results of laryngeal in-vivo and in-vitro animal studies will be presented. We will discuss the system setup, fiber performance and clinical outcomes. In addition we will present the results of the first human treatment and highlight additional otolaryngology conditions, which will likely benefit from the new technology herein presented.
Transcriptomic similarities and differences in host response between SARS-CoV-2 and other viral infections (2020)

The pandemic 2019 novel coronavirus disease (COVID-19) shares certain clinical characteristics with other acute viral infections. We studied the whole-blood transcriptomic host response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using RNAseq from 24 healthy controls and 62 prospectively enrolled patients with COVID-19. We then compared these data to non-COVID-19 viral infections, curated from 23 independent studies profiling 1,855 blood samples covering six viruses (influenza, respiratory syncytial virus (RSV), human rhinovirus (HRV), severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1), Ebola, dengue). We show gene expression changes in COVID-19 versus non-COVID-19 viral infections are highly correlated (r = 0.74, p < 0.001). However, we also found 416 genes specific to COVID-19. Inspection of top genes revealed dynamic immune evasion and counter host responses specific to COVID-19. Statistical deconvolution of cell proportions maps many cell type proportions concordantly shifting. Discordantly increased in COVID-19 were CD56<sup>bright</sup> natural killer cells and M2 macrophages. The concordant and discordant responses mapped out here provide a window to explore the pathophysiology of the host response to SARS-CoV-2.
Synchronisation of apical constriction and cell cycle progression is a conserved behaviour of pseudostratified neuroepithelia informed by their tissue geometry (2022)

Neuroepithelial cells balance tissue growth requirement with the morphogenetic imperative of closing the neural tube. They apically constrict to generate mechanical forces which elevate the neural folds, but are thought to apically dilate during mitosis. However, we previously reported that mitotic neuroepithelial cells in the mouse posterior neuropore have smaller apical surfaces than non-mitotic cells. Here, we document progressive apical enrichment of non-muscle myosin-II in mitotic, but not non-mitotic, neuroepithelial cells with smaller apical areas. Live-imaging of the chick posterior neuropore confirms apical constriction synchronised with mitosis, reaching maximal constriction by anaphase, before division and re-dilation. Mitotic apical constriction amplitude is significantly greater than interphase constrictions. To investigate conservation in humans, we characterised early stages of iPSC differentiation through dual SMAD-inhibition to robustly produce pseudostratified neuroepithelia with apically enriched actomyosin. These cultured neuroepithelial cells achieve an equivalent apical area to those in mouse embryos. iPSC-derived neuroepithelial cells have large apical areas in G2 which constrict in M phase and retain this constriction in G1/S. Given that this differentiation method produces anterior neural identities, we studied the anterior neuroepithelium of the elevating mouse mid-brain neural tube. Instead of constricting, mid-brain mitotic neuroepithelial cells have larger apical areas than interphase cells. Tissue geometry differs between the apically convex early midbrain and flat posterior neuropore. Culturing human neuroepithelia on equivalently convex surfaces prevents mitotic apical constriction. Thus, neuroepithelial cells undergo high-amplitude apical constriction synchronised with cell cycle progression but the timing of their constriction if influenced by tissue geometry.
CNN-Based Classification of Degraded Images Without Sacrificing Clean Images (2021)

Image classification needs to consider image degradations in practice because an image classification network trained with clean images works poorly for degraded images while digital images usually include some degradations such as JPEG compression. To tackle this problem, a common approach is training classification networks on degraded images with various levels of degradation, e.g. various quality factors for JPEG compression. However, the classification networks do not usually have enough accuracy for clean images because the classification networks have been averagely trained for various levels of degradation. This paper aims to construct a classification network of degraded images without sacrificing the performance of clean images. This paper proposes a network to learn the classification of degraded images and degradation levels of degraded images as multi-task learning. Learning the classification of degraded images is the main task of multi-task learning. On the other hand, learning degradation levels is a sub-task of multi-task learning and reinforces the classification ability. In the proposed network, a feature extractor of the classification is trained with image features acquired from a classification network of clean images by using consistency regularization with the cosine similarity loss. The experimental results using different types of degradations, including JPEG compression, Gaussian blur, Gaussian noise, and salt-and-pepper noise, show that our proposed network has enough ability to classify degraded images without sacrificing the performance for clean images.