gebhart/patrepeval huggingface dataset:
Automatic Visual Tracking and Social Behaviour Analysis with Multiple Mice (2013)

Social interactions are made of complex behavioural actions that might be found in all mammalians, including humans and rodents. Recently, mouse models are increasingly being used in preclinical research to understand the biological basis of social-related pathologies or abnormalities. However, reliable and flexible automatic systems able to precisely quantify social behavioural interactions of multiple mice are still missing. Here, we present a system built on two components. A module able to accurately track the position of multiple interacting mice from videos, regardless of their fur colour or light settings, and a module that automatically characterise social and non-social behaviours. The behavioural analysis is obtained by deriving a new set of specialised spatio-temporal features from the tracker output. These features are further employed by a learning-by-example classifier, which predicts for each frame and for each mouse in the cage one of the behaviours learnt from the examples given by the experimenters. The system is validated on an extensive set of experimental trials involving multiple mice in an open arena. In a first evaluation we compare the classifier output with the independent evaluation of two human graders, obtaining comparable results. Then, we show the applicability of our technique to multiple mice settings, using up to four interacting mice. The system is also compared with a solution recently proposed in the literature that, similarly to us, addresses the problem with a learning-by-examples approach. Finally, we further validated our automatic system to differentiate between C57B/6J (a commonly used reference inbred strain) and BTBR T+tf/J (a mouse model for autism spectrum disorders). Overall, these data demonstrate the validity and effectiveness of this new machine learning system in the detection of social and non-social behaviours in multiple (>2) interacting mice, and its versatility to deal with different experimental settings and scenarios.
Molecular Detection of Circulating Prostate Cells in Cancer II: Comparison of Prostate Epithelial Cells Isolation Procedures (1998)

The sensitive and specific detection of circulating tumor cells holds great promise for more accurate staging of cancer patients. Several reverse transcription-PCR (RT-PCR) procedures based on tissue-specific mRNA expression are now able to detect one cell derived from a given tissue among >10 peripheral nucleated blood cells [PNBCs; for a review, see (1)]. However, even for a single marker, highly discrepant results have been observed among the available clinical studies; e.g., the frequencies of positive prostate-specific antigen (PSA) RT-PCR results range from 25% (2) to 80% (3) in patients with metastatic prostate cancer (CaP), blurring the clinical relevance of these assays. Standardization and quality control in molecular diagnosis are crucial to the solution of this issue. We have previously studied factors potentially affecting RT-PCR results (4), and this current work focuses on the approaches for harvesting prostate cells among nucleated blood cells.

Since the first 1992 clinical report describing the RT-PCR detection of circulating prostatic cells in CaP, the majority of reported assays have used gradient separations to recover nucleated cells from the peripheral blood (1). We (5) and others (6) rather choose overnight hypo-osmotic red blood cell lysis as an easier and more cost-effective protocol. Because the approach used to harvest PNBCs may account for discrepancies in clinical results, we have compared a panel of nucleated blood cell separation methods.

Fresh blood from four healthy blood donors (total volume, 400 mL) was sampled in 40 × 10-mL EDTA-treated tubes (Becton-Dickinson). The LNCaP cell line, derived from a metastatic prostate carcinoma, was cultured as described (7). After trypsinization (2.5 mL/L trypsin), 10 confluent LNCaP cells were added into each of the 40 tubes, which were gently mixed. Six tubes were processed immediately by overnight hypoosmotic red blood cell lysis, as described (5)(6): Two volumes of ammonium chloride (9 …
[The progress of electrical treatment of arrhythmia]. (2002)

Described here is the progress of the electrical treatment for arrhythmia during the past half a century. The mechanism, their expression and the principles of electrical treatment for bradycardia, tachycardia and fatal arrhythmia--ventricular fibrillation (VF) are introduced respectively. The current situation and future development of the pacemaker, RF ablation and implantable cardioversion defibrillator are also discussed in the paper.
Using neuroimaging to detect awareness in disorders of consciousness. (2009)

The assessment of residual brain function in the vegetative state is extremely difficult and depends frequently on subjective interpretations of observed spontaneous and volitional behaviours. For those patients who retain peripheral motor function, rigorous behavioural assessment supported by structural imaging and electrophysiology is usually sufficient to establish a patient's level of wakefulness and awareness. However, it is becoming increasingly apparent that, in some patients, damage to the peripheral motor system may prevent overt responses to commands, even though the cognitive ability to perceive and understand such commands may remain intact. Advances in functional neuroimaging suggest a novel solution to this problem; in several recent cases, so-called activation studies have been used to identify residual cognitive function and even conscious awareness in patients who are assumed to be vegetative, yet retain cognitive abilities that have evaded detection using standard clinical methods.
Combining radiation plus immunotherapy to improve systemic immune response (2018)

Over the past decade, the fields of oncology have made great strides in therapies. The development of new therapeutics and increased understanding of the role of the immune system in the development and treatment of cancer has led to increased collaboration between oncologic fields. Recent technologic advancements in radiation therapy (RT), including stereotactic beam radiation therapy (SBRT), have improved local control and offer an alternative to surgery for the control of oligometastatic disease. Immunotherapy has proven a promising therapeutic in the treatment of metastatic disease but treatment resistance remains a significant obstacle in the majority of patients. Together, radiation and immunotherapy offer potential to eliminate metastatic disease, reduce time to recurrence and improve overall survival. Major obstacles to these positive outcomes include high tumor burden, intratumoral heterogeneity, and the negative effects of tumor stroma, to name a few. Multimodality treatments are under heavy investigation. Promising data from clinical trials is emerging to highlight the value of RT in combination with immunotherapy. However, the mechanisms behind their synergistic effects remain to be fully elucidated. This review aims to highlight the existing literature and offers hypotheses to explain mechanisms behind the synergy of RT and immunotherapy.
OR2M3: A Highly Specific and Narrowly Tuned Human Odorant Receptor for the Sensitive Detection of Onion Key Food Odorant 3-Mercapto-2-methylpentan-1-ol (2016)

The detection of key food odorants appears to be an important capability of odorant receptors. Here, thiols occupy an outstanding position among the 230 known key food odorants because of their very low odor thresholds. Members of the homologous series of 3-mercapto-2-methylalkan-1-ols have been described as onion key food odorants or food constituents and are detected at logarithmically different thresholds. 3-Mercapto-2-methylpentan-1-ol being the only key food odorant within this series also has the lowest odor threshold. Most odorants typically activate combinations of odorant receptors, which may be narrowly or broadly tuned. Consequently, a specific receptor activation pattern will define an odor quality. In contrast, here we show that just 1 of the 391 human odorant receptors, OR2M3, responded exclusively to 3-mercapto-2-methylpentan-1-ol of the 190 key food odorants tested, with a half maximal effective concentration at submicromolar concentration. Moreover, neither the Denisovan OR2M3 nor the closest OR2M3 homologs from five species did respond to this compound. This outstanding specificity of extremely narrowly tuned human OR2M3 can explain both odor qualities and odor threshold trend within a homologous series of 3-mercapto-2-methylalkan-1-ols and suggests a modern human-specific, food-related function of OR2M3 in detecting a single onion key food odorant.
Inhibition of Both Protease and Helicase Activities of Hepatitis C Virus NS3 by an Ethyl Acetate Extract of Marine Sponge Amphimedon sp (2012)

Combination therapy with ribavirin, interferon, and viral protease inhibitors could be expected to elicit a high level of sustained virologic response in patients infected with hepatitis C virus (HCV). However, several severe side effects of this combination therapy have been encountered in clinical trials. In order to develop more effective and safer anti-HCV compounds, we employed the replicon systems derived from several strains of HCV to screen 84 extracts from 54 organisms that were gathered from the sea surrounding Okinawa Prefecture, Japan. The ethyl acetate-soluble extract that was prepared from marine sponge Amphimedon sp. showed the highest inhibitory effect on viral replication, with EC₅₀ values of 1.5 and 24.9 µg/ml in sub-genomic replicon cell lines derived from genotypes 1b and 2a, respectively. But the extract had no effect on interferon-inducing signaling or cytotoxicity. Treatment with the extract inhibited virus production by 30% relative to the control in the JFH1-Huh7 cell culture system. The in vitro enzymological assays revealed that treatment with the extract suppressed both helicase and protease activities of NS3 with IC₅₀ values of 18.9 and 10.9 µg/ml, respectively. Treatment with the extract of Amphimedon sp. inhibited RNA-binding ability but not ATPase activity. These results suggest that the novel compound(s) included in Amphimedon sp. can target the protease and helicase activities of HCV NS3.
Wavelength-Dependent Differential Interference Contrast Microscopy: Selectively Imaging Nanoparticle Probes in Live Cells (2009)

Gold and silver nanoparticles display extraordinarily large apparent refractive indices near their plasmon resonance (PR) wavelengths. These nanoparticles show good contrast in a narrow spectral band but are poorly resolved at other wavelengths in differential interference contrast (DIC) microscopy. The wavelength dependence of DIC contrast of gold/silver nanoparticles is interpreted in terms of Mie's theory and DIC working principles. We further exploit this wavelength dependence by modifying a DIC microscope to enable simultaneous imaging at two wavelengths. We demonstrate that gold/silver nanoparticles immobilized on the same glass slides through hybridization can be differentiated and imaged separately. High-contrast, video-rate images of living cells can be recorded both with and without illuminating the gold nanoparticle probes, providing definitive probe identification. Dual-wavelength DIC microscopy thus presents a new approach to the simultaneous detection of multiple probes of interest for high-speed live-cell imaging.
Ly-6A.2 Expression Regulates Antigen-Specific CD4+ T Cell Proliferation and Cytokine Production (2002)

Ly-6 proteins appear to serve cell adhesion and cell signaling function, but the precise role of Ly-6A.2 in CD4+ T lymphocytes is still unclear. Overexpression of Ly-6A.2 in T lymphocytes has allowed us to analyze the influence of elevated Ly-6A.2 expression on T cell function. In this study we report reduced proliferation of CD4+ T cells overexpressing Ly-6A.2 in response to a peptide Ag. Moreover, the Ly-6A.2-overexpressing CD4+ cells generated elevated levels of IL-4, a key factor that propels the differentiation of naive CD4+ T cells into Th2 subset. The hyporesponsiveness of Ly-6A.2 transgenic CD4+ T cells is dependent on the interaction of Ly-6A.2 T cells with the APCs and can be reversed by blocking the interaction between Ly-6A.2 and a recently reported candidate ligand. Overexpression of Ly-6A.2 in CD4+ T cells reduced their Ca(2+) responses to TCR stimulation, therefore suggesting effects of Ly-6A.2 signaling on membrane proximal activation events. In contrast to the observed Ag-specific hyporesponsiveness, the Ly-6A.2 transgenic CD4+ T cells produced IL-4 independent of the interactions between Ly-6A.2 and the candidate Ly-6A.2 ligand. Our results suggest that 1) interaction of Ly-6A.2 with a candidate ligand regulates clonal expansion of CD4+ Th cells in response to an Ag (these results also provide further functional evidence for presence of Ly-6A.2 ligand on APC); and 2) Ly-6A.2 expression on CD4+ T cells promotes production of IL-4, a Th2 differentiation factor.
New strategies for probing crystal dissolution kinetics at the microscopic level (1995)

P. R. Unwin and J. V. Macpherson, Chem. Soc. Rev., 1995, 24, 109 DOI: 10.1039/CS9952400109
Preliminary Study for Automated Recognition of Anatomical Structure from Torso CT images (2005)

The anatomical human structure recognition is very important and necessary during the development of computer-aided diagnosis (CAD) system. In this paper, we propose an image processing scheme that can recognize the general structure of human torso by identifying the human torso region from CT images automatically and separating it into 7 parts: skin, subcutaneous fat, muscle, bone, diaphragm, thoracic cavity and abdominal cavity based on CT number distribution and spatial relations between different organ and tissue regions. We applied this scheme to 313 patient cases of torso CT images and confirmed its usefulness from the preliminary experiment.
Ray mapping and illumination control (2013)

Canonical illumination control problems are studied through the calculation of an appropriate ray mapping. We show that when the problem enjoys certain symmetries, the ray mapping can be calculated independently of the lens design. Once the ray mapping is known, the lens can be constructed. Such a separation of ray mapping and lens determination greatly simplifies the design task. We provide a few examples to illustrate this concept.
Collagen‐derived dipeptide, proline‐hydroxyproline, stimulates cell proliferation and hyaluronic acid synthesis in cultured human dermal fibroblasts (2010)

Orally ingested collagen undergoes degradation to small di- or tripeptides, which are detected in circulating blood 2 h after ingestion. The influence of collagen-derived peptides on dermal extracellular matrix components and cell proliferation was studied using cultured human dermal fibroblasts. Of the various collagenous peptides tested here, the dipeptide proline-hydroxyproline (Pro-Hyp) enhanced cell proliferation (1.5-fold) and hyaluronic acid synthesis (3.8-fold) at a dose of 200 nmol/mL. This was concomitant with a 2.3-fold elevation of hyaluronan synthase 2 (HAS2) mRNA levels. Small interfering RNA (siRNA)-mediated knockdown of the HAS2 gene in human dermal fibroblasts inhibited Pro-Hyp-induced HAS2 mRNA transcription and cell mitotic activity. Addition of genistein or H7, a protein kinase inhibitor, abolished the Pro-Hyp-induced HAS2 mRNA stimulation. Pro-Hyp elevated phosphorylation of signal transducer and activator of transcription 3 (STAT3) within a short time period (60 min). These results suggest that Pro-Hyp stimulates both cell mitotic activity and hyaluronic acid synthesis, which is mediated by activation of HAS2 transcription.
Synergistic Effects of Danshen (Salvia Miltiorrhiza Radix et Rhizoma) and Sanqi (Notoginseng Radix et Rhizoma) Combination in Inhibiting Inflammation Mediators in RAW264.7 Cells (2016)

<i>Aims</i>. This study aims to investigate the possible synergistic interactions of the Danshen-Sanqi combination on vascular disease via their anti-inflammatory activities. <i>Methods</i>. Nine combination ratios of Danshen-Sanqi extracts were screened in the RAW264.7 cell line and their anti-inflammatory effects were examined in lipopolysaccharide- (LPS-) induced nitric oxide (NO), tumor necrosis factor (TNF), and monocyte chemoattractant protein-1 (MCP-1) generation pathways. The interaction between Danshen and Sanqi on each target was analysed using combination index (CI) and isobologram models. Additionally, the anti-inflammatory activities of key bioactive compounds from Danshen and Sanqi were tested using the same models. The compounds from each herb that exerted the most potent activity were combined to evaluate their possible synergistic/antagonistic interactions. <i>Results</i>. Danshen-Sanqi 8 : 2 was found to be the optimal ratio and exerted a synergistic effect in inhibiting NO, TNF, and MCP-1 when the concentrations were higher than 1.24, 1.89, and 2.17 mg/mL, respectively. Although dihydrotanshinone I (DT) and ginsenoside Rd (Rd) from Danshen and Sanqi, respectively, exhibited the greatest individual bioactivity in the assays, antagonistic effects were observed for the DT-Rd combination 7 : 3. <i>Conclusion</i>. This study provided scientific evidence to support the traditional use of the Danshen-Sanqi combination for vascular disease through their synergistic interactions on anti-inflammatory pathways.
Performance-oriented dependency parsing (2013)

In the last decade a lot of dependency parsers have been developed. This book describes the motivation for the development of yet another parser - MDParser. The state of the art is presented and the deficits of the current developments are discussed. The main problem of the current parsers is that the task of dependency parsing is treated independently of what happens before and after it. However, in practice parsing is rarely done for the sake of parsing itself, but rather in order to use the results in a follow-up application. Additionally, current parsers are accuracy-oriented and focus only on the quality of the results, neglecting other important properties, especially efficiency. The evaluation of some NLP technologies is sometimes as difficult as the task itself. For dependency parsing it was long thought not to be the case, however, some recent works show that the current evaluation possibilities are limited. This book proposes a methodology to account for the weaknesses and combine the strengths of the current approaches. Finally, MDParser is evaluated against other state-of-the-art parsers. The results show that it is the fastest parser currently available and it is able to process plain text, which other parsers usually cannot. The results are slightly behind the top accuracies in the field, however, it is demonstrated that it is not decisive for applications.
Novel nanohydrogel of hyaluronic acid loaded with quercetin alone and in combination with temozolomide as new therapeutic tool, CD44 targeted based, of glioblastoma multiforme (2017)

Glioblastoma multiforme is the most common and aggressive primary brain cancer with only ∼3% of patients surviving more than 3 years from diagnosis. Several mechanisms are involved in drug and radiation resistance to anticancer treatments and among them one of the most important factors is the tumor microenvironment status, characterized by cancer cell hypersecretion of interleukins and cytokines. The aim of our research was the synthesis of a nanocarrier of quercetin combined with temozolomide, to enhance the specificity and efficacy of this anticancer drug commonly used in glioblastoma treatment. The nanohydrogel increased the internalization and cytotoxicity of quercetin in human glioblastoma cells and, when co-delivered with temozolomide, contribute to an improved anticancer effect. The nanohydrogel loaded with quercetin had the ability to recognize CD44 receptor, a brain cancer cell marker, through an energy and caveolae dependent mechanism of internalization. Moreover, nanohydrogel of quercetin was able to reduce significantly IL-8, IL-6, and VEGF production in pro-inflammatory conditions with interesting implications on the mechanism of glioblastoma cells drug resistance. In summary, novel CD44 targeted polymeric based nanocarriers appear to be proficient in mediating site-specific delivery of quercetin via CD44 receptor in glioblastoma cells. This targeted therapy lead to an improved therapeutic efficacy of temozolomide by modulating the brain tumor microenvironment.
Thermal stability of heat‐reflective films consisting of oxide–Ag–oxide deposited by dc magnetron sputtering (1986)

Transparent heat‐reflective films consisting of ITO–Ag–ITO or ZnO–Ag–ZnO were deposited onto soda‐lime glass by dc magnetron sputtering. In particular, the oxide layers were deposited from an electrically conductive oxide target. The transmittance in the visible range of the ITO–Ag–ITO film was more than 80% and the reflectance at 10 μm was nearly 95%. After the heat treatment at 650 °C, the transmittance of the films increased to nearly 85% and the reflectance at 10 μm was the same value of 95% as it was before the heat treatment. Moreover, the sheet resistance decreased to less than 4 Ω/cm2 by the heat treatment. Further, there were no visual changes or damage to the film up to 650 °C. The results showed that the ITO–Ag–ITO film was durable for the glass bending process. The ZnO–Ag–ZnO film also had high transmittance in the visible range and high reflectance in the infrared range, i.e., the transmittance in the visible range was more than 80% and the reflectance at 10 μm was 95%. However, these properties are much deteriorated by the heat treatment as compared with those of the ITO–Ag–ITO film.
Cyclic performance and fracture of wide flanged concentrically steel braced frames (2020)

Concentrically braced steel frames (CBFs) are often used in buildings to resist lateral loads induced by wind and seismic excitations. Large-size wide-flange (WF) steel brace members could be selected and used in these frames. In the current study, a finite element model (FEM) with a strain-based fracture rule is presented to investigate the performance of a large-size WF brace member in single-storey CBF with different sizes of beams and columns when subjected to reversed axial displacements. The effects of restraining the far ends of the beam bottom-flange, increasing the thickness of tab-plates, increasing the number of bolts used to connect the tab-plates to the web of the beam, and the location of the work-point along the brace with respect the beam-column assembly, on the hysteresis response of the frame are investigated. Results suggest that it may be advantageous to reduce the number of bolts and to increase the bolt size to allow for an increase in the thickness of the tab-plates to resist the extreme rotational demand in high seismic regions, thereby preventing fracture of the weld between the tab-plates and the column flange.