gebhart/patrepeval huggingface dataset:
Abstract 118: A comprehensive profile of the genomic architecture of curable prostate cancer (2016)

Abstract There is an urgent need to develop novel biomarkers of treatment response for precision medicine in prostate cancer, particularly in the setting of localized, non-indolent disease, which represents the vast majority of cases at initial clinical presentation. The Canadian Prostate Cancer Genome Network (CPC-GENE) - a member of the International Cancer Genome Consortium - aims to identify multi-modal prognostic and predictive signatures of therapeutic outcome based on intrinsic tumour genomics, transcriptomics, and epigenomics, which are being incorporated into novel clinical trials of treatment escalation/de-escalation for image-guided radiotherapy and/or radical prostatectomy. Herein we report the results of the largest prostate cancer whole-genome sequencing study to date, consisting of 194 patients and whole-exome sequencing of 479 patients with localized, potentially curable disease; a sample size that allows for saturating discovery of genes mutated at ≥1% frequency. We show that tumours treated by curative local therapy have a paucity of clinically-actionable mutations relative to high-risk localized or metastatic disease, but instead harbor a significant number of recurrent non-coding aberrations and genomic rearrangements, including a novel inversion - and an associated reduction in gene expression - of the PTEN tumour suppressor gene on chromosome 10. The median tumour contains three distinct driver mutations, with &amp;gt;86% of tumours possessing at least one known driver. Importantly, multiple driver aberrations are associated with patient outcome, including copy number aberrations and methylation events, but notably excluding well-described recurrent events such as TMPRSS2:ERG fusions and SPOP point mutations. Localized hypermutation events (e.g. kataegis) were detected in &amp;gt;20% of tumours, and were strongly enriched for aggressive disease. Taken together, these data provide a comprehensive analysis of the genomic landscape of localized, non-indolent prostate cancer. Moreover, our results strongly suggest that specific molecular aberrations may serve as useful biomarkers for improved pre-treatment stratification of patients with localized, low/intermediate risk disease into escalation/de-escalation protocols, and support the development of clinical trials to assess this hypothesis, based on patient-specific molecular profiles. Citation Format: Michael E. Fraser, Theodorus van der Kwast, John McPherson, Colin C. Collins, Yves Fradet, Bernard Tetu, Alain Bergeron, Rob G. Bristow, Paul C. Boutros. A comprehensive profile of the genomic architecture of curable prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 118.
Imaging of dense cell cultures by multiwavelength lens‐free video microscopy (2017)

They present results for lens-free microscopy for the imaging of dense cell culture. With this aim, they use a multiwavelength LED illumination with well separated wavelengths, together with the implementation of an appropriate holographic reconstruction algorithm. This allows for a fast and efficient reconstruction of the phase image of densely packed cells (up to 700 cells/mm<sup>2</sup> ) over a large field of view of 29.4 mm<sup>2</sup> . Combined with the compactness of the system which fits altogether inside an incubator, lens-free microscopy becomes a unique tool to monitor cell cultures over several days. The high contrast phase shift images provide robust cell segmentation and tracking, and enable high throughput monitoring of individual cell dimensions, dry mass, and motility. They tested the multiwavelength lens-free video-microscope over a broad range of cell lines, including mesenchymal, endothelial, and epithelial cells. © 2017 International Society for Advancement of Cytometry.
Design and validation of magnetic particle spectrometer for characterization of magnetic nanoparticle relaxation dynamics (2017)

The design and validation of a magnetic particle spectrometer (MPS) system used to study the linear and nonlinear behavior of magnetic nanoparticle suspensions is presented. The MPS characterizes the suspension dynamic response, both due to relaxation and saturation effects, which depends on the magnetic particles and their environment. The system applies sinusoidal excitation magnetic fields varying in amplitude and frequency and can be configured for linear measurements (1 mT at up to 120 kHz) and nonlinear measurements (50 mT at up to 24 kHz). Time-resolved data acquisition at up to 4 MS/s combined with hardware and software-based signal processing allows for wide-band measurements up to 50 harmonics in nonlinear mode. By cross-calibrating the instrument with a known sample, the instantaneous sample magnetization can be quantitatively reconstructed. Validation of the two MPS modes are performed for iron oxide and cobalt ferrite suspensions, exhibiting Néel and Brownian relaxation, respectively.
Rationale and Methods of the Study Protocol: Streptococcus pneumoniae Serotypes in Adults 18 Years and Older with Radiographically-Confirmed Community-Acquired Pneumonia (CAP) (2017)

This study was an active, prospective surveillance study of adults 18 years and older hospitalized with community-acquired pneumonia (CAP) due to Streptococcus pneumoniae conducted at 21 hospitals in ten cities across the United States. This report describes the surveillance methodology applied between October 7, 2013 and September 30, 2016, including the identification and description of surveillance areas and populations at-risk for CAP hospitalization for estimation of incidence rates for selected study sites.
A Preliminary Study of Transient Confusional States following Bilateral Subthalamic Stimulation for Parkinson’s Disease (2005)

Transient postoperative confusion (POC) occurs in 5-25% of patients following bilateral subthalamic nucleus stimulation. We retrospectively reviewed data on 96 patients who underwent bilateral subthalamic nucleus deep brain stimulation for Parkinson's disease. Nine percent of patients developed POC. There was no significant correlation between age/perioperative factors and POC. The POC group had a significantly higher incidence of depression and frontal-subcortical dysfunction on preoperative evaluation than patients without POC. Postoperative neuropsychological evaluations revealed declines on measures of general cognitive function and memory in the POC group. We provide preliminary evidence that patients with depression and frontal-subcortical dysfunction are more likely to develop POC, and that POC is more often associated with cognitive decline following surgery.
Design Space Exploration for the Profitability of a Rule-Based Aggregator Business Model Within a Residential Microgrid (2014)

The microgrid has been shown to be profitable, reliable, and efficient for military, commercial, and university-like installations. However, until now, there has been no study to show how and when a residential microgrid may be profitable. Therefore, in this paper, we present a design space exploration methodology of the microgrid by modeling all the energy resources at the residential level and conducting numerous simulations with various parameters. Moreover, a set of rules are defined to make the stakeholders in the microgrid profitable. Also, by analyzing the number of houses in the microgrid, we observe that the number of years it takes to return the capital costs invested in the microgrid may become adequately short for a certain range of the number of houses. For instance, if the aggregator owns the renewable energy resources, e.g., solar panels, it may profit in less than five years when 500 houses participate in the microgrid where each house owns 500 sf solar panels. On the other hand, if the prosumers own the renewable energy resources, e.g., solar panels, the aggregator may profit in about a year. Typically, for an apartment-block type housing area in U.S. there are more than 1000 houses, therefore the aggregator profitability may improve furthermore.
Diffusion and interaction dynamics of the cytosolic peroxisomal import receptor PEX5 (2022)

Cellular functions rely on proper actions of organelles such as peroxisomes. These organelles rely on the import of proteins from the cytosol. The peroxisomal import receptor PEX5 takes up target proteins in the cytosol and transports them to the peroxisomal matrix. However, its cytosolic molecular interactions have so far not directly been disclosed. Here, we combined advanced optical microscopy and spectroscopy techniques such as fluorescence correlation spectroscopy and stimulated emission depletion microscopy with biochemical tools to present a detailed characterization of the cytosolic diffusion and interaction dynamics of PEX5. Among other features, we highlight a slow diffusion of PEX5, independent of aggregation or target binding, but associated with cytosolic interaction partners via its N-terminal domain. This sheds new light on the functionality of the receptor in the cytosol as well as highlighting the potential of using complementary microscopy tools to decipher molecular interactions in the cytosol by studying their diffusion dynamics.
Commentary on A Rare and Unusual Cause of Unilateral Ureteric Obstruction in a Child (2020)

sustained increases in plasma free metanephrine concentrations, making them more sensitive and specific than plasma catecholamines. The recommended initial biochemical analyses include measurements of plasma free metanephrines or urinary fractionated metanephrine by liquid chromatography with mass spectrometric or electrochemical detection methods. In patients who are highly suspect for PPLG, it may be best to screen by measuring plasma free fractionated metanephrines, while 24-h urinary fractionated metanephrines may be used as the first test for low suspicion cases and as confirmatory studies in patients whose plasma free fractionated metanephrines are less than 2-fold increased.
Carrier detection in the Wiskott Aldrich syndrome (1988)

The Wiskott-Aldrich syndrome (WAS) is an X-linked recessive disease characterized by immunodeficiency and severe thrombocytopenia in affected males, but no demonstrable clinical abnormalities in carrier females. Through analysis of the methylation patterns of X-linked genes that display restriction fragment length polymorphisms (RFLPs), we studied the pattern of X-chromosome inactivation in various cell populations from female relatives of patients with WAS. The peripheral blood T cells, granulocytes, and B cells of eight obligate WAS carriers were found to display specific patterns of X-chromosome inactivation clearly different from these of normal controls. Thus, carriers of WAS could be accurately identified using this analysis.
Synthesis of 2,3,5,6‐tetrahydroimidazo[1,2‐c]quinazoline derivatives as potential narcotic antagonists (1980)

Abstract The synthesis of a series of N 6 ‐alkyl derivatives of the 2,3,5,6‐tetrahydroimidazo[1,2‐ c ]quinazoline as potential narcotic antagonists is reported.
Kidney Hormones (1997)

The tissue kallikrein gene family is a subset of closely related serine proteinases that exhibit a narrow range of substrate specificities. Members of the family are involved in processing of polypeptide precursors to generate biologically active peptide hormones and growth factors. The best-known physiological function of tissue kallikrein is the cleavage of low-mol-wt kininogen substrate to release the vasoactive kinin peptide. Kinin binds to its receptor in target tissues and exerts a broad spectrum of biological activities, including vasodilation, blood pressure reduction, smooth muscle relaxation and contraction, pain induction, and inflammation. There are two types of kinin receptors, B1 and B2, which differ in pharmacological properties, biological activities, and primary structures. The B2-receptor has a greater affinity to intact kinin than to kinin’s metabolites. The B1-receptor binds weakly to intact bradykinin (a nonapeptide), but strongly to the metabolites desArg9-bradykinin and des-Arg10-kallidin (Lys-bradykinin), which are generated by kininase I (Fig. 1).
PRORETA 3: An Integrated Approach to Collision Avoidance and Vehicle Automation (2021)

The article describes first results of the research project PRORETA 3 that aims at the development of an integral driver assistance system for collision avoidance and automated vehicle guidance based on a modular system architecture. For this purpose, relevant information is extracted from a dense environment model and fed into a potential field-based trajectory planner that calculates reference signals for underlying vehicle controllers. In addition, the driver is supported by a human-machine interface.
3D modeling of the total electric field induced by transcranial magnetic stimulation using the boundary element method (2009)

Transcranial magnetic stimulation (TMS) delivers highly localized brain stimulations via non-invasive externally applied magnetic fields. This non-invasive, painless technique provides researchers and clinicians with a unique tool capable of stimulating both the central and peripheral nervous systems. However, a complete analysis of the macroscopic electric fields produced by TMS has not yet been performed. In this paper, we addressed the importance of the secondary E-field created by surface charge accumulation during TMS using the boundary element method (BEM). 3D models were developed using simple head geometries in order to test the model and compare it with measured values. The effects of tissue geometry, size and conductivity were also investigated. Finally, a realistically shaped head model was used to assess the effect of multiple surfaces on the total E-field. Secondary E-fields have the greatest impact at areas in close proximity to each tissue layer. Throughout the head, the secondary E-field magnitudes typically range from 20% to 35% of the primary E-field's magnitude. The direction of the secondary E-field was generally in opposition to the primary E-field; however, for some locations, this was not the case (i.e. going from high to low conductivity tissues). These findings show that realistically shaped head geometries are important for accurate modeling of the total E-field.
Failure Mechanisms in Semiconductor Devices (1987)

Introduction Reliability Theory Failure Mechanisms Failure Mechanisms and Device Technologies Packaging Screening Accelerated Testing Physical Failure Analysis Techniques Reliability Prediction and Failure Modelling Quality Assurance Conclusions.
A High-Efficiency Active Battery-Balancing Circuit Using Multiwinding Transformer (2012)

This paper presents a simple circuit for balancing series-connected battery cells. The circuit is composed of one low-voltage metal–oxide–semiconductor field-effect transistor (MOSFET) for each cell and a symmetrical multiwinding transformer for a group of cells. Only one control signal is needed for all MOSFETs, and energy can be directly transferred from higher voltage cells to lower voltage cells. A small capacitor is added to form a resonant circuit with the transformer magnetizing inductance so that soft switching can be achieved in some operation range to obtain high efficiency. The circuit balance function and soft-switching condition are analyzed and verified by simulation and experiments. A circuit for balancing a 4- and 12-cell battery group is tested. The experimental results showed the effectiveness of the circuit. The energy transfer efficiency between cells can reach up to 93%. The circuit can be easily scaled to battery strings containing up to 12 battery cells, directly applicable to consumer electronics application where the number of cells is typically less than 12. A battery pack containing a large number of battery cells, such as the ones used in electric vehicles, can be balanced in groups, for example, in modules containing 12 cells each and with one additional circuit to balance among the modules.
Hybrid wafer-level vacuum hermetic micropackaging technology for MOEMS-MEMS (2009)

Packaging constitutes one of the most costly steps of MEMS/MOEMS manufacturing. The package protects the MEMS devices and, in the case of MOEMS, it also provides light access to the device. In many cases, MEMS require a specific atmosphere for their proper functioning. The atmosphere should be kept invariable during the lifetime of the package in order to not degrade the performance of the device. Maintaining a constant atmosphere inside the package becomes more challenging as the cavity volume is decreased to the microliter and nanoliter range. Other packaging requirements are compatibility with wafer-level microfabrication techniques (cost reduction) and low temperature assembly in cases where temperature sensitive devices are to be packaged. In recent years, INO has performed a great amount of work towards the development of uncooled IR microbolometer detectors using VOx technology. Different pixel designs have been optimized for different applications. The bolometer pixels require a vacuum atmosphere below 10 mTorr to be maintained during the lifetime of the device in order to operate at their highest sensitivity. INO's micropackaging technology has been demonstrated to provide base pressures below 5 mTorr. An equivalent flow rate of 2.5&times;10<sup>-14</sup> Torr.l/sec has been obtained for a device packaged without any getter. The advantages of INO's micropackaging technology are the possibility of achieving very low base pressures, the low temperatures required for the assembly (the package device is never exposed to a temperature above 150 &deg;C) and its compatibility with hybrid wafer-level packaging. The technology has been developed for the micropackaging of INO's 160&times;120 pixel uncooled microbolometer FPA, but it is compatible with any other kinds of MOEMS-MEMS devices requiring vacuum hermetic packaging. In order to increase the lifetime of the package, knowledge of the gases outgassing inside the package is crucial. A hybrid approach has been chosen as it permits packaging only known-good dies and saving considerable quantities of IR window material. In INO's hybrid wafer-level packaging, dicing is performed only through one of the wafers, therefore reducing the risk of perturbing the vacuum during the separation of the different dies.
Soft actuators by electrochemical oxidation of liquid metal surfaces (2020)

The surface energy of liquid metals can be electrochemically controlled over a wide range of values - from near zero to 500 mJ m<sup>-2</sup>- using a low voltage potential (∼1 V). This enables the ability to create soft-matter actuators that exhibit a high work density on small scales. We demonstrate that a liquid metal (LM) meniscus wetted between two copper pads can function as an electrochemical soft actuator whose force and shape are controllable by tuning the LM surface energy. Energy minimization models are presented in order to predict the actuator performance as a function of LM droplet and Cu pad dimensions. The results suggest that the electrochemical LM actuator has a unique combination of high work density, biologically-relevant activation frequency, and low operational voltage that stands out from other classes of soft-matter actuators.
Molecular imaging of endogenous and exogenous chromophores using ground state recovery pump-probe optical coherence tomography (2006)

We present a novel molecular imaging technique which combines the 3-D tomographic imaging capability of optical coherence tomography with the molecular sensitivity of pump-probe spectroscopy. This technique, based on transient absorption, is sensitive to any molecular chromophore. It is particularly promising for the many important biomarkers, such as hemoglobin, which are poor fluorophores and therefore difficult to image with current optical techniques without chemical labeling. Previous implementations of pump-probe optical coherence tomography have suffered from inefficient pump-probe schemes which hurt the sensitivity and applicability of the technique. Here we optimize the efficiency of the pump-probe approach by avoiding the steady-state kinetics and spontaneous processes exploited in the past in favor of measuring the transient absorption of fully allowed electronic transitions on very short time scales before a steady-state is achieved. In this article, we detail the optimization and characterization of the prototype system, comparing experimental results for the system sensitivity to theoretical predictions. We demonstrate in situ imaging of tissue samples with two different chromophores; the transfectable protein dsRed and the protein hemoglobin. We also demonstrate, with a simple sample vessel and a mixture of human whole blood and rhodamine 6G, the potential to use ground state recovery time to separate the contributions of multiple chromophores to the ground state recovery signal.
An Application of Optimization Methods to Evaluate Conditioning Intervals (1985)

A decision rule is obtained to determine when exercise is beneficial. The term beneficial used in this context refers to the extension of lifetime based on studies of cardiovascular conditioning. Models are used to characterize changes in heart rate with intense exercise. In addition, it is necessary to consider a model involving a heartbeat bank to help determine the conditioning interval. Optimization procedures are used to develop the decision rule, to examine the assumptions in the problem, and to point out when a unique solution exists. This procedure is applied to empirical data for one individual (inter-subject study) and a unique conditioning interval is obtained.
Down modulation of IL‐18 expression by human papillomavirus type 16 E6 oncogene via binding to IL‐18 (2001)

To understand modulation of a novel immune-related cytokine, interleukin-18, by human papillomavirus type (HPV) 16 oncogenes, HaCaT, normal keratinocyte cell line, and C-33A, HPV-negative cervical cancer cell line, were prepared to establish stable cell lines expressing E6, E6 mutant (E6m), E6E7, or E7 constitutively. Expressions of various HPV oncogene transcripts were identified by RT-PCR. Expression of HPV oncogene E6 was reversely correlated to the expression of interleukin-18, a novel pro-inflammatory cytokine. The expression of E6 in C-33A, independent of E6 splicing, resulted in decreased IL-18 expression and that of IL-18 was also significantly reduced in HaCaT cells expressing E6. The level of p53 was reduced in C-33A cells expressing E6 whereas not altered in HaCaT cells expressing E6, suggesting that E6 downregulated IL-18 expression via an independent pathway of p53 degradation in HaCaT cells which have a mutated p53 form. However, E7 did not affect IL-18 expression significantly in both C-33A and HaCaT cells. Cotransfection experiments showed that E6 oncogene did not inhibit the activities of IL-18 promoter P1 and P2, suggesting that E6 oncogene indirectly inhibited IL-18 expression. Taken together, E6, E6m and E6/E7 inhibited IL-18 expression with some variation, assuming that cells expressing E6 oncogene can evade immune surveillance by downregulating the expression of immune stimulating cytokine gene, IL-18, and inhibiting the cascade of downstream effects that follow activation of the IL-18 receptor.