gebhart/patrepeval huggingface dataset:
Morphological study of testicular descent in the rabbit. (1981)

We studied the morphologic changes in the rabbit gubernaculum that occur just before and at the time of testicular descent. Our findings suggest that in the rabbit the gubernaculum may be the target tissue responsible for the movement of the testis from the abdomen into the scrotum.
CryoSIM: super resolution 3D structured illumination cryogenic fluorescence microscopy for correlated ultra-structural imaging (2020)

Abstract Rapid cryo-preservation of biological specimens is the gold standard for visualising cellular structures in their true structural context. However, current commercial cryo-fluorescence microscopes are limited to low resolutions. To fill this gap, we have developed cryoSIM, a microscope for 3D super-resolution fluorescence cryo-imaging for correlation with cryo electron microscopy or cryo soft X-ray tomography. We provide the full instructions for replicating the instrument mostly from off-the-shelf components and accessible, user-friendly open source Python control software. Therefore, cryoSIM democratises the ability to detect molecules using super-resolution fluorescence imaging of cryo-preserved specimens for correlation with their cellular ultrastructure.
The positive P representation and the laser equations (1986)

The drift in the Fokker-Planck equation in the positive P representation describing a gas laser is shown to have a continuum of stable steady states. Only a small subset is physically acceptable. It is demonstrated that the diffusion does manage to average over the unphysical steady states to give correct correlation properties in the lasing region. However, in the chaotic region, the positive P representation equations have additional instabilities. As a consequence the positive P representation in the chaotic region leads to behaviour either different from known solutions or breaks down.
Tumour genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: a retrospective cohort study (2014)

Movember Foundation, Prostate Cancer Canada, Ontario Institute for Cancer Research, Canadian Institute for Health Research, NIHR Cambridge Biomedical Research Centre, The University of Cambridge, Cancer Research UK, Cambridge Cancer Charity, Prostate Cancer UK, Hutchison Whampoa Limited, Terry Fox Research Institute, Princess Margaret Cancer Centre Foundation, PMH-Radiation Medicine Program Academic Enrichment Fund, Motorcycle Ride for Dad (Durham), Canadian Cancer Society.
Characterization of XPR1/SLC53A1 variants located outside of the SPX domain in patients with primary familial brain calcification (2019)

Primary familial brain calcification (PFBC) is a rare neurological disease characterized by deposits of calcium phosphate in the basal ganglia and other regions of the brain. Pathogenic variants in the XPR1/SLC53A1 gene, which encodes the only known inorganic phosphate exporter, cause an autosomal dominant form of PFBC. These variants are typically located in the SPX N-terminal domain of the protein. Here, we characterize three XPR1 variants outside of SPX in three PFBC patients with an apparently sporadic presentation: c.1375C > T p.(R459C), c.1855A > G p.(N619D) and c.1886T > G p.(I629S), with the latter identified as the first XPR1/SLC53A1 de novo mutation to occur in a PFBC proband. When tested in an in vitro physiological complementation assay, the three XPR1 variants were impaired in phosphate export function, although they were normally expressed at the cell surface and could serve as functional receptors for retrovirus entry. Moreover, peripheral blood cells from the p.N619D patient could be assayed ex vivo and displayed significantly impaired phosphate export. Our results establish for the first time the clinical and molecular characteristics of XPR1 variants located outside the SPX domain and assert a direct link between these variants, deficient phosphate export, and PFBC. Moreover, we unveiled new structural features in XPR1 C-terminal domain that play a role in phosphate export and disease.
<title>Novel color transformation algorithm and its applications</title> (1990)

We propose a new algorithm available to variety of real-time color space transformations : color correction for hardcopy system, perceptual color control in CIE-LAB space, color coordinate conversions, and color recognition. This algorithm consists of color look up tables and a new 3D color space interpolator. This interpolator makes it easy to design a simple real-time color processor. The simulation shows how the flexible transformations can be performed without degrading the color and tone.
Characterization of Ebola Virus Disease (EVD) in Rhesus Monkeys for Development of EVD Therapeutics (2020)

Recent Ebola virus (EBOV) outbreaks in West Africa and the Democratic Republic of the Congo have highlighted the urgent need for approval of medical countermeasures for treatment and prevention of EBOV disease (EVD). Until recently, when successes were achieved in characterizing the efficacy of multiple experimental EVD therapeutics in humans, the only feasible way to obtain data regarding potential clinical benefits of candidate therapeutics was by conducting well-controlled animal studies. Nonclinical studies are likely to continue to be important tools for screening and development of new candidates with improved pharmacological properties. Here, we describe a natural history study to characterize the time course and order of progression of the disease manifestations of EVD in rhesus monkeys. In 12 rhesus monkeys exposed by the intramuscular route to 1000 plaque-forming units of EBOV, multiple endpoints were monitored for 28 days following exposure. The disease progressed rapidly with mortality events occurring 7-10 days after exposure. Key disease manifestations observed consistently across the infected animals included, but were not limited to, viremia, fever, systemic inflammation, coagulopathy, lymphocytolysis, renal tubular necrosis with mineralization, and hepatocellular degeneration and necrosis.
Specificity of human tissue kallikrein towards substrates containing Phe‒Phe pair of amino acids (1999)

We have explored in detail the determinants of specificity for the hydrolysis by human tissue kallikrein (hK1) of substrates containing the Phe–Phe amino acid pair, after which hK1 cleaves kallistatin (human kallikrein-binding protein), a specific serpin for this protease, as well as somatostatin 1–14. Internally quenched fluorogenic peptides were synthesized with the general structure Abz-peptidyl-EDDnp [Abz, o-aminobenzoic acid; EDDnp, N-(2,4-dinitrophenyl)ethylenediamine], based on the natural reactive-centre loop sequence of kallistatin from P9 to P´13, and the kinetic parameters of their hydrolysis by hK1 were determined. All these peptides were cleaved after the Phe–Phe pair. For comparison, we have also examined peptides containing the reactive-centre loop sequences of human protein-C inhibitor (PCI) and rat kallikrein-binding protein, which were hydrolysed after Phe–Arg and Leu–Lys bonds, respectively. Hybrid peptides containing kallistatin–PCI sequences showed that the efficiency of hK1 activity on the peptides containing kallistatin and PCI sequences depended on both the nature of the P1 amino acid as well as on residues at the P- and P´-sides. Moreover, we have made systematic modifications on the hydrophobic pair Phe–Phe, and on Lys and Ile at the P3 and P4 positions according to the peptide substrate, Abz-AIKFFSRQ-EDDnp. All together, we concluded that tissue kallikrein was very effective on short substrates that are cleaved after the Phe–Arg pair; however, hydrolysis after Phe–Phe or other hydrophobic pairs of amino acids was more restrictive, requiring additional enzyme–substrate interaction and/or particular substrate conformations.
Immunohistochemical Detection of Telomerase (hTERT) Protein in Human Cancer Tissues and a Subset of Cells in Normal Tissues (2001)

We examined human telomerase reverse transcriptase (hTERT) protein distribution by immunohistochemistry in cultured cells and tissue sections. Cells with telomerase activity had nuclear positive signals whereas cells without telomerase activity did not. In most normal epithelial tissues, hTERT expression was prominent in the early proliferative descendent progenitors cells. In cancers with high telomerase activity, hTERT expression was detected in almost all neoplastic cells and correlated with telomerase activity levels, whereas cancers with low telomerase activity had fewer hTERT-positive cancer cells. In pediatric neuroblastomas with a favorable outcome, both the percentage of positive cells and the signal intensities of each hTERT-expressing cell decreased. These studies indicate that detection of telomerase at the cellular level is achievable and may have utility in cancer diagnostics.
The importance of integrin‐linked kinase in the regulation of bladder cancer invasion (2011)

It is important to understand the molecular mechanisms of bladder cancer progression not only to prevent cancer progression but also to detect new therapeutic targets against advanced bladder cancer. The integrin-linked kinase (ILK) is a major signaling integrator in mammalian cells and plays an important role in epithelial-mesenchymal transition (EMT) of human cancers, but its mechanisms are not completely understood. In this study, we investigated the importance and mechanisms of ILK in bladder cancer progression. When the expression of ILK in bladder cancer cell lines and N-butyl-N-(4-hydroxybutyl) nitrosamine (BBN)-induced murine bladder cancer was evaluated, ILK has a tendency to be overexpressed in invasive cell lines and invasive BBN-induced murine bladder cancer. Overexpression of ILK in 253J bladder cancer cells suppressed E-cadherin expression, resulting in the promotion of cell invasion. Conversely, ILK knockdown by siRNA suppresses cell invasion in invasive bladder cancer cells through the regulation of E-cadherin or matrix metalloprotease 9 (MMP-9). To regulate E-cadherin expression, our results showed that the glycogen synthase kinase 3β (GSK3β)-Zeb1 pathway may play an important role downstream of ILK. Finally, the results of a human bladder tissue microarray (TMA) showed that ILK expression correlates with the invasiveness of human bladder cancer. Our study suggests that ILK is overexpressed in invasive bladder cancer and plays an important role in the EMT of bladder cancer via the control of E-cadherin and MMP-9 expression. ILK may be a new molecular target to suppress tumor progression in advanced and high-risk bladder cancer patients.
The SeaView security model (2003)

A formal security policy model that uses basic view concepts for a secure multilevel relational database system is described. The model is formulated in two layers, one corresponding to a security kernel of reference monitor that enforces mandatory security, and the other defining multilevel relations and formalizing policies for labeling new and derived data, data consistency, discretionary security, and transaction consistency. This includes the policies for sanitization, aggregation, and downgrading. The model also defines application-independent properties for entity integrity, referential integrity, and polyinstantiation integrity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Thermisch und anodisch oxidierte Titanlegierungen (2005)

Kurzfassung Im Rahmen der vorliegenden Arbeit wurden Umlaufbiegeversuche und axiale Ermüdungsversuche an den Implantatwerkstoffen cp-Ti grade 2 und TiAl6Nb7, deren Oberflächen mit Hilfe thermischer sowie anodischer Oxidation modifiziert wurden, in Ringerlösung durchgeführt. Das Wechselverformungsverhalten sowie ermüdungsbedingte Oberflächenschäden wurden durch den zeitlichen Verlauf des freien Korrosionspotentials bzw. des Korrosionsstromes charakterisiert. Zusätzlich wurde die Veränderung der Grenzflächenimpedanz in Abhängigkeit des Ermüdungszustandes erfasst. Mit Hilfe rasterelektronenmikroskopischer Methoden wurden beanspruchungsbedingte mikrostrukturelle Veränderungen an der Oberfläche mit den Ergebnissen der elektrochemischen Messungen korreliert.
Ultra‐Low‐Loss Silicon Nitride Photonics Based on Deposited Films Compatible with Foundries (2023)

Abstract The fabrication processes of silicon nitride (Si 3 N 4 ) photonic devices used in foundries require low temperature deposition, which typically leads to high propagation losses. Here, it is shown that propagation loss as low as 0.42 dB cm −1 can be achieved using foundry compatible processes by solely reducing waveguide surface roughness. By postprocessing the fabricated devices using rapid thermal anneal (RTA) and furnace anneal, propagation losses down to 0.28 dB cm −1 and 0.06 dB cm −1 , respectively, are achieved. These low losses are comparable to the conventional devices using high temperature, high‐stress LPCVD films. The dispersion of the devices is also tuned, and it is proved that these devices can be used for linear and nonlinear applications. Low threshold parametric oscillation, broadband frequency combs, and narrow‐linewidth laser are demonstrated. This work demonstrates the feasibility of scalable photonic systems based on foundries.
Recipient of the RSC Haworth Lectureship (1999)

P. George W. J. Fleet, J. Chem. Soc., Perkin Trans. 1, 1999, 6-ix DOI: 10.1039/A901533G
Optimization Approach to Hybrid Electric Propulsion System Design∗ (1999)

Abstract Environmentally friendly ground vehicles with range and performance capabilities surpassing those of conventional vehicles require a careful balance among competing goals for fuel efficiency, performance, and emissions. The research objective here is to integrate hybrid electric vehicle simulations with high-fidelity engine modules, to increase the accuracy of predictions, and to allow design studies in the concept evaluation stage. This paper describes a methodology for integrating vehicle and engine simulations. The feed-forward model of the engine is modified to allow its linking with the vehicle model, and an engine component scaling routine is added to facilitate system sizing studies. A design optimization framework is then used to find the best overall engine size, battery pack, and motor combination for minimum fuel consumption within proposed US government performance criteria.
Dual-platform affinity proteomics identifies links between the recurrence of ovarian carcinoma and proteins released into the tumor microenvironment (2019)

The peritoneal fluid (ascites), replete with abundant tumor-promoting factors and extracellular vesicles (EVs) reflecting the tumor secretome, plays an essential role in ovarian high-grade serous carcinoma (HGSC) metastasis and immune suppression. A comprehensive picture of mediators impacting HGSC progression is, however, not available. <b>Methods:</b> Proteins in ascites from HGSC patients were quantified by the aptamer-based SOMAscan affinity proteomic platform. SOMAscan data were analyzed by bioinformatic methods to reveal clinically relevant links and functional connections, and were validated using the antibody-based proximity extension assay (PEA) Olink platform. Mass spectrometry was used to identify proteins in extracellular microvesicles released by HGSC cells. <b>Results:</b> Consistent with the clinical features of HGSC, 779 proteins in ascites identified by SOMAscan clustered into groups associated either with metastasis and a short relapse-free survival (RFS), or with immune regulation and a favorable RFS. In total, 346 proteins were linked to OC recurrence in either direction. Reanalysis of 214 of these proteins by PEA revealed an excellent median Spearman inter-platform correlation of ρ=0.82 for the 46 positively RFS-associated proteins in both datasets. Intriguingly, many proteins strongly associated with clinical outcome were constituents of extracellular vesicles. These include proteins either linked to a poor RFS, such as HSPA1A, BCAM and DKK1, or associated with a favorable outcome, such as the protein kinase LCK. Finally, based on these data we defined two protein signatures that clearly classify short-term and long-term relapse-free survivors. <b>Conclusion:</b> The ascites secretome points to metastasis-promoting events and an anti-tumor response as the major determinants of the clinical outcome of HGSC. Relevant proteins include both bone fide secreted and vesicle-encapsulated polypeptides, many of which have previously not been linked to HGSC recurrence. Besides a deeper understanding of the HGSC microenvironment our data provide novel potential tools for HGSC patient stratification. Furthermore, the first large-scale inter-platform validation of SOMAscan and PEA will be invaluable for other studies using these affinity proteomics platforms.
Magnetostrictive Devices (2016)

Magnetostrictive materials exhibit coupling between magnetic and mechanical energies. This bidirectional energy exchange can be employed for actuation, sensing, and energy harvesting. All ferromagnetic materials exhibit the magnetostrictive effect, but only certain iron–rare earth alloys, iron–gallium alloys, amorphous metals, and iron‐ aluminum alloys exhibit sufficiently high magnetostriction for commercial use. Because the magnetostrictive effect is an intrinsic material property that is robust against external factors such as stress and cyclic fatigue, magnetostrictive devices are suitable for harsh environments. This article provides an overview ofmagnetostrictivematerials and devices, particularly focused on Metglas, Terfenol‐D, and Galfenol. Various transducer topologies are presented and discussed, along with quantification of performance metrics and experimental aspects related to understanding and harnessing the intrinsic nonlinearities of magnetostrictive materials. Selected modeling approaches considering both constitutive material behavior and system response are presented.
Quantitative kinetic analysis of DNA nanocomplex self-assembly with Quantum Dots FRET in a microfluidic device (2008)

The demand for safer and more efficient non-viral gene vectors has increased with the recent progress of genetic medicine. Appropriate nanocomplex assembly of DNA and gene carriers is critical for successful cellular entry and transfection. However, there is a lack of knowledge on this self-assembly process, let alone the controllability of monodisperse nanocomplexes. This paper describes a novel platform integrating nanobiophotonics (Quantum Dots-mediated FRET) and microfluidic technology to determine binding kinetics that govern the structural and chemical properties of DNA nanocomplexes. We anticipate that this method will elucidate mechanistic and kinetic insights into the self-assembly process of nanocomplexes which may facilitate the rational design of more efficient gene carriers. In addition, a microfluidic platform offers many advantages, including small volume, fast response to external stimulations, continuous monitoring and real-time control of reaction environments, which may be potentially used to generate more monodisperse complexes.
A memristive deep belief neural network based on silicon synapses (2022)

Memristor-based neuromorphic computing could overcome the limitations of traditional von Neumann computing architectures -- in which data are shuffled between separate memory and processing units -- and improve the performance of deep neural networks. However, this will require accurate synaptic-like device performance, and memristors typically suffer from poor yield and a limited number of reliable conductance states. Here we report floating gate memristive synaptic devices that are fabricated in a commercial complementary metal-oxide-semiconductor (CMOS) process. These silicon synapses offer analogue tunability, high endurance, long retention times, predictable cycling degradation, moderate device-to-device variations, and high yield. They also provide two orders of magnitude higher energy efficiency for multiply-accumulate operations than graphics processing units. We use two 12-by-8 arrays of the memristive devices for in-situ training of a 19-by-8 memristive restricted Boltzmann machine for pattern recognition via a gradient descent algorithm based on contrastive divergence. We then create a memristive deep belief neural network consisting of three memristive restricted Boltzmann machines. We test this on the modified National Institute of Standards and Technology (MNIST) dataset, demonstrating recognition accuracy up to 97.05%.
Improved Performance Measures for Voice Activity Detection (2014)

Voice activity detection is an essential part of many speech processing algorithms. The requirements of the speech application determine the design of voice activity detection. Some applications need low-latency results whereas the accuracy of speech detection is more important for other applications. The performance is generally evaluated by Receiver Operating Characteristic (ROC) curves, which perform a static analysis averaged over speech and nonspeech segments, respectively. We adopt the ROC curves but evaluate them for specific speech classes, e.g., voiced or unvoiced speech, to describe the overall accuracy of speech detection. In addition, we present a new measure for the dynamic behavior that considers the delay and latency of speech on- and offset detection. Finally, we present a unified measure for both aspects. This measure may be used to find appropriate voice activity detection features for a given application. An automotive noise scenario is employed to demonstrate the measures as it contains stationary and non-stationary noise.
A high efficiency, miniaturized Ka band traveling wave tube based on a novel finned ladder RF circuit design (2003)

Summary form only given. Space communications architectures are being planned to meet the high rate data of future NASA Enterprise missions. These will require the use of traveling wave tube amplifiers (TWTAs) to provide the high frequency, RF power and efficiency needed for many of the communications links. A program addressing these requirements is underway for the development of a high efficiency, 20 watt, 32 GHz TWT of reduced size and weight that is based on a novel high gain slow-wave circuit design, termed the "finned ladder". The finned ladder slow-wave circuit, has an exceptionally high gain per unit length. The very high RF/electron beam interaction impedance (>100 ohms) enables more than 40 dB of gain over a 5 cm length and an RF efficiency greater than 20%, which offers a significant reduction in RF circuit length and the potential for TWT miniaturization. Fabrication by micromachining techniques is being investigated.
Unexpected role of lipocalin-type prostaglandin D synthase in brain (2012)

Lipocalin-type prostaglandin D synthase (L-PGDS) is one of the most abundant proteins in the cerebrospinal fluid. Nevertheless, its role in the central nervous system is far from clear. Here, we present evidence that L-PGDS induces glial cell migration and morphological changes in vitro and in vivo. We also identified myristoylated alanine-rich C-kinase substrate (MARCKS), heat shock proteins and actin as L-PGDS-binding proteins, demonstrating that MARCKS/Akt/Rho/Jnk pathways are involved in the L-PGDS actions in glia. We further show that the cell migration-promoting activity of L-PGDS is independent of PGD 2 production. The results suggest a novel non-enzymatic function of L-PGDS protein in brain inflammation, and may have an impact on glial cell biology and brain pathology related with reactive gliosis. L-PGDS is a potential drug target that can be exploited for therapeutic intervention of glia-driven neuroinflammation and related diseases.