gebhart/patrepeval huggingface dataset:
Cross-scanner and cross-protocol diffusion MRI data harmonisation: A benchmark database and evaluation of algorithms (2019)

Diffusion MRI is being used increasingly in studies of the brain and other parts of the body for its ability to provide quantitative measures that are sensitive to changes in tissue microstructure. However, inter-scanner and inter-protocol differences are known to induce significant measurement variability, which in turn jeopardises the ability to obtain 'truly quantitative measures' and challenges the reliable combination of different datasets. Combining datasets from different scanners and/or acquired at different time points could dramatically increase the statistical power of clinical studies, and facilitate multi-centre research. Even though careful harmonisation of acquisition parameters can reduce variability, inter-protocol differences become almost inevitable with improvements in hardware and sequence design over time, even within a site. In this work, we present a benchmark diffusion MRI database of the same subjects acquired on three distinct scanners with different maximum gradient strength (40, 80, and 300 mT/m), and with 'standard' and 'state-of-the-art' protocols, where the latter have higher spatial and angular resolution. The dataset serves as a useful testbed for method development in cross-scanner/cross-protocol diffusion MRI harmonisation and quality enhancement. Using the database, we compare the performance of five different methods for estimating mappings between the scanners and protocols. The results show that cross-scanner harmonisation of single-shell diffusion data sets can reduce the variability between scanners, and highlight the promises and shortcomings of today's data harmonisation techniques.
Junction Temperature Measurement of InAs Quantum-Dot Laser Diodes by Utilizing Voltage–Temperature Method (2008)

Junction temperature of InAs quantum-dot laser diodes (LDs) is measured by utilizing a forward voltage- temperature method. Although the forward voltage decrease with junction temperature increment is low, the linear relation between forward voltage and temperature clearly occurs. It is found that SiN <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</i> is more useful than SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> to keep junction temperature low. Injection current to shift the lasing wavelength from ground to excited state is increased over 200 mA by using SiN <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</i> instead of SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> as the insulating layer. As a result, ground state optical power is doubled.
Story-Driven Summarization for Egocentric Video (2013)

We present a video summarization approach that discovers the story of an egocentric video. Given a long input video, our method selects a short chain of video sub shots depicting the essential events. Inspired by work in text analysis that links news articles over time, we define a random-walk based metric of influence between sub shots that reflects how visual objects contribute to the progression of events. Using this influence metric, we define an objective for the optimal k-subs hot summary. Whereas traditional methods optimize a summary's diversity or representative ness, ours explicitly accounts for how one sub-event "leads to" another-which, critically, captures event connectivity beyond simple object co-occurrence. As a result, our summaries provide a better sense of story. We apply our approach to over 12 hours of daily activity video taken from 23 unique camera wearers, and systematically evaluate its quality compared to multiple baselines with 34 human subjects.
Purification of chimeric heavy chain monoclonal antibody EG2‐hFc using hydrophobic interaction membrane chromatography: An alternative to protein‐A affinity chromatography (2014)

Heavy chain monoclonal antibodies are being considered as alternative to whole-IgG monoclonal antibodies for certain niche applications. Protein-A chromatography which is widely used for purifying IgG monoclonal antibodies is also used for purifying heavy chain monoclonal antibodies as these molecules possess fully functional Fc regions. However, the acidic conditions used to elute bound antibody may sometimes also leach protein-A, which is immunotoxic. Low pH conditions also tend to make the mAb molecules unstable and prone to aggregation. Moreover, protein-A affinity chromatography does not remove aggregates already present in the feed. Hydrophobic interaction membrane chromatography (or HIMC) has already been studied as an alternative to protein-A chromatography for purifying whole-IgG monoclonal antibodies. This paper describes the use of HIMC for capturing a humanized chimeric heavy chain monoclonal antibody (EG2-hFC). Binding and eluting conditions were suitably optimized using pure EG2-hFC. Based on this, an HIMC method was developed for capture of EG2-hFC directly from cell culture supernatant. The EG2-hFc purity obtained in this single-step process was high. The glycan profiles of protein-A and HIMC purified monoclonal antibody samples were similar, clearly demonstrating that both techniques captured similarly glycosylated population of EG2-hFc. Moreover, this technique was able to resolve aggregates from monomeric form of the EG2-hFc.
Highly efficient 1.064 µm upconversion pumped1.47 µm thulium doped fluoride fibre laser (1994)

Results are presented on a 1064 nm upconversion pumped thulium doped fluoride fibre laser operating on the 3F4 – 3H4 transition around 1.47 µm. A minimum threshold of 8.7mW (3.6mW absorbed), and a maximum slope efficiency of 58% (80% photon conversion efficiency), with respect to launched pump power has been observed. In addition a maximum gain efficiency of 0.22 dB/mW has been demonstrated.
Enhancing early bladder cancer detection with fluorescence-guided endoscopic optical coherent tomography (2003)

We report an experimental study of the possibility of enhancing early bladder cancer diagnosis with fluorescence-image-guided endoscopic optical coherence tomography (OCT). After the intravesical instillation of a 10% solution of 5-aminolevulinic acid, simultaneous fluorescence imaging (excitation of 380-420 nm, emission of 620-700 nm) and OCT are performed on rat bladders to identify the photochemical and morphological changes associated with uroepithelial tumorigenesis. The preliminary results of our ex vivo study reveal that both fluorescence and OCT can identify early uroepithelial cancers, and OCT can detect precancerous lesions (e.g., hyperplasia) that fluorescence may miss. This suggests that a cystoscope combining 5-aminolevulinic acid fluorescence and OCT imaging has the potential to enhance the efficiency and sensitivity of early bladder cancer diagnosis.
Generation of an Artificial Double Promoter for Protein Expression in Bacillus subtilis through a Promoter Trap System (2013)

Bacillus subtilis is an attractive host for production of recombinant proteins. Promoters and expression plasmid backbones have direct impacts on the efficiency of gene expression. To screen and isolate strong promoters, a promoter trap vector pShuttleF was developed in this study. Using the vector, approximately 1000 colonies containing likely promoters from Bacillus licheniformis genomic DNA were obtained. Amongst them, pShuttle-09 exhibited the highest β-Gal activities in both Escherichia coli and B. subtilis. The activity of pShuttle-09 in B. subtilis was eight times of that of the P43 promoter, a commonly used strong promoter for B. subtilis. A sequence analysis showed that pShuttle-09 contained P(luxS) and truncated luxS in-frame fused with the reporter gene as well as another fragment upstream of P(luxS) containing a putative promoter. This putative promoter was a hybrid promoter and its β-Gal activity was higher than P(luxS). Reconstructing the hybrid promoter from pShuttle-09 to P(lapS) further improved the β-Gal production by 60%. The usefulness of our promoter trap system is likely due to random shuffling and recombination of DNA fragments and adoption of a rapid and high-throughput screening. Thus, our data provide additional evidence to support the concept of using a promoter trap system to create new promoters.
Visualization of oxygen‐concentration‐dependent production of nitric oxide in rat hippocampal slices during aglycemia (2001)

Our novel fluorescent indicator, DAF-FM, permits the bioimaging of nitric oxide (NO) in living cells with high resolution in space and time, with stable intensity above pH 5.8. A membrane-permeable derivative, DAF-FM DA, was applied to imaging of NO generated in rat hippocampal slices by exposure to an aglycemic medium. NO production was observed mainly in the CA1 area, and was dependent on the concentration of O(2). During exposure to an anoxic-aglycemic medium, NO was hardly produced, while marked elevation of intracellular Ca(2+) was observed. Production of NO increased sharply as soon as the perfusate was changed to the normal medium. These results suggest that NO synthase is activated after reperfusion rather than during ischemia.
The nervous system (1988)

The nervous system is a communications network whose functions range from simple reflex activities to the complexities of awareness and conscious thought. Elements of the nervous system ramify to every part of the body, giving it a universal functional influence.
Role for highly regulated rep gene expression in adeno-associated virus vector production. (2020)

Recent success achieving long-term in vivo gene transfer without a significant immune response by using adeno-associated virus (AAV) vectors (X. Xiao, J. Li, and R. J. Samulski, J. Virol. 70:8098-8108, 1996) has encouraged further development of this vector for human gene therapy. Currently, studies focus on the generation of high-titer vectors by using the two-plasmid helper-vector system in adenovirus (Ad)-infected cells. To examine the effects of the AAV replication (rep) genes on recombinant AAV (rAAV) vector production, we have constructed a series of AAV helper plasmids that contain strong heterologous promoters in place of the endogenous p5 promoter. Although high-level rep gene expression was achieved, rAAV DNA failed to replicate in the absence of Ad infection. Moreover, unregulated overexpression of Rep78/68 led to substantially lower rAAV yields in the presence of Ad (10(4-5) versus 10(7-8)). In contrast, under similar conditions, reduced Rep78/68 expression resulted in much higher rAAV yields (10(9)). Molecular characterization showed that overexpression of the rep gene decreased rAAV DNA replication and severely inhibited capsid (cap) gene expression. Interestingly, a reduced rep level enhanced cap gene expression and supported normal rAAV DNA replication. These studies suggest a critical role for regulated rep gene expression in rAAV production and have facilitated the development of a new AAV helper plasmid that increases vector production eightfold over currently used constructs.
[Dementing disorders. What benefits do the new anti-dementia drugs have?]. (2002)

A critical analysis of the latest studies and meta-analyses dealing with antidementia agents, show that the efficacy of donepezil, galantamine, ginkgo biloba EGb 761, memantine, rivastigmine and tacrine in Alzheimer's disease is adequately confirmed. With the exception of tacrine, none of these substances are commonly associated with severe side effects. In the case of vascular dementia, the efficacy of ginkgo biloba EGb 761 and memantine has been demonstrated. Studies on the effectiveness of the cholinesterase inhibitors for this indication have been initiated. Antidementia agents can delay progression of the disease by about 6 to 12 months. Further studies are needed to confirm evidence of a prophylactic effect and a synergistic action of combinations.
Going far beyond the near-field diffraction limit via plasmonic cavity lens with high spatial frequency spectrum off-axis illumination (2015)

For near-field imaging optics, minimum resolvable feature size is highly constrained by the near-field diffraction limit associated with the illumination light wavelength and the air distance between the imaging devices and objects. In this study, a plasmonic cavity lens composed of Ag-photoresist-Ag form incorporating high spatial frequency spectrum off-axis illumination (OAI) is proposed to realize deep subwavelength imaging far beyond the near-field diffraction limit. This approach benefits from the resonance effect of the plasmonic cavity lens and the wavevector shifting behavior via OAI, which remarkably enhances the object's subwavelength information and damps negative imaging contribution from the longitudinal electric field component in imaging region. Experimental images of well resolved 60-nm half-pitch patterns under 365-nm ultra-violet light are demonstrated at air distance of 80 nm between the mask patterns and plasmonic cavity lens, approximately four-fold longer than that in the conventional near-field lithography and superlens scheme. The ultimate air distance for the 60-nm half-pitch object could be theoretically extended to 120 nm. Moreover, two-dimensional L-shape patterns and deep subwavelength patterns are illustrated via simulations and experiments. This study promises the significant potential to make plasmonic lithography as a practical, cost-effective, simple and parallel nano-fabrication approach.
Quantitative regional blood volume studies in rat myocardium <i>in Vivo</i> (1998)

Many pathophysiological processes in the myocardium are in close relation to changes of the regional blood volume and regional myocardial blood flow or perfusion. Only few methods exist to obtain quantitative values for these parameters. Quantitative regional blood volume (RBV) studies in rat myocardium are presented using snapshot fast low angle shot (FLASH) inversion recovery T1 measurements with two different blood pool contrast agents, gadolinium diethylenetriaminopentaacetic acid (Gd-DTPA) albumin and Gd-DTPA polylysine. In contrast to previous attempts, each snapshot FLASH image acquisition was ECG-triggered under breathhold conditions. To measure relaxation times shorter than a heart cycle, each T1 sequence was repeated two times with different delays between inversion pulse and first image acquisition. The experiments were performed on a Bruker Biospec 70/21 using a homogeneous transmitter coil and a circularly polarized surface receiver coil, a special ECG trigger unit, and a respirator that is controlled by the pulse program. Based on a fast exchange model RBVm maps were calculated from the relaxation time maps for different concentrations of the two blood pool contrast agents. A significant dependence of the RBVm values on blood T1 was found. This is in accordance with a model that has been developed recently relating the dependence of RBVm on T1 of blood to perfusion. For Gd-DTPA albumin, the application of the model to the experimental data yields realistic values for RBV and perfusion. The values, which are in accordance with literature data, were obtained at highest contrast agent concentrations i.e., lowest relaxation times of blood (ca. 200 ms).
The Functional Genomics of Noncoding RNA (2005)

Large numbers of noncoding RNA transcripts (ncRNAs) are being revealed by complementary DNA cloning and genome tiling array studies in animals. The big and as yet largely unanswered question is whether these transcripts are relevant. A paper by Willingham et al. shows the way forward by developing a strategy for large-scale functional screening of ncRNAs, involving small interfering RNA knockdowns in cell-based screens, which identified a previously unidentified ncRNA repressor of the transcription factor NFAT. It appears likely that ncRNAs constitute a critical hidden layer of gene regulation in complex organisms, the understanding of which requires new approaches in functional genomics.
Nuestra entrevista del mes: entrevista de táctica a Gonzalo Arconada (2006)

Muy variados aspectos de tactica y de organizacion del juego colectivo planteamos en esta entrevista. Se incluyen conceptos generales, asi como conceptos relativos a las situaciones de defensa y de ataque. Tambien se vierten criterios sobre la decisiva incidencia de la Regla del Fuera de Juego. El entrevistado es un tecnico que posee un perfecto conocimiento del juego y de todos los parametros inherentes a la metodologia de entrenamiento, ademas, atesora un extraordinaria inquietud. Siempre esta presente en las jornadas tecnicas importantes que se celebran en cualquier punto de Espana. Actualmente esta cursando el Master Profesional para Entrenadores Nacionales de Futbol impartido por Cesfutbol con la colaboracion academica del Instituto Universitario de Ciencias del Deporte de la Universidad de Murcia. Despues de demostrar su gran valia, por trabajo y resultados, como entrenador de la Real Sociedad B, se hizo cargo del primer equipo de la Real Sociedad, asumiendo una tarea desesperada con un equipo inmerso en una profunda crisis de juego y resultados. No se le dio tiempo para arreglar el gran desaguisado que era el equipo, se le ceso tras pocas semanas en el cargo. Pero auguro un magnifico futuro profesional a Gonzalo Arconada, cuenta con una alta capacidad tecnica y una gran valia personal. (Jesus Cuadrado Pino, director de 
TRAINING FUTBOL)
Empirical Amide I Vibrational Frequency Map: Application to 2D-IR Line Shapes for Isotope-Edited Membrane Peptide Bundles (2008)

The amide I vibrational mode, primarily associated with peptide-bond carbonyl stretches, has long been used to probe the structures and dynamics of peptides and proteins by infrared (IR) spectroscopy. A number of ab initio-based amide I vibrational frequency maps have been developed for calculating IR line shapes. In this paper, a new empirical amide I vibrational frequency map is developed. To evaluate its performance, we applied this map to a system of isotope-edited CD3-zeta membrane peptide bundles in aqueous solution. The calculated 2D-IR diagonal line widths vary from residue to residue and show an asymmetric pattern as a function of position in the membrane. The theoretical results are in fair agreement with experiments on the same system. Through analysis of the computed frequency time-correlation functions, it is found that the 2D-IR diagonal widths are dominated by contributions from the inhomogeneous frequency distributions, from which it follows that these widths are a good probe of the extent of local structural fluctuations. Thus, the asymmetric pattern of line widths follows from the asymmetric structure of the bundle in the membrane.
Isolated cleft palate in mice with a targeted mutation of the LIM homeobox gene <i>Lhx8</i> (1999)

Formation of the mammalian secondary palate is a highly regulated and complex process whose impairment often results in cleft palate, a common birth defect in both humans and animals. Loss-of-function analysis has linked a growing number of genes to this process. Here we report that Lhx8, a recently identified LIM homeobox gene, is expressed in the mesenchyme of the mouse palatal structures throughout their development. To test the function of Lhx8 in vivo, we generated a mutant mouse with a targeted deletion of the Lhx8 gene. Our analysis of the mutant animals revealed a crucial role for Lhx8 in palatogenesis. In Lhx8 homozygous mutant embryos, the bilateral primordial palatal shelves formed and elevated normally, but they often failed to make contact and to fuse properly, resulting in a cleft secondary palate. Because development of other craniofacial structures appeared normal, the impaired palatal formation in Lhx8-mutant mice was most likely caused by an intrinsic primary defect in the mesenchyme of the palatal shelves. The cleft palate phenotype observed in Lhx8-mutant mice suggests that Lhx8 is a candidate gene for the isolated nonsyndromic form of cleft palate in humans.
<title>Nonuniformity correction using a flood technique and 1:1 mapping</title> (2001)

Although the sparse grid Non-Uniformity Correction (NUC) technique can accurately correct individual emitters on a resistor array, it is not a good solution for all projection applications. Due to busbar robbing, the sparse grid NUC breaks down when a large number of emitters are turned on simultaneously. For this case, a more appropriate NUC data collection method is needed. This method involves measuring the entire resistor array at once with a 1:1 mapping between the projector and NUC sensor. Then busbar effects, measured during the NUC data collection, can be accounted for and corrected. This paper presents details pertaining to the flood NUC technique and results. This NUC system is implemented at the Kinetic Kill Vehicle Hardware In the Loop Simulator (KHILS) at Eglin AFB, Florida.
Immunological detection of membrane-associated human luteinizing hormone correlates with gene expression in cultured human cancer and fetal cells. (1995)

We have demonstrated the expression of membrane-associated hCG and its subunits and fragments by cells from 78 human cancer cell lines of different types and origins, indicating that such expression is a common phenotypic characteristic of cultured human malignant cells. Because human (h) LH beta has 80% homology with hCG beta and is coded by one of the seven genes in the gene cluster located in chromosome 19, it was important to determine whether hLH and its beta-subunit are also expressed as membrane-associated proteins by cells from human cancer cell lines. Thus, 11 cancer cell lines of different types and origins were adapted to grow in serumless medium, with Nutridoma-HU or SP as serum substitute, and analyzed by flow cytometry using two monoclonal antibodies directed to different conformational epitopes of intact hLH and a monoclonal antibody reacting with an epitope of hLH beta-free. The cells were also analyzed simultaneously for the expression of hCG and its subunits and fragments. Determination of translatable levels of hLH beta and hCG beta messenger RNAs (mRNAs) was performed in cells from some of the cancer cell lines, including the JEG-3 choriocarcinoma cell line, and in cells from a human fetal lung cell line. The analytical flow cytometry studies showed that in addition to the expression of membrane-associated hCG in all of its forms, expression of membrane-associated intact (holo) hLH and its free beta-subunit occurred in every case. These findings were corroborated by the presence of translatable levels of hLH beta and hCG beta mRNAs in all of the cancer cell lines analyzed, indicating that the expression of these membrane-associated glycoproteins is a phenotypic characteristic of human cancer cells and that the activation of the hCG beta-hLH beta gene cluster is nonselective. The presence of translatable levels of hCG beta-hLH beta mRNAs in the cultured human fetal lung cells punctuates once more the in vivo and in vitro biochemical similarities between fetal and cancer cells.
A Noise Robust Front-End Using Wiener Filter, Probability Model And CMS For ASR (2006)

A novel and noise robust front-end based on the combination of spectral noise reduction and probability model-based feature compensation and cepstral mean subtraction (CMS) is proposed. Mel filter-bank outputs can be affected by additive noise primarily because of the vulnerable spectral valleys. An instantaneous Wiener filter is used to improve SNR of the spectral valley. Because the compensated MFCC is an approximation of the clean one and retains a residual mismatch, features are further processed by CMS in order to remove the global shift of the mean. In the presence of additive noise, ASR experiments reveal that a cascade fashion use of these techniques improves recognition performance greatly. For the 863 continuous Chinese speech databases, the average recognition rate across different noise types is improved from 34.63% (using unmodified MFCCs) to 84.63% (using the proposed techniques) at best.