gebhart/patrepeval huggingface dataset:
Metabolic Activation of CPT-11, 7-Ethyl-10-(4-(1-piperidino)-1-piperidino)carbonyloxycamptothecin, a Novel Antitumor Agent, by Carboxylesterase. (1994)

We measured the plasma concentrations of 7-ethyl-10-[4-(1-piperidino)-1- piperidine]carbonyloxycamptothecin (CPT-11) and the active metabolite 7-ethyl-10-hydroxycamptothecin (SN-38), after treatment with CPT-11 to rats pretreated with bis-p-nitrophenylphosphate (BNPP) which is a specific inhibitor of carboxylesterase, and non-pretreated rats. The plasma level of SN-38 was decreased in the BNPP-pretreated group compared with these of non-pretreated group, indicating that the esterase involved in CPT-11 metabolism is a carboxylesterase. We also characterized the molecular species of carboxylesterase involved in CPT-11 metabolism using enzyme preparations purified from liver microsomes. Thirteen carboxylesterase isozyme activities towards CPT-11 were compared and guinea pig GLP1 was found to have the highest activity, while human HU1 isozyme had relatively lower activity than those of animal species. In studies on the kinetic parameters of the hydrolysis of CPT-11 by the purified carboxylesterase isozymes the highest Vmax value of the isozymes was found in human HU1 and the smallest was seen in rat RL1. The Vmax/Km for RL1 showed the largest value of 21.7 nmol/mg protein/mM.
Learning to Extract Semantic Structure from Documents Using Multimodal Fully Convolutional Neural Networks (2017)

We present an end-to-end, multimodal, fully convolutional network for extracting semantic structures from document images. We consider document semantic structure extraction as a pixel-wise segmentation task, and propose a unified model that classifies pixels based not only on their visual appearance, as in the traditional page segmentation task, but also on the content of underlying text. Moreover, we propose an efficient synthetic document generation process that we use to generate pretraining data for our network. Once the network is trained on a large set of synthetic documents, we fine-tune the network on unlabeled real documents using a semi-supervised approach. We systematically study the optimum network architecture and show that both our multimodal approach and the synthetic data pretraining significantly boost the performance.
Flexible layout and optimal cancellation of the orthonormality error for spherical microphone arrays (2004)

This paper describes an approach to achieving a flexible layout of microphones on the surface of a spherical microphone array for beamforming. Our approach achieves orthonormality of spherical harmonics to higher order for relatively distributed layouts. This gives great flexibility in microphone layout on the spherical surface. One direct advantage is that it makes it much easier to build a real world system, such as those with cable outlets and a mounting base, with minimal effects on the performance. Simulation results are presented.
Plasmon-Induced Magneto-Optical Activity in Nanosized Gold Disks (2010)

In this Letter we show that nanostructures made out of pure noble metals can exhibit measurable magneto-optic activity at low magnetic fields. This phenomenon occurs when the localized surface plasmon resonance of the nanostructure is excited in the presence of a static magnetic field parallel to the propagation of incident light. The large magneto-optical response observed comes from an increase of the magnetic Lorentz force induced by the large collective movement of the conduction electrons in the nanostructures when the resonance is excited.
Phase II trial of denileukin diftitox for relapsed/refractory T‐cell non‐Hodgkin lymphoma (2006)

This phase II study evaluated the safety and efficacy of denileukin diftitox, an interleukin-2-diphtheria toxin fusion protein, in relapsed/refractory T-cell non-Hodgkin lymphoma (T-NHL), excluding cutaneous T-cell lymphoma. Eligible patients received denileukin diftitox 18 microg/kg/d x 5 d every 3 weeks for up to eight cycles. Tumour staging was performed every two cycles and the primary endpoint was the objective response rate [complete response (CR) + partial response (PR)]. For 27 patients enrolled, median age: 55 years (range 26-80 years), 70.4% male, and mean prior therapies: 2.5 (range 1-6). Objective responses (six CRs, seven PRs) were achieved in 13 patients (48.1%), stable disease in eight (29.6%) and six (22.2%) had progressive disease. An objective response was achieved in eight of 13 patients (61.5%) with CD25(+) tumours (four CR/four PR) and five of 11 patients (45.5%) with CD25(-) tumours (two CR/three PR). Median progression-free survival was 6 months (range, 1-38+ months). Most adverse reactions were grade 1/2 and transient. No grade 4-5 toxicities were reported. Denileukin diftitox had significant activity and was well tolerated in relapsed/refractory T-NHL, with responses observed in both CD25(+) and CD25(-) tumours. Further studies of denileukin diftitox in combination with other agents are warranted in previously untreated and relapsed/refractory T-NHL.
Algal transgenics and biotechnology (2007)

Transgenesis in algae is a complex and fast-growing technology. Selectable marker genes, promoters, reporter genes, transformation techniques, and other genetic tools and methods are already available for various species and currently ~25 species are accessible to genetic transformation. Fortunately, large-scale sequencing projects are also planned, in progress, or completed for several of these species; the most advanced genome projects are those for the red alga Cyanidioschyzon merolae, the diatom Thalassiosira pseudonana, and the three green algae Chlamydomonas reinhardtii, Volvox carteri and Ostreococcus tauri. The vast amount of genomic and EST data coming from these and a number of other algae has the potential to dramatically enlarge not only the algae’s molecular toolbox. A powerful driving force in algal transgenics is the prospect of using genetically modified algae as bioreactors. In general, today’s non-transgenic, commercial algal biotechnology produces food additives, cosmetics, animal feed additives, pigments, polysaccharides, fatty acids, and biomass. But recent progress in algal transgenics promises a much broader field of application: molecular farming, the production of proteins or metabolites that are valuable to medicine or industry, seems to be feasible with transgenic algal systems. Indeed, the ability of transgenic algae to produce recombinant antibodies, vaccines, insecticidal proteins, or bio-hydrogen has already been demonstrated. Genetic modifications that enhance physiological properties of algal strains and optimization of algal production systems should further improve the potential of this auspicious technology in the future.
Tamoxifen decreases the rate of proliferation of rat vascular smooth-muscle cells in culture by inducing production of transforming growth factor β (1993)

Tamoxifen selectively and reversibly decreased the rate of proliferation of adult rat aortic vascular smooth-muscle cells (VSMCs). Half-maximal inhibition of proliferation occurred at 2-5 microM tamoxifen for VSMCs and at > 50 microM for adventitial fibroblasts. The cell cycle time for all the VSMCs in the population was increased from 35 +/- 2 h to 54 +/- 4 h in the presence of 33 microM tamoxifen. Tamoxifen did not affect the time of entry into DNA synthesis, but delayed arrival at mitosis by > 24 h. It therefore extended the duration of the G2-to-M phase of the cell cycle. However, the rate of proliferation of VSMCs was not decreased by tamoxifen (at concentrations up to 50 microM) in the presence of neutralizing antibody to transforming growth factor beta (TGF-beta). The level of mRNA for TGF-beta 1 in VSMCs was strongly induced by 10 microM tamoxifen, and TGF-beta activity in conditioned medium from tamoxifen-treated cells was more than 50-fold higher than from control cells. Tamoxifen therefore extended the G2-to-M phase of the cell cycle in VSMCs by increasing TGF-beta activity in the culture.
Phase dynamics in cerebral autoregulation (2005)

Complex continuous wavelet transforms are used to study the dynamics of instantaneous phase difference delta phi between the fluctuations of arterial blood pressure (ABP) and cerebral blood flow velocity (CBFV) in a middle cerebral artery. For healthy individuals, this phase difference changes slowly over time and has an almost uniform distribution for the very low-frequency (0.02-0.07 Hz) part of the spectrum. We quantify phase dynamics with the help of the synchronization index gamma = (sin delta phi)2 + (cos delta phi)2 that may vary between 0 (uniform distribution of phase differences, so the time series are statistically independent of one another) and 1 (phase locking of ABP and CBFV, so the former drives the latter). For healthy individuals, the group-averaged index gamma has two distinct peaks, one at 0.11 Hz [gamma = 0.59 +/- 0.09] and another at 0.33 Hz (gamma = 0.55 +/- 0.17). In the very low-frequency range (0.02-0.07 Hz), phase difference variability is an inherent property of an intact autoregulation system. Consequently, the average value of the synchronization parameter in this part of the spectrum is equal to 0.13 +/- 0.03. The phase difference variability sheds new light on the nature of cerebral hemodynamics, which so far has been predominantly characterized with the help of the high-pass filter model. In this intrinsically stationary approach, based on the transfer function formalism, the efficient autoregulation is associated with the positive phase shift between oscillations of CBFV and ABP. However, the method is applicable only in the part of the spectrum (0.1-0.3 Hz) where the coherence of these signals is high. We point out that synchrony analysis through the use of wavelet transforms is more general and allows us to study nonstationary aspects of cerebral hemodynamics in the very low-frequency range where the physiological significance of autoregulation is most strongly pronounced.
Divide-and-conquer programming on MIMD computers (1995)

We have developed a programming template to implement divide and conquer algorithms on MIMD computers. The template is based on the parallel divide and conquer function of Z.G. Mou and P. Hudak (1988). We explore the programmability and performance of this approach by solving some well known numerical problems on a shared memory multiprocessor and a multicomputer. A byproduct of this work is a new parallel algorithm for solving tridiagonal systems of equations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Detecting anti-Treponema hyodysenteriae antibodies in swine serum using immunofluorometry. (1983)

An indirect fluorescent antibody test was adapted for measuring serum anti-Treponema hyodysenteriae antibodies with a fluorometer. The immunofluorescence was recorded as fluorescent signal units. Cultures of T. hyodysenteriae and Treponema innocens were used as antigen. There was a significant (P less than 0.01) correlation between the immunofluorescence recorded with the fluorometer and that evaluated visually with a microscope. The swine exposed orally to swine dysentery infective inoculum and subsequently hyperimmunized by the intravenous inoculation of live cultures of T. hyodysenteriae had the highest average fluorescent signal unit, which was 104.5. There was a significant (P less than 0.01) correlation between the level of anti-T. hyodysenteriae antibody and the interval length between the last day of diarrhea and the day of bleeding. However, in measuring fluorescent signal units in serum from swine infected with nonpathogenic large spirochetes, (T. innocens), there was also a significant (P less than 0.01) correlation between T. hyodysenteriae and T. innocens as antigen. The coefficient of variation of the average fluorescent signal unit for a highly positive serum and a highly negative serum between 16 runs of assays were 5.7% and 19% respectively; the coefficient of variation of the average fluorescent signal unit for duplicate samples on 358 serum samples tested was 5.8%.
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 (2014)

In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html webcite.
Rotate intra block copy for still image coding (2015)

This paper proposes a method called rotate intra block copy, which extends the intra block copy technique by making the block matching process invariant to rotation. HEVC intra prediction plus rotate intra block copy gives an average of 20% reduction in residual energy (i.e. prediction error) compared to HEVC intra prediction plus intra block copy. As the motion vector correlation in rotate intra block copy is different from the intra block copy, a new method of motion vector coding is presented. The impact of angular resolution on residual energy reduction is also evaluated. In a full codec pipeline, this reduction in residual energy translates into a coding gain in BD-rate of 3.4% over HEVC intra prediction plus intra block copy for both screen content and camera-captured gray scale images.
Sporogonic Development of a Malaria Parasite in Vitro (1992)

The sporogonic cycle of the avian malaria parasite Plasmodium gallinaceum was completed in vitro. Ookinetes (motile zygotes) were seeded onto a murine basement membrane-like gel (Matrigel) in coculture with Drosophila melanogaster cells (Schneider's L2). Transformation into oocysts as well as subsequent growth and differentiation were observed in parasites attached to Matrigel and depended on the presence of L2 cells. Sporozoites were first observed on day 10 in culture. Specific circumsporozoite protein antigenicity was identified in mature oocysts and in sporozoites. It is now possible to follow the entire life cycle of Plasmodium in vitro.
Optical Coherence Tomography in the Gastrointestinal Tract (2000)

Optical coherence tomography (OCT) is a high-resolution, cross-sectional optical imaging technique that allows in situ imaging of tissue by measuring back-reflected light. OCT provides images in real time with a resolution approaching that of conventional histopathology, but without the need for tissue removal. OCT imaging can be performed endoscopically to visualize gastrointestinal tissue using a fiberoptic catheter passed through the instrument channel of a conventional endoscope. The resolution of OCT allows visualization of the different layers of gastrointestinal epithelium and the differentiation of Barrett's epithelium from normal gastric and squamous mucosa. OCT has also been used to image esophageal adenocarcinoma and colonic polyps. Recent developments include Doppler OCT, spectroscopic OCT, and ultrahigh-resolution OCT, which can visualize nuclei within single cells. Although still in its infancy as a clinical tool, OCT currently provides high-resolution images over the same imaging depth as conventional mucosal biopsy, and may prove to be a useful and minimally invasive technique for evaluating gastrointestinal tissue, particularly for early neoplastic changes.
Rod Outer Segment Development Influences AAV-Mediated Photoreceptor Transduction After Subretinal Injection (2017)

Vectors based on the adeno-associated virus (AAV) are currently the preferred tools for delivering genes to photoreceptors (PR) in small and large animals. AAVs have been applied successfully in various models of PR dystrophies. However, unknown barriers still limit AAV's efficient application in several forms of severe PR degenerations due to insufficient transgene expression and/or treated cells at the time of injection. Optimizations of PR gene therapy strategies will likely benefit from the identification of the cellular factors that influence PR transduction. Interestingly, recent studies have shown that the AAV transduction profile of PRs differs significantly between neonatal and adult mouse retinas after subretinal injection. This phenomenon may provide clues to identify host factors that influence the efficiency of AAV-mediated PR transduction. This study demonstrates that rod outer segments are critical modulators of efficient AAV-mediated rod transduction. During retinal development, rod transduction correlated temporally and spatially with the differentiation order of PRs when vectors were introduced subretinally but not when introduced intravitreally. All subretinally injected vectors had an initial preference to transduce cones in the absence of formed rod outer segments and then displayed a preference for rods as the cells matured, independently of the expression cassette or AAV serotype. Consistent with this observation, altered development of rod outer segments was associated with a strong reduction of rod transduction and an increase in the percentage of transduced cones by 2- to 2.8-fold. A similar increase of cone transduction was observed in the adult retinal degeneration 1 (rd1) retina compared to wild-type mice. These results suggest that the loss of rod outer segments in diseased retinas could markedly affect gene transfer efficiency of AAV vectors by limiting the ability of AAVs to infect dying rods efficiently. This information could be exploited for the development of more efficient AAV-based PR gene delivery procedures.
Expression of Iμ-Cγ hybrid germline transcripts subsequent to immunoglobulin heavy chain class switching (1994)

Germline CH transcripts initiate from a non-coding I exon and terminate downstream of the associated CH exons. Ig heavy chain class switch recombination from the VDJ-C mu gene to particular downstream CH genes appears to be regulated by a process that involves mitogen and/or cytokine induction of germline CH transcripts from the downstream genes. We have examined the expression of germline C mu transcripts (I mu-C mu transcripts) in splenic B cells and pre-B cell lines after cytokine and mitogen stimulation. In contrast to the expression of the germline transcripts from downstream CH genes, expression of germline C mu transcripts was constitutive and unaffected by mitogen and cytokine treatment. After a primary switch recombination event, the germline I mu promoter, which is now associated with a downstream CH gene, continues to be active--leading to the generation of a novel germline transcript consisting of the I mu exon spliced to the CH exons of the switched CH gene. We discuss the potential role of the expression of hybrid I mu-containing transcripts in the class switch process. We also describe a novel and sensitive assay, based on the detection of the hybrid I mu-containing transcripts, that allows detection of class switch recombination events even in heterogeneous populations of cells.
Estimating source position accuracy of a large-aperture hydrophone array for bioacoustics (2001)

A linear error propagation analysis was applied to a hydrophone array used to locate sperm whales [see Møhl et al., J. Acoust. Soc. Am. 107, 638–648 (2000)]. The accuracy of two-dimensional (2D) and three-dimensional (3D) array configurations was investigated. The precision in source location was estimated as a function of inaccuracies in measurements of sound velocity, time-of-arrival differences (TOADs), and receiver positions. The magnitude of additional errors caused by geometric simplification was also assessed. The receiver position uncertainty had the largest impact on the precision of source location. A supplementary vertical linear array consisting of three receivers gave information on the vertical bearing and distance to the sound sources. The TOAD data from an additional receiver as well as from surface reflections were used to form an overdetermined location system. This system rendered positions within two standard deviations of the estimated errors from the original 3D array.
Triple negative breast cancer: looking for the missing link between biology and treatments (2015)

The so called "Triple Negative Breast Cancer" (TNBC) represents approximately 15-20% of breast cancers. This acronym simply means that the tumour does not express oestrogen receptor (ER) and progesterone receptor (PR) and does not exhibit amplification of the human epidermal growth factor receptor 2 (HER2) gene. Despite this unambiguous definition, TNBCs are an heterogeneous group of tumours with just one common clinical feature: a distinctly aggressive nature with higher rates of relapse and shorter overall survival in the metastatic setting compared with other subtypes of breast cancer. Because of the absence of well-defined molecular targets, cytotoxic chemotherapy is currently the only treatment option for TNBC. In the last decades, the use of more aggressive chemotherapy has produced a clear improvement of the prognosis in women with TNBC, but this approach results in an unacceptable deterioration in the quality of life, also if some support therapies try to relieve patients from distress. In addition, there is the general belief that it is impossible to further improve the prognosis of TNBC patients with chemotherapy alone. In view of that, there is a feverish search for new "clever drugs" able both to rescue chemo-resistant, and to reduce the burden of chemotherapy in chemo-responsive TNBC patients. A major obstacle to identifying actionable targets in TNBC is the vast disease heterogeneity both inter-tumour and intra-tumour and years of study have failed to demonstrate a single unifying alteration that is targetable in TNBC. TNBC is considered the subtype that best benefits from the neoadjuvant model, since the strong correlation between pathological Complete Response and long-term Disease-Free-Survival in these patients. In this review, we discuss the recent discoveries that have furthered our understanding of TNBC, with a focus on the subtyping of TNBC. We also explore the implications of these discoveries for future treatments and highlight the need for a completely different type of clinical trials.
Dual EGFR/HER2 Inhibition Sensitizes Prostate Cancer Cells to Androgen Withdrawal by Suppressing ErbB3 (2011)

These studies indicate that dual EGFR/HER2 inhibition, administered together with AWT, sensitize prostate cancer cells to apoptosis during AWT.