gebhart/patrepeval huggingface dataset:
Clinical utility of external immunoscintigraphy with the IMMU-4 technetium-99m Fab' antibody fragment in patients undergoing surgery for carcinoma of the colon and rectum: results of a pivotal, phase III trial. The Immunomedics Study Group. (1996)

CEA-Scan affords high-quality, same-day imaging, uses an inexpensive and readily available radio-nuclide, adds clinically significant information in assessing extent and location of disease in colorectal cancer patients, and only rarely induces a HAMA response.
Empirical error based optimization of SVM kernels: application to digit image recognition (2003)

We address the problem of optimizing kernel parameters in support vector machine modeling, especially when the number of parameters is greater than one as in polynomial kernels and KMOD, our newly introduced kernel. The present work is an extended experimental study of the framework proposed by Chapelle et al. (2001) for optimizing SVM kernels using an analytic upper bound of the error. However our optimization scheme minimizes an empirical error estimate using a quasi-Newton optimization method. To assess our method, the approach is further used for adapting KMOD, RBF and polynomial kernels on synthetic data and NIST database. The method shows a much faster convergence with satisfactory results in comparison with the simple gradient descent method.
From the Editor: The Vision for a National Quality Report (2001)

By now, most readers are familiar with the far-reaching Institute of Medicine (IOM) reports on American medical care. Taken together, To Err is Human1 and Crossing the Quality Chasm2 reveal a health system that is disjointed, inefficient, and, too frequently, harmful to patients. “Americans ought to be able to count on receiving care that is safe and uses the best scientific knowledge…there is strong evidence that this is not the case.”1 It is not my intent to summarize these widely publicized reports in this space. Rather, I want readers to focus on another task directly related to these reports; that is, former President Clinton’s Advisory Commission on Consumer Protection and Quality (in the Healthcare Industry) call for a national commitment to improve quality. This Presidential Advisory Commission recommended that there be an annual report to the President and Congress on the nation’s progress in improving healthcare quality. As a result, Congress enacted the Healthcare Research and Quality Act of 1999 directing the Agency for Healthcare Research and Quality (AHRQ) to prepare an annual report on national trends in the quality of healthcare provided to the
Glucagon Secretion from the Perfused Rat Pancreas STUDIES WITH GLUCOSE AND CATECHOLAMINES (1974)

The isolated in situ perfused rat pancreas was used to study glucose and catecholamine control of glucagon secretion, and to investigate the possible role of endogenous cyclic AMP as a mediator of this secretory process. When perfusate glucose was acutely dropped from 100 to 25 mg/100 ml, glucagon was released in a biphasic pattern with an early spike and a later plateau-like response. 300 mg/100 ml glucose suppressed glucagon secretion to near the detection limit of the radioimmunoassay (15 pg/ml). When perfusate glucose was dropped from 300 to 25 mg/100 ml, a delayed, relatively small peak occurred suggesting persisting alpha cell suppression by prior high glucose exposure. 2-Deoxy d-glucose stimulated glucagon secretion and inhibited insulin secretion. Glucagon was secreted in a biphasic pattern in response to both 2.7 x 10(-7) M epinephrine and norepinephrine. The glucagon response to epinephrine was markedly suppressed by glucose at 300 mg/100 ml, and the biphasic response pattern was obliterated. Glucose evoked a two-phase insulin secretory pattern, and the second phase was markedly and rapidly inhibited by epinephrine. Pancreases were perfused with glucose at 300 mg/100 ml which was then lowered to 80 mg/100 ml. 5 min later, epinephrine was infused and definite blunting of the first-phase spike occurred. 10 mM theophylline produced modest rapid uniphasic stimulation of glucagon release, and, in addition, caused enhancement of epinephrine-stimulated glucagon release. An inhibitory influence upon epinephrine-stimulated glucagon was observed as well. Insulin secretion was stimulated by 10 mM theophylline, and this stimulation was inhibited by epinephrine.
Serum cytokine profiles and their correlations with disease activity in Takayasu's arteritis (2005)

Serum IL-18 and IL-6 levels were elevated in patients with TA, especially in those with active disease. Serum IL-18 levels correlated well with disease activity of TA. These results suggest that IL-6 and IL-18 might contribute to the pathogenesis of TA and that IL-18 could be a useful marker for monitoring disease activity of TA.
Human serum albumin: twenty‐three genetic variants and their population distribution (1973)

Peer Reviewed
The t(9;14)(p13;q32) chromosomal translocation associated with lymphoplasmacytoid lymphoma involves the PAX-5 gene (1996)

The t(9;14)(p13;q32) translocation is associated with approximately 50% of lymphoplasmacytoid lymphoma (LPL), a subtype of B-cell non-Hodgkin's lymphoma (NHL). We cloned the chromosomal breakpoint of der (14) from an LPL case (1052) and showed that it involved a junction between 9p13 and the switch micro region of the Ig heavy chain locus (IgH) on 14q32. Using a YAC contig spanning 1.5 megabase (Mb), we determined that the 9p13 breakpoint in one case (1052) mapped within a 270-kb restriction fragment containing two previously reported 9p breakpoints associated with a alpha-heavy chain disease case (MAL) and KI-1 positive diffuse large cell lymphoma (DLCL) cell line (KIS-1). The same fragment also contained the PAX-5 gene which encodes a B-cell specific transcription factor involved in the control of B-cell proliferation and differentiation. The breakpoints of KIS-1 and 1052 were mapped within the 5' noncoding region of PAX-5, while the 9p13 breakpoint of MAL mapped 230 to 270 kb upstream to PAX-5. In all three cases, the translocation caused the juxtaposition of the PAX-5 gene to the IgH locus in the opposite direction of transcription. When compared with six other DLCL cell lines lacking t(9;14)(p13;q32), the KIS-1 cell line showed an 11-fold overexpression of PAX-5 mRNA and a significantly reduced expression of the p53 gene, which is normally regulated by PAX-5. Moreover, metaphase and interphase fluorescence in situ hybridization (FISH) analysis using a YAC clone spanning 1 Mb including the PAX-5 as a probe identified chromosomal translocations in 5 of 7 cases carrying 9p13 translocations. These findings suggest that the PAX-5 gene is the target of the t(9;14) in LPL whereby its expression may be deregulated by juxtaposition to IgH regulatory elements, thus contributing to lymphomagenesis.
Dihydroquinone Ansamycins:  Toward Resolving the Conflict between Low in Vitro Affinity and High Cellular Potency of Geldanamycin Derivatives (2006)

Heat shock protein 90 (Hsp90) is critical for the maturation of numerous client proteins, many of which are involved in cellular transformation and oncogenesis. The ansamycins, geldanamycin (GA) and its derivative, 17-allylaminogeldanamycin (17-AAG), inhibit Hsp90. As such, the prototypical Hsp90 inhibitor, 17-AAG, has advanced into clinical oncology trials. GA and 17-AAG potently inhibit tumor cell proliferation and survival but have been reported to bind weakly to Hsp90 in vitro. Recent studies have suggested that the in vitro potency of ansamycins against Hsp90 may be enhanced in the presence of cochaperones. Here, we present evidence of an alternative explanation. Ansamycins reduced to their dihydroquinones in the presence of common reducing agents in vitro have approximately 40-fold greater affinity than the corresponding oxidized quinones. The dihydroquinone of 17-AAG is not generated in an aqueous environment in the absence of reducing agents but is produced in both tumor and normal quiescent epithelial cells. The reduced form of 17-AAG is differentiated from its oxidized form not only by the higher affinity for Hsp90 but also by a protracted K(off) rate. Therefore, the in vivo accumulation of the high-affinity dihydroquinone ansamycins in tumor cells contributes to the antitumor activity of these compounds and alters our understanding of the active species driving the efficacy of this class of compounds.
Practical lessons from protein structure prediction (2005)

Despite recent efforts to develop automated protein structure determination protocols, structural genomics projects are slow in generating fold assignments for complete proteomes, and spatial structures remain unknown for many protein families. Alternative cheap and fast methods to assign folds using prediction algorithms continue to provide valuable structural information for many proteins. The development of high-quality prediction methods has been boosted in the last years by objective community-wide assessment experiments. This paper gives an overview of the currently available practical approaches to protein structure prediction capable of generating accurate fold assignment. Recent advances in assessment of the prediction quality are also discussed.
Design of Robust Steerable Broadband Beamformers with Spiral Arrays and the Farrow Filter Structure (2010)

This paper extends the design of steerable broadband beamformers by incorporating robustness in the design formulation to cater for microphone mismatches and other non-ideal characteristics. In our method, a 2 norm constraint on the filter weights is imposed in the design optimisation problem. This constraint limits the 2-norm of the filter weights, thus reducing the sensitivity of the beamformer towards the non-ideal characteristics of the microphones. Design examples and comparisons are presented to illustrate our approach.
Increased fetal nuchal translucency at 11–14 weeks (2002)

Nuchal translucency (NT) is the sonographic appearance of a subcutaneous collection of fluid behind the fetal neck. The measurement of fetal NT thickness at the 11-14-week scan has been combined with maternal age to provide an effective method of screening for trisomy 21; for an invasive testing rate of 5%, about 75% of trisomic pregnancies can be identified. When maternal serum free-beta human chorionic gonadotrophin (beta-hCG) and pregnancy-associated plasma protein-A (PAPP-A) at 11-14 weeks are also taken into account, the detection rate of chromosomal defects is about 90%. Increased NT can also identify a high proportion of other chromosomal abnormalities and is associated with major defects of the heart and great arteries, and a wide range of skeletal dysplasias and genetic syndromes. In monochorionic twins, discordancy for increased NT is an early marker of twin-to-twin transfusion syndrome (TTTS). As with the introduction of any new technology into routine clinical practice, it is essential that those undertaking the 11-14-week scan are adequately trained and their results are subjected to rigorous audit.
Biologically Active Constituents of Leaves and Roots of Aloe arborescens var. natalensis (1977)

Several biologically active substances, such as aloenin (1), magnesium lactate, aloe-emodin (4), barbaloin (5), and succinic acid, were found to be contained in the leaf juice of Aloe arborescens Mill. var. natalensis Berger, which has widely been used in domestic medicines. Aloenin (1) and magnesium lactate were elucidated to exhibit an inhibitory action on the gastric juice secretion of rats. Various constituents other than the above bioactive substances were found in the leaves and the roots of the plant.
Expression of estrogen receptor β in prostate carcinoma cells inhibits invasion and proliferation and triggers apoptosis (2004)

The involvement of estrogen receptor beta (ERbeta) in prostate carcinogenesis has been hypothesized. Several reports have shown that ERbeta expression was decreased when prostate cells undergo neoplastic transformation, suggesting that it could play a tumor-suppressor role. By restoring ERbeta expression in prostatic carcinoma cells by adenoviral delivery, we aimed to test this hypothesis. We observed that ERbeta strongly inhibited the invasiveness and the growth of these cells. In addition, ERbeta cells were undergoing apoptosis, as shown by quantification of Bax, poly(ADP-ribose) polymerase and caspase-3 expression. Our data suggest that ERbeta acts as a tumor-suppressor by its anti-proliferative, anti-invasive and pro-apoptotic properties.
Improvement in performance of a TeO2acousto-optic imaging spectrometer (2007)

This paper concerns the problem of the optimization of parameters in acousto-optic image processing systems. The optimization was carried out with the purpose of obtaining the best performance and minimum driving power. A choice of optimal geometry of acousto-optic interaction in the crystal is discussed. Longitudinal aberrations in the device caused by dispersion of refractive indices of acousto-optic media are studied. Calculations prove that a specific choice of distances between optical elements in the device can reduce the aberration to a value less than the focal depth of a filtered image. Spectral analysis of radiation reflected from artificial test objects demonstrates operationaal capability of the imager.
Output power changes in laser diodes subject to sub-wavelength variations in external cavity length: theory and experiment (2000)

Summary form only. Recent experiments have shown that the five regimes of feedback commonly used to characterise the dynamical performance of laser diodes subject to optical feedback poorly describe the behaviour for short external cavity laser diodes. Experimental investigations have shown that the output power of the laser can be dramatically affected by sub-wavelength variation in the external cavity length. A theoretical investigation using the Lang-Kobayashi model has shown excellent agreement with experimental results, and has thus elucidated the mechanisms that induces the observed experimental behaviour.
Spectrogram-channels u-net: a source separation model viewing each channel as the spectrogram of each source (2018)

Sound source separation has attracted attention from Music Information Retrieval(MIR) researchers, since it is related to many MIR tasks such as automatic lyric transcription, singer identification, and voice conversion. In this paper, we propose an intuitive spectrogram-based model for source separation by adapting U-Net. We call it Spectrogram-Channels U-Net, which means each channel of the output corresponds to the spectrogram of separated source itself. The proposed model can be used for not only singing voice separation but also multi-instrument separation by changing only the number of output channels. In addition, we propose a loss function that balances volumes between different sources. Finally, we yield performance that is state-of-the-art on both separation tasks.
Micropower CMOS Integrated Low-Noise Amplification, Filtering, and Digitization of Multimodal Neuropotentials (2009)

Electrical activity in the brain spans a wide range of spatial and temporal scales, requiring simultaneous recording of multiple modalities of neurophysiological signals in order to capture various aspects of brain state dynamics. Here, we present a 16-channel neural interface integrated circuit fabricated in a 0.5 mum 3M2P CMOS process for selective digital acquisition of biopotentials across the spectrum of neural signal modalities in the brain, ranging from single spike action potentials to local field potentials (LFP), electrocorticograms (ECoG), and electroencephalograms (EEG). Each channel is composed of a tunable bandwidth, fixed gain front-end amplifier and a programmable gain/resolution continuous-time incremental DeltaSigma analog-to-digital converter (ADC). A two-stage topology for the front-end voltage amplifier with capacitive feedback offers independent tuning of the amplifier bandpass frequency corners, and attains a noise efficiency factor (NEF) of 2.9 at 8.2 kHz bandwidth for spike recording, and a NEF of 3.2 at 140 Hz bandwidth for EEG recording. The amplifier has a measured midband gain of 39.6 dB, frequency response from 0.2 Hz to 8.2 kHz, and an input-referred noise of 1.94 muV rms while drawing 12.2 muA of current from a 3.3 V supply. The lower and higher cutoff frequencies of the bandpass filter are adjustable from 0.2 to 94 Hz and 140 Hz to 8.2 kHz, respectively. At 10-bit resolution, the ADC has an SNDR of 56 dB while consuming 76 muW power. Time-modulation feedback in the ADC offers programmable digital gain (1-4096) for auto-ranging, further improving the dynamic range and linearity of the ADC. Experimental recordings with the system show spike signals in rat somatosensory cortex as well as alpha EEG activity in a human subject.
Plant Genome Engineering with Sequence-Specific Nucleases (2013)

Recent advances in genome engineering provide newfound control over a plant's genetic material. It is now possible for most bench scientists to alter DNA in living plant cells in a variety of ways, including introducing specific nucleotide substitutions in a gene that change a protein's amino acid sequence, deleting genes or chromosomal segments, and inserting foreign DNA at precise genomic locations. Such targeted DNA sequence modifications are enabled by sequence-specific nucleases that create double-strand breaks in the genomic loci to be altered. The repair of the breaks, through either homologous recombination or nonhomologous end joining, can be controlled to achieve the desired sequence modification. Genome engineering promises to advance basic plant research by linking DNA sequences to biological function. Further, genome engineering will enable plants' biosynthetic capacity to be harnessed to produce the many agricultural products required by an expanding world population.
Antiangiogenic Agents Can Increase Lymphocyte Infiltration into Tumor and Enhance the Effectiveness of Adoptive Immunotherapy of Cancer (2010)

Adoptive cell transfer (ACT)-based immunotherapies can mediate objective cancer regression in animal models and in up to 70% of patients with metastatic melanoma; however, it remains unclear whether the tumor vasculature impedes the egress of tumor-specific T cells, thus hindering this immunotherapy. Disruption of the proangiogenic interaction of vascular endothelial growth factor (VEGF) with its receptor (VEGFR-2) has been reported to "normalize" tumor vasculature, enhancing the efficacy of chemotherapeutic agents by increasing their delivery to the tumor intersitium. We thus sought to determine whether disrupting VEGF/VEGFR-2 signaling could enhance the effectiveness of ACT in a murine cancer model. The administration of an antibody against mouse VEGF synergized with ACT to enhance inhibition of established, vascularized, B16 melanoma (P = 0.009) and improve survival (P = 0.003). Additive effects of an antibody against VEGFR-2 in conjunction with ACT were seen in this model (P = 0.013). Anti-VEGF, but not anti-VEGFR-2, antibody significantly increased infiltration of transferred cells into the tumor. Thus, normalization of tumor vasculature through disruption of the VEGF/VEGFR-2 axis can increase extravasation of adoptively transferred T cells into the tumor and improve ACT-based immunotherapy. These studies provide a rationale for the exploration of combining antiangiogenic agents with ACT for the treatment of patients with cancer.
Viral drug resistance (1990)

University of California, San Diego, and Veterans Administration Medical Center, San Diego, California, USA
A NewN-Spiro C2-Symmetric Chiral Quaternary Ammonium Bromide Consisting of 4,6-Disubstituted Biphenyl Subunit as an Efficient Chiral Phase-Transfer Catalyst (2003)

A new N-spiro chiral quaternary ammonium bromide has been designed and assembled from optically active 4,6-disubstitute­d biphenyl subunits. Its utility as an efficient chiral phase-transfer catalyst has been clearly demonstrated by application to the highly enantioselective alkylation of tert-butyl glycinate benzophenon­e Schiff base.
Cytokine cascade in dengue hemorrhagic fever: implications for pathogenesis (2000)

Dengue virus produces a mild acute febrile illness, dengue fever (DF) and a severe illness, dengue hemorrhagic fever (DHF). The characteristic feature of DHF is increased capillary permeability leading to extensive plasma leakage in serous cavities resulting in shock. The pathogenesis of DHF is not fully understood. This paper presents a cascade of cytokines, that in our view, may lead to DHF. The main feature is the early generation of a unique cytokine, human cytotoxic factor (hCF) that initiates a series of events leading to a shift from Th1-type response in mild illness to a Th2-type response resulting in severe DHF. The shift from Th1 to Th2 is regulated by the relative levels of interferon-gamma and interleukin (IL)-10 and between IL-12 and transforming growth factor-beta, which showed an inverse relationship in patients with DF.
Multi-Gb/s silicon bipolar clock recovery IC (1991)

A novel clock recovery IC for optical fiber communication systems with data rates up to several Gb/s is presented. It combines nonlinear signal preprocessing directly with a regenerative frequency divider scheme and an external filter in the divider loop. Hence, the center frequency of the filter and the working frequency of the amplifier are halved. The extracted clock frequency corresponds to half the bit rate, as required for many clocked circuit components within fiber optic lines. Two versions of the same IC design, scheduled for two bit rate ranges between 0.3-4 Gb/s, are realized with a conventional Si bipolar process. Clock recovery is demonstrated at 2.2 and 3.52 Gb/s, using both cavity and surface acoustic wave (SAW) filters.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Probabilistic Approach to Large-Scale Association Scans: A Semi-Bayesian Method to Detect Disease-Predisposing Alleles (2005)

Recent analytic and technological breakthroughs have set the stage for genome-wide linkage disequilibrium studies to map disease-susceptibility variants. This paper discusses a probabilistic methodology for making disease-mapping inferences in large-scale case-control genetic studies. The semi-Bayesian approach promoted compares the probability of the observed data under disease hypotheses to the probability of the data under a null hypothesis defined by data at all the markers interrogated in a large study. This method automatically adjusts for the effects of diffuse population stratification. It is claimed that this characterization of the evidence for or against disease models may facilitate more appropriate inductions for large-scale genetic studies. Results include (i) an analytic solution for the population stratification-adjusted Bayes' factor, (ii) the relationship between sample size and Bayes' factors, (iii) an extension to an approximate Bayes' factor calculated across closely-linked sites, and (iv) an extension across multiple studies. Although this paper deals exclusively with genetic studies, it is possible to generalize the approach to treat many different large-scale experiments including studies of gene expression and proteomics.
The VC Dimension and Pseudodimension of Two-Layer Neural Networks with Discrete Inputs (1996)

We give upper bounds on the Vapnik-Chervonenkis dimension and pseudodimension of two-layer neural networks that use the standard sigmoid function or radial basis function and have inputs from {−D, …,D} n . In Valiant's probably approximately correct (pac) learning framework for pattern classification, and in Haussler's generalization of this framework to nonlinear regression, the results imply that the number of training examples necessary for satisfactory learning performance grows no more rapidly than W log (WD), where W is the number of weights. The previous best bound for these networks was O(W 4 ).