gebhart/patrepeval huggingface dataset:
Controlled Ovarian Hyperstimulation for In Vitro Fertilization Alters Endometrial Receptivity in Humans: Protocol Effects1 (2009)

The impact of gonadotropin-releasing hormone (GnRH) agonist long compared with GnRH antagonist protocols, under in vitro fertilization conditions on endometrial receptivity, is still debated. Therefore, we compared the effect of both GnRH antagonist and agonist long protocols on the endometrial receptivity by analyzing, to our knowledge for the first time, the global gene expression profile shift during the prereceptive and receptive stages of stimulated cycles under the two GnRH analogue protocols compared with natural cycles in the same patients. For the same normal-responder patients, endometrial biopsies were collected on the day of oocyte retrieval and on the day of embryo transfer after human chorionic gonadotropin administration of a stimulated cycle with either GnRH agonist long or GnRH antagonist protocols and compared with the prereceptive and receptive stages of a natural cycle. Samples were analyzed using DNA microarrays. Gene expression profiles and biological pathways involved during the prereceptive stage to the receptive endometrial transition of stimulated and natural cycles were analyzed and compared for each patient. Both protocols affect endometrial receptivity in comparison with their natural cycle in the same patients. Major differences in endometrial chemokines and growth factors under stimulated cycles in comparison with natural cycles were observed. Such an effect has been associated with gene expression alterations of endometrial receptivity. However, the endometrial receptivity under the GnRH antagonist protocol was more similar to the natural cycle receptivity than that under the GnRH agonist protocol.
Content-based filtering for efficient online materialized view maintenance (2008)

Real-time materialized view maintenance has become increasingly popular, especially in real-time data warehousing and data streaming environments. Upon updates to base relations, maintaining the corresponding materialized views can bring a heavy burden to the RDBMS. A traditional method to mitigate this problem is to use the where clause condition in the materialized view definition to detect whether an update to a base relation is relevant and can affect the materialized view. However, this detection method does not consider the content in the base relations and hence misses a large number of filtering opportunities. In this paper, we propose a content-based method for detecting irrelevant updates to base relations of a materialized view. At the cost of using more space, this method increases the probability of catching irrelevant updates by judiciously designing filtering relations to capture the content in the base relations. Based on the content-based method, a prototype real-time data warehouse has been implemented on top of IBM's System S using IBM DB2. Using an analytical model and our prototype, we show that the content-based method can catch most (or all) irrelevant updates to base relations that are missed by the traditional method. Thus, when the fraction of irrelevant updates is non-negligible, the load on the RDBMS due to materialized view maintenance can be significantly reduced.
Prostate cancer prognosis via integrative and co-localized glandular morphometry and immunofluorescent protein biomarker expression. (2015)

262 Background: Quantitative image analysis of both the prostate needle biopsy (PNB) and the radical prostatectomy sample (RPS) have proven to be robust and predictive for prostate cancer (PCa) prognosis. While metrics assessing morphology and protein biomarker expression separately have been published in prognostic risk prediction models, we sought to determine the performance of novel approaches which combine protein biomarker expression with the morphometry of the gland wherein they express. In order to assess robustness, we evaluated these metrics in both PNB and RPS cohorts. Methods: Novel quantitative biometric features were derived from computerized analysis of morphology and immunofluorescent (IF) biomarker expression in PCa images. A Bayesian probabilistic approach to co-locate and quantify IF biomarker expression within various glandular sub-types was developed. This permitted differentiable analysis of PCa biomarkers such as androgen receptor (AR) in high and low Gleason grade glands of the same patient. Performance in predicting significant clinical disease progression (including metastasis and death-of-disease) was assessed via the concordance index (CI). Performance was evaluated independently in a cohort of 326 PNB samples (median 8-year follow up) and a cohort of 373 RPS (median 5-year follow up). Results: In a univariate analysis, previously published glandular morphology features had a CI of 0.68 (PNB) and 0.76 (RPS). Quantitative AR had a CI of 0.67 (PB) and 0.72 (RPS). Novel metrics of integrative co-localization resulted in a significant increase in prognostic accuracy; CIs of 0.72 (PNB) and 0.83 (RPS). These features separately assessed AR expression depending on the multiple glandular sub-types within the tumor sample. Conclusions: Integrating quantitative image analysis of morphology and IF biomarker expression in the PNB and RPS outperformed previous quantitative metrics. Such robust and reproducible metrics may prove beneficial in improving risk stratification models for future treatment decision making.
The Proliferative Effect of “Anti-Androgens” on the Androgen-Sensitive Human Prostate Tumor Cell Line LNCaP (1990)

The effect of steroidal and nonsteroidal "anti-androgens" on the proliferative capacity of androgen-sensitive LNCaP-FGC human prostate tumor cells in culture was studied using charcoal-dextran stripped human serum-supplemented media. Cyproterone and medroxyprogesterone acetates, flutamide, hydroxyflutamide, and anandron (R23908) were administered alone at concentrations between 3 X 10(-12) and 3 X 10(-6) M. Results indicated that although medroxyprogesterone induced maximal proliferation at 3 X 10(-9) M, the other "anti-androgens" (with the exception of flutamide that was ineffective) were effective at 3 X 10(-8) M and higher concentrations; the amplitude of the proliferative response by these compounds was comparable to that elicited by estradiol-17 beta (3 to 5-fold over control). None of the anti-androgens tested triggered the shutoff effect characteristic of androgen action. When 3 X 10(-10) M DHT and the above mentioned anti-androgens were administered simultaneously, a synergistic pattern was seen; on the contrary, 3 X 10(-8) M DHT cancelled the proliferative effect of each of the anti-androgens when administered simultaneously. The relative binding affinity of these anti-androgens to androgen receptors present in LNCaP-FGC cells did not correlate well with their proliferative efficiency. The data collected were interpreted within the premises of the negative control hypotheses for the regulation of cell proliferation in metazoans. Within those premises, results became compatible with the notion that first, "anti-androgens" elicited the proliferation of androgen-sensitive cells by neutralizing the effect of a serum-borne inhibitor (androcolyone-I); this event seems not to be mediated by androgens receptors. Second, anti-androgens did not trigger a proliferative shutoff response like androgens do, i.e. the proliferative pattern induced by anti-androgens was comparable to that elicited by estrogens and progestins. Third, when administered simultaneously with 3 X 10(-10) M DHT, anti-androgens behaved synergistically. Fourth, the DHT-induced shutoff effect consistently overrode the proliferative effect generated by anti-androgens and estrogens when added alone. Finally, taken together these results raise important questions regarding the therapeutic role of anti-androgens in prostate cancer.
Low-complexity Bayer-pattern video compression using distributed video coding (2008)

Most consumer digital color cameras capture video using a single chip. Single chip cameras do not capture RGB triples for every pixel, but a subsampled version with only one color component per pixel (e.g. Bayer pattern). Conventionally, a full resolution video is constructed from the Bayer pattern by demosaicing before being converted to YUV domain for compression. In order to lower the encoding complexity, we propose in this work a novel color space conversion in the pre-processing step. Compared to the conventional method, the proposed scheme reduces the encoding complexity almost by half. Moreover, it improves the reconstructed video quality by up to 1.5 dB in CPSNR, when H.264/AVC is used for compression. To further lower the encoding complexity, we additionally use our Wyner-Ziv video coder for compression. Again, we observe in our experiments a similar gain of the proposed scheme over the conventional one.
High thermoelectric figure of merit and improved mechanical properties in melt quenched PbTe–Ge and PbTe–Ge1−xSix eutectic and hypereutectic composites (2009)

We report the synthesis, microstructure, and transport properties of composite thermoelectric materials based on the eutectic phase relationship between PbTe and Ge. When quenched, these eutectic mixtures exhibit considerably stronger mechanical strength and reduced brittleness compared to PbTe itself, while at the same time they possess lower lattice thermal conductivity. Thermal conductivity measurements show values lower than expected based on the law of mixtures and multiphase composites. We find that the thermoelectric performance in these composites can be tuned through the use of hypereutectic compositions and alloying of Ge with Si. PbI2 was used as an n-type dopant, and precise control of the carrier concentration was achieved to optimize the electrical transport and thermoelectric properties. ZT values approaching 1.3 at 778 K have been obtained in samples of PbTe–Ge0.8Si0.2(5%), which represent an ∼62% improvement over that of PbTe.
Ovarian stimulation with HMG: results of a prospective randomized phase III European study comparing the luteinizing hormone-releasing hormone (LHRH)-antagonist cetrorelix and the LHRH-agonist buserelin (2000)

In this prospective and randomized study, 188 patients received the luteinizing hormone-releasing hormone (LHRH) antagonist cetrorelix, and 85 patients the LHRH agonist buserelin to prevent endogenous luteinizing hormone (LH) surges during ovarian stimulation in in-vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) cycles. Ultimately, 181 patients (96.3%) in the cetrorelix group, and 77 (90.6%) in the buserelin group, reached the day of the human chorionic gonadotrophin (HCG) injection. The mean number of human menopausal gonadotrophin (HMG) ampoules administered and the mean number of stimulation days with HMG were significantly less in the cetrorelix group than in the buserelin group (P < 0.01). A rise in LH and progesterone concentrations was observed in three of the 188 patients (1.6%) who received cetrorelix. On the day of the HCG administration, more follicles of a small diameter (11-14 mm) were observed in the buserelin group than in the cetrorelix group (P = 0. 02) and the mean serum oestradiol concentration was significantly higher in patients who received buserelin than in those who received cetrorelix (P < 0.01). Similar results were observed in fertilization, cleavage and pregnancy rates in the two groups. In conclusion, the use of the LHRH antagonists might be considered more advantageous because of the short-term application needed to inhibit gonadotrophin secretion, so allowing a reduction in the treatment time in a clinically significant manner.
Proteinaceous inhibitors of phospholipase A2 purified from inflammatory sites in rats. (1990)

We have purified two phospholipase A2 inhibitory proteins (37 and 33 kDa) from peritoneal fluid of dexamethasone-treated rats. The extracellular phospholipase A2 found in inflammatory sites differed from the exocrine phospholipase A2 in susceptibility to these endogenous inhibitors; both proteins inhibited the activity of the extracellular phospholipase A2 purified from sites of inflammation but did not affect appreciably the activity of either porcine pancreatic or Naja naja venom phospholipase A2. The amino acid sequence of the NH2-terminal portion of the purified proteins did not resemble that of lipocortins so far reported, but it was almost identical to that of parts of human or mouse complement component C3. These findings may indicate that degraded products of C3 are involved in the regulation of activity of a class of mammalian phospholipase A2.
Continuously-tunable microwave photonic true-time-delay based on a fiber-coupled beam deflector and diffraction grating (2011)

This paper reports the demonstration of a continuously-tunable true-time delay line for microwave photonics and optical communications capable of high-resolution phase control throughout the 1-100 GHz modulation range. A fiber-coupled device is demonstrated with 75 ps of continuous delay tuning range, 3 dB optical insertion loss, and minimal RF amplitude and phase variation over the 4-18 GHz band. Measured delay ripple was less than 0.2 ps. Theoretical analysis is also presented which indicates scalability to delay tuning ranges over 1000 ps and modulation bandwidths over 10 THz.
Scattering parameter model of low level electrical contacts in electro-mechanical microwave switches-a switch manufacturer approach (2003)

A model that predicts the variation of the scattering parameters with contact resistance for RF microwave switches is presented. The studies encompass analyses and measurements of electro-mechanical coaxial microwave switches as well as RF MEMS switches. The model accounts for the effects of the contact geometry, contact force and surface texture on the discontinuity in the transmission line generated by the contacts of microwave switches. The model demonstrates the influence of high frequency signals on constriction resistance and insulation resistance of the contacts. An experimental setup is presented for the validation of the model. The experimental data correlates very closely with the performance predicted by analyses for all three studied frequencies covering L-band through C-band to Ku-band. The same model is relevant for standard electro-mechanical switches as well as for RF MEMS switches. The usefulness of the model is evident in the manufacturing environment for electro-mechanical RF switches. The model establishes a method for monitoring RF characteristics by performing a DC contact resistance test that is easier to implement especially over temperature extremes and over a large number of switching operations.
Predicate Derivation and Monotonicity Detection in DB2 UDB (2005)

DB2 universal database allows database schema designers to specify generated columns. These generated columns are useful for maintaining rollup hierarchy variables in warehouses (e.g., date, month, quarter). In order for the generated columns to be useful for query processing, queries must automatically make use of such columns when applicable. In particular, query predicates on the original columns should be rewritten to make use of the generated columns. In this paper, we describe two main aspects of this predicate rewriting technique that allows usage of the generated columns for a variety of query predicate types. The first aspect, monotonicity detection, allows for rewrites in the case of range predicates. The second aspect, predicate derivation, is the technique for using generating expressions for query processing. We show the value of this technique for providing significant performance improvement when combined with indexing or multidimensional clustering in DB2.
Internal Language Model Training for Domain-Adaptive End-To-End Speech Recognition (2021)

The efficacy of external language model (LM) integration with existing end-to-end (E2E) automatic speech recognition (ASR) systems can be improved significantly using the internal language model estimation (ILME) method [1]. In this method, the internal LM score is subtracted from the score obtained by interpolating the E2E score with the external LM score, during inference. To improve the ILME-based inference, we propose an internal LM training (ILMT) method to minimize an additional internal LM loss by updating only the E2E model components that affect the internal LM estimation. ILMT encourages the E2E model to form a standalone LM inside its existing components, without sacrificing ASR accuracy. After ILMT, the more modular E2E model with matched training and inference criteria enables a more thorough elimination of the source-domain internal LM, and therefore leads to a more effective integration of the target-domain external LM. Experimented with 30K-hour trained recurrent neural network transducer and attention-based encoder- decoder models, ILMT with ILME-based inference achieves up to 31.5% and 11.4% relative word error rate reductions from standard E2E training with Shallow Fusion on out-of-domain LibriSpeech and in-domain Microsoft production test sets, respectively.
The cytoplasmic 'linker region' in Toll-like receptor 3 controls receptor localization and signaling (2004)

Toll-like receptor 3 (TLR3) recognizes double-stranded RNA and transmits signals to activate NF-kappaB and the interferon (IFN)-beta promoter via the newly identified adaptor, TICAM-1. The extracellular LRR domain of TLR3 is engaged in the ligand recognition, while the intracellular TIR domain is crucial for the adaptor binding and signal transduction upon ligand stimulation. Here, we analyzed TLR3 localization in human monocyte-derived immature dendritic cells (iDCs) and stable transfectants expressing human TLR3 by immunofluorescence staining and confocal microscopy. TLR3 was predominantly localized in specific but as yet unidentified intracellular vesicles where TLR3 signaling was initiated. Expression analysis of TLR3-tail-truncated mutants revealed that the cytoplasmic 'linker' region (residues 730-755) determines the intracellular localization of TLR3. Site-directed mutagenesis of the linker region allowed us to identify the relevant determinants as Arg(740) and Val(741) residues for intracellular expression of TLR3. Furthermore, alanine scanning of the linker region demonstrated that the Phe(732), Leu(742) and Gly(743) in the TLR3 cytoplasmic linker region are essential for ligand-induced NF-kappaB and IFN-beta promoter activation. Thus, the cytoplasmic linker region of TLR3 regulates receptor retention inside the organelle and signaling, which may be closely linked to TLR3 function in DCs.
A novel multi-resolution based PSD estimation method based on expectation maximization algorithm (2014)

Power spectral density (PSD) estimation is used in many applications such as spectrum sensing for cognitive radio (CR). For a fixed number of samples, one must trade-off estimation accuracy against frequency resolution. We propose a multi-resolution method based on the expectation-maximization (EM) algorithm that provides both high frequency resolution and low estimation error variance. First a high resolution PSD estimate with high estimation error variance is produced. Then, from the same set of samples, we produce a low frequency resolution PSD estimate with low estimation error variance. Using information from the first PSD estimate, the EM algorithm is used to estimate the missing frequency bins of the PSD with low frequency resolution. It is shown by analysis and simulation that the proposed method improves both the resolution and estimation error variance compared to conventional PSD estimation.
Use of monoclonal antibodies as sensitive and specific probes for biologically active human gamma-interferon. (1984)

Mouse monoclonal antibodies B1 and B3 are specific for natural and Escherichia coli-derived recombinant human gamma-interferon (IFN-gamma). The two antibodies recognize different epitopes of the IFN-gamma molecule and do not compete with each other's binding. We have used these two antibodies to construct a solid-phase, sandwich immunoradiometric assay for human IFN-gamma. Purified antibody B1 was coated on polystyrene beads (0.64 cm in diameter) and used as the solid-phase immunoadsorbent and antibody B3 was labeled with 125I and used as tracer. This assay can be completed in about 4 hr and is capable of detecting IFN-gamma levels in human serum or tissue culture fluids as low as 0.1 NIH reference unit/ml. Recombinant human IFN-gamma derived from E. coli was detectable at a concentration of 0.02 ng/ml. The assay appears to be specific for the biologically active forms of IFN-gamma, since after exposure to pH 2, 37 degrees C, or 56 degrees C, biological activity and reactivity in the immunoradiometric assay decreased in parallel. The immunoradiometric assay can be employed for the analysis of the structural characteristics of the human IFN-gamma molecule.
The Multiple Multicomponent Approach to Natural Product Mimics: Tubugis, N-Substituted Anticancer Peptides with Picomolar Activity (2011)

The synthesis of a new generation of highly cytotoxic tubulysin analogues (i.e., tubugis) is described. In the key step, the rare, unstable, and synthetically difficult to introduce tertiary amide-N,O-acetal moiety required for high potency in natural tubulysins is replaced by a dipeptoid element formed in an Ugi four-component reaction. Two of the four components required are themselves produced by other multicomponent reactions (MCRs). Thus, the tubugis represent the first examples of the synthesis of natural-product-inspired compounds using three intertwined isonitrile MCRs.
Assessment of a Modified Acoustic Lens for Electromagnetic Shock Wave Lithotripters in a Swine Model (2013)

With lens modification the Modularis lithotripter demonstrates significantly improved stone fragmentation with minimal tissue injury at a clinically relevant acoustic pulse energy. This new lens design could potentially be retrofitted to existing lithotripters, improving the effectiveness of electromagnetic lithotripters.
Dual-Phase Virtual Metrology Scheme (2007)

This paper proposes a dual-phase virtual metrology scheme. To consider both promptness and accuracy, this scheme generates dual-phase virtual metrology (VM) values. Phase I emphasizes promptness, that is to immediately calculate and output the Phase-I VM value (denoted ) of a workpiece (wafer or glass) once the entire process data of the workpiece are completely collected. Phase II improves accuracy, that is not to recalculate and output the Phase-II VM values (denoted ) of all the workpieces in the cassette (also called FOUP in the semiconductor industry) until an actual metrology value (required for tuning or retraining purposes) of a workpiece in the same cassette is collected. Also, in this scheme, the accompanying reliance index (RI) and global similarity index (GSI) of each and are also generated. The RI and GSI are applied to gauge the degree of reliance. If the reliance level of a VM value is lower than the threshold, this VM value may not be adopted. An illustrative example involving fifth-generation thin-film transistor liquid crystal display (TFT-LCD) chemical-vapor deposition equipment is presented. Experimental results demonstrate that the proposed scheme is applicable to the wafer-to-wafer or glass-to-glass advanced process control for semiconductor or TFT-LCD factories.