gebhart/patrepeval huggingface dataset:
Carbohydrate Sequence of the Prostate Cancer-associated Antigen F77 Assigned by a Mucin O-Glycome Designer Array (2014)

Monoclonal antibody F77 was previously raised against human prostate cancer cells and has been shown to recognize a carbohydrate antigen, but the carbohydrate sequence of the antigen was elusive. Here, we make multifaceted approaches to characterize F77 antigen, including binding analyses with the glycolipid extract of the prostate cancer cell line PC3, microarrays with sequence-defined glycan probes, and designer arrays from the O-glycome of an antigen-positive mucin, in conjunction with mass spectrometry. Our results reveal F77 antigen to be expressed on blood group H on a 6-linked branch of a poly-N-acetyllactosamine backbone. We show that mAb F77 can also bind to blood group A and B analogs but with lower intensities. We propose that the close association of F77 antigen with prostate cancers is a consequence of increased blood group H expression together with up-regulated branching enzymes. This is in contrast to other epithelial cancers that have up-regulated branching enzymes but diminished expression of H antigen. With knowledge of the structure and prevalence of F77 antigen in prostate cancer, the way is open to explore rationally its application as a biomarker to detect F77-positive circulating prostate cancer-derived glycoproteins and tumor cells.
Mass Preserving Image Registration: Results of Evaluation of Methods for Pulmonary Image Registration 2010 Challenge (2010)

The paper presents results the mass preserving image registration method in the Evaluation of Methods for Pulmonary Image Registration 2010 (EMPIRE10) Challenge. The mass preserving image registration algorithm was applied to the 20 image pairs. Registration was evaluated using four different scores: lung boundary alignment, major fissure lignment, landmark alignment and transform singularity scores. The registration algorithm achieved an average landmark alignment score of 2.20 } 2.05 mm and the median of 1.29 mm. In 19 out of 20 image pairs, the method produced invertible deformations. Overall, the masspreserving image registration method was ranked 20th out of 34 participants <br/>
Thoracic empyema associated with recurrent colon cancer (2001)

Many types of infections associated with colorectal cancer have been reported. Here, we describe a rare case of thoracic empyema that was observed during immunotherapy for recurrent colon cancer. Culture of the pleural fluid yielded Streptococcus bovis, which is known to be associated with gastrointestinal lesions, especially colorectal malignancies. The possible correlation between these two clinical entities-empyema and colon cancer-is discussed.
IS-IS Flooding Speed advertisement (2020)

This document proposes a mechanism that can be used to increase the
speed at which link state information is flooded across a network when
multiple LSPDUs need to be flooded, such as in case of a node failure.
It also reduces the likelihood of overloading the downstream flooding
neighbors. This document defines a new TLV to be advertised in IS-IS
Hello messages. This TLV carries two parameters indicating the
performance capacity to receive LSPDUs: the minimum delay between two
consecutive LSPDUs and the number of LSPDUs which can the received
back to back.
Applying Different Artificial Intelligence Techniques in Dynamic Poisson’s Ratio Prediction Using Drilling Parameters (2021)

Abstract Rock geomechanical properties impact wellbore stability, drilling performance, estimation of in situ stresses, and design of hydraulic fracturing. One of these properties is Poisson’s ratio which is measured from lab testing or derived from well logs, the former is costly, time-consuming, and does not provide continuous information, and the latter may not be always available. An alternative prediction technique from drilling parameters in real time is proposed in this paper. The novel contribution of this approach is that the drilling data is always available and obtained from the first encounter with the well. These parameters are easily obtainable from drilling rig sensors such as rate of penetration (ROP), weight on bit (WOB), and torque. Three machine-learning methods were utilized: support vector machine (SVM), functional network (FN), and random forest (RF). Dataset (2905 data points) from one well were used to build the models, while a dataset from another well with 2912 data points was used to validate the constructed models. Both wells have diverse lithology consists of carbonate, shale, and sandstone. To ensure optimal accuracy, sensitivity and optimization tests on various parameters in each algorithm were performed. The three machine-learning tools provided good estimations; however, SVM and RF yielded close results, with correlation coefficients of 0.99 and the average absolute percentage error (AAPE) values were mostly less than 1%. While in FN the outcomes were less efficient with correlation coefficients of 0.92 and AAPE around 3.8%. Accordingly, the presented approach provides an effective tool for Poisson's ratio prediction on a real-time basis at no additional expense. In addition, the same approach could be used in other rock mechanical properties.
Investigations of Chain Shuttling Olefin Polymerization Using Deuterium Labeling (2008)

Chain shuttling among olefin polymerization catalysts with differing monomer responses has been developed for the preparation of block copolymers with enhanced performance. The chain shuttling agent (CSA) is usually a main group alkyl complex that is able to exchange polymeryl chains with the catalysts. We have performed a diverse yet complementary set of polymerization experiments using a hafnium pyridyl−amide catalyst (1) and Oct3Al as CSA. Ethylene/1-hexene copolymerization experiments using different amounts of CSA were quenched with D2O after varied reaction times. In ethylene homopolymerizations with fairly constant polymer yields, Mw/Mn is less than 2 and decreases monotonically with the addition of CSA, indicative of chain shuttling. However, less than half of the available Al sites are occupied by polymer chains. This indicates that chain shuttling (polymeryl−polymeryl exchange) is kinetically competitive with chain transfer (polymer−alkyl exchange) in this system. This approach also allows a more complete accounting of the fates of each polymeryl and alkyl chain by using multiple characterization techniques (GPC, GC, and 2H NMR). The mass balance agreement among these techniques is excellent, which validates our techniques and our basic understanding of chain shuttling processes. The results indicate that chain transfer to aluminum is the dominant termination mechanism under these conditions. Furthermore, 2H and 13C NMR experiments indicate that chain transfer from 1 to Oct3Al occurs significantly faster after an ethylene insertion than after a hexene insertion.
PROLONGED PANCREAS PRESERVATION USING A SIMPLIFIED UW SOLUTION CONTAINING POLYETHYLENE GLYCOL (1991)

The University of Wisconsin solution is considered the most effective universal flush and cold storage solution to date, and is now being widely applied clinically in organ transplantation. The results of this study show that Cardiosol, a modified cardioplegic solution containing 5% polyethylene glycol (PEG20M, MW 17,000 daltons), is significantly superior to UW (P less than 0.001) in the flush perfusion and hypothermic storage of pancreases for more than 36 hr prior to transplantation into streptozotocin-induced diabetic rats. When the pancreases were stored in Cardiosol, the 1-week survival rate was 7 of 10 (70%) after 24 hr of preservation; 7 of 12 (58%) after 36 hr; and 3 of 10 (30%) after 48 hr. In contrast, when the pancreases were stored in UW solution, the 1-week survival rate was 8 of 12 (67%) after 24 hr of preservation; after 36 hr, no animal survived (0 of 14). Intravenous glucose tolerance test K-values (decline in glucose concentration, percentage per minute) were normal in both groups receiving 24-hr-preserved pancreases, ranging from 2.60 to 4.16. Of interest, the peak insulin response 1 min following intravenous glucose was significantly higher (P less than 0.01) in the Cardiosol-preserved organs (303 +/- 29.8 microU/ml) (+/- SEM) than in the glands preserved in UW solution (112 +/- 47.9 microU/ml). We conclude that Cardiosol allows prolonged whole organ pancreas preservation in the rat transplant model.
Investigating the effects of Inonotus rickii extracts on the muscle contraction intensity (2021)

The aim of this study is to test the effect of aqueous, ethereal and alcoholic extracts of the fruit bodies of the wood-destroying fungus Inonotus rickii on locomotor activity resulting from contraction of both cross-striated and smooth muscles. The pharmacological activity of I. rickii raw materials was determined in vitro using the dose-response curve method (smooth muscles) and in experiments with oral intake of extracts (CNS-mediated effects on cross-lacing muscles). The aqueous extract of fungal material showed an increase in the motor activity of smooth muscles compared to standard caffeine, which indicates the ability of fungal extract to have a stimulating effect on the synapses. It was found that I. rickii extracts have an effect on smooth muscle contraction similar to the acetylcholine. It was shown that the greatest stimulating activity demonstrates an aqueous extract that may be a result of inhibitory effect of diethyl ether and ethanol on synapses. The described effects put on the agenda both the fractionation of active extracts and further experiments on the therapeutic applications of their described properties. As a field of possible application of this kind of substances can be considered the cardiovascular remodeling, the maintenance of smooth muscle tone during a number of surgical interventions, and the palliative cure of disseminated cancers.
Receiver driven layered multicast with layer-aware forward error correction (2008)

A wide range of different capabilities and connection qualities typically characterizes receivers of mobile television services. Receiver driven layered multicast (RDLM) offers an efficient way for providing different capabilities over such a broadcast channel. Scalable video coding (SVC) allows for the transmission of multiple video qualities within one media stream. Using SVC generates a video bit stream with various inter layer dependencies due to references between the layers. This work proposes a layer-aware forward error correction (L-FEC) approach in combination with SVC. L-FEC increases robustness of the more important layers by generating protection across layers following existing dependencies of the media stream. The L-FEC is integrated as an extension of a Raptor FEC implementation in a DVB-H broadcast system. It is shown by experimental results that L-FEC outperforms traditional UEP protection schemes.
A Defined N-Heterocyclic Carbene Complex for the Palladium-Catalyzed Suzuki Cross-Coupling of Aryl Chlorides at Ambient Temperatures (2002)

Highly active but sterically demanding: Ambient-temperature Suzuki cross-coupling of aryl chlorides is possible with a palladium(0) complex bearing two bulky, N-heterocyclic carbene ligands (see structure). Nearly quantitative yields are obtained within two hours with some reagents, which makes this compound the most active catalyst known to date under these conditions.
Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens’ theorem (2012)

Metagenomic project design has relied variously upon speculation, semi-empirical and ad hoc heuristic models, and elementary extensions of single-sample Lander-Waterman expectation theory, all of which are demonstrably inadequate. Here, we propose an approach based upon a generalization of Stevens' Theorem for randomly covering a domain. We extend this result to account for the presence of multiple species, from which are derived useful probabilities for fully recovering a particular target microbe of interest and for average contig length. These show improved specificities compared to older measures and recommend deeper data generation than the levels chosen by some early studies, supporting the view that poor assemblies were due at least somewhat to insufficient data. We assess predictions empirically by generating roughly 4.5 Gb of sequence from a twelve member bacterial community, comparing coverage for two particular members, Selenomonas artemidis and Enterococcus faecium, which are the least ([Formula: see text]3 %) and most ([Formula: see text]12 %) abundant species, respectively. Agreement is reasonable, with differences likely attributable to coverage biases. We show that, in some cases, bias is simple in the sense that a small reduction in read length to simulate less efficient covering brings data and theory into essentially complete accord. Finally, we describe two applications of the theory. One plots coverage probability over the relevant parameter space, constructing essentially a "metagenomic design map" to enable straightforward analysis and design of future projects. The other gives an overview of the data requirements for various types of sequencing milestones, including a desired number of contact reads and contig length, for detection of a rare viral species.
Impact of non-ideal pulse carving induced phase distortions on QPSK based modulation format (2009)

We investigate impact of non-ideal pulse carver induced phase distortions on QPSK format. The results show that only 0.5 dB amplitude imbalance of sinusoidal wave applied into carver produces 2 dB ONSR penalty in case of 67 % pulse carving.
Pharmacokinetic interactions between ritonavir and quinine in healthy volunteers following concurrent administration (2009)

Downward dosage adjustment of quinine appears necessary when concurrently administered with ritonavir.
FPGA implementation of multiplierless M-QAM modulator (2002)

Adaptive multilevel QAM (M-QAM) modulation can increase throughput in a wireless packet data network. A technique is discussed for efficiently realising M-QAM modulators on field programmable gate arrays (FPGAs) using ‘multiplierless’ finite impulse response (FIR) filters with carry-save addition and canonic signed-digit coefficients. An adaptive M-QAM modulator supporting 4, 16, 64 and 256-QAM is presented.
Gonadotropin-Releasing Hormone (GnRH) Antagonists Promote Proapoptotic Signaling in Peripheral Reproductive Tumor Cells by Activating a Gαi-Coupling State of the Type I GnRH Receptor (2004)

Gonadotropin-releasing hormone (GnRH) receptor agonists are extensively used in the treatment of sex hormone-dependent cancers via the desensitization of pituitary gonadotropes and consequent decrease in steroid sex hormone secretion. However, evidence now points to a direct inhibitory effect of GnRH analogs on cancer cells. These effects appear to be mediated via the Galpha(i)-type G protein, in contrast to the predominant Galpha(q) coupling in gonadotropes. Unlike Galpha(q) coupling, Galpha(i) coupling of the GnRH receptor can be activated by both agonists and antagonists. This unusual pharmacology suggested that the receptor involved in the cancer cells may not be the classical gonadotrope type I GnRH receptor. However, we have previously shown that a functional type II GnRH receptor is not present in man. In the present study, we show that GnRH agonists and selective GnRH antagonists exert potent antiproliferative effects on JEG-3 choriocarcinoma, benign prostate hyperplasia (BPH-1), and HEK293 cells stably expressing the type I GnRH receptor. This antiproliferative action occurs through a Galpha(i)-mediated activation of stress-activated protein kinase pathways, resulting in caspase activation and transmembrane transfer of phosphatidlyserine to the outer membrane envelope. Structurally related antagonistic GnRH analogs displayed divergent antiproliferative efficacies but demonstrated equal efficacies in inhibiting GnRH-induced Galpha(q)-based signaling. Therefore the ability of GnRH receptor antagonists to exert an antiproliferative effect on reproductive tumors may be dependent on ligand-selective activation of the Galpha(i)-coupled form of the type I GnRH receptor.
Photoluminescent ZrO2:Eu3+ Nanofibers Prepared via Electrospinning (2010)

Europium-doped zirconium oxide (ZrO 2 :Eu 3+ ) nanofibers were prepared via electrospinning, in which a mixture of zirconium chloride oxide octahydrate, europium nitrate hexahydrate, poly(vinyl pyrrolidone), dimethylformamide, and ethanol were electrospun at atmospheric conditions. Subsequent calcination to produce ZrO 2 :Eu 3+ nanofibers with diameters around 300 nm. The crystal structure and photoluminescence of the ZrO 2 :Eu 3+ nanofibers were studied as a function of dopant concentration and heating temperature. At a dopant concentration of 5 mol %, tetragonal phase crystals were observed. Photoluminescence spectra revealed several emission bands in the red region corresponding to the transition of 5 D 0 → 7 F J ( J =1,2,3,4). Two most intense emission bands were observed at wavelengths of 606 and 591 nm due to the forced electric dipole ( 5 D 0 → 7 F 2 ) and magnetic dipole ( 5 D 0 → 7 F 1 ) transitions, respectively. This work demonstrates that one-dimensional photoluminescent materials can be generated by a two step electrospinning and calcination process.
Targeted protein S-nitrosylation of ACE2 as potential treatment to prevent spread of SARS-CoV-2 infection (2022)

Prevention of infection and propagation of SARS-CoV-2 is of high priority in the COVID-19 pandemic. Here, we describe S-nitrosylation of multiple proteins involved in SARS-CoV-2 infection, including angiotensin converting enzyme 2 (ACE2), the receptor for viral entry. This reaction prevents binding of ACE2 to the SARS-CoV-2 Spike protein, thereby inhibiting viral entry, infectivity, and cytotoxicity. Aminoadamantane compounds also inhibit coronavirus ion channels formed by envelope (E) protein. Accordingly, we developed dual-mechanism aminoadamantane nitrate compounds that inhibit viral entry and thus spread of infection by S-nitrosylating ACE2 via targeted delivery of the drug after E-protein channel blockade. These non-toxic compounds are active <i>in vitro</i> and <i>in vivo</i> in the Syrian hamster COVID-19 model, and thus provide a novel avenue for therapy.
Text-to-Speech (TTS) Synthesis (2018)

The goal of text-to-speech (TTS) synthesis is to convert arbitrary input text to intelligible and natural sounding speech so as to transmit information from a machine to a person. The methodology used in TTS is to exploit acoustic representations of speech for synthesis, together with linguistic analyses of text to extract correct pronunciations and prosody in context. The text analysis and normalization module in the front-end determines to a large extend the “what” and “how” of the resulting synthetic speech. Linguistic analysis in the front-end encompasses the determination of parts-of-speech, word sense, emphasis, appropriate speaking style, and speech acts. With the availability of good automatic speech labeling tools, concatenative speech synthesis has embraced the use of multi-hour voice databases. Eliciting the desired voice characteristics from a voice talent that is being recorded for a unit-selection synthesis voice database could be essential for customers accepting an automated dialog system that speaks with a TTS voice.
Wear Rate to Stainless Steel Pipe From Liquid-Solid Slurry (2016)

The United States Department of Energy is building a Waste Treatment Plant (WTP) at the DOE Hanford Site in the state of Washington to process stored radioactive wastes for long-term storage and disposal. The Savannah River National Laboratory (SRNL) is helping resolve technical concerns with the WTP, which are related to piping erosion/corrosion (wear). SRNL is assisting in the design of a flow loop to obtain long term wear that will use prototypic simulant chemistry, operating conditions, and materials for total wear rate. The challenge is to accurately measure slurry wear to a pipe wall thickness tolerance of ∼47 microns/year anywhere in the test flow loop in a timely manner. To help in the design of the flow loop a test was performed with a smaller loop, which contained many of the pipe fittings expected in WTP to determine where high wear locations exist. One aspect of this test was to understand the rate of wear to straight pipe and to protrusions from the surface of the pipe. Initially, wear to straight pipe was studied because wear in other flow loop situations, e.g., around bends, through tees, etc. will be higher. To measure such low wear rates requires sensitive measurement techniques. To that end, twelve wear coupons were placed in one section of the pipe system and at different protrusion heights into the flow stream. They were made of 316L stainless steel, which is the expected material of pipe to be utilized. From the wear coupons, an estimate of wear rate was obtained, as well as illustrating when a protrusion above a pipe surface no longer disturbs the flow streams with respect to slurry wear. It appears when a surface is just above the laminar sublayer it produces a wear rate equivalent to a surface with no protrusions. The slurry was a mixture of water and 30 wt% of sand, d50 ∼ 200 microns. The test flow conditions were a velocity of 4 m/s in a 0.07793-m inside diameter (3-inch, Schedule 40) pipe system, resulting in Reynolds number just above 3 × 105, i.e., turbulent flow at a temperature of 25°C. The wear was to a vertically oriented straight section of pipe that was 1.86 meter long. The twelve wear coupons were located on the inside surface starting from 10 diameters from the pipe entrance to 21 diameters, with a separation of 1-pipe diameter between each successive coupon. Furthermore, each set of two adjacent coupons were rotated 180 degrees apart which were then rotated 30 degrees from the next set to minimize disturbance to the flow for the downstream coupon. This paper describes the wear rates obtained, the effect of increasing a wear coupon’s protrusion into the flow stream, and the overall operation of the test apparatus.
Selective and Practical Graphene-Based Arsenite Sensor at 10 ppb (2022)

Arsenic detection in field water samples at concentrations of relevance with affordable and simple equipment is of global interest. We report a biomimetic electrode using electrochemically reduced graphene oxide (ERGO) for highly selective and sensitive reagent-free arsenite (As3+) detection in field water samples, down to the ten parts per billion level, enabling measurement of drinking water quality affordably for millions of arsenic-affected people. This electronically and structurally optimized ERGO electrode shows selective detection of As3+ in both phosphate buffered saline (PBS, pH ∼7) and field water samples, even though more than 100 times larger conductivity and total dissolved solids (TDS), respectively, are present in them. Raman and FTIR spectroscopies were used to understand the mechanism of selectivity and sensitivity. The sensing mechanism involved two processes, namely, selective binding of As3+ with the −COOH groups of ERGO followed by its electro-oxidation by an applied potential. Density functional theory (DFT) and force-field calculations were used to obtain crucial insights into the site selectivity and mechanism of oxidation of As3+. A two-electron transfer process from As3+ to ERGO followed by associative O ligand addition to As3+ by a ketone oxygen atom, and concomitant regeneration of −COOH group is presented. The ion selectivity depends both on structural and electronic factors. First, the compact pyramidal-shaped As3+ species may closely approach the edge −COOH functional group to a greater extent than the other ions enabling covalent binding of the As center with the ketone O atom. Furthermore, closer proximity of the lowest unoccupied molecular orbital (LUMO) acceptor level of the positively charged ERGO and the highest occupied molecular orbital (HOMO) donor level of the As3+ species suggests that a uniquely selective resonant charge-transfer effect occurs between the As3+ species and ERGO.