gebhart/patrepeval huggingface dataset:
Removing undersampling artifacts in DCE‐MRI studies using independent components analysis (2008)

In breast MRI mammography both high temporal resolution and high spatial resolution have been shown to be important in improving specificity. Adaptive methods such as projection reconstruction time-resolved imaging of contrast kinetics (PR-TRICKS) allow images to be reconstructed at various temporal and spatial resolutions from the same data set. The main disadvantage is that the undersampling, which is necessary to produce high temporal resolution images, leads to the presence of streak artifacts in the images. We present a novel method of removing these artifacts using independent components analysis (ICA) and demonstrate that this results in a significant improvement in image quality for both simulation studies and for patient dynamic contrast-enhanced (DCE)-MRI images. We also investigate the effect of artifacts on two quantitative measures of contrast enhancement. Using simulation studies we demonstrate that streak artifacts lead to pronounced periodic oscillations in pixel concentration curves which, in turn, lead to increased errors and introduce bias into heuristic measurements. ICA filtering significantly reduces this bias and improves accuracy. Pharmacokinetic modeling was more robust and there was no evidence of bias due to the presence of streak artifacts. ICA filtering did not significantly reduce the errors in the estimated pharmacokinetic parameters; however, the chi-squared error was greatly reduced after ICA filtering.
Growth phase and low pH affect the thermal regulation of the <i>Yersinia enterocolitica inv</i> gene (1994)

The inv gene encodes the protein invasin, which is the primary invasion factor for Yersinia enterocolitica in vitro and in vivo. Previous studies of Yersinia species have shown that inv expression and entry into mammalian cells are temperature regulated. Invasin production is reduced at the host temperature of 37 degrees C as compared to production at ambient temperature; consequently, this study was initiated to determine whether other host environmental signals might induce inv expression at 37 degrees C. An inv::phoA translational fusion was recombined on to the Y. enterocolitica chromosome by allelic exchange to monitor inv expression. Molecular characterization of expression of the wild-type inv gene and the inv::phoA fusion showed that invasin is not produced until early stationary phase in bacteria grown at 23 degrees C. Y. enterocolitica grown at 37 degrees C and pH 5.5 showed levels of inv expression comparable to those observed in bacteria grown at 23 degrees C. An increase in Na+ ions caused a slight increase in expression at 37 degrees C. However, expression at 37 degrees C was unaffected by anaerobiosis, growth medium, calcium levels, or iron levels. Additionally, Y. enterocolitica expressed invasin in Peyer's patches two days after being introduced intragastrically into BALB/c mice. These results suggest that invasin expression in Y. enterocolitica may remain elevated early during interaction with the intestinal epithelium, a site at which invasin was shown to be necessary.
Repression of IS200 transposase synthesis by RNA secondary structures (1999)

The IS 200 transposase, a 16 kDa polypeptide encoded by the single open reading frame (ORF) of the insertion element, has been identified using an expression system based on T7 RNA polymerase. In wild-type IS 200, two sets of internal inverted repeats that generate RNA secondary structures provide two independent mechanisms for repression of transposase synthesis. The inverted repeat located near the left end of IS 200 is a transcriptional terminator that terminates read-through transcripts before they reach the IS 200 ORF. The terminator is functional in both directions and may terminate >80% of transcripts. Another control operates at the translational level: transposase synthesis is inhibited by occlusion of the ribosome-binding site (RBS) of the IS 200 ORF. The RBS (5'-AGGGG-3') is occluded by formation of a mRNA stem-loop structure whose 3' end is located only 3 nt upstream of the start codon. This mechanism reduces transposase synthesis approximately 10-fold. Primer extension experiments with AMV reverse transcriptase have provided evidence that this stem-loop RNA structure is actually formed. Tight repression of transposase synthesis, achieved through synergistic mechanisms of negative control, may explain the unusually low transposition frequency of IS 200.
Helicobacter pylori infection density and gastric inflammation in duodenal ulcer and non-ulcer subjects. (1995)

The factors that determine which Helicobacter pylori infected subjects develop duodenal ulcer (DU) are unclear. This study tested the hypothesis that infection density and urease activity are higher in DU than non-DU subjects. Fifty five DU and 55 age and sex matched non-DU subjects were studied. Quantitative methods were used for measuring infection density (viable organism count) and urease activity (Berthelot reaction). DU subjects had a greater antral infection density (geometric mean of colony forming units/mg biopsy protein; 10.5 x 10(5) v 1.3 x 10(5), p < 0.001). They also had higher biopsy urease activity (geometric mean of NH3 nmol/min-1/mg protein-1; 103 v 25, p < 0.001). Urease activity per organism, however, was similar in the two groups showing that high antral urease activity in DU was a reflection of organism density. DU was not present in subjects with an antral infection density less than 10(5) colony forming units/mg protein. A correlation was present between H pylori viable counts and the severity and activity of gastritis. Both severity and activity of gastritis were greater in the antrum of DU compared with non-DU subjects but there was no difference in the body between the two groups. It is concluded that antral H pylori infection density is probably an important determinant of DU development, and that there is a baseline of infection density that is necessary for ulcer formation.
Coordinating Disaster Emergency Response with Heuristic Reinforcement Learning (2018)

A crucial and time-sensitive task when any disaster occurs is to rescue victims and distribute resources to the right groups and locations. This task is challenging in populated urban areas, due to the huge burst of help requests generated in a very short period. To improve the efficiency of the emergency response in the immediate aftermath of a disaster, we propose a heuristic multi-agent reinforcement learning scheduling algorithm, named as ResQ, which can effectively schedule the rapid deployment of volunteers to rescue victims in dynamic settings. The core concept is to quickly identify victims and volunteers from social network data and then schedule rescue parties with an adaptive learning algorithm. This framework performs two key functions: 1) identify trapped victims and rescue volunteers, and 2) optimize the volunteers' rescue strategy in a complex time-sensitive environment. The proposed ResQ algorithm can speed up the training processes through a heuristic function which reduces the state-action space by identifying the set of particular actions over others. Experimental results showed that the proposed heuristic multi-agent reinforcement learning based scheduling outperforms several state-of-art methods, in terms of both reward rate and response times.
The Identification of the Single‐Stranded DNA‐Binding Domain of the <i>Escherichia coli</i> RecA Protein (1995)

To identify the ssDNA-binding domain of Escherichia coli RecA protein, we examined the ssDNA-binding capabilities of synthetic peptides, the sequences of which were derived from the C- and N-termini and from sequences within loops L1 and L2 of the RecA molecule identified from the crystal structure. Synthetic peptides derived from amino acid residues 185-219 of several bacterial RecA proteins, which include loop L2 of RecA, bound to ssDNA in filter-binding assays, whereas three separate synthetic peptides corresponding to single point mutants of E. coli RecA in this region did not. The binding of RecA to ssDNA examined using a gel-shift assay was inhibited by a synthetic peptide derived from this ssDNA-binding region, but not by synthetic peptides derived from amino acid residues 301-329 of the C-terminus or from N-terminal residues 6-39. A peptide corresponding to amino acid positions 152-169 of the RecA molecule and spanning loop L1 and its flanking regions did not bind ssDNA at peptide concentrations up to 250 microM. We have also defined a synthetic 20-amino-acid peptide that comprises amino acid residues 193-212 and includes loop L2 of RecA as the minimum unit that can bind to ssDNA from this region of RecA. Finally, two maltose-binding protein-RecA fusion proteins were made, one containing amino acid residues 185-224 of RecA and the other the last 51 C-terminal residues of RecA (amino acid residues 303-353). In contrast to the C-terminus-derived fusion protein, the fusion protein containing the putative DNA-binding site demonstrated significant binding to single-stranded oligonucleotides in both filter-binding and gel-shift assays. These findings suggest that a portion of the region extending from amino acid residues 193-212 is either part of or the whole ssDNA-binding domain of the RecA protein.
Provable Security for Outsourcing Database Operations (2006)

Database outsourcing, whilst becoming more popular in recent years, is creating substantial security and privacy risks. In this paper, we assess cryptographic solutions to the problem that some client party (Alex) wants to outsource database operations on sensitive data sets to a service provider (Eve) without having to trust her. Contracts are an option, but for various reasons their effectiveness is limited [2]. Alex would rather like to use privacy homomorphisms [6], i.e., encryption schemes that transform relational data sets and queries into ciphertext such that (i) the data is securely hidden from Eve; and (ii) Eve computes hidden results from hidden queries that Alex can efficiently decrypt. Unfortunately, all privacy homomorphisms we know of lack a rigorous security analysis. Before they can be used in practice, we need formal definitions that are both sound and practical to assess their effectiveness.
Future Trajectory Prediction via RNN and Maximum Margin Inverse Reinforcement Learning (2018)

In this paper, we propose a future trajectory prediction framework based on recurrent neural network (RNN) and maximum margin inverse reinforcement learning (IRL) for the task of predicting future trajectories of agents in dynamic scenes. Given the current position of a target agent and the corresponding static scene information, a RNN is trained to produce the next position, which is the closest to the true next position while maximizing the proposed reward function. The reward function is also trained at the same time to maximize the margin between the rewards from the true next position and its estimate. The reward function plays the role of a regularizer when training the parameters of the proposed network so the trained network is able to reason the next position of the agent much better. We evaluated our model on a public KITTI dataset. Experimental results show that the proposed method significantly improves the prediction accuracy compared to other baseline methods.
Aluminium from fly ash (1982)

The authors describe the Calsinter process for recovering aluminium from fly ash, which at present is at the laboratory stage.
On a class of N-dimensional associated random walks and the hitting point identity (1989)

N-dimensional random walks on the lattice S with nonnegative integer valued coordinates in RN play an important rate in the modelling of computer preformance.For N>2 the analysis of those random walks presents difficult analytical problems.The available techniques for N=2 are hard to generalize for N>2.An interesting identity will be derived for the distribution of the hitting point of the bounding hyperplanes of S. With the aid of this identity it is possible to construct a class of associated N-dimensional random walks on S which are quite accessible for detailed analysis.
A recursive algorithm for the calculation of identity coefficients (1981)

SUMMARY Based on a theory of generalized kinship coefficients a recursive algorithm for the calculation of the coefficient of kinship and all nine condensed identity coefficients for any two individuals with given pedigree is described. Furthermore, the algorithm also permits the calculation of all fifteen detailed coefficients for two individuals neither of whom is an ancestor of the other one. Results for standard as well as highly inbred relationships are given.
Scalable-distributed-arbitration ATM switch supporting multiple QoS classes (2003)

This paper proposes a multi-QoS scalable-distributed-arbitration (MSDA) ATM switch that supports both the high-priority class and the low-priority class under the head-of-line-priority discipline. It has a crosspoint buffer and a transit buffer, each consisting of a high-priority buffer and a low-priority buffer. Arbitration is executed between the crosspoint buffer and the transit buffer in a distributed manner. The MSDA switch extends the advantage of our previously proposed single-QoS scalable-distributed-arbitration (SSDA) switch. It is expandable while permitting high output-line speeds due to the distributed arbitration. The SSDA switch has a problem when its delay-time-based cell selection mechanism is applied to the low-priority class due to the limitation of the number of bits for the delay measure in the cell overhead. We solved this problem by introducing a distributed-ring-arbiter-based cell selection mechanism at each crosspoint for the low-priority class. The low-priority transit buffer at each crosspoint has virtual queues in accordance with the upper input ports. Cells for the low-priority class are selected by distributed ring arbitration among the low-priority crosspoint buffer and the virtual queues at the low-priority transit buffer. Simulations confirm that the MSDA switch ensures fairness in terms of delay time for the high-priority class, while it ensures fairness in terms of throughput for the low-priority class.
Impact of dispersion compensation gratings on OC-192 systems (2002)

This paper analyzes the system impact of dispersion compensation gratings (DCG) with regards to its group delay ripple amplitude, frequency, as well as dispersion deviation. Computer simulations in terms of power penalty and bit error rate (BER) tests on OC-192 systems are correlated and presented. Requirements on DCG delay ripple are derived.
Predictability of Peripheral Lymphocyte Reduction of Novel S1P1 Agonists by In Vitro GPCR Signaling Profile (2013)

Surrogate readouts of G-protein-coupled receptor signaling pathways using highly engineered systems are often employed in the drug discovery process. However, accumulating data have demonstrated the importance of selecting relevant biological activity rather than technically facile assays to support high-throughout screening and subsequent structure-activity relationship studies. Here we report a case study using sphingosine-1-phosphate receptor 1 (S1P(1)) as the model system to compare compound activity in six different in vitro assays with their ability to predict in vivo efficacy. S1P(1) has long been validated as a therapeutic target for autoimmune diseases. In this article, in vivo and in vitro studies on 19 S1P1 agonists are reported. In vitro activities of these S1P(1) agonists, together with S1P and FTY720p, on Ca(2+) mobilization, adenylyl cyclase inhibition, extracellular signal-related kinase (ERK) phosphorylation, β-arrestin recruitment, and receptor internalization, were determined. The in vitro potency of these compounds was correlated with their ability to induce peripheral lymphocyte reduction. The results revealed that inhibition of adenylyl cyclase and induction of β-arrestin recruitment and receptor internalization are good indicators to predict in vivo efficacy, whereas induction of Ca(2+) mobilization through G(qi/5) coupling and ERK phosphorylation is irrelevant. This study demonstrated the importance of identifying an appropriate in vitro assay to predict in vivo activity based on the biological relevance in the drug discovery setting.
Dynamic Energy Resource Control of Power Electronics in Local Area Power Networks (2010)

In a local area power system, all components of the system, including sources, loads, and distribution have multiple commitments and responsibilities. These commitments include serving the energy needs of a local load, but also maintaining the efficiency and stability of the overall system. Then, the control law of a power converter should consider these objectives, but also needs to anticipate the reaction of other converters within the power network. A differential game-theoretic approach is proposed to derive sliding surfaces that uses a component's objective and operating characteristics to plan an optimal state trajectory during a transient without the need for communication channels or centralized control. The optimal trajectory includes considerations for maintaining local operation of the converter, as well as the stability of the system as a whole. This paper introduces a geometric control surface based on a change of variables that simply and effectively implements a power buffer function in multiple load converters within a power network and microgrids. The formulation and implementation of the optimal surfaces are presented, in addition to experimental validation of the new power buffer control law.
Controlling postoperative ileus by vagal activation (2010)

Postoperative ileus is a frequently occurring surgical complication, leading to increased morbidity and hospital stay. Abdominal surgical interventions are known to result in a protracted cessation of bowel movement. Activation of inhibitory neural pathways by nociceptive stimuli leads to an inhibition of propulsive activity, which resolves shortly after closure of the abdomen. The subsequent formation of an inflammatory infiltrate in the muscular layers of the intestine results in a more prolonged phase of ileus. Over the last decade, clinical strategies focusing on reduction of surgical stress and promoting postoperative recovery have improved the course of postoperative ileus. Additionally, recent experimental evidence implicated antiinflammatory interventions, such as vagal stimulation, as potential targets to treat postoperative ileus and reduce the period of intestinal hypomotility. Activation of nicotinic receptors on inflammatory cells by vagal input attenuates inflammation and promotes gastrointestinal motility in experimental models of ileus. A novel physiological intervention to activate this neuroimmune pathway is enteral administration of lipid-rich nutrition. Perioperative administration of lipid-rich nutrition reduced manipulation-induced local inflammation of the intestine and accelerated recovery of bowel movement. The application of safe and easy to use antiinflammatory interventions, together with the current multimodal approach, could reduce postoperative ileus to an absolute minimum and shorten hospital stay.
Visualizing feedback‐enhanced contrast in magnetic resonance imaging (2007)

Abstract A new approach to magnetic resonance imaging (MRI) contrast enhancement has recently been developed that exploits nonlinear feedback interactions to amplify contrast arising from small variations in the underlying MRI parameters. A unified framework for understanding feedback‐enhanced contrast is presented here based on the concepts of instability and positive feedback. The specific mechanisms governing contrast enhancement under the feedback interactions of radiation damping, the distant dipolar field, and their joint effect are elucidated through numerical simulations illustrating the involved spin dynamics. Experimental demonstrations of feedback‐enhanced contrast are shown on samples of in vitro human brain tissue, and applications to improving lesion detection in disease states such as epilepsy and cancer are discussed. © 2007 Wiley Periodicals, Inc. Concepts Magn Reson Part A 30A: 378–393, 2007.
Variant of Hepatitis B Virus with Primary Resistance to Adefovir (2006)

The reverse-transcriptase inhibitor lamivudine (Zeffix, GlaxoSmithKline) is often used to treat chronic infection with hepatitis B virus (HBV) until resistance develops. Treatment may then be switched to the reverse-transcriptase inhibitor adefovir (Hepsera, Gilead), which has a lower frequency of resistance. Here, we describe three cases of primary adefovir resistance that were sensitive to tenofovir (Viread, Gilead). All three cases involved a rare HBV variant with a valine at position 233 of the reverse-transcriptase domain instead of isoleucine (rtI233V), as in the wild-type virus. This HBV variant also displayed resistance to adefovir and sensitivity to tenofovir in vitro.
Microfluidic Electrochemical Sensor Array for Characterizing Protein Interactions with Various Functionalized Surfaces (2011)

We present a unique microfluidic platform to allow for quick and sensitive probing of protein adsorption to various functionalized surfaces. The ability to tailor a sensor surface for a specific analyte is crucial for the successful application of portable gas and fluid sensors and is of great interest to the drug screening community. However, choosing the correct surface chemistry to successfully passivate against nonspecific binding typically requires repeated trial and error experiments. The presented device incorporates an array of integrated electrochemical sensors for fast, sensitive, label-free detection of these binding interactions. The layout of the electrodes allows for loading various surface chemistries in one direction while sensing their interactions with particular compounds in another without any cross-contamination. Impedance data is collected for three commonly used passivation compounds (mercaptohexanol, polyethylene glycol, and bovine serum albumin) and demonstrates their interaction with three commonly studied proteins in genetic and cancer research (cAMP receptor protein, tumor necrosis factor α, and tumor necrosis factor β). The ability to quickly characterize various surface interactions provides knowledge for selecting optimal functionalization for any biosensor.
The influence of radiation therapy quality control on survival, response and sites of relapse in oat cell carcinoma of the lung. Preliminary report of a Southwest Oncology group study (1982)

Two hundred and ninety-eight patients with limited (confined to chest and supraclavicular area, encompassable by a single radiation portal) small cell carcinoma of the lung were entered on Southwest Oncology Group Protocol 7628. Patients were treated with multi-agent chemotherapy and radiation therapy with or without BCG. Radiation therapy quality control analysis, including dosimetric reconstruction and port film review was introduced after the protocol was activated and was retrospectively applied. Patients who were considered major protocol variations had statistically worse survival (40 weeks versus 60 weeks; P = 0.002), a lesser improvement in response rate after induction chemotherapy (27 versus 48%; P = 0.05) and a higher chest failure rate (77 versus 55%; P = 0.047) than evaluable patients. Five patients relapsed in the brain, all associated with chest failure. Quality control is essential in cooperative group studies.