gebhart/patrepeval huggingface dataset:
A Real-Time Well Site Log Analysis Application Using MRI Logs (2000)

Abstract With any complex logging tool, there exists a need for a "qualitative and reasonable" analysis, run in real-time at the well site that both provides a preliminary interpretation of the data and also serves as a means for enhancing quality control. Such an application has been developed to provide a quicklook analysis of data from NUMAR’s MRIL® -Prime tool. The application takes advantage of the Prime tool’s ability to simultaneously acquire data from multiple nuclear magnetic resonance (NMR) activations for purposes of fluid identification. The application is based on several well-established NMR fluid-characterization methods. These methods compute total porosity, effective porosity, bulk volume irreducible, flushed-zone fluid volume, and fluid type in a variety of reservoirs. The methods used in quick-look analyses include the Differential Spectral Method (DSM™), Time Domain Analysis (TDA™), Shifted Spectrum Method (SSM™), Enhanced Diffusion Method (EDM™), and the Total Porosity Method (TPM™). Accomplishing these objectives, i.e., computation of total porosity, effective porosity, etc., in a real-time environment requires consideration of the wellsite engineer’s level of experience and responsibilities. In addition, the dynamics of the real-time wellsite analysis presents several competing and important challenges: acquiring quality measurements, working with limited data and information, and providing results in a timely and efficient manner. Thus, a real-time analysis should be robust and consistent with any additional analysis done in the post-acquisition environment. A set of procedures has been developed to guide the process so that reasonable interpretations can be obtained over a broad range of operating conditions. To simplify the engineer’s tasks, the analysis procedure is automatically driven by the type of NMR data being obtained. Thus, meaningful results can be obtained without increasing the burden on the field engineer. This paper briefly describes the techniques that have been developed and demonstrates their application through field examples.
Decreased Surfactant Protein-B Expression and Surfactant Dysfunction in a Murine Model of Acute Lung Injury (2001)

This study examines the relationships between inflammation, surfactant protein (SP) expression, surfactant function, and lung physiology in a murine model of acute lung injury (ALI). 129/J mice received aerosolized endotoxin lipopolysaccharide [LPS] daily for up to 96 h to simulate the cytokine release and acute inflammation of ALI. Lung elastance (E(L)) and resistance, lavage fluid cell counts, cytokine levels, phospholipid and protein content, and surfactant function were measured. Lavage and lung tissue SP content were determined by Western blot and immunohistochemistry, and tissue messenger RNA (mRNA) levels were assessed by Northern blot and in situ hybridization. Tumor necrosis factor-alpha and neutrophil counts in bronchoalveolar lavage fluid increased within 2 h of LPS exposure, followed by increases in total protein, interleukin (IL)-1beta, IL-6, and interferon-gamma. E(L) increased within 24 h of LPS exposure and remained abnormal up to 96 h. SP-B protein and mRNA levels were decreased at 24, 48, and 96 h. By contrast, SP-A protein and mRNA levels and SP-C mRNA levels were not reduced. Surfactant dysfunction occurred coincident with changes in SP-B levels. This study demonstrates that lung dysfunction in mice with LPS-ALI corresponds closely with abnormal surfactant function and reduced SP-B expression.
Utility-Based Optimal Service Selection for Business Processes in Service Oriented Architectures (2010)

Service Oriented Architectures enable markets of functionally equivalent service providers delivering services at different Quality of Service (QoS) and cost levels. Under these circumstances, there is a need for mechanisms to optimally select service providers at run-time to support a business process execution so that a utility function for the business process is maximized subject to QoS and cost constraints. This is an NP-hard problem. This paper investigates this problem when the utility function is expressed in terms of multiple QoS metrics. An efficient optimal algorithm is presented, which eliminates the need to exhaustively search the state space. This algorithm can be used for small to medium size problems. A very efficient heuristic solution is also presented and scientifically evaluated against the optimal solution on a large set of randomly generated business processes.
Research on adaptive fusion algorithm for image stitching (2017)

An adaptive multi-direction image fusion algorithm is proposed to solve the problem that one fusion algorithm is not suitable for many kinds of image stitching, and there will be significant seam-line at the boundary of the overlap region after image fusion. According to the positional relation of the two images in the coordinate system after projection deformation, we divide the image stitching into two types. We design different image fusion algorithm against the characteristics of each type of stitching, and seam-line be in all boundary direction is eliminated. The algorithm can estimate the type of image stitching rapidly and accurately and perform the corresponding multi-direction image fusion and eventually eliminate the seam-line. Adding brightness adjustment before stitching will make the final result achieve consistency in brightness if the two images for stitching have a considerable difference in brightness.
Enforcing Alias Analysis for Weakly Typed Languages (2005)

Static analysis of programs in weakly typed languages such as C and C++ generally is not guaranteed to be sound because programs in these languages may have undetected memory errors such as dangling pointer references, references using uninitialized pointers, and array bounds overflow. Optimizing compilers can produce undefined results for programs with memory access errors, but this is quite undesirable for many tools that aim to analyze security and reliability properties with guarantees of soundness. We describe a relatively simple compilation strategy for standard C programs that guarantees sound semantics for a call graph, an aggressive interprocedural pointer analysis, and type information for a subset of memory. These provide the foundation for sophisticated static analyses to be applied to such programs with a guarantee of soundness. Our work builds on a previously published transformation called Automatic Pool Allocation to ensure that hard-to-detect memory errors (dangling pointer references and certain array bounds errors) cannot invalidate the call graph, points-to information or type information. The key insight behind our approach is that pool allocation can be used to create a run-time partitioning of memory that matches the compile-time memory partitioning in a points-to graph, and efficient checks can be used to isolate the run-time partitions.&#13;\n&#13;\nFurthermore, we show that the sound analysis information enable static checking techniques that reliably eliminate many run-time checks. Our approach requires no source code changes, allows memory to be managed explicitly, and do not use meta-data on pointers or individual tag bits for memory thus avoiding any external library compatibility issues. Using many benchmarks and system codes, we show experimentally that the run-time overheads are low (less than 10% in nearly all cases and 30% in the worst case we have seen). We also show the effectiveness of reliable static analyses for eliminating run-time checks.
Microbiota-directed biotherapeutics: considerations for quality and functional assessment (2023)

Mounting evidence points to causative or correlative roles of gut microbiome in the development of a myriad of diseases ranging from gastrointestinal diseases, metabolic diseases to neurological disorders and cancers. Consequently, efforts have been made to develop and apply therapeutics targeting the human microbiome, in particular the gut microbiota, for treating diseases and maintaining wellness. Here we summarize the current development of gut microbiota-directed therapeutics with a focus on novel biotherapeutics, elaborate the need of advanced -omics approaches for evaluating the microbiota-type biotherapeutics, and discuss the clinical and regulatory challenges. We also discuss the development and potential application of <i>ex vivo</i> microbiome assays and <i>in vitro</i> intestinal cellular models in this context. Altogether, this review aims to provide a broad view of promises and challenges of the emerging field of microbiome-directed human healthcare.
The thymus: A pictorial review of thymic pathology (2013)

Poster: ECR 2013 / C-1692 / The thymus: A pictorial review of thymic pathology by: D. J. Conces , S. Rissing, P. J. Loehrer; Indianapolis, IN/US
Efficient n-doping of graphene films by APPE (aminophenyl propargyl ether): a substituent effect (2013)

We report the synthesis and applications of APPE (aminophenyl propargyl ether) as a novel n-type dopant for graphene. The characteristics of APPE-doped graphene films were investigated using Raman spectroscopy as well as electron transport measurements. The Raman 2D/G peak ratio decreased by more than 40%, and the minimum conductivity voltage (Dirac voltage) was shifted to -133 V as the pristine graphene was doped with APPE, indicating that the graphene was strongly n-doped. We suppose that the electron donating property of the amine group (-NH2) is the origin of such an intense n-doping effect. In contrast, a similar molecule with an electron withdrawing nitro group (-NO2) (nitrophenyl propargyl ether, NPPE) showed a slight p-doping effect. Thus, we conclude that the doping effect of a molecular framework strongly depends on the functional substituents, which can be represented by the Hammett equation. We also confirmed that the sheet resistance of the APPE doped graphene film was reduced by ∼70%, which is crucial to enhance the electrical conductivity of graphene for various electronic applications. In addition, the acetylene group of APPE appears promising to be utilized in "click chemistry" to further functionalize the π-surface of graphene for sensors and bio applications.
A Reconstruction Filter for Saturated Accelerometer Signals Due to Insufficient FSR in Foot-mounted Inertial Navigation System (2021)

In pedestrian inertial navigation, one possible placement of Inertial Measurement Units (IMUs) is on a footwear. This placement allows to limit the accumulation of navigation errors due to the bias drift of inertial sensors and is generally a preferable placement of sensors to achieve the highest precision of pedestrian inertial navigation. However, inertial sensors mounted on footwear experience significantly higher accelerations and angular velocities during regular pedestrian activities than during more conventional navigation tasks, which could exceed Full Scale Range (FSR) of many commercial-off-the-shelf IMUs, therefore degrading accuracy of pedestrian navigation systems. This paper proposes a reconstruction filter to mitigate localization error in pedestrian navigation due to insufficient FSR of inertial sensors. The proposed reconstruction filter approximates immeasurable accelerometer's signals with a triangular function and estimates the size of the triangles using a Gaussian Process regression. To evaluate performance of the proposed reconstruction filter, we conducted two series of indoor pedestrian navigation experiments with a VectorNav VN-200 IMU and an Analog Device ADIS16497-3 IMU. In the first series of experiments, forces experienced by the IMUs did not exceed the FSRs of the sensors, while in the second series, the forces surpassed the FSR of the VN-200 IMU and saturated the accelerometer's readings. The saturated readings reduced the accuracy of estimated positions using the VN-200 by 1.34× and 3.37× along horizontal and vertical directions. When applying our proposed reconstruction filter to the saturated measurements, the navigation accuracy was increased by 5% horizontally and 50% vertically, as compared to using unreconstructed signals.
Honeyvine Milkweed (Ampelamus albidus) Response to Foliar Herbicides (1986)

A 3-yr experiment and a 1-yr experiment in continuous winter wheat ( Triticum aestivum L. ‘Newton’) and two 3-yr experiments in continuous grain sorghum [ Sorghum bicolor L. (Moench.) ‘Co-op SG-10’ or ‘DeKalb DX-42Y’] were conducted to evaluate selected foliage-applied herbicides for control of honeyvine milkweed [ Ampelamus albidus (Nutt.) Britt # AMPAL]. Glyphosate [ N -(phosphonomethyl)-glycine] applied at 3.4 kg ae/ha, glyphosate plus dicamba (3,6-dichloro-2-methoxybenzoic acid) applied at 1.7 plus 0.6 kg ae/ha, and glyphosate plus 2,4-D [(2,4-dichlorophenoxy)acetic acid] applied at 1.7 plus 1.1 kg ae/ha in summer between harvesting and planting winter wheat and in spring prior to planting grain sorghum effectively reduced honeyvine milkweed regrowth 1 yr after initial application in both cropping systems. One or two additional annual applications did not provide complete control in either cropping system. Applications of 2,4-D at 2.2 kg ae/ha dicamba at 1.1 kg ae/ha and 2,4-D plus dicamba at 1.1 plus 0.6 kg ae/ha were effective if applied consecutively for 3 yr in continuous winter wheat but not in continuous grain sorghum.
Successful spontaneous nesting of the hawksbill turtle (Eretmochelys imbricate) at Yaeyama Station, National Center for Stock Enhancement, Japan (2005)

Organized by Graduate School of Informatics, Kyoto University ; JSPS Bangkok Liaison Office ; Japanese Society of Bio-logging Science ; Informatics Research Center for Development of Knowledge Society Infrastructure
Whole‐body vibration induces pain and lumbar spinal inflammation responses in the rat that vary with the vibration profile (2016)

Whole-body vibration (WBV) is linked epidemiologically to neck and back pain in humans, and to forepaw mechanical allodynia and cervical neuroinflammation in a rodent model of WBV, but the response of the low back and lumbar spine to WBV is unknown. A rat model of WBV was used to determine the effect of different WBV exposures on hind paw behavioral sensitivity and neuroinflammation in the lumbar spinal cord. Rats were exposed to 30 min of WBV at either 8 or 15 Hz on days 0 and 7, with the lumbar spinal cord assayed using immunohistochemistry at day 14. Behavioral sensitivity was measured using mechanical stimulation of the hind paws to determine the onset, persistence, and/or recovery of allodynia. Both WBV exposures induce mechanical allodynia 1 day following WBV, but only the 8 Hz WBV induces a sustained decrease in the withdrawal threshold through day 14. Similarly, increased activation of microglia, macrophages, and astrocytes in the superficial dorsal horn of the lumbar spinal cord is only evident after the painful 8 Hz WBV. Moreover, extracellular signal-regulated kinase (ERK)-phosphorylation is most robust in neurons and astrocytes of the dorsal horn, with the most ERK phosphorylation occurring in the 8 Hz group. These findings indicate that a WBV exposure that induces persistent pain also induces a host of neuroimmune cellular activation responses that are also sustained. This work indicates there is an injury-dependent response that is based on the vibration parameters, providing a potentially useful platform for studying mechanisms of painful spinal injuries. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 34:1439-1446, 2016.
A novel correspondence searching strategy in multiocular vision (2012)

Correspondence searching among different images is a fundamental problem in computer vision. It is important to find correspondences correctly and rapidly, especially for real-time tracking systems. Therefore, the definition of search areas in images is crucial. Traditional epipolar constraint is not noise-enduring; some reformative methods lack explicit geometric meanings. All of them cannot help defining rational search areas under noises. This paper proposes two new binocular imaging constraints with clear geometric meanings and strong restraining forces. Based on them, a novel searching strategy among multiimages is developed which can define optimal search areas with smallest sizes but best reliability. Practical algorithms for implementation are presented and experiments with real images are performed, validating the effectiveness of the proposed strategy.
Molecular Evidence that Nasal Carriage of Staphylococcus aureus Plays a Role in Respiratory Tract Infections of Critically Ill Patients (2005)

The relationship between nasal Staphylococcus aureus carriage and lower respiratory tract infections was studied in 16 critically ill patients. S. aureus strains from nasal and bronchial samples were characterized by pulsed-field gel electrophoresis. In all but one case, nasal and bronchial strains were genetically identical in the same patients.
MODERATE HYPOTHERMIA PROTECTS AGAINST SYSTEMIC OXIDATIVE STRESS IN A RAT MODEL OF INTESTINAL ISCHEMIA AND REPERFUSION INJURY (2005)

Multisystem organ failure represents a major cause of mortality in intestinal ischemia and reperfusion (I/R), and oxidative stress plays a key role in its pathogenesis. Hypothermia is beneficial in I/R injury, but its effects on systemic oxidative stress have not been elucidated. The aim of this study was to evaluate the effects of moderate hypothermia on systemic oxidative stress after intestinal I/R injury. Anaesthetized adult rats (n = 10 per group) underwent 60 min of intestinal ischemia followed by 120 min of reperfusion or sham operation at normothermia (36 degrees C-38 degrees C) or moderate hypothermia (30 degrees C-32 degrees C). At sacrifice, ileum, liver, lungs, and kidneys were removed to determine the concentration of malondialdehyde (a marker of lipid peroxidation), reduced and oxidized glutathione (a major endogenous antioxidant), and glutathione redox state. Plasma malondialdehyde and nitrate plus nitrite (reflecting nitric oxide production) were also analyzed. A marked elevation of malondialdehyde was observed after I/R at normothermia in plasma, ileum, and lungs; however, hypothermia during I/R prevented this increase. I/R at normothermia caused a profound decrease in reduced glutathione and glutathione redox state in the ileum, but this was not observed in I/R at hypothermia. Interestingly, hypothermia increased glutathione content of control intestine. Nitric oxide production was increased only in normothermic I/R animals. Moderate hypothermia attenuates systemic oxidative stress associated with experimental intestinal I/R in an animal model by decreasing lipid peroxidation in plasma, ileum, lungs, and kidneys, by preventing the depletion of gut glutathione, and by reducing systemic nitric oxide production. However, whether these effects persist after rewarming is unknown.
Induction of Heme Oxygenase-1 with Hemoglobin Depresses Vasoreactivity in Rat Aorta (1999)

Septic shock induced by lipopolysaccharide (LPS) produces systemic hypotension and decreased responsiveness to vasoconstrictors. Recently, intravenous injection of hemoglobin (HGB) into rats was found to be protective from a subsequent lethal dose of LPS and was correlated with induction of the enzyme heme oxygenase-1 (HO-1). To determine whether the HGB modulated the vasomotor tone of systemic arteries, we evaluated the effect of in vivo treatment with HGB and LPS on vasoconstrictor responses to phenylephrine (PE) in the isolated rat aorta. Rats (n = 4, for each group) were injected intravenously with rat HGB (200 mg/kg i.v.) or normal saline control (CON) 16 h before sacrifice, and/or LPS (20 mg/kg) or CON 4 h before sacrifice. The descending aorta was dissected into rings and suspended in a modified Krebs solution where vasoconstrictor responses were determined to KCl (60 mM) and PE (10(-8) to 10(-5) M). LPS, but not HGB, inhibited the vasoconstrictor response to KCl. LPS, HGB, and HGB+LPS inhibited the maximal vasoconstrictor response to PE (PEmax). Induction of HO-1 RNA in the aorta by HGB and by LPS was demonstrated by Northern blot analysis. To determine if induction of HO-1 was related to the effect of LPS or HGB on vascular reactivity, vessels were treated with the HO-1 inhibitor, SnPP9 (30 microM). PEmax in SnPP9+HGB vessels was not different from control, whereas SnPP9+LPS vessels had a marked decrease in PEmax. We conclude that induction of HO-1 does not protect the rat aorta from the vasodepressor effects of LPS in vitro. Our results demonstrate, however, that the induction of HO-1 causes vasodepression, possibly via increased production of carbon monoxide.
Photochemical Internalization: From Bench to Bedside with a Novel Technology for Targeted Macromolecule Therapy (2013)

The utilization of macromolecules in the therapy of cancer and other diseases is becoming increasingly relevant to successful tumor therapy. Recent advances in molecular biology and biotechnology have made it possible to improve the targeting and design of cytotoxic agents, DNA complexes, and other macromolecules for clinical applications. To achieve the expected biological effect of these macromolecules, in many cases, internalization to the cell cytosol is crucial. Macromolecules are frequently prohibited from penetrating cell membranes, but are instead endocytosed and without any active intervention become degraded by hydrolytic enzymes in the lysosomes. Thus, at an intracellular level, the most fundamental obstruction for cytosolic localization of therapeutic macromolecules is the membrane barrier of the endocytic vesicles (Varkouhi et al. 2010). Photochemical internalization (PCI) is a novel technology for release of endocytosed macromolecules into the cytosol. PCI has been shown to potentiate the biological activity of a large variety of macromolecules and other molecules that do not readily penetrate the plasma membrane (Berg et al. 1999; Selbo et al. 2010). PCI may therefore be utilized for treatment of most solid tumors, and the first phase I/II clinical trial with PCI of bleomycin (Berg et al. 2005) for several cancer indications has recently been completed. This review will describe the mechanistic basis for the PCI technology, the present status, the potential clinical advantages, and future perspectives.
Recent Advances in Next Generation Snakebite Antivenoms (2018)

With the inclusion of snakebite envenoming on the World Health Organization's list of Neglected Tropical Diseases, an incentive has been established to promote research and development effort in novel snakebite antivenom therapies. Various technological approaches are being pursued by different research groups, including the use of small molecule inhibitors against enzymatic toxins as well as peptide- and oligonucleotide-based aptamers and antibody-based biotherapeutics against both enzymatic and non-enzymatic toxins. In this article, the most recent advances in these fields are presented, and the advantages, disadvantages, and feasibility of using different toxin-neutralizing molecules are reviewed. Particular focus within small molecules is directed towards the inhibitors varespladib, batimastat, and marimastat, while in the field of antibody-based therapies, novel recombinant polyclonal plantivenom technology is discussed.