gebhart/patrepeval huggingface dataset:
An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology (2023)

As exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian influenza virus in Europe, North America, and elsewhere raises the need for similarly rapid sequencing to aid in appropriate response and mitigation activities. To facilitate this objective, we investigate a next-generation sequencing platform that uses a portable nanopore sequencing device to generate and present data in real time. This platform offers the potential to extend in-house sequencing capacities to laboratories that may otherwise lack resources to adopt sequencing technologies requiring large benchtop instruments. We evaluate this platform for routine use in a diagnostic laboratory. In this study, we evaluate different primer sets for the whole genome amplification of influenza A virus and evaluate five different library preparation approaches for sequencing on the nanopore platform using the MinION flow cell. A limited amplification procedure and a rapid procedure are found to be best among the approaches taken.
Food choices and health during military service: increases in sugar- and fibre-containing foods and changes in anthropometric and clinical risk factors (2012)

OBJECTIVE To analyse changes in food choices, diet-related risk factors and their association during 6 months of military service. DESIGN Longitudinal cohort study in Finland, where all men are liable to military service and a clear majority of each age group completes service. Dietary intake data were collected by self-administered questionnaire before and at 6 months of service. Three dietary indices based on food frequencies were developed to characterize the diet: Sugar Index, Fibre Index and Fat Index. Thirteen diet-related risk factors were measured at the beginning and at 6 months of service. SETTING Military environment, two geographically distinct garrisons. SUBJECTS Male conscripts aged 18-21 years (n 256) performing military service. RESULTS During 6 months of service, positive changes concerned more frequent use of fibre-rich foods (P = 0·011), improved body composition (BMI, waist circumference, muscle mass, fat mass and percentage body fat, P ≤ 0·003 for all), decreased systolic blood pressure and increased HDL cholesterol (P < 0·001 for both). Negative changes concerned more frequent use of sugar-rich foods and increased total cholesterol, TAG and blood glucose (P < 0·001 for all). The consumption of fibre-rich foods was inversely associated with anthropometric risk factors at baseline and with sugar-rich foods at both time points. CONCLUSIONS Despite more frequent consumption of sweet foods, military service with a unified, nutritionally planned diet, a controlled environment and high physical load has a positive effect on conscripts' health risk factors. The negative changes in blood lipids and glucose may reflect more varied free-time eating.
SUMO-mediated regulation of NLRP3 modulates inflammasome activity (2018)

The NLRP3 inflammasome responds to infection and tissue damage, and rapidly escalates the intensity of inflammation by activating interleukin (IL)-1β, IL-18 and cell death by pyroptosis. How the NLRP3 inflammasome is negatively regulated is poorly understood. Here we show that NLRP3 inflammasome activation is suppressed by sumoylation. NLRP3 is sumoylated by the SUMO E3-ligase MAPL, and stimulation-dependent NLRP3 desumoylation by the SUMO-specific proteases SENP6 and SENP7 promotes NLRP3 activation. Defective NLRP3 sumoylation, either by NLRP3 mutation of SUMO acceptor lysines or depletion of MAPL, results in enhanced caspase-1 activation and IL-1β release. Conversely, depletion of SENP7 suppresses NLRP3-dependent ASC oligomerisation, caspase-1 activation and IL-1β release. These data indicate that sumoylation of NLRP3 restrains inflammasome activation, and identify SUMO proteases as potential drug targets for the treatment of inflammatory diseases.
Electromyographic Analysis of Thoracic and Lumbar Erector Spinae Activity Using the Abdominal Drawing-in Maneuver and Chin Tuck During Prone Thoracic Extension Exercises (2012)

This present study investigated the effects of the abdominal drawing-in maneuver (ADIM) and chin tuck (CT) on middle thoracic erector spinae, lower thoracic erector spinae, and lumbar erector spinae muscle activity during three prone thoracic extension (PTE) exercises. Twelve healthy subjects performed preferred PTE, ADIM PTE, and ADIM-CT PTE. Surface electromyography was used to collect data on the muscle activity of dominant middle and lower thoracic erector spinae muscles and the lumbar erector spinae. Middle and lower thoracic erector spinae muscle activity significantly increased when ADIM and CT was performed (p<.05). However, lumbar erector spinae muscle activity significantly decreased in ADIM PTE compared to preferred PTE (p=.017) and significantly increased in ADIM-CT PTE compared to ADIM PTE (p=.004). In conclusion, ADIM-CT PTE effectively increased middle and lower thoracic erector spinae muscle activity, and ADIM PTE decreased lumbar erector spinae muscle activity. Hence, ADIM PTE could be a recommended exercise maneuver to strengthen thoracic erector spinae without over activation of lumbar erector spinae.
An Efficient, Novel Microstrip Collector Architecture for Digital Radiographic Imaging CZT Semiconductor Sensors (2005)

The purpose of this paper is to study the impact of a novel microstrip collector design on the temporal response of CdZnTe (CZT) semiconductor detectors for digital radiographic imaging applications. The experimental results of this paper clearly indicate a significant improvement of the temporal response of the CZT imaging detectors due to the enhanced collection efficiency.
Effect of Extracorporeal Shock Wave Therapy on Cultured Tenocytes (2009)

BACKGROUND: Little has been reported about the biologic effect of shock waves on human normal or pathologic tendon tissue. We hypothesized that inflammatory cytokine and MMP production would be down-regulated by shock wave stimulation.\n\nMATERIALS AND METHODS: Diseased Achilles tendon tissue and healthy flexor hallucis longus tissue were used. Shock wave treatment was applied to cultured cells at 0.17 mJ/mm(2)energy 250, 500, 1000, and 2000 times.\n\nRESULTS: A dose-dependent decrease in cell viability was noted in cells receiving 1000 and 2000 shocks (86.0 +/- 5.6%, p = 0.01 and 72.4 +/- 8.9%, p = 0.001) as compared with the normal control. Cell count in the 500-shock group increased by 23.4% as compared with the control (p = 0.05). The concentration of MMP 1, 2, and 13 was higher in diseased tenocytes as compared with normal cells (p = 0.04, all comparisons). IL-6 levels were higher in the diseased tenocytes as compared with normal tenocytes (44.10 +/- 16.72 versus 0.21 +/- 0.55 ng/ml, (p &lt; 0.05). IL-1 levels in normal cells increased (2.24 +/- 5.02 ng/ml to 9.31 +/- 6.85 ng/ml) after shock wave treatment (p = 0.04). In diseased tenocytes, levels of MMP-1 (1.12 +/- 0.23 to 0.75 +/- 0.24 ng/ml; p = 0.04) and MMP-13 (1.43 +/- 0.11 to 0.80 +/- 0.15 ng/ml; p = 0.04) were significantly decreased after shock wave treatment. The IL-6 level in diseased tenocytes was decreased (44.10 +/- 16.72 to 14.66 +/- 9.49 ng/ml) after shock wave treatment (p = 0.04).\n\nCONCLUSION: Higher levels of MMPs and ILs were found in human tendinopathy-affected tenocytes as compared with normal cells. ESWT decreased the expression of several MMPs and ILs.\n\nCLINICAL RELEVANCE: This mechanism may play an important role in shock wave treatment of tendinopathy clinically
Phase motion in the scalar low-mass ππ amplitude in D+→π−π+π+ decay (2005)

Applying the amplitude difference method to Fermilab experiment E791 D+→π−π+π+ data, we measure the low mass π+π− phase motion. Our results suggest a significant phase variation, compatible with the existence of an isoscalar σ(500) meson, as previously reported using an isobar model fit to the full Dalitz-plot density.
Detecting out-of-context objects using contextual cues (2022)

This paper presents an approach to detect out-of-context (OOC) objects in an image. Given an image with a set of objects, our goal is to determine if an object is inconsistent with the scene context and detect the OOC object with a bounding box. In this work, we consider commonly explored contextual relations such as co-occurrence relations, the relative size of an object with respect to other objects, and the position of the object in the scene. We posit that contextual cues are useful to determine object labels for in-context objects and inconsistent context cues are detrimental to determining object labels for out-of-context objects. To realize this hypothesis, we propose a graph contextual reasoning network (GCRN) to detect OOC objects. GCRN consists of two separate graphs to predict object labels based on the contextual cues in the image: 1) a representation graph to learn object features based on the neighboring objects and 2) a context graph to explicitly capture contextual cues from the neighboring objects. GCRN explicitly captures the contextual cues to improve the detection of in-context objects and identify objects that violate contextual relations. In order to evaluate our approach, we create a large-scale dataset by adding OOC object instances to the COCO images. We also evaluate on recent OCD benchmark. Our results show that GCRN outperforms competitive baselines in detecting OOC objects and correctly detecting in-context objects.
Analysis of Sagittal Alignment in Thoracic and Thoracolumbar Curves in Adolescent Idiopathic Scoliosis (2007)

An increased pelvic incidence, associated with both thoracic and thoracolumbar curves when compared with the normal adolescent population, does not appear to be the potential determinant of the development of thoracic versus thoracolumbar scoliosis, but may be a risk factor for the development of adolescent idiopathic scoliosis. The theory of anterior overgrowth may be supported by the identification of thoracic hypokyphosis, despite an increased pelvic incidence and lumbar lordosis, in patients with thoracic scoliosis. The association between sagittal measurements and the etiology of thoracolumbar curve formation is less clear; however, regional anterior overgrowth in the lumbar spine may also be responsible for the deformity.
Dynamic-focusing Microscope Objective for Optical Coherence Tomography (2006)

This paper presents a novel method for dynamic focusing in biological tissue samples using a variable-focus microscope objective within an OCT probe for a resolution of 5 microns. © 2006 Optical Society of America.
Gene therapy for C1 esterase inhibitor deficiency in a Murine Model of Hereditary angioedema (2018)

A single treatment with AAVrh.10hC1EI has the potential to provide long-term protection from angioedema attacks in affected individuals.
Metabolic effects of activation of CCK receptor signaling pathways by twice-daily administration of the enzyme-resistant CCK-8 analog, (pGlu-Gln)-CCK-8, in normal mice (2012)

Cholecystokinin (CCK) is a hormone that has important physiological effects on energy balance. This study has used a stable CCK(1) receptor agonist, (pGlu-Gln)-CCK-8, to evaluate the metabolic effects of prolonged administration in normal mice. Twice-daily injection of (pGlu-Gln)-CCK-8 for 28 days resulted in significantly lowered body weights (P<0.05) on days 24 and 28, which was associated with decreased accumulated calorie intake (P<0.01) from day 12 onward. Nonfasting plasma glucose was significantly reduced (P<0.05) on day 28, while plasma insulin concentrations were increased (P<0.05). After 28 days, glucose tolerance and glucose-mediated insulin secretion were not significantly different in (pGlu-Gln)-CCK-8-treated mice. However, following a 15-min refeeding period in 18-h fasted mice, glucose levels were significantly (P<0.05) decreased by (pGlu-Gln)-CCK-8 despite similar food intake and nutrient-induced insulin levels. Insulin sensitivity in (pGlu-Gln)-CCK-8-treated mice was significantly (P<0.01) improved compared with controls. Accumulation of triacylglycerol in liver was reduced (P<0.01) but there were no differences in circulating cholesterol and triacylglycerol concentrations, as well as triacylglycerol content of pancreatic, muscle, and adipose tissue in (pGlu-Gln)-CCK-8 mice. These data highlight the beneficial metabolic effects of prolonged (pGlu-Gln)-CCK-8 administration and confirm a lack of detrimental effects.
PBCCF: Accelerated Deduplication by Prefetching Backup Content Correlated Fingerprints (2020)

Deduplication provides significant benefits for accelerating large-scale storage systems, particularly backup systems, by eliminating the redundancy of the streaming data. Given the extraordinary growth of data, modern deduplication backup systems are challenged with the task of effectively and efficiently identifying data duplicates while having limited memory for fingerprint indexing. Based on our observation about an enterprise backup system, for the newly created client, there are no historical backups so that the prefetching algorithm has no reference basis to perform effective fingerprint prefetching. The generic prefetching approach such as Progressive Sampling requires large memory to maintain the prefetching performance. In our paper, we discovered the backup content correlation exists among the backups from some different clients based on the study of the real-world dataset. We propose a fingerprint prefetching algorithm, prefetching backup content correlated fingerprint (PBCCF) to improve the prefetching performance, by applying lightweight machine learning and statistical techniques to discover the backup patterns and generalize their features only using the high-level meta data. The experimental results reveal that PBCCF succeeds at identifying the highly correlated backups and fingerprints to maintain a good deduplication rate while significantly saving memory compared to the Progressive Sampling.
Information Retrieval: Uncertainty and Logics: Advanced Models for the Representation and Retrieval of Information (1998)

List of Figures. List of Tables. Preface. Part I: Genesis. 1. A Non-Classical Logic for Information Retrieval C.J. van Rijsbergen. Part II: Logical Models. 2. Toward a Broader Logical Model for Information Retrieval Jian-Yun Nie, F. Lepage. 3. Experiences in Information Retrieval Modelling Using Structured Formalisms and Modal Logic J.-P. Chevallet, Y. Chiaramella. 4. Preferential Models of Query by Navigation P. Bruza, B. van Linder. 5. A Flexible Framework for Multimedia Information Retrieval A. Muller. 6. The Flow of Information in Information Retrieval: Towards a General Framework for the Modelling of Information Retrieval M. Lalmas. 7. Mirlog: A Logic for Multimedia Information Retrieval C. Meghini, et al. Part III: Uncertainty Models. 8. Semantic Information Retrieval G. Amati, K. van Rijsbergen. 9. Information Retrieval with Probabilistic Datalog T. Roelleke, N. Fuhr. 10. Logical Imaging and Probabilistic Information Retrieval F. Crestani. 11. Simplicity and Information Retrieval G. Amati, K. van Rijsbergen. Part IV: Meta-Models. 12. Towards an Axiomatic Aboutness Theory for Information Retrieval T. Huibers, B. Wondergem.
Interdisciplinary Team Training for Occupational Therapists (1986)

No abstract available for this article.
A Gripper System for Robustly Picking Various Objects Placed Densely by Suction and Pinching (2018)

Suction is an effective method for picking various objects because it makes trajectory planning and control easy. However, suction has not been used due to misalignment and leakage of suction air when handling a variety of shapes. We therefore develop a hand to handle these characteristics. First, we model the vacuum pump and pad characteristics to allow evaluation of momentum and suction force in the case of leakage. Utilizing this, we select a configuration suitable for the items in the Amazon Robotics Challenge 2017. In addition, we design a mechanism for switching from suction to pinching for grasping items that cannot be sucked. Moreover, robust pinching is made possible by equipping the fingertips with a passive linear motion mechanism. In the Amazon Robotics Challenge 2017, it was shown possible to stably grasp items with irregularities and items with large moments. Furthermore, items that cannot be grasped by suction can also be grasped robustly by switching to the pinching mechanism.
On the andvantages of free choice (1981)

It is shown that distributed systems of probabilistic processors are essentially more powerful than distributed systems of deterministic processors, i.e., there are certain useful behaviors that can be realized only by the former. This is demonstrated on the dining philosophers problem. It is shown that, under certain natural hypotheses, there is no way the philosophers can be programmed (in a deterministic fashion) so as to guarantee the absence of deadlock (general starvation). On the other hand, if the philosophers are given some freedom of choice one may program them to guarantee that every hungry philosopher will eat (with probability one) under any circumstances (even an adversary scheduling). The solution proposed here is fully distributed and does not involve any central memory or any process with which every philosopher can communicate.
Performance evaluation of the LabPET&#x2122; APD-based digital PET scanner (2007)

The LabPET <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TM</sup> is a fully digital avalanche photodiode (APD) based PET scanner designed for state-of-the- art molecular and genomic imaging of small animals. Two versions of the scanner were evaluated, having 3.75 (LabPET4) and 7.5 cm axial FOV (LabPET8). The detectors are made of 2x2x10/12 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> LYSO and LGSO crystals assembled in phoswich pairs read out by an APD. After digital crystal identification, the average energy resolution is 24 plusmn 6% for LYSO and 25 plusmn 6% for LGSO. The scanner overall timing resolution is 6.6 ns for LYSO/LYSO and 10.7 ns for LGSO/LGSO coincidences after coarse timing alignment. The FBP reconstructed tangential/radial resolution is 1.3/1.4 mm FWHM (2.5/2.4 mm FWTM) at the FOV center and remains below 2.1 mm FWHM (3.6 mm FWTM) within the central 4-cm diameter FOV. MLEM reconstruction of a micro resolution phantom provided clear separation of the 1.35 mm spots and fair identification of 1 mm spots. With an energy window of 250-650 keV, the sensitivity is 1.1% for LabPET4 and 2.1% for LabPET8. The imaging capabilities of the scanner are demonstrated with in vivo images of rats and mice.
Fast mixing device inside a nuclear magnetic resonance magnet: A tool for observing early steps in protein folding (2000)

We describe a device designed to perform a fast mixing of two solutions inside the magnet of a nuclear magnetic resonance (NMR) spectrometer. The apparatus is totally nonmagnetic; it operates via a system of pneumatic valves, which drives a syringe to inject the first solution into the NMR tube that already contains the other solution. An important point is that before and after the injection, the solution in the NMR tube is free of any perturbing injecting device. The injection is controlled by the spectrometer software in the NMR pulse sequence. Simple experiments have been performed to assess the viability of the device, and evaluate the dead time after injection, as well as the loss of homogeneity and the mixing capabilities. The device described can mix up to 200 μl of solution with the solution already present in the NMR tube in less than 50 ms, with a negligible loss of homogeneity during injection. The device was specifically designed for protein folding studies but can find a general purpose for chemical reactions involving small amounts of compounds.
Effect of insulin and insulin-like growth factors I and II on phosphatidylinositol and phosphatidylinositol 4,5-bisphosphate breakdown in liver from humans with and without type II diabetes (1989)

We have characterized a plasma membrane phosphatidylinositol 4,5-bisphosphate (PIP2)-specific phospholipase C (PLC) and a cytosolic phosphatidylinositol (PI)-specific PLC in human liver. Epinephrine, 1 x 10(-5) M, and vasopressin, 1 x 10(-8) M, stimulated PIP2-PLC which was enhanced by guanosine 5'-O-(3-thiotriphosphate) (GTP gamma S). PI-PLC stimulation was not observed by these agents. Insulin and insulin-like growth factors (IGF-I and IGF-II) in the presence and absence of GTP gamma S did not stimulate PIP2-PLC or PI-PLC in plasma membranes and cytosol preparations nor phosphoinositide breakdown in isolated human hepatocytes. Furthermore, serendipitly we found that PIP2-PLC activity was increased in liver membranes from obese patients with type II diabetes when compared to obese and lean controls. We conclude that in human liver, insulin and IGFs are not members of the family of hormones generating inositol trisphosphate (IP3) as a second messenger. Furthermore, the increased PIP2-PLC in diabetic liver may result in: (a) increased intracellular concentrations of IP3 and thus increased Ca2+, which has been postulated to induce insulin resistance; and (b) increased diacylglycerol and thus increased protein kinase C which phosphorylates the insulin receptor at serine residues inactivating the insulin receptor kinase. While the mechanism of increased PIP2-PLC activity in diabetes is unknown, it may initiate a cascade of events that result in insulin resistance.
A multimodal imaging agent for intrinsic surface enhanced Raman scattering of biological tissue (2015)

Raman imaging is an optical method that provides chemo-selective contrast, microscopic resolution and multiplexing capability. Medical applications, however, still suffer from weak signals and resulting long acquisition times. Plasmon resonance effects can drastically increase signals for Surface Enhanced Raman Scattering (SERS). Here, we present concepts towards an ideal, multimodal SERS agent for medical applications. Enhancement of intrinsic spectra of biological tissue is combined with contrast in Photoacoustic- and Magnetic Resonance Tomography, making this imaging agent highly promising for clinical radiology.