gebhart/patrepeval huggingface dataset:
3D distance fields: a survey of techniques and applications (2006)

A distance field is a representation where, at each point within the field, we know the distance from that point to the closest point on any object within the domain. In addition to distance, other properties may be derived from the distance field, such as the direction to the surface, and when the distance field is signed, we may also determine if the point is internal or external to objects within the domain. The distance field has been found to be a useful construction within the areas of computer vision, physics, and computer graphics. This paper serves as an exposition of methods for the production of distance fields, and a review of alternative representations and applications of distance fields. In the course of this paper, we present various methods from all three of the above areas, and we answer pertinent questions such as How accurate are these methods compared to each other? How simple are they to implement?, and What is the complexity and runtime of such methods?
Substrate Distortion by aβ-Mannanase: Snapshots of the Michaelis and Covalent-Intermediate Complexes Suggest aB2,5 Conformation for the Transition State (2002)

Der konformative Reaktionspfad, der hier für β-Mannosidasen vorgeschlagen wird, unterscheidet sich von dem von Glucosidasen und Cellulasen. Der Vorschlag beruht auf Substratverzerrungen entlang dem Reaktionspfad einer β-Mannosidase (siehe Bild), die röntgenographisch nachgewiesen wurden und dem Konformationsraum bekannter β-Mannosidase-Inhibitoren nahestehen.
Ecologic vulnerabilities and capacities related to population health: a test of a model (2008)

Peer Reviewed
Effect of Long-Term Ammonia Starvation on the Oxidation of Ammonia and Hydroxylamine by Nitrosomonas europaea (1998)

Axenic cultures of the ammonia-oxidizing bacterium Nitrosomonas europaea were starved of ammonia (energy source) for up to 342 d. During this time the bacteria retained the ability to respond instantly to ammonia (1 mM) or hydroxylamine (0.1 mM) amendment by oxidizing it to nitrite without initial protein synthesis. In vivo, the ability to oxidize amended ammonia stayed almost constant during the starvation period, but a drop in the hydroxylamine oxidation rate (to 33%) was observed after 4 wk of starvation when exogenous hydroxylamine was supplied as sole energy source. In contrast, it has been shown that the level and in vitro activity of hydroxylamine oxidoreductase were not significantly affected during the starvation period. Only minor changes were detected between the protein patterns on one-dimensional SDS-PAGE of growing and starved cells. Thus, it is concluded that the activities of the energy-generating enzymes in N. europaea were not affected during long-term ammonia starvation.
Evaluation of an orthotopically implanted calcium phosphate cement containing gelatin microparticles (2008)

This study focused on the degradation properties of gelatin microparticles incorporated in calcium phosphate (CaP) cement and the subsequent effect of these composites on bone formation. Positively charged alkaline gelatin (type A) microparticles or negatively charged acidic gelatin (type B) microparticles were incorporated in CaP cement, which was implanted in critical-sized cranial defect in rats and left in place for 2, 4, and 8 weeks. The degradation of the gelatin was monitored using radioiodinated microparticles. After 4 and 8 weeks of implantation, a significantly faster degradation of type A gelatin over type B gelatin was found. Light microscopic analysis of the specimens showed similar bone response concerning implants containing either type A or B gelatin microparticles. At 2 weeks of implantation, a minimal amount of bone formation was observed from the cranial bone toward the implant, while after 8 weeks of implantation an entire layer of newly formed bone was present from the cranial bone toward the implant periphery. Bone ingrowth into the implant was observed at sites of gelatin microparticle degradation, predominantly at the implant periphery. Histomorphometrical evaluation did not reveal significant differences in bone formation between CaP cement incorporated with either type A or B gelatin microparticles during implantation periods up to 8 weeks. In conclusion, this study demonstrates that gelatin type influences the degradation of gelatin microparticles incorporated in CaP cements. However, this difference in degradation and the concomitant subsequent macroporosity did not induce differences in the biological response.
Synthesis and Ligand‐Exchange Kinetics of the Solvated Trigonal‐Prismatic Clusters [W6CCl12L6]2+ (L=dmf, py) (2007)

Trading places: The first terminal-ligand substitution reactions on the trigonal-prismatic cluster [W6CCl18]2− are reported. The new cluster [W6CCl12(SO3CF3)6]2− is a convenient precursor for solvated [W6CCl12]2+ cluster cores. Self-exchange kinetics experiments on a pyridine-substituted variant (see picture; black W, green Cl, blue N, dark gray C) reveal that the core is classified as inert.
Ranking Production Potential Based on Key Geological Drivers - Bakken Case Study (2011)

Abstract The Bakken Play is a lithologically complex, mixed carbonate-clastic and low porosity-permeability petroleum system comprised of juxtaposed source rocks and reservoir intervals. The play spans variable source maturity, reservoir pressure and temperature, and fluid type. The target reservoirs are thin (below seismic resolution), gently-dipping and variably affected by subtle structure, faults or natural fractures. As a continuous oil accumulation with an unconventional development model, numerous horizontal wells with multi-stage completions will be required to develop the Bakken Play. Ranking future drilling locations is a critical step in planning the development strategy and optimizing the economics of the play. Ranking methods are typically based on prior well performance; however, in the Bakken Play we recognize that numerous non-geological parameters associated with drilling, completions, and production operations contribute to well performance. In this paper we describe a methodology to assess the underlying productivity potential of the reservoirs based on key geological drivers. With an extensive well log database, petrophysical uncertainty can be addressed and stock-tank oil originally in place (STOOIP) calculated and mapped. Nevertheless, the relationship of STOOIP to production performance remains weak due to drilling, completion, and production variables. In this study we apply geological modifiers to the calculated in-place resource to better represent the productivity potential. Geological modifiers include source maturity and charge access, reservoir facies and properties, structure (trap and natural fractures), overpressure, and fluid properties.
On the Combination of IMU and Optical Flow for Action Recognition (2019)

Different Action recognition methods use Inertial Measurement Unit (IMU) and optical flow independently. This research aims to explore the usefulness of combining IMU and Optical flow for action recognition. We are investigating the effectiveness of using statistical features to build an expandable feature vector space.
First Demonstration of Antigen Induced Cytokine Expression by CD4-1+ Lymphocytes in a Poikilotherm: Studies in Zebrafish (Danio rerio) (2015)

Adaptive immunity in homeotherms depends greatly on CD4+ Th cells which release cytokines in response to specific antigen stimulation. Whilst bony fish and poikilothermic tetrapods possess cells that express TcR and CD4-related genes (that exist in two forms in teleost fish; termed CD4-1 and CD4-2), to date there is no unequivocal demonstration that cells equivalent to Th exist. Thus, in this study we determined whether CD4-1+ lymphocytes can express cytokines typical of Th cells following antigen specific stimulation, using the zebrafish (Danio rerio). Initially, we analyzed the CD4 locus in zebrafish and found three CD4 homologues, a CD4-1 molecule and two CD4-2 molecules. The zfCD4-1 and zfCD4-2 transcripts were detected in immune organs and were most highly expressed in lymphocytes. A polyclonal antibody to zfCD4-1 was developed and used with an antibody to ZAP70 and revealed double positive cells by immunohistochemistry, and in the Mycobacterium marinum disease model CD4-1+ cells were apparent surrounding the granulomas typical of the infection. Next a prime-boost experiment, using human gamma globulin as antigen, was performed and revealed for the first time in fish that zfCD4-1+ lymphocytes increase the expression of cytokines and master transcription factors relevant to Th1/Th2-type responses as a consequence of boosting with specific antigen.
Convergent evolution as an indicator for selection during acute HIV-1 infection (2021)

Convergent evolution describes the process of different populations acquiring similar phenotypes or genotypes. Complex organisms with large genomes only rarely and only under very strong selection converge to the same genotype. In contrast, independent virus populations with very small genomes often acquire identical mutations. Here we test the hypothesis of whether convergence in early HIV-1 infection is common enough to serve as an indicator for selection. To this end, we measure the number of convergent mutations in a well-studied dataset of full-length HIV-1envgenes sampled from HIV-1 infected individuals during early infection. We compare this data to a neutral model and find an excess of convergent mutations. Convergent mutations are not evenly distributed across the env gene, but more likely to occur in gp41, which suggests that convergent mutations provide a selective advantage and hence are positively selected. In contrast, mutations that are only found in an HIV-1 population of a single individual are significantly affected by purifying selection. Our analysis suggests that comparisons between convergent and private mutations with neutral models allow us to identify positive and negative selection in small viral genomes. Our results also show that selection significantly shapes HIV-1 populations even before the onset of the adaptive immune system.
Management of anticoagulation during cardiopulmonary bypass in a patient with allergy to heparin and heparin-like compounds (2014)

Hypersensitivity to heparin and heparin-like compounds is a rare condition that represents therapeutic challenges for patients requiring a cardiopulmonary bypass (CPB). We here report the case of a woman with a combined allergy to heparins (fractionated and unfractionated), danaparoid and fondaparinux. She underwent a mitral valve replacement under CBP using lepirudin for systemic anticoagulation. The use of lepirudin instead of unfractionated heparin (UFH) in this setting has many important implications. Lepirudin therapeutic index is narrow and so, overdosing can lead to catastrophic bleeding, whereas underdosing can result in clotting in the CPB tubing. Monitoring of lepirudin activity is essential. The usual activated clotting time monitoring is not a reliable method to monitor anticoagulation with lepirudin in the operating theater. Our experience suggests that the diluted thrombin time provides a valuable alternative during CPB.
Blindness limitations in optical coherence domain reflectometry (1993)

The theoretical and measured limitations on dynamic range near strong reflections in optical coherence domain reflectometry arc examined. A model and data are presented that show that such blindness limitations can be caused by broad spectral tails from the superluminescent diodes typically used in such measurements.
Induced conjugate addition of simple 2-lithio-1,3-dithians to cyclic αβ-unsaturated ketones (1979)

In sharp contrast to prior observations that 2-lithio-1,3-dithians undergo only carbonyl (1,2–) additions to enones, the successful conjugate (1,4–) addition of the parent 2-lithio-1,3-dithian and its simple derivatives has been achieved by the addition of 1·0–2·0 equiv. of hexamethylphosphoramide to the reaction mixture.
The gene for -glutamylcysteine synthetase from Thiobacillus ferrooxidans has low homology to its Escherichia coli equivalent and is linked to the gene for citrate synthase (1996)

The gene for gamma-glutamylcysteine synthetase (gshA) from Thiobacillus ferrooxidans was isolated from a family of cosmids by its ability to complement an Escherichia coli gshA trxA double mutant which was unable to grow on minimal medium lacking glutathione. The predicted sequence of the gamma-glutamylcysteine synthetase was found to have only 18% amino acid sequence identity to the equivalent enzyme from E. coli. In spite of this low sequence homology, concentrations of GSH in a cell extract prepared from the E. coli gshA trxA mutant containing the cloned gene were almost as high as in a cell extract prepared from a wild-type E. coli strain. The gshA gene was found to be physically and transcriptionally linked to the T. ferrooxidans gene for citrate synthase (gltA). The T. ferrooxidans and E. coli citrate synthases shared 37% amino acid sequence identity and the cloned T. ferrooxidans citrate synthase gene was able to complement an E. coli gltA mutant.
A novel ship identification system based on polarimetric ASAR data (2007)

The use of satellite imagery and specifically SAR data for vessel detection and identification has attracted researchers during the last decade. The objective of this work is to provide a novel approach for ship identification based mainly on polarimetric data, taking into consideration the different behaviour of the ship in various polarizations. For this purpose new measures and accordingly a new feature vector is proposed. The feature vector is employed in order to create a vessel signatures database and its efficiency is tested on ASAR data.
Capacitive-faradaic fuel cells (CFFCs) for ion separation: Macro-scale configurations and polarization mechanism (2021)

The polarization mechanism of capacitive-faradaic fuel cells is reported. The mixed potentials of faradaic (Pt and Ti/Pt-IrO2) and capacitive (activated carbon powder and fleece) electrodes were measured in aerated and hydrogenated NaCl solutions at various pH values. Next, two configurations featuring divided and undivided macro-scale CFFCs were investigated: (i) a system with two fixed electrodes made of Ti/Pt-IrO2 and activated carbon fleece, and (ii) a CFFC with one fixed Ti/Pt-IrO2 electrode and one flowing carbon electrode. The salt adsorption capacities obtained in both systems were low compared to conventional capacitive deionization, and therefore optimization of materials and cell architecture is needed. The behaviour of pH and Cl−, SO42− anions conforms to the proposed capacitive-faradaic mechanism, but that of NH4+ and Na+ cations contradicts it. This phenomenon is attributed to faradaic processes and the competitive adsorption–desorption of H+ and OH− ions, which require further detailed investigation.
A Study on the Price Behavior of Chinese Copper Future (2009)

This paper studies the price behavior of Chinese copper future by Zipf-type analysis model. We transformed the closing copper future price data to series only contained up-down information by certain thresholds. We have observed phase transitions phenomena in copper future market, and identified three critical points, at which the heterogeneous agents transit their trading behaviors. We found the first phase is affected by noise traders, the second and third phase is controlled by fundamentalists, the forth phase is controlled by noise traders.
Design, Calibration, and Evaluation of Depth-of-Interaction-Capable PET Detector Modules (2012)

High-resolution, small-bore PET systems suffer from a tradeoff between system sensitivity, and image quality degradation. In these systems long crystals allow mispositioning of the line of response due to parallax error and this mispositioning causes resolution blurring, but long crystals are necessary for high system sensitivity. One means to allow long crystals without introducing parallax errors is to determine the depth of interaction (DOI) of the gamma ray interaction within the detector module. While DOI has been investigated previously, newly available solid state photomultipliers (SSPMs) well-suited to PET applications and allow new modules for investigation. Depth of interaction in full modules is a relatively new field, and so even if high performance DOI capable modules were available, the appropriate means to characterize and calibrate the modules are not. This work presents an investigation of DOI capable arrays and techniques for characterizing and calibrating those modules. The methods introduced here accurately and reliably characterize and calibrate energy, timing, and event interaction positioning. Additionally presented is a characterization of the spatial resolution of DOI capable modules and a measurement of DOI effects for different angles between detector modules. These arrays have been built into a prototype PET system that delivers better than 2.0 mm resolution with a single-sided-stopping-power in excess of 95% for 511 keV g's. The noise properties of SSPMs scale with the active area of the detector face, and so the best signal-to-noise ratio is possible with parallel readout of each SSPM photodetector pixel rather than multiplexing signals together. This work additionally investigates several algorithms for improving timing performance using timing information from multiple SSPM pixels when light is distributed among several photodetectors.
Supplementary Figure 4 from Targeted Disruption of the <i>S1P</i><sub><i>2</i></sub> Sphingosine 1-Phosphate Receptor Gene Leads to Diffuse Large B-Cell Lymphoma Formation (2023)

Supplementary Figure 4 from Targeted Disruption of the &lt;i&gt;S1P&lt;/i&gt;&lt;sub&gt;&lt;i&gt;2&lt;/i&gt;&lt;/sub&gt; Sphingosine 1-Phosphate Receptor Gene Leads to Diffuse Large B-Cell Lymphoma Formation
Effect of Variation of Heated Bottom Wall Area on Natural Convection in Square Enclosure with Inner Circular Cylinder (2013)

본 연구에서는 Ra =10? 일 때, 사각 밀폐계 내부에 고온의 원형 실린더가 존재하는 자연대류에 대한 수치해석을 수행하였다. 밀폐계는 상부 벽면을 통해 냉각되고 양측 벽면과 고온의 국소 영역을 제외한 하부 벽면은 단열 조건이다. 하부 벽면에서 고온 영역이 차지하는 비를 w 로 정의 하였다. 반경이 밀폐계 한 변의 길이의 0.2 배인 원형 실린더를 구현하기 위해 유한체적법(FVM)에 기초한 가상경계법(IBM)을 사용하였다. 본 연구에서는 w 가 고온의 원형 실린더를 갖는 밀폐계 내부의 자연대류에 미치는 영향을 10?의 Rayleigh 수에 대해 2 차원 해를 구하였다. 10?의 Rayleigh 수에서는 유동장과 온도장은 시간에 따라 변하는 특성을 보였다.
Differential expression of PSP94 in rat prostate lobes as demonstrated by an antibody against recombinant GST‐PSP94 (1999)

Prostate secretory protein (PSP94, 94 amino acids) is one of the most abundant proteins secreted from the prostate. Its biological role is unknown and still controversial, although it is assumed to have the potential to be a biomarker and a suppressor of prostate cancer. In order to establish an animal model to further elucidate its biological role, we expressed the mature form of rat PSP94 in Escherichia coli, using a glutathione S-transferase (GST) fusion expression vector; we generated a polyclonal rabbit antibody against the recombinant protein. The antibody specifically recognized recombinant rat PSP94 and cross-reacted only very weakly with its human homologue. Using the characterized anti-rat PSP94 antibody, we found that PSP94 was located primarily in rat prostate. Furthermore, PSP94 is present at different levels in different lobes of rat prostate, with significant levels detectable only in the lateral lobe (LP). In addition, the most abundant PSP94 expression was found in the prostate lobe secretions, and PSP94 levels in LP secretions were at least seven times higher than in secretions from the dorsal prostate (DP). The rat ventral prostate (VP) and other regions of the male accessory glands were found to be almost completely devoid of PSP94. Since most rat prostate dysplasia induced by steroid hormone treatment occurs only in dorsolateral prostate, prostate tissue-specific expression and the expression of PSP94 in dorsolateral, but not other, lobes of the prostate suggest a potential role in prostate targeting and prostate cancer development. J. Cell. Biochem. 74:406–417, 1999. © 1999 Wiley-Liss, Inc.
Solid-State Physical Transducers for Biomedical Research (1986)

The development of solid-state sensors and actuators during the last decade is reviewed, with emphasis on solid-state physical transducers for the measurement or control of the physical parameters in biomedical instrumentation systems. The principles and performance of electrodes, sensors for temperature, position, motion, pressure, fluid flow, and humidity, as well as actuators, are briefly discussed. Selective references on physical sensors and actuators are listed.
Polycation-Based Ternary Gene Delivery System (2015)

Recent progress in gene therapy has opened the door for various human diseases. The greatest challenge that gene vectors still face is the ability to sufficiently deliver nucleic acid into target cells. To overcome various barriers, plenty of researches have been undertaken utilizing diverse strategies, among which a wide variety of polycation/pDNA vectors have been developed and explored frequently. For enhanced transfection efficiency, polycations are constantly utilized with covalent modifications, which however lead to reduced positive charge density and changed properties of polycation/pDNA complexes. Accordingly, non-covalent or ternary strategy is proposed. The cationic properties of polycations can be retained and the transfection efficiency can be enhanced by introducing additional polymers with functional groups via non-covalent assembly. This review will discuss the construction and advantages of ternary complexes gene delivery system, including low toxicity and enhanced gene expression both in vitro and in vivo. Recent progress and expectations with promising results that may have some reference for clinical application are also discussed.
Evaluation of SPOT and TM data for forest stratification: a case study for small-size poplar stands (1993)

The value of SPOT and TM data for stratification of poplar stands prior to volume inventory is assessed. The stratification is based upon the poplar development stage, which is determined by canopy closure and tree height. The effect of development stage and type of understorey vegetation on the spectral radiance of poplar stands is analyzed throughout the vegetation period. The optimal acquisition date(s) and spectral range(s) and the most suited classification approach for discrimination of poplar development stages are determined. Satellite images recorded during the full growing season are preferred for poplar stand stratification according to development stage. In this period the interfering effect of the understory vegetation is minimal in proportion to the effect of the poplar stand development stage. Young poplar stands can accurately be classified as long as the appropriate spectral range of an image registered during the full growing period is selected. The discrimination between young and other popular development stages is accurate enough for use in a stratification prior to volume inventory.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>