gebhart/patrepeval huggingface dataset:
Virulence of luminous vibrios to Artemia franciscana nauplii (2003)

From healthy and diseased penaeid shrimp from Asia and the Americas, 25 luminous and 2 non-luminous bacterial strains were isolated, and 14 were phenotypically identified as Vibrio harveyi; 9 isolates produced significant mortalities (45 to 80%) in Artemia franciscana nauplii at inoculation densities of 10(5) to 10(6) CFU ml(-1) compared to the controls (unchallenged nauplii). The maximum number of bacteria ingested (bioencapsulated) by the Artemia nauplii varied from less than 10 to 10(3) CFU nauplius(-1) and no significant relationship was observed between the density of bacteria inoculated, the amount of bacteria ingested, and naupliar mortality. Significant correlations were obtained between naupliar mortality and production of proteases, phospholipases or siderophores, but not between mortality and lipase production, gelatinase production, hydrophobicity or hemolytic activity. The results suggest that virulence of the strains tested was more related to the production of particular exoenzymes than to the measured colonization factors.
Chemistry with ADF (2001)

Abstract We present the theoretical and technical foundations of the Amsterdam Density Functional (ADF) program with a survey of the characteristics of the code (numerical integration, density fitting for the Coulomb potential, and STO basis functions). Recent developments enhance the efficiency of ADF (e.g., parallelization, near order‐N scaling, QM/MM) and its functionality (e.g., NMR chemical shifts, COSMO solvent effects, ZORA relativistic method, excitation energies, frequency‐dependent (hyper)polarizabilities, atomic VDD charges). In the Applications section we discuss the physical model of the electronic structure and the chemical bond, i.e., the Kohn–Sham molecular orbital (MO) theory, and illustrate the power of the Kohn–Sham MO model in conjunction with the ADF‐typical fragment approach to quantitatively understand and predict chemical phenomena. We review the “Activation‐strain TS interaction” (ATS) model of chemical reactivity as a conceptual framework for understanding how activation barriers of various types of (competing) reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis. Finally, we include a brief discussion of exemplary applications in the field of biochemistry (structure and bonding of DNA) and of time‐dependent density functional theory (TDDFT) to indicate how this development further reinforces the ADF tools for the analysis of chemical phenomena. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 931–967, 2001
Risk Aware Provisioning and Resource Aggregation Based Consolidation of Virtual Machines (2012)

Server consolidation has emerged as an important technique to save on energy costs in virtualized datacenters. The issue of instantiation of a given set of Virtual Machines (VMs) on a set of Physical Machines (PMs) can be thought of as consisting of a provisioning step where we determine the amount of resources to be allocated to a VM and a placement step which decides which VMs can be placed together on a physical machines thereby allocating VMs to PMs. In this paper, we introduce a provisioning scheme which takes into account acceptable intensity of violation of provisioned resources. In addition we identify a serious shortcoming of existing placement schemes that correct in our correlation aware placement scheme. We consider correlation among aggregated resource demands of VMs while finding the VM-PM mapping. Experimental results reveal that our approach leads to a significant amount of reduction in the number of servers (up to 32% in our settings) required to host 1000 VMs and thus enables us to turn off unnecessary servers. It achieves this by packing VMs more tightly by correlating resource requirements across the entire set of VMs to be placed. We present a comprehensive set of experimental results comparing our scheme with the existing provisioning and placement schemes.
Centroid fluctuations of speckled targets (1991)

We present a statistical description of the centroid fluctuations of imaged targets under coherent illumination. We derive analytic expressions that take into account the illumination and imaging geometries. The fluctuations are shown to be insensitive to linear filtering and constitute a physical limitation to remote sensing devices making use of lasers.
A new silicon micro-transducer for the measurement of the magnitude and direction of a magnetic-field vector (1980)

This paper describes a new Silicon Micro-Transducer (SMT) which is capable of measuring the magnitude and direction of a magnetic-field vector. This vector sensor --made by standard bipolar technology-is a four-collector npn-transistor giving output signals which are a linear function of the two components of an in-plane magnetic field. A centrally injected current is divided into four equal parts. The current differences of the two pairs of opposite collectors, affected by the two in-plane field components, are the output signals. Consequently, the amplitude and direction of the applied field can be derived from these independent signals. The vector sensor was developed from a one-dimensional sensor having two collectors only. As the basic operating principles are the same, most of the one-dimensional characteristics also apply to the vector sensor. Non-linearity: ≤ 0.3% for |B| ≤ 1 T. Typical sensitivity per collector pair: δI <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</inf> /(I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</inf> .B) = 3 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> T <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> at U <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">cb</inf> = 5 V.
Radiation therapy and hyperthermia improve the oxygenation of human soft tissue sarcomas. (1996)

The adverse prognostic impact of tumor hypoxia has been demonstrated in human malignancy. We report the effects of radiotherapy and hyperthermia (HT) on soft tissue sarcoma oxygenation and the relationship between treatment-induced changes in oxygenation and clinical treatment outcome. Patients receiving preoperative radiotherapy and HT underwent tumor oxygenation measurement pretreatment after the start of radiation/pre-HT and one day after the first HT treatment. The magnitude of improvement in tumor oxygenation after the first HT fraction relative to pretreatment baseline was positively correlated with the amount of necrosis seen in the resection specimen. Patients with <90% resection specimen necrosis experienced longer disease-free survival than those with > or = 90% necrosis. Increasing levels of tumor hypoxia were also correlated with diminished metabolic status as measured by P-31 magnetic resonance spectroscopy.
INTERNATIONAL MULTI-CENTER TRIAL OF ISLET TRANSPLANTATION USING THE EDMONTON PROTOCOL IN PATIENTS WITH TYPE 1 DIABETES (2004)

O449* The Immune Tolerance network international multicenter trial using the Edmonton Protocol was designed to explore the safety and efficacy of islet-alone transplantation in patients with Type 1 diabetes. Stringent enrollment criteria included metabolic lability, recurrent hypoglycemic or progressive complications of diabetes. Only optimal patients were selected based on strict weight limitation (70kg) and adequate renal reserve (CC>80ml/min/1.73m). The trial involved nine sites in Canada, the US and Europe, with a target enrollment of 36 patients. All 36 participants have been enrolled and have received at least one islet transplant. We anticipate all transplants to be completed in the next several months. Clinical follow-up will continue for three years post final transplant with the primary endpoint assessed at one-year post the patient’s final transplant. Updated information regarding the number of transplants, insulin independence, glucose control, complications related to transplantation and overall safety will be available for presentation. Conclusions: The preliminary findings from this trial support the safety and efficacy of islet-alone transplantation, and indicate that the Edmonton Protocol may be successfully replicated across centers internationally. Standardization of islet processing between centers remains a major challenge, but it should not delay the development of successful clinical protocols in the field of islet transplantation.
Differential cytotoxicity of phospholipid analogues to pathogenic Acanthamoeba species and mammalian cells (2007)

These results demonstrate that hexadecyl-PC has the highest therapeutic index and is the most promising for the treatment of acanthamoebiasis.
MR compatible brain PET using tileable GAPD arrays (2009)

The aim of this study is to develop a MR compatible PET that is insertable to MRI and allows simultaneous PET and MR imaging of human brain. The brain PET having 72 detector modules arranged in a ring of 330 mm diameter was designed. Each PET module composed of 4 ? 4 matrix of 3 mm ? 3 mm ? 20 mm LYSO crystals coupled to a tileable 4 ? 4 array Geigermode avalanche photodiode (GAPD) and designed to locate between RF and gradient coils. Signals of the each module were transferred to preamplifiers using flexible flat cable of 3 m long, and then sent to a position decoder circuit (PDC), which outputs digital address and an analog pulse of the one interacted channel from preamplifier signals. The PDC outputs were fed into FPGA-embedded DAQ boards. The analog signal was digitized, and arrival time and energy of the signal were calculated and stored. All electronics were located outside MR bore to minimize signal interference between PET and MR. Basic performance of the PET components and cross-compatibilities of the PET module and MR were evaluated. Imaging performance of the designed brain PET was investigated using Monte Carlo simulation and experimental measurement. The degradation of PET performance caused by the 3 m long cable and the PDC was negligibly small. No obvious differences of the PET module performance measured inside/outside MR bore were observed. The SNR of various MR sequence phantom images acquired with/without the PET module were also similar. Activity distribution patterns of hot-rod phantoms were well imaged without distortion, and rods down to a diameter of 3.5 mm were resolved in both simulation and experiment. Grayand white matter of the Hoffman brain phantom was also well imaged. Preliminary experimental results demonstrate that MR compatible high quality PET imaging is feasible using the GAPD arrays, electronics, signal processing method and MR insertable PET design schemes developed in this study.
The crystal structure of human α‐thrombin complexed with LY178550, a nonpeptidyl, active site‐directed inhibitor (1997)

Abstract The crystal structure of human α‐thrombin in complex with LY178550, a nonpeptidyl, active site‐directed inhibitor, has been solved to 2.07 α resolution by the method of X‐ray crystallography. The final model of the complex has a crystallographic R ‐value of 21.5% ( R free = 23.1%) with 0.014 Å and 2.4° standard deviation from ideal bond lengths and angles, respectively. Well‐defined electron density was observed for the inhibitor in the active site. The inhibitor binds to the active site in an L‐shaped manner, mimicking the bound conformation of the tripeptide arginal series of thrombin inhibitors (Chirgadze NY et al., 1992, American Crystallographic Association Meeting 20 :116 [Abstr. PB311]). The basic amidine of LY178550 forms a salt bridge with Asp 189 within the specificity pocket, while the 4‐benzylpiperidine side chain engages in a number of hydrophobic interactions at the S 2 and S 3 binding sites. The inhibitor does not interact in any fashion with the active site sequence Ser 214‐Gly 216, as occurs with many of the inhibitors studied previously. The indole N‐H of the inhibitor forms a hydrogen bond to the γ‐oxygen of the catalytic serine (Ser 195).
Prediction of High-Amplitude Forces during Propeller Crashback (2008)

Propeller crashback, an emergency maneuver undertaken when a forward-moving vessel needs to stop quickly, involves reversing the propeller rotation and running the propeller in reverse into the oncoming flow. This maneuver generates low frequency, high amplitude forces on the blades which impart pitch and yaw moments on the vessel. The origins of these forces are uncertain and there are no tools based on first principles with which propeller designers can predict the maximum loadings during crashback. In order to better understand the origins of these phenomena and develop a loading prediction tool a large eddy simulation (LES) methodology using an unstructured, finite volume, incompressible LES code with a 2nd-order accurate central difference (CD) flux reconstruction methodology, and a dynamic sub-grid scale model is being applied to crashback. In this paper, we compare results of this code with experimental data and a commercially-available unstructured finite volume LES code with upwind (UW) flux reconstruction without sub-grid scale model. Crashback simulations have been performed on the 0.3048 m diameter, zero-skew angle, 5-bladed Propeller 4381operating at J=-0.5. We compare the mean, RMS higher order statistical moments for the integrated forces and moments to experimental data. Comparison to the experimental power spectral density (PSD) functions shows that both codes correctly predict the low-frequency blade loading and the blade rate energy concentrations. However, the CD code predicts a wider range of turbulence scales around the blade rate peak that may be important for loading dynamics. The CD LES data reveals that the flow has a bi-modal behavior that switches between vortex ring (VR) and axial jet (AJ) modes which are associated with minimum and maximum loadings, respectively.
Novel lipolytic genes from the microbial metagenomic library of the South China Sea marine sediment (2010)

Metagenomic cloning is a powerful tool for the discovery of novel genes and biocatalysts from environmental microorganisms. Based on activity screening of a marine sediment microbial metagenomic library, a total of 19 fosmid clones showing lipolytic activity were identified. After subcloning, 15 different lipolytic genes were obtained; their encoded proteins showed 32-68% amino acid identity with proteins in the database. Multiple sequence alignment and phylogenetic tree analysis demonstrated that most of these predicted proteins are new members of known families of bacterial lipolytic enzymes. However, two proteins, FLS18C and FLS18D, could not be assigned to any known family, thus probably representing a novel family of the bacterial lipolytic enzyme. The activity assay results indicated that most of these lipolytic enzymes showed optimum temperature for hydrolysis at 40-50 degrees C with p-nitrophenol butyrate as a substrate. The lipolytic gene fls18D was overexpressed, and the resulting protein FLS18D was characterized as an alkaline esterase. Furthermore, the whole sequence of fosmid pFL18 containing FLS18C and FLS18D was shotgun sequenced, and a total of 26 ORFs on it were analyzed and annotated.
Recent developments in black phosphorus transistors (2015)

The discovery of graphene has inspired great research interest in two-dimensional (2D) layered nanomaterials during the past decade.
Diabetic foot disorders. A clinical practice guideline. For the American College of Foot and Ankle Surgeons and the American College of Foot and Ankle Orthopedics and Medicine. (2000)

Foot ulcerations, infections, and Charcot neuropathic osteoarthropathy are three serious foot complications of diabetes mellitus that can too frequently lead to gangrene and lower limb amputation. Consequently, foot disorders are one of the leading causes of hospitalization for persons with diabetes and can account for expenditures in the billions of dollars annually in the U.S. alone. Although not all foot complications can be prevented, dramatic reductions in their frequency have been obtained through the implementation of a multidisciplinary team approach to patient management. Using this concept, the authors present a Clinical Practice Guideline for diabetic foot disorders based on currently available evidence. The underlying pathophysiology and treatment of diabetic foot ulcers, infections, and the diabetic Charcot foot are thoroughly reviewed. Although these guidelines cannot and should not dictate the standard of care for all affected patients, they are intended to provide evidence-based guidance for general patterns of practice. The goal of a major reduction in diabetic limb amputations is certainly possible if these concepts are embraced and incorporated into patient management protocols.
A Preliminary Study on the Toxic Combustion Products Testing of Polymers Used in High-Pressure Oxygen Systems (2004)

One likely cause of polymer ignition in a high-pressure oxygen system is adiabatic-compression heating of polymers caused by pneumatic impact. Oxidative _ pyrolysis or combustion of polymers in a high-pressure oxygen system could generate toxic gases. This paper reports the preliminary results of toxic combustion product testing of selected polymers in a pneumatic-impact test system. Five polymers commonly used in high-pressure oxygen systems, Nylon 6/6, polychlorotrifluoroethylene (CTFE), polytetrafluoroethylene (PTFE), fluoroelastomer (Viton(TradeMark) A), and nitrile rubber (Buna N), were tested in a pneumatic-impact test system at 2500- or 3500-psia oxygen pressure. The polymers were ignited and burned, then combustion products were collected in a stainless-steel sample bottle and analyzed by GC/MS/IRD, GC/FID, and GC/Methanizer/FID. The results of adiabatic-compression tests show that combustion of hydrocarbon polymers, nitrogen-containing polymers, and halogenated polymers in high-pressure oxygen systems are relatively complete. Toxicity of the combustion product gas is presumably much lower than the combustion product gas generated from ambient-pressure oxygen (or air) environments. The NASA-Lewis equilibrium code was used to determine the composition of combustion product gas generated from a simulated, adiabatic-compression test of nine polymers. The results are presented and discussed.
Inhibitory effects of 2-guanidinebenzimidazole and 1-phenylbiguanide on gastric acid secretion in rats. (1984)

In this study 2-guanidinebenzimidazole (GBI) and 1-phenylbiguanide (PBG) appear to be capable of decreasing gastric acid secretion, while the compounds dimethylbiguanide and cyanoguanidine do not. Thus, the antisecretory effect is present when the biguanide groups are associated with lipophilic molecules. GBI and PBG depress gastric acid secretion, even when it has been stimulated by carbamoylcholine (carbachol) or betazole. The antihistamine effects of GBI and PBG on betazole-stimulated gastric acid secretion were confirmed by the inhibitory activity of these compounds on the isolated guinea pig auricle stimulated by histamine. The antimuscarine activity of GBI and PBG on carbachol-stimulated gastric acid secretion in rats is also supported by the way in which these same drugs depress the motility of the duodenum and colon of the anaesthetized cat stimulated by prostigmine. The above mentioned effects of these compounds are also associated with myolytic activity, since they decrease the spontaneous and histamine-stimulated motility of the duodenum and colon. GBI and PBG probably depress gastric acid secretion by interfering with both histamine and acetylcholine receptors and with other sites involved in the secretory process.
Decreased expression of both the low-density lipoprotein receptor-related protein/alpha(2)-macroglobulin receptor and its receptor-associated protein in late stages of cutaneous melanocytic tumor progression. (1996)

We recently found that the proteins of the proteolytic system of plasminogen activation emerge in late stages of melanocytic tumor progression. A large body of evidence suggests a role for two proteins, the low-density lipoprotein receptor-related protein (LRP)/alpha(2)-macroglobulin receptor and its receptor-associated protein (RAP), in the internalization of components of the plasminogen activation system. Here, we present data on the presence of these two proteins in human melanoma cell lines which differ in metastatic capacity, their corresponding xenografts, and in cutaneous melanocytic lesions. With flow cytometry, we found surface expression of LRP to be restricted to urokinase plasminogen activator, producing highly metastatic cell lines. These cell lines also produce higher levels of LRP mRNA, whereas RAP mRNA and protein are expressed at equal levels in all cell lines and not expressed at the cell surface. Xenografts of cell lines producing high levels of LRP remarkably contain only a small fraction of LRP-positive tumor cells. Using immunohistochemistry on frozen sections of 107 human melanocytic lesions comprising the various stages of melanocytic tumor progression, we found that expression of both LRP and RAP decreased in tumor progression. Furthermore, we noted that LRP and RAP are coexpressed within the same lesion. Using immunofluorescence double staining, we found that LRP and RAP colocalize in the same cells in the lesions studied and in the same cell structures in the cell lines studied. In conclusion, our results indicate that LRP and RAP are coordinately expressed in a decreased fashion in melanocytic tumor progression. Based on the staining results in xenografts and in human melanocytic lesions, we conclude that a strong correlation between expression of LRP and urokinase-type plasminogen activator seems not to exist in in vivo melanomas.
Isolation of Dieldrin Resistance from Field Populations of Drosophila melanogaster (Diptera: Drosophilidae) (1990)

High levels (about 4,000-fold) of resistance to dieldrin were isolated by screening field-collected populations of Drosophila melanogaster (Meigen). The resistance was made homozygous following 2-4 generations of selection. A single, major gene mapping to the left arm of chromosome III was solely responsible for resistance. The implications of the recovery of resistant mutants from field populations of D. melanogaster are discussed.
A $192\times128$ Time Correlated SPAD Image Sensor in 40-nm CMOS Technology (2019)

A <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$192 \times 128$ </tex-math></inline-formula> pixel single photon avalanche diode (SPAD) time-resolved single photon counting (TCSPC) image sensor is implemented in STMicroelectronics 40-nm CMOS technology. The 13% fill factor, <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$18.4\,\,\mu \text {m} \times 9.2\,\,\mu \text{m}$ </tex-math></inline-formula> pixel contains a 33-ps resolution, 135-ns full scale, 12-bit time-to-digital converter (TDC) with 0.9-LSB differential and 5.64-LSB integral nonlinearity (DNL/INL). The sensor achieves a mean 219-ps full-width half-maximum (FWHM) impulse response function (IRF) and is operable at up to 18.6 kframes/s through 64 parallelized serial outputs. Cylindrical microlenses with a concentration factor of 3.25 increase the fill factor to 42%. The median dark count rate (DCR) is 25 Hz at 1.5-V excess bias. A digital calibration scheme integrated into a column of the imager allows off-chip digital process, voltage, and temperature (PVT) compensation of every frame on the fly. Fluorescence lifetime imaging microscopy (FLIM) results are presented.