gebhart/patrepeval huggingface dataset:
Hospital Wastewater Treatment With the Hydrolysis Oxidization Technology (2005)

Objective To study the application of contact oxidization and hydrolysis acidifying technology in hospital wastewater treatment. Methods Hydrolysis combined with chlorine dioxide disinfection was used in the engineering of treatment. Results Even if CODCr was 300 mg/L, BOD5 was 150 mg/L, SS was 300 mg/L, pH was 6-9 and large intestine bacteria number was 50 000/L, the wastewater quality met the requirement of related standard after treated with the present method. Conclusion The present technology was efficient, practical and economical.
Realistic conductivity geometry model of the human head for interpretation of neuromagnetic data (1989)

In this paper, the computational and practical aspects of a realistically-shaped multilayer model for the conductivity geometry of the human head are discussed. A novel way to handle the numerical difficulties caused by the presence of the poorly conducting skull is presented. Using our method, both the potential on the surface of the head and the magnetic field outside the head can be computed accurately. The procedure was tested with the multilayer sphere model, for which analytical expressions are available. The method is then applied to a realistically-shaped head model, and it is numerically shown that for the computation of B, produced by cerebral current sources, it is sufficient to consider a brain-shaped homogeneous conductor only since the secondary currents on the outer interfaces give only a negligible contribution to the magnetic field outside the head. Comparisons with the sphere model are also included to pinpoint areas where the homogeneous conductor model provides essential improvements in the calculation of the magnetic field outside the head.
<i>In vitro</i> response of MC3T3‐E1 preosteoblasts within three‐dimensional apatite‐coated PLGA scaffolds (2005)

Biomimetic apatites have been reported to promote osteogenic activities in numerous in vivo and in vitro models, but the precise mechanism by which the apatite microenvironment promotes such activities is not well understood. Such mechanistic studies require reproducible model systems that are relevant to tissue engineering practices. Although two-dimensional (2D) apatite-coated polystyrene culture dishes provide practicality and reproducibility, they do not simulate the effects of the three-dimensional (3D) microenvironment and degrading polymeric substrates. A simple 3D model system to address these relevant effects, and its utilization in the investigation of apatite-promoted osteoblastic differentiation in vitro is reported in this paper. Apatite coating was achieved by sequentially immersing poly(lactide-co-glycolide) (PLGA) scaffolds into different simulated body fluids (SBF). SEM, EDX, FTIR, TEM electron diffraction confirmed the apatite coating to comprise of calcium-deficient carbonated hydroxyapatite crystals. While both apatite-coated and non-coated PLGA scaffolds supported MC3T3-E1 attachment, spreading, and proliferation, significant differences in osteoblastic differentiation were observed. Relative to non-coated controls, quantitative real-time PCR revealed significant apatite-associated suppression of alkaline phosphatase (ALP), early upregulation of osteopontin (OPN) at 3 days, and upregulation of osteocalcin (OCN) and bone sialoprotein (BSP) at 4 weeks. In summary, apatite-promoted osteoblastic differentiation can be observed in a 3D model system that is relevant to tissue engineering.
Aerial Measuring System (AMS)/Israel Atomic Energy Commission (IAEC) Joint Comparison Study Report (2013)

Under the 13th Bilateral Meeting to Combat Nuclear Terrorism conducted on January 8–9, 2013, the committee approved the development of a cost-effective proposal to conduct a Comparison Study of the Aerial Measuring System (AMS) of the U.S. Department of Energy (DOE), National Nuclear Security Administration (NNSA) and Israel Atomic Energy Commission (IAEC). The study was to be held at the Remote Sensing Laboratory (RSL), Nellis Air Force Base, Las Vegas, Nevada, with measurements at the Nevada National Security Site (NNSS). The goal of the AMS and the IAEC joint survey was to compare the responses of the two agencies’ aerial radiation detection systems to varied radioactive surface contamination levels and isotopic composition experienced at the NNSS, and the differing data processing techniques utilized by the respective teams. Considering that for the comparison both teams were using custom designed and built systems, the main focus of the short campaign was to investigate the impact of the detector size and data analysis techniques used by both teams. The AMS system, SPectral Advanced Radiological Computer System, Model A (SPARCS-A), designed and built by RSL, incorporates four different size sodium iodide (NaI) crystals: 1" × 1", 2" × 4" × 4", 2" × 4" ×16", and an “up-looking” 2" × 4" × 4". The Israel AMS System, Air RAM 2000, was designed by the IAEC Nuclear Research Center – Negev (NRCN) and built commercially by ROTEM Industries (Israel) and incorporates two 2" diameter × 2" long NaI crystals. The operational comparison was conducted at RSL-Nellis in Las Vegas, Nevada, during week of June 24–27, 2013. The Israeli system, Air RAM 2000, was shipped to RSL-Nellis and mounted together with the DOE SPARCS on a DOE Bell-412 helicopter for a series of aerial comparison measurements at local test ranges, including the Desert Rock Airport and Area 3 at the NNSS. A 4-person Israeli team from the IAEC NRCN supported the activity together with 11 members of the RSL team, which consisted of pilots, mechanics, scientists, a data analyst, equipment operators, and operation specialists. All planned flight activities followed by scientific discussions on the collected data were completed. For IAEC, the joint survey provided an opportunity to characterize their system’s response to extended sources of various fission products at the NNSS. As both systems play an important role in their respective countries’ (United States and Israel) national framework of radiological emergency response and are subject to multiple mutual cooperation agreements, it was important for each country to obtain more thorough knowledge of how they would employ these important assets and define the roles that they would each play in an actual response.
Spin Transfer Torques in MnSi at Ultralow Current Densities (2010)

Spin manipulation using electric currents is one of the most promising directions in the field of spintronics. We used neutron scattering to observe the influence of an electric current on the magnetic structure in a bulk material. In the skyrmion lattice of manganese silicon, where the spins form a lattice of magnetic vortices similar to the vortex lattice in type II superconductors, we observe the rotation of the diffraction pattern in response to currents that are over five orders of magnitude smaller than those typically applied in experimental studies on current-driven magnetization dynamics in nanostructures. We attribute our observations to an extremely efficient coupling of inhomogeneous spin currents to topologically stable knots in spin structures.
Photolysis of Nitrous Oxide. I. 1236 A (1961)

The photolysis of nitrous oxide containing an N15 atom in the external position has been investigated using 1236-A light. The products include N229, N15O, N14O, and small amounts of N230. The appearance of N230 shows that there are two primary processes occurring at this wavelength, one of which is dissociation to a nitrogen atom and a nitric oxide molecule, the other dissociation to an oxygen atom and a nitrogen molecule. The latter process is approximately 10 times as important as the former. The quantum yield of nitrogen is 1.34±0.04.
The Metal Homeostasis Protein, Lsp, of <i>Streptococcus pyogenes</i> Is Necessary for Acquisition of Zinc and Virulence (2009)

"Cluster 9" family lipoproteins function as ligand-binding subunits of ABC-type transporters in maintaining transition metal homeostasis and have been implicated in the virulence of several bacteria. While these proteins share high similarity, the specific metal that they recognize and whether their role in virulence directly involves metal homeostasis cannot be reliably predicted. We examined the cluster 9 protein Lsp of Streptococcus pyogenes and found that specific deletion of lsp produced mutants highly attenuated in a murine model of soft tissue infection. Under standard in vitro conditions, growth of the Lsp(-) mutant was indistinguishable from that of the wild type, but growth was defective under zinc-limited conditions. The growth defect could be complemented by plasmids expressing wild-type Lsp but not Lsp engineered to lack its putative lipidation residue. Furthermore, Zn(2+) but not Mn(2+) rescued Lsp(-) growth, implicating Zn(2+) as the physiological ligand for Lsp. Mutation of residues in the putative Zn(2+)-binding pocket generated variants both hypo- and hyper-resistant to zinc starvation, and both mutant classes displayed attenuated virulence. Together, these data suggest that Lsp is a ligand-binding component of an ABC-type zinc permease and that perturbation of zinc homeostasis inhibits the ability of S. pyogenes to cause disease in a zinc-limited host milieu.
Effects of Co-occurring Genomic Alterations on Outcomes in Patients with <i>KRAS</i> -Mutant Non–Small Cell Lung Cancer (2017)

<b>Purpose:</b><i>KRAS</i> mutations occur in approximately 25% of patients with non-small cell lung cancer (NSCLC). Despite the uniform presence of <i>KRAS</i> mutations, patients with <i>KRAS</i>-mutant NSCLC can have a heterogeneous clinical course. As the pattern of co-occurring mutations may describe different biological subsets of patients with <i>KRAS</i>-mutant lung adenocarcinoma, we explored the effects of co-occurring mutations on patient outcomes and response to therapy.<b>Experimental Design:</b> We identified patients with advanced <i>KRAS</i>-mutant NSCLC and evaluated the most common co-occurring genomic alterations. Multivariate analyses were performed incorporating the most frequent co-mutations and clinical characteristics to evaluate association with overall survival as well as response to platinum-pemetrexed chemotherapy and immune checkpoint inhibitors.<b>Results:</b> Among 330 patients with advanced <i>KRAS</i>-mutant lung cancers, the most frequent co-mutations were found in <i>TP53</i> (42%), <i>STK11</i> (29%), and <i>KEAP1</i>/<i>NFE2L2</i> (27%). In a multivariate analysis, there was a significantly shorter survival in patients with co-mutations in <i>KEAP1</i>/<i>NFE2L2</i> [HR, 1.96; 95% confidence interval (CI), 1.33-2.92; <i>P</i> ≤ 0.001]. <i>STK11</i> (HR, 1.3; <i>P</i> = 0.22) and <i>TP53</i> (HR 1.11, <i>P</i> = 0.58) co-mutation statuses were not associated with survival. Co-mutation in <i>KEAP1</i>/<i>NFE2L2</i> was also associated with shorter duration of initial chemotherapy (HR, 1.64; 95% CI, 1.04-2.59; <i>P</i> = 0.03) and shorter overall survival from initiation of immune therapy (HR, 3.54; 95% CI, 1.55-8.11; <i>P</i> = 0.003).<b>Conclusions:</b> Among people with <i>KRAS</i>-mutant advanced NSCLC, <i>TP53, STK11</i>, and <i>KEAP1</i>/<i>NFE2L2</i> are the most commonly co-occurring somatic genomic alterations. Co-mutation of <i>KRAS</i> and <i>KEAP1</i>/ <i>NFE2L2</i> is an independent prognostic factor, predicting shorter survival, duration of response to initial platinum-based chemotherapy, and survival from the start of immune therapy. <i>Clin Cancer Res; 24(2); 334-40. ©2017 AACR</i>.
Covariation of a Specificity-Determining Structural Motif in an Aminoacyl-tRNA Synthetase and a tRNA Identity Element (2001)

Transfer RNA (tRNA) identity determinants help preserve the specificity of aminoacylation in vivo, and prevent cross-species interactions. Here, we investigate covariation between the discriminator base (N73) element in histidine tRNAs and residues in the histidyl-tRNA synthetase (HisRS) motif 2 loop. A model of the Escherichia coli HisRS--tRNA(His) complex predicts an interaction between the prokaryotic conserved glutamine 118 of the motif 2 loop and cytosine 73. The substitution of Gln 118 in motif 2 with glutamate decreased discrimination between cytosine and uracil some 50-fold, but left overall rates of adenylation and aminoacylation unaffected. By contrast, substitutions at neighboring Glu 115 and Arg 121 affected both adenylation and aminoacylation, consistent with their predicted involvement in both half-reactions. Additional evidence for the involvement of the motif 2 loop was provided by functional analysis of a hybrid Saccharomyces cerevisiae-- E. coli HisRS possessing the 11 amino acid motif 2 loop of the yeast enzyme. Despite an overall decreased activity of nearly 1000-fold relative to the E. coli enzyme, the chimera nevertheless exhibited a modest preference for the yeast tRNA(His) over the E. coli tRNA, and preferred wild-type yeast tRNA(His) to a variant with C at the discriminator position. These experiments suggest that part of, but not all of, the specificity is provided by the motif 2 loop. The close interaction between enzyme loop and RNA sequence elements suggested by these experiments reflects a covariation between enzyme and tRNA that may have acted to preserve aminoacylation fidelity over evolutionary time.
An analysis of security issues for cloud computing (2013)

Cloud Computing is a flexible, cost-effective, and proven delivery platform for providing business or consumer IT services over the Internet. However, cloud Computing presents an added level of risk because essential services are often outsourced to a third party, which makes it harder to maintain data security and privacy, support data and service availability, and demonstrate compliance. Cloud Computing leverages many technologies (SOA, virtualization, Web 2.0); it also inherits their security issues, which we discuss here, identifying the main vulnerabilities in this kind of systems and the most important threats found in the literature related to Cloud Computing and its environment as well as to identify and relate vulnerabilities and threats with possible solutions.
Distribution of de novo synthesized betaine in rat kidney: role of renal synthesis on medullary betaine accumulation (1997)

The trimethylamine glycine-betaine is accumulated to high concentrations in medullary cells of mammalian kidneys, whereas betaine synthesis from choline is predominant in the renal cortex. We investigated the contribution of renal betaine synthesis to medullary betaine accumulation. De novo synthesis of betaine in situ was accomplished by injecting [14C]choline into the renal artery of male Sprague-Dawley rats. [14C]betaine was measured in the renal cortex and medulla, as well as in serum and urine samples. Betaine concentration in the cortex decreased from 3.5 +/- 1.3 at 5 min to 0.4 +/- 0.2 nmol/mg protein at 60 min, but it increased from 1.4 +/- 0.1 to 2.5 +/- 0.6 nmol/mg protein in the medulla. Serum and total urine [14C]betaine increased from 2.7 +/- 1.3 and 0.9 +/- 0.1 nmol/ml at 5 min to 5.3 +/- 0.3 and 2.1 +/- 0.4 nmol/ml at 60 min, respectively. Concentrations of newly synthesized betaine were not decreased by the ligation of the hepatic artery and portal vein, suggesting that most [14C]betaine was synthesized in the kidney. Coinjection with 5 mM dimethylamino-ethanol, a choline oxidase inhibitor, and 100 mM cold betaine reduced medullary betaine accumulation by 80 and 76%, respectively. Water deprivation for 60 h increased both cortical and medullary [14C]betaine, whereas furosemide diuresis decreased the medullary [14C]betaine concentration. We concluded that betaine synthesized in the kidney can be accumulated in the medulla and that the medullary concentrations of newly synthesized betaine are closely related to the hydration state of the animal.
Insulin-like growth factor I and epidermal growth factor regulate the expression of transferrin receptors at the cell surface by distinct mechanisms. (1987)

The transferrin receptor cycles rapidly between cell surface and endosomal membrane compartments. Treatment of cultured cells with epidermal growth factor (EGF) or insulin-like growth factor I (IGF-I) at 37 degrees C causes a rapid redistribution of transferrin receptors from an intracellular compartment to the cell surface. The effects of EGF and IGF-I on the kinetics of the cycling of the transferrin receptor in A431 human epidermoid carcinoma cells were compared. The primary site of EGF action was found to be an increase in the rate of transferrin receptor exocytosis. The exocytotic rate constant was measured to be 0.11 min-1 in control cells and 0.33 min-1 in EGF-treated cells. In contrast, IGF-I was found to increase the cell surface expression of transferrin receptors by causing a small increase in the rate of exocytosis (from 0.11 to 0.17 min-1) and a decrease in the rate of endocytosis (from 0.33 to 0.24 min-1). It is concluded that the mechanisms for EGF and IGF-I action to increase the cell surface expression of the transferrin receptor are distinct. A kinetic model of the cycling of the transferrin receptor based on experimentally determined rate constants is presented. The model predicts that a consequence of IGF-I action on transferrin receptor cycling is to decrease the apparent Km for the uptake of diferric transferrin by cells. This prediction is confirmed by direct measurement of the accumulation of 59Fe-labeled diferric transferrin by A431 cells. These data demonstrate that the accumulation of iron by cultured cells is a complex function of the rate of cycling of the transferrin receptor and that this process is under acute regulation by growth factors.
NuClick: A Deep Learning Framework for Interactive Segmentation of Microscopy Images (2020)

Object segmentation is an important step in the workflow of computational pathology. Deep learning based models generally require large amount of labeled data for precise and reliable prediction. However, collecting labeled data is expensive because it often requires expert knowledge, particularly in medical imaging domain where labels are the result of a time-consuming analysis made by one or more human experts. As nuclei, cells and glands are fundamental objects for downstream analysis in computational pathology/cytology, in this paper we propose a simple CNN-based approach to speed up collecting annotations for these objects which requires minimum interaction from the annotator. We show that for nuclei and cells in histology and cytology images, one click inside each object is enough for NuClick to yield a precise annotation. For multicellular structures such as glands, we propose a novel approach to provide the NuClick with a squiggle as a guiding signal, enabling it to segment the glandular boundaries. These supervisory signals are fed to the network as auxiliary inputs along with RGB channels. With detailed experiments, we show that NuClick is adaptable to the object scale, robust against variations in the user input, adaptable to new domains, and delivers reliable annotations. An instance segmentation model trained on masks generated by NuClick achieved the first rank in LYON19 challenge. As exemplar outputs of our framework, we are releasing two datasets: 1) a dataset of lymphocyte annotations within IHC images, and 2) a dataset of segmented WBCs in blood smear images.
Highly Efficient, Regioselective, and Stereospecific Oxidation of Aliphatic C–H Groups with H<sub>2</sub>O<sub>2</sub>, Catalyzed by Aminopyridine Manganese Complexes (2012)

Aminopyridine manganese complexes [LMn(II)(OTf)(2)] having a similar coordination topology catalyze the oxidation of unactivated aliphatic C-H groups with H(2)O(2), demonstrating excellent efficiency (up to TON = 970), site selectivity, and stereospecificity (up to >99%).
Die Nachkriegsaufgaben der Fremdenverkehrspolitik (1947)

In der Zeit zwischen den beiden Weltkriegen ist der Fremdenverkehr dank der technischen Fortschritte im Verkehrswesen und der dadurch bedingten Erfüllung der Reisesebnsucht breiter Volksschichten zu einer weltweiten Erscheinung geworden und hat daher aufgehört, ausschliesslich eine innere Angelegenheit einzelner mit besonderer Anziehungskraft ausgestatteten Länder zu sein. Für Europa wurde diese Erkenntnis in erster Reihe durch eine Steigerung des Zuzugs aus Übersee zur bewussten Tatsache. Dies war der Grund, weshalb wir uns zeitweilig in gemeinsamen Werbeaktionen zusammengefunden haben, weshalb wir alle gemeinsam die Abschaffung des Pass‐ und Sichtvermerkzwanges forderten, und eben aus diesem Grunde waren wir auch bestrebt, die bald bier, bald dort auftretenden strengen Devisenbeschränkungen in ihren ungünstigen Auswirkungen auf den Fremdenverkehr mit alien zur Verfügung stehenden zulässigen Mitteln zu mildern oder abzuwenden.
Dose dependence of microstructural development of buried oxide in oxygen implanted silicon-on-insulator material (1997)

The effect of implantation dose on microstructural development of the buried oxide (BOX) of 200 keV oxygen implanted Si was studied by electron microscopy. A continuous BOX layer with a low density of Si islands was obtained for a dose of 0.45×1018 cm−2, following high temperature annealing. At a lower dose of 0.225×1018 cm−2 a layer did not form, but only disjointed, isolated, oxide precipitates developed. At a higher dose, 0.675×1018 cm−2, a continuous BOX layer with a high density of Si islands formed. Microstructures of intermediate-temperature annealed samples showed the formation of oxide precipitates at preferred depths, the morphology being dose dependent. The final microstructure of the BOX is strongly influenced by the evolution of the oxide precipitates during annealing. A qualitative mechanism is proposed for the dose-dependent behavior of BOX formation during the annealing process.
Autonomous conformational regulation of β <sub>3</sub> integrin and the conformation-dependent property of HPA-1a alloantibodies (2018)

Integrin α/β heterodimer adopts a compact bent conformation in the resting state, and upon activation undergoes a large-scale conformational rearrangement. During the inside-out activation, signals impinging on the cytoplasmic tail of β subunit induce the α/β separation at the transmembrane and cytoplasmic domains, leading to the extended conformation of the ectodomain with the separated leg and the opening headpiece that is required for the high-affinity ligand binding. It remains enigmatic which integrin subunit drives the bent-to-extended conformational rearrangement in the inside-out activation. The β<sub>3</sub> integrins, including α<sub>IIb</sub>β<sub>3</sub> and α<sub>V</sub>β<sub>3</sub>, are the prototypes for understanding integrin structural regulation. The Leu33Pro polymorphism located at the β<sub>3</sub> PSI domain defines the human platelet-specific alloantigen (HPA) 1a/b, which provokes the alloimmune response leading to clinically important bleeding disorders. Some, but not all, anti-HPA-1a alloantibodies can distinguish the α<sub>IIb</sub>β<sub>3</sub> from α<sub>V</sub>β<sub>3</sub> and affect their functions with unknown mechanisms. Here we designed a single-chain β<sub>3</sub> subunit that mimics a separation of α/β heterodimer on inside-out activation. Our crystallographic and functional studies show that the single-chain β<sub>3</sub> integrin folds into a bent conformation in solution but spontaneously extends on the cell surface. This demonstrates that the β<sub>3</sub> subunit autonomously drives the membrane-dependent conformational rearrangement during integrin activation. Using the single-chain β<sub>3</sub> integrin, we identified the conformation-dependent property of anti-HPA-1a alloantibodies, which enables them to differently recognize the β<sub>3</sub> in the bent state vs. the extended state and in the complex with α<sub>IIb</sub> vs. α<sub>V</sub> This study provides deeper understandings of integrin conformational activation on the cell surface.