gebhart/patrepeval huggingface dataset:
Stereotactic body radiation therapy for non-small cell lung cancer patients with prior history of thoracic surgery and/or radiation therapy: the influence of smoking, size, and central location on risk of complications (2017)

Abstract Purpose The purpose of this retrospective cohort study was to evaluate the effect of tumor location and other major factors on the risk of complications from stereotactic body radiation therapy (SBRT) in non-small cell lung cancer (NSCLC) patients with a history of thoracic surgery and/or radiation therapy. Methods Medical records of patients with recurrent or second primary NSCLC treated with SBRT between 2005 and 2015 were reviewed. All patients had prior thoracic surgery and/or radiation therapy and were treated with image-guided, robotic SBRT. Time to local failure and toxicity was evaluated by using cumulative incidence and competing risk regression analysis. Overall survival was estimated using the Kaplan-Meier method. Results Fifty-six patients with 74 tumors treated with SBRT were included for analysis. Of the 74 tumors, 19 (26%) were centrally located within 2 cm of the proximal bronchial tree. At a median follow-up of 27 months (range = 5–129), the 2-year cumulative incidence of LF was 13% for peripheral tumors and 16% for central tumors ( p = 0.95). Neither prior thoracic surgery nor radiation therapy was associated with increased LF or toxicity. Among the 56 patients, eight (14%), three (5%), and one (2%) experienced grade 2, 3, and 4 complications following SBRT. Patients with a ≥ 50 pack-year smoking history were more likely to develop ≥ grade 2 toxicity (HR 5.3; 95% CI 1.4–19.9, p = 0.01). Central tumor location was associated with higher risk of toxicity (HR 3.4; 95% CI 1.1–10.5, p = 0.04) as was planning tumor volume &gt; 30 mL (HR 4.3; 95% CI 1.1–16.3, p = 0.047). In a multivariable model, central location remained significant after adjusting for smoking history and planning tumor volume. Conclusions After prior thoracic surgery and/or radiation, SBRT retreatment for NSCLC provided durable local control and was well tolerated in most patients. Patients with a history of previously operated and/or radiated lung cancer with new central tumors, PTV volume &gt; 30 mL, or smoking history ≥ 50 pack-years were at higher risk of complications from SBRT.
Replication and expression of thymidine kinase and human globin genes microinjected into mouse fibroblasts. (1980)

A mixture of two recombinant plasmids was microinjected into mouse thymidine kinase-negative fibroblasts (L cells). One plasmid contained the thymidine kinase gene of herpes simplex virus type I and the other contained the human beta globin gene. Seven fibroblast colonies arising from injected cells incubated in hypoxanthine/aminopterin/thymidine medium were analyzed. These microinjected cells were shown to: (i) produce functionally active herpes simplex type I thymidine kinase enzyme, (ii) replicate the human beta globin gene, and (iii) produce human beta globin mRNA sequences at low levels. Thus, the genetic defect (lack of thymidine kinase activity) was corrected by the microinjected thymidine kinase gene, and a coinjected human beta globin gene was replicated and weakly expressed.
Mucoid Pseudomonas aeruginosa growing in a biofilm in vitro are killed by opsonic antibodies to the mucoid exopolysaccharide capsule but not by antibodies produced during chronic lung infection in cystic fibrosis patients (1995)

Serum opsonophagocytic-killing titers often indicate the level of immune resistance to bacterial pathogens, yet in almost all cystic fibrosis (CF) patients that have chronic lung infections with mucoid Pseudomonas aeruginosa, high titers of opsonic-killing Abs can be measured and the infectious pathology still progresses through pulmonary failure and death. This anomalous finding may be due to the use of suspended cells of P. aeruginosa to evaluate phagocytic killing, whereas in the lungs of CF patients the organisms grow in a microcolony or biofilm, encased in mucoid exopolysaccharide (MEP, also called alginate). To determine whether the microcolony mode of growth contributes to bacterial resistance to host defenses, we evaluated opsonophagocytic killing of mucoid P. aeruginosa growing in a biofilm. Abs from infected CF patients were poorly able to mediate opsonic killing of biofilm, but not suspended, mucoid P. aeruginosa cells. Bacterial resistance to killing could be overcome by disruption of the biofilm layer with an enzyme that degrades MEP. Chronically infected CF patients also fail to produce opsonic-killing Abs specific to MEP, and when these Abs were evaluated in sera of older, noninfected CF patients and humans vaccinated with MEP, comparable killing of P. aeruginosa in biofilms and suspensions was obtained. In this case, C3 was deposited onto the MEP layer and could be visualized by fluorescence microscopy deposited throughout the biofilm. We conclude that opsonic Abs made by CF patients in response to chronic infection are ineffective at mediating phagocytic killing and elimination of bacterial cells growing as microcolonies in their lungs.
Urinary TIMP-1 and MMP-2 levels detect the presence of pancreatic malignancies (2014)

Taken together, our results suggest that the detection of uMMP-2 and uTIMP-1 may have diagnostic value in the detection of pancreatic malignancies and that uTIMP-1 may be useful in distinguishing between pancreatic adenocarcinoma and neuroendocrine tumours.
Protein kinase inhibitors prevent junction dissociation induced by low extracellular calcium in MDCK epithelial cells (1992)

When epithelial cell cultures are transferred from a medium with a normal extracellular calcium concentration (1-2 mM) to a medium with a low extracellular calcium concentration (LC, less than 50 microM free Ca2+) cell-cell contacts are disrupted, and the tight junction-dependent transepithelial resistance drops. In this study, I used MDCK epithelial cells to investigate the effects of LC on the localization of the tight junction protein cingulin, and the role of protein kinases in the events induced by LC. Immunofluorescence analysis showed that within 15 min of incubation of confluent monolayers in LC, cingulin labeling was dislocated from the cell periphery, as an array of granules forming a ring-like structure. At later times after calcium removal, cingulin labeling appeared mostly cytoplasmic, in a diffuse and granular pattern, and cells appeared rounded and smaller. These events were not influenced by lack of serum, or by preincubation with 10 mM sodium azide or 6 mg/ml of cycloheximide. However, the disruption of cell-cell contacts, the cell shape changes, and the redistribution of cingulin and other junctional proteins induced by LC were inhibited when cells were pretreated with the protein kinase inhibitor H-7 (greater than or equal to 30 microM). The inhibitors H-8 and, to a lesser degree, staurosporine were also effective, whereas HA-1004 and ML-7 showed essentially no activity, suggesting a specificity of action of different inhibitors. Measurement of the transepithelial resistance showed that the kinase inhibitors that could prevent junction disassembly could also reduce the drop in transepithelial resistance induced by LC. Dose-response curves demonstrated that H-7 is the most effective among the inhibitors, and the transepithelial resistance was 70% of control up to 1 h after calcium removal. These results suggest that low extracellular calcium modulates junctional integrity and cytoskeletal organization through an effector system involving protein kinases.
Spatially Correlated Qubit Errors and Burst-Correcting Quantum Codes (1997)

We explore the design of quantum error-correcting codes for cases where the decoherence events of qubits are correlated. In particular, we consider the case where only spatially contiguous qubits decohere, which is analogous to the case of burst errors in classical coding theory. We present several different efficient schemes for constructing families of such codes. For example, one can find one-dimensional quantum codes of length n=13 and 15 that correct burst errors of width b &lt; 4; as a comparison, a random-error correcting quantum code that corrects t=3 errors must have length n &gt; 18. In general, we show that it is possible to build quantum burst-correcting codes that have near optimal dimension. For example, we show that for any constant b, there exist b-burst-correcting quantum codes with length n, and dimension k=n-log n -O(b); as a comparison, the Hamming bound for the case with t (constant) random errors yields k &lt; n - t log n - O(1) .
ChemInform Abstract: Phases in the Boundary Range of the Zintl‐Phase Class: Sr5Sn2P6 (I) and SrSnP (II). (1986)

Abstract The novel compound (I) (prepared from the elements) crystallizes in the orthorhombic system, space group Pbam with Z=2.
Vapor−Solid Growth of Sn Nanowires:  Growth Mechanism and Superconductivity (2005)

A noncatalytic and template-free vapor transport process has been employed to prepare single-crystalline Sn nanowires with diameters of 10-20 nm. The growth of one-dimensional Sn nanowires follows the mechanism similar to the vapor-solid (V-S) mechanism. Two-dimensional square-shaped nanostructures were also found to form in the region of lower deposition temperatures. The rich morphology may be attributed to the competition in growth rate among different crystallographic planes. Structural characterization with high-resolution transmission electron microscopy showed that the nanowires and nanosquares grew in a preferential direction of [200]. The superconducting transition temperatures for Sn nanowires and Sn nanosquares were about 3.7 K, which was very close to that of bulk beta-Sn. Magnetization measurements showed that the critical magnetic fields for both Sn nanowires and Sn nanosquares increased significantly as compared to that of bulk Sn.
Network bucket testing (2011)

Bucket testing, also known as A/B testing, is a practice that is widely used by on-line sites with large audiences: in a simple version of the methodology, one evaluates a new feature on the site by exposing it to a very small fraction of the total user population and measuring its effect on this exposed group. For traditional uses of this technique, uniform independent sampling of the population is often enough to produce an exposed group that can serve as a statistical proxy for the full population.In on-line social network applications, however, one often wishes to perform a more complex test: evaluating a new social feature that will only produce an effect if a user and some number of his or her friends are exposed to it. In this case, independent uniform draws from the population will be unlikely to produce groups that contains users together with their friends, and so the construction of the sample must take the network structure into account. This leads quickly to challenging combinatorial problems, since there is an inherent tension between producing enough correlation to select users and their friends, but also enough uniformity and independence that the selected group is a reasonable sample of the full population.Here we develop an algorithmic framework for bucket testing in a network that addresses these challenges. First we describe a novel walk-based sampling method for producing samples of nodes that are internally well-connected but also approximately uniform over the population. Then we show how a collection of multiple independent subgraphs constructed this way can yield reasonable samples for testing. We demonstrate the effectiveness of our algorithms through computational experiments on large portions of the Facebook network.
An empirical study of realvideo performance across the internet (2001)

The tremendous increase in computer power and bandwidth connectivity has fueled the growth of streaming video over the Internet to the desktop. While there have been large scale empirical studies of Internet, Web and multimedia traffic, the performance of popular Internet streaming video technologies and the impact of streaming video on the Internet is still largely unkown. This paper presents analysis from a wide-scale empirical study of RealVideo traffic from several Internet servers to many geographically diverse users. We find typical RealVideos to have high quality, achieving an average frame rate of 10 frames per second and very smooth playout, but very few videos achieve full-motion frame rates. Overall video performance is most influenced by the bandwidth of the end-user connection to the Internet, but high-bandwidth Internet connections are pushing the video performance bottleneck closer to the server.
A Space-Economical Suffix Tree Construction Algorithm (1976)

A new algorithm is presented for constructing auxiliary digital search trees to aid in exact-match substring searching. This algorithm has the same asymptotic running time bound as previously published algorithms, but is more economical in space. Some implementation considerations are discussed, and new work on the modification of these search trees in response to incremental changes in the strings they index (the update problem) is presented.
The prognostic significance of p16INK4a/p14ARF locus deletion and MDM‐2 protein expression in adult acute myelogenous leukemia (2000)

The authors concluded that 1) deletions of p16(INK4a)/p14(ARF) and/or p15(INK4b) occur with low incidence in patients with AML; 2) patients with deletions of p16(INK4a)/p14(ARF) and/or p15(INK4b) have a significantly shorter CR duration, EFS rate, and overall survival rate than do patients without deletions; (3) overexpression of MDM-2 is common in AML and is associated with shorter CR duration and EFS rate. Mechanisms other than p14(ARF) deletion are responsible for MDM-2 overexpression, and this overexpression may play a role in the biology of the disease.
Site-directed Mutagenesis Identifies Residues Involved in Ligand Recognition in the Human A2a Adenosine Receptor (1995)

The A2a adenosine receptor is a member of the G-protein coupled receptor family, and its activation stimulates cyclic AMP production. To determine the residues which are involved in ligand binding, several residues in transmembrane domains 5-7 were individually replaced with alanine and other amino acids. The binding properties of the resultant mutant receptors were determined in transfected COS-7 cells. To study the expression levels in COS-7 cells, mutant receptors were tagged at their amino terminus with a hemagglutinin epitope, which allowed their immunological detection in the plasma membrane by the monoclonal antibody 12CA5. The functional properties of mutant receptors were determined by measuring stimulation of adenylate cyclase. Specific binding of [3H]CGS 21680 (15 nM) and [3H]XAC (4 nM), an A2a agonist and antagonist, respectively, was absent in the following Ala mutants: F182A, H250A, N253A, I274A, H278A, and S281A, although they were well expressed in the plasma membrane. The hydroxy group of Ser-277 is required for high affinity binding of agonists, but not antagonists. An N181S mutant lost affinity for adenosine agonists substituted at N6 or C-2, but not at C-5'. The mutant receptors I274A, S277A, and H278A showed full stimulation of adenylate cyclase at high concentrations of CGS 21680. The functional agonist potencies at mutant receptors that lacked radioligand binding were > 30-fold less than those at the wild type receptor. His-250 appears to be a required component of a hydrophobic pocket, and H-bonding to this residue is not essential. On the other hand, replacement of His-278 with other aromatic residues was not tolerated in ligand binding. Thus, some of the residues targeted in this study may be involved in the direct interaction with ligands in the human A2a adenosine receptor. A molecular model based on the structure of rhodopsin, in which the 5'-NH in NECA is hydrogen bonded to Ser-277 and His-278, was developed in order to visualize the environment of the ligand binding site.
Extreme wettability and tunable adhesion: biomimicking beyond nature? (2011)

In this critical review, we summarize the recent developments of extreme wettability in nature and biomimetic examples, and then we focus on surface wetting behavior beyond nature, which means surface wetting properties that cannot be found in nature. They are: switchable wettability between (super)hydrophobicity and (super)hydrophilicity, switchable water/oil droplet adhesion between superhydrophobic pinning states and superhydrophobic rolling states, superoleophobicity at the air–solid interface or even under vacuum, and self-healing (super)amphiphobicity at the air–solid interface.
Expression and Characterization of Soluble and Membrane-bound Human Nucleoside Triphosphate Diphosphohydrolase 6 (CD39L2) (2000)

Ecto-nucleoside-triphosphate diphosphohydrolase-6 (eNTPDase6(1), also known as CD39L2) cDNA was expressed in mammalian COS-1 cells and characterized using nucleotidase assays as well as size exclusion, anion exchange, and cation exchange chromatography. The deduced amino acid sequence of eNTPDase6 is more homologous with the soluble E-type ATPase, eNTPDase5, than other E-type ATPases, suggesting it may also be soluble. To test this possibility, both the cell membranes and the growth media from eNTPDase6-transfected COS-1 cells were assayed for nucleotidase activities. Activity was found in both the membranes and the media. Soluble eNTPDase6 preferentially exhibits nucleoside diphosphatase activity, which is dependent on the presence of divalent cations. Western blot analysis of eNTPDase6 treated with PNGase-F indicated both soluble and membrane-bound forms are glycosylated. However, unlike some membrane-bound ecto-nucleotidases, the eNTPDase6 activity was not specifically inhibited by deglycosylation with peptide N-glycosidase F. Soluble eNTPDase6 hydrolyzed nucleoside triphosphates poorly and nucleoside monophosphates not at all. Analysis of the relative rates of hydrolysis of nucleoside diphosphates (GDP = IDP > UDP > CDP >> ADP) suggests that soluble eNTPDase6 is a diphosphatase most likely not involved in regulation of ADP levels important for circulatory hemostasis.
Expression patterns of the ATM gene in mammary tissues and their associations with breast cancer survival (2007)

The ATM gene expression was down-regulated in breast cancer tissues and a high ATM gene expression level in breast cancer tissue was associated with a favorable prognosis.
Refractive index maps and membrane dynamics of human red blood cells parasitized by Plasmodium falciparum (2008)

Parasitization by malaria-inducing Plasmodium falciparum leads to structural, biochemical, and mechanical modifications to the host red blood cells (RBCs). To study these modifications, we investigate two intrinsic indicators: the refractive index and membrane fluctuations in P. falciparum-invaded human RBCs (Pf-RBCs). We report experimental connections between these intrinsic indicators and pathological states. By employing two noninvasive optical techniques, tomographic phase microscopy and diffraction phase microscopy, we extract three-dimensional maps of refractive index and nanoscale cell membrane fluctuations in isolated RBCs. Our systematic experiments cover all intraerythrocytic stages of parasite development under physiological and febrile temperatures. These findings offer potential, and sufficiently general, avenues for identifying, through cell membrane dynamics, pathological states that cause or accompany human diseases.
Allele-Specific Competitive Blocker–PCR Detection of Rare Base Substitution (2004)

Methods that detect rare base substitutions within populations of DNA molecules are valuable tools for studying the DNA-damaging effects of chemicals and for pool screening for single-nucleotide polymorphisms. Allele-specific competitive blocker-polymerase chain reaction (ACB-PCR) uses a mutant-specific PCR primer with more 3'-terminal mismatches to an abundant or wild-type sequence than to a rare or mutant sequence in order to amplify specifically an allele that differs from the wild-type by a single base pair. ACB-PCR reactions include a blocker primer to reduce the amount of background signal generated from the abundant wild-type template. The nonextendable blocker primer preferentially anneals to the wild-type DNA sequence, thereby excluding the annealing of the extendable mutant-specific primer to the wild-type sequence. Inclusion of single-strand DNA binding protein in the ACB-PCR reaction and use of the Stoffel fragment of Taq DNA polymerase both significantly increase allele discrimination. The concurrent analysis of mutant fraction standards and equivalent PCR products amplified from genomic DNA samples makes ACB-PCR a quantitative method that can detect a base pair substitution in the presence of a 105-fold excess of wild-type DNA. Methods for the ACB-PCR measurement of the mouse H-ras codon 61 CAA --> AAA mutation are presented.
Multicarrier CDMA with adaptive frequency hopping for mobile radio systems (1996)

A modified multicarrier (MC) direct-sequence code-division multiple-access (DS-CDMA) system has been proposed for use over slow multipath fading channels with frequency selectivity in the reverse link transmission of a cellular network. Instead of transmitting data substreams uniformly through subchannels, data substreams hop over subchannels with the hopping patterns adaptively adjusted to the channel fading characteristics. The problem of determining the optimal hopping pattern is formulated as a multiobjective optimization problem, for which an efficient algorithm, based on the water-filling (WF) principle, is designed to solve the problem practically. Simulation results show that the performance in terms of the average bit-error probability (BEP) (over all users) is better than that of single carrier RAKE receiver systems, conventional MC CDMA systems applying moderate error protection, or diversity systems with different combining techniques.
Training health workers for primary care in a developing health service. (1978)

Summary

To provide primary health care in a thinly populated mountainous country with few doctors presents great difficulties. The Royal Government of Bhutan decided to base their primary medical care service on appropriately trained medical auxiliaries. The training programme is described, and the problems of assessing the field activities discussed.