gebhart/patrepeval huggingface dataset:
Intraperitoneal delivery of a small interfering RNA targeting NEDD1 prolongs the survival of scirrhous gastric cancer model mice (2012)

The prognosis of patients with advanced diffuse-type gastric cancer (GC), especially scirrhous gastric cancer (SGC) remains extremely poor. Peritoneal carcinomatosis is a frequent form of metastasis of SGC. With survival rates of patients with peritoneal metastasis at 3 and 5 years being only 9.8% and 0%, respectively, development of a new treatment is urgently crucial. For such development, the establishment of a therapeutic mouse model is required. Among the 11 GC cell lines we examined, HSC-60 showed the most well-preserved expression profiles of the Hedgehog and epithelial-mesenchymal transition pathways found in primary SGCs. After six cycles of harvest of ascitic tumor cells and their orthotopic inoculation in scid mice, a highly metastatic subclone of HSC-60, 60As6 was obtained, by means of which we successfully developed peritoneal metastasis model mice. The mice treated with small interfering (si) RNA targeting NEDD1, which encodes a gamma-tubulin ring complex-binding protein, by the atelocollagen-mediated delivery system showed a significantly prolonged survival. Our mouse model could thus be useful for the development of a new therapeutic modality. Intraperitoneal administration of siRNAs of targeted genes such as NEDD1 could provide a new opportunity in the treatment of the peritoneal metastasis of SGC.
State of the Art: Coordinated &amp; Multiple Views in Exploratory Visualization (2007)

The area of coordinated and multiple views has been steadily developing and maturing over the past fifteen years. Some may say that it is a "solved problem', while others argue that we are only just scratching the surface of the subject. Considering merely the CMV conference series, it is clear to see that in the early years researchers were concerned with models and techniques, while in latter years authors presented more work on how to apply these ideas to different domains. It is our view that there is still much research to be done, but the subject is changing and developing as a tool for visual analytics. This paper provides the "state of the art' of CMV, it describes areas that should be developed further and looks at what the future may hold for coordinated and multiple views.
FastCap: a multipole accelerated 3-D capacitance extraction program (1991)

A fast algorithm for computing the capacitance of a complicated three-dimensional geometry of ideal conductors in a uniform dielectric is described and its performance in the capacitance extractor FastCap is examined. The algorithm is an acceleration of the boundary-element technique for solving the integral equation associated with the multiconductor capacitance extraction problem. The authors present a generalized conjugate residual iterative algorithm with a multipole approximation to compute the iterates. This combination reduces the complexity so that accurate multiconductor capacitance calculations grow nearly as nm, where m is the number of conductors. Performance comparisons on integrated circuit bus crossing problems show that for problems with as few as 12 conductors the multipole accelerated boundary element method can be nearly 500 times faster than Gaussian-elimination-based algorithms, and five to ten times faster than the iterative method alone, depending on required accuracy.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cloning of the Human Equilibrative, Nitrobenzylmercaptopurine Riboside (NBMPR)-insensitive Nucleoside Transporter ei by Functional Expression in a Transport-deficient Cell Line (1998)

Mammalian cells obtain nucleic acid precursors through the de novo synthesis of nucleotides and the salvage of exogenous nucleobases and nucleosides. The first step in the salvage pathway is transport across the plasma membrane. Several transport activities, including equilibrative and concentrative mechanisms, have been identified by their functional properties. We report here the functional cloning of a 2.6-kilobase pair human cDNA encoding the nitrobenzylmercaptopurine riboside (NBMPR)-insensitive, equilibrative nucleoside transporter ei by functional complementation of the transport deficiency in a subline of CEM human leukemia cells. Expression of this cDNA conferred an NBMPR-insensitive, sodium-independent nucleoside transport activity to the cells that exhibited substrate specificity and inhibitor sensitivity characteristic of the ei transporter. The cDNA contained a single open reading frame that encoded a 456-residue protein with 11 potential membrane-spanning regions and two consensus sites for N-glycosylation in the first predicted extracellular loop. The predicted protein was 50% identical to the recently cloned human NBMPR-sensitive, equilibrative nucleoside transporter ENT1 and thus was designated ENT2. Surprisingly, the carboxyl-terminal portion of the ENT2 protein was nearly identical to a smaller protein in the GenBankTM data base (human HNP36, 326 residues) that has been identified as a growth factor-induced delayed early response gene of unknown function. Comparison of the ENT2 and HNP36 nucleotide sequences suggested that HNP36 was translated from a second start codon within the ENT2 open reading frame. Transient expression studies with the full-length ENT2 and a 5'-truncated construct that lacks the first start codon (predicted protein 99% identical to HNP36) demonstrated that only the full-length construct conferred uridine transport activity to the cells. These data suggest that the delayed early response gene HNP36 is a truncated form of ENT2 and that the full-length open reading frame of ENT2 is required for production of a functional plasma membrane ei transporter.
Description of Six New Capsular Types (29–34) ofStreptococcus Suis (1995)

Streptococcus suis is probably the most important veterinary pathogen among streptococcal species belonging to the Lancefield group D. During the last 2 decades, it has been associated with a variety of infections in pigs and was recognized as an important zoonotic agent. Since its official recognition as a species in 1987, S. suis has been found in many other animal species, including cattle, small ruminants, horses, dogs, and cats . The number of capsular types has increased from 9 in 1983 to 29 in 1991. Among all S. suis capsular types, capsular type 2 is always the most prevalent type isolated from diseased pigs in most countries where the swine industry is important. This type also is practically the only one that causes human cases of septicemia, meningitis, and endocarditis. The majority of other isolates associated with pathologic processes belongs to capsular types 1/2, 3, 4, 6, 7, 8, and 9. Some capsular types such as 18, 19, and 21 are generally recovered from clinically healthy animals. 10 The number of untypeable S. suis isolates is now relatively low. Because some of these isolates are recovered in large numbers from several tissues of a diseased animal, they are considered potential pathogens for animals and they become candidates for new capsular types. In this article, we describe and propose 6 new capsular types of S. suis, designated as 29, 30, 31, 32, 33, and 34. Bacterial strains included in this study were reference strains of S. suis capsular types 1-28 and 1/2 and 6 other strains representing proposed capsular types 29-34. Strains representing capsular types 29, 30, 32, and 34 were recovered from diseased pigs, whereas strains representing capsular types 31 and 33 were isolated from a diseased calf and a diseased lamb, respectively. One of the diseased pigs had meningitis and 1 had septicemia, and the last 2 were aborted fetuses. The 2-month-old Holstein calf was affected with a cerebral edema and a generalized vasculitis, and S. suis was isolated in large numbers from the brain and lungs. The lamb had marked posterior paresis, and the right coxal femoral joint had marked thickening of the joint capsule with fibrin present in the joint space. Bacteriologic culturing of the synovial fluid resulted in the recovery of a large pure population of S. suis. Capsular types 29, 30, 31, and 34 reference strains originated from the Clinical Bacteriology Laboratory of the Faculty of Veterinary Medicine at the University of Montreal, and capsular types 32 and 33 reference strains were provided by S. A. Rawiuk, Bacteriology Section, Animal Health Laborato-
Irritable Bowel Syndrome (1993)

Irritable bowel syndrome is one of a group of disorders that includes chest pain of unexplained origin, nonulcer dyspepsia, and biliary dyskinesia. These chronic disorders are frequently considered functional, because no specific structural or biochemical cause has been found1. In all likelihood, the pathogenesis involves disordered motility or altered visceral sensation, although no consistent abnormality has been identified. In addition, psychosocial factors affect the clinical expression of these disorders.Definition and Clinical PresentationPatients with irritable bowel syndrome have a broad range of symptoms well known to most clinicians. The symptoms may be continuous or intermittent but should be . . .
Microplate alamar blue assay versus BACTEC 460 system for high-throughput screening of compounds against Mycobacterium tuberculosis and Mycobacterium avium (1997)

In response to the need for rapid, inexpensive, high-throughput assays for antimycobacterial drug screening, a microplate-based assay which uses Alamar blue reagent for determination of growth was evaluated. MICs of 30 antimicrobial agents against Mycobacterium tuberculosis H37Rv, M. tuberculosis H37Ra, and Mycobacterium avium were determined in the microplate Alamar blue assay (MABA) with both visual and fluorometric readings and compared to MICs determined in the BACTEC 460 system. For all three mycobacterial strains, there was < or = 1 dilution difference between MABA and BACTEC median MICs in four replicate experiments for 25 to 27 of the 30 antimicrobics. Significant differences between MABA and BACTEC MICs were observed with 0, 2, and 5 of 30 antimicrobial agents against H37Rv, H37Ra, and M. avium, respectively. Overall, MICs determined either visually or fluorometrically in MABA were highly correlated with those determined in the BACTEC 460 system, and visual MABA and fluorometric MABA MICs were highly correlated. MICs of rifampin, rifabutin, minocycline, and clarithromycin were consistently lower for H37Ra compared to H37Rv in all assays but were similar for most other drugs. M. tuberculosis H37Ra may be a suitable surrogate for the more virulent H37Rv strain in primary screening of compounds for antituberculosis activity. MABA is sensitive, rapid, inexpensive, and nonradiometric and offers the potential for screening, with or without analytical instrumentation, large numbers of antimicrobial compounds against slow-growing mycobacteria.
Silver Iodide Formation in Methyl Ammonium Lead Iodide Perovskite Solar Cells with Silver Top Electrodes (2015)

Silver is a low‐cost candidate electrode material for perovskite solar cells. However, in such cells the silver electrodes turn yellow within days of device fabrication. The color change is also accompanied by a dramatic decrease in the power conversion efficiency when compared to otherwise identical devices using gold electrodes. Here, it is shown that the color change results from silver oxidation to silver iodide, due to a reaction with iodine in methyl ammonium lead perovskite. The change in X‐ray diffraction and X‐ray photo­electron spectroscopy is discussed. Exposure to air accelerates corrosion of the Ag electrodes when compared to dry nitrogen gas exposure. However, iodine not reacted with silver is observed by X‐ray photoelectron spectroscopy even for the perovskite solar cell kept in dry nitrogen gas. It is proposed that silver iodide is formed when methyl ammonium iodide migration is facilitated by the small pinholes in the hole transport layer spiro‐MeOTAD.
RNase L Mediates Transient Control of the Interferon Response through Modulation of the Double-stranded RNA-dependent Protein Kinase PKR (2003)

The transient control of diverse biological responses that occurs in response to varied forms of stress is often a highly regulated process. During the interferon (IFN) response, translational repression due to phosphorylation of eukaryotic initiation factor 2alpha, eIF2alpha, by the double-stranded RNA-dependent protein kinase, PKR, constitutes a means of inhibiting viral replication. Here we show that the transient nature of the IFN response against acute viral infections is regulated, at least in part, by RNase L. During the IFN antiviral response in RNase L-null cells, PKR mRNA stability was enhanced, PKR induction was increased, and the phosphorylated form of eIF2alpha appeared with extended kinetics compared with similarly treated wild type cells. An enhanced IFN response in RNase L-null cells was also demonstrated by monitoring inhibition of viral protein synthesis. Furthermore, ectopic expression of RNase L from a plasmid vector prevented the IFN induction of PKR. These results suggest a role for RNase L in the transient control of the IFN response and possibly of other cytokine and stress responses.
High performance stacked crystal filters for GPS and wide bandwidth applications (2002)

Stacked Crystal Filters, (SCF), are composed of multi-layers of piezoelectric and metal layers. Normally these filters have a complex frequency spectrum containing near-in spurious responses. However, by having the SCF formed in a Solidly Mounted Resonator (SMR) format, the performance of the device is greatly improved by the finite bandwidth of the SMR reflector. The conventional SCF also has a bandwidth that is too small for some wireless applications. This paper will describe the design and performance issues associated with stacked crystal filters using bulk wave thin films with aluminum nitride as the piezoelectric. Filters without spurious responses, filters having wide bandwidths, and filters operating at frequencies up to 8.5 GHz will be described in addition to GPS filters.
Propranolol hydrochloride enhancement of tumor perfusion and uptake of gallium-67 in a mouse sarcoma. (1986)

The effect of propranolol hydrochloride on the blood perfusion of a mouse sarcoma and other tissues has been studied using 86Rb. The maximum increase in relative tumor perfusion (2x controls) occurred 15 min after an i.v. administration of 10 mg per kg propranolol hydrochloride. To study the effect of this drug on the uptake of 67Ga, it was injected at a concentration of 10 mg/kg 10 min before administering 3 microCi (110 kBq) [67Ga]citrate. Tissue uptakes were measured 4 hr later. The tumor: blood ratio increased from 1.16 +/- 0.17 to 3.41 +/- 2.27 (s.d.) and tumor: liver ratio increased from 2.39 +/- 0.30 to 7.13 +/- 3.52 (s.d.). The results showed that propranolol hydrochloride can improve the relative tumor blood flow and radiopharmaceutical concentration in an animal model. It is hoped that this and other agents will yield similar results in the human situation.
Evaluation of plasma levels of tumour necrosis factor alpha and interleukin-6 as rejection markers in a cohort of 142 heart-grafted patients followed by endomyocardial biopsy (1997)

The rejection reaction after cell or organ transplantation has to be detected as early as possible in order to conduct optimal immunosuppressive treatment. Among the numerous events leading to rejection, cytokine production, especially of tumour necrosis factor alpha, is particularly important. Interleukin-6 and tumour necrosis factor alpha were investigated in 142 heart-grafted patients in order to define an early peripheral non-invasive marker of an acute rejection that could fit well with myocardial biopsy results. Cytokines were immunoenzymatically measured in blood specimens collected on the day of the endomyocardial biopsy. The values were compared to the grade of heart graft rejection established according to pathological criteria. Plasma interleukin-6 and especially tumour necrosis factor alpha determined on the day of the rejection diagnosis were significantly increased in the patient sample with moderate or severe rejection when compared with mean values of interleukin-6 and tumour necrosis factor alpha in the patient sample without rejection or with mild rejection (P = 0.04 and 0.001 respectively). Because high levels of tumour necrosis factor alpha may appear before histological signs, this biological marker could be useful in the follow-up of heart-grafted patients.
Atomic Decomposition by Basis Pursuit (1998)

The time-frequency and time-scale communities have recently developed a large number of overcomplete waveform dictionaries --- stationary wavelets, wavelet packets, cosine packets, chirplets, and warplets, to name a few. Decomposition into overcomplete systems is not unique, and several methods for decomposition have been proposed, including the method of frames (MOF), Matching pursuit (MP), and, for special dictionaries, the best orthogonal basis (BOB). Basis Pursuit (BP) is a principle for decomposing a signal into an "optimal" superposition of dictionary elements, where optimal means having the smallest l1 norm of coefficients among all such decompositions. We give examples exhibiting several advantages over MOF, MP, and BOB, including better sparsity and superresolution. BP has interesting relations to ideas in areas as diverse as ill-posed problems, in abstract harmonic analysis, total variation denoising, and multiscale edge denoising. BP in highly overcomplete dictionaries leads to large-scale optimization problems. With signals of length 8192 and a wavelet packet dictionary, one gets an equivalent linear program of size 8192 by 212,992. Such problems can be attacked successfully only because of recent advances in linear programming by interior-point methods. We obtain reasonable success with a primal-dual logarithmic barrier method and conjugate-gradient solver.
IBD: Microbiota Manipulation through Diet and Modified Bacteria (2014)

Strategies that target the microbiota or the host defence against it appear to be good prospects for therapy and deserve greater investment.
Perspectives on holoprosencephaly: Part II. Central nervous system, craniofacial anatomy, syndrome commentary, diagnostic approach, and experimental studies. (1993)

This paper presents an updated analytic review of the holoprosencephalic disorders. Central nervous system findings and craniofacial anatomy are discussed in depth. Associated anomalies and syndromes are updated with a syndrome commentary that attempts to separate durable syndromes from associated anomalies and spurious entities. The differential diagnosis of various conditions that may simulate the holoprosencephalic disorders is also discussed. Various experimental approaches to holoprosencephaly are reviewed, indicating that holoprosencephaly appears to be both etiologically and pathogenetically heterogeneous.
Comparison of background EEG activity of different groups of patients with idiopathic epilepsy using Shannon spectral entropy and cluster-based permutation statistical testing (2017)

Idiopathic epilepsy is characterized by generalized seizures with no apparent cause. One of its main problems is the lack of biomarkers to monitor the evolution of patients. The only tools they can use are limited to inspecting the amount of seizures during previous periods of time and assessing the existence of interictal discharges. As a result, there is a need for improving the tools to assist the diagnosis and follow up of these patients. The goal of the present study is to compare and find a way to differentiate between two groups of patients suffering from idiopathic epilepsy, one group that could be followed-up by means of specific electroencephalographic (EEG) signatures (intercritical activity present), and another one that could not due to the absence of these markers. To do that, we analyzed the background EEG activity of each in the absence of seizures and epileptic intercritical activity. We used the Shannon spectral entropy (SSE) as a metric to discriminate between the two groups and performed permutation-based statistical tests to detect the set of frequencies that show significant differences. By constraining the spectral entropy estimation to the [6.25-12.89) Hz range, we detect statistical differences (at below 0.05 alpha-level) between both types of epileptic patients at all available recording channels. Interestingly, entropy values follow a trend that is inversely related to the elapsed time from the last seizure. Indeed, this trend shows asymptotical convergence to the SSE values measured in a group of healthy subjects, which present SSE values lower than any of the two groups of patients. All these results suggest that the SSE, measured in a specific range of frequencies, could serve to follow up the evolution of patients suffering from idiopathic epilepsy. Future studies remain to be conducted in order to assess the predictive value of this approach for the anticipation of seizures.
Crystal structure of the catalytic core domain of the family 6 cellobiohydrolase II, Cel6A, from Humicola insolens, at 1.92 Å resolution (1999)

The three-dimensional structure of the catalytic core of the family 6 cellobiohydrolase II, Cel6A (CBH II), from Humicola insolens has been determined by X-ray crystallography at a resolution of 1.92 Å. The structure was solved by molecular replacement using the homologous Trichoderma reesei CBH II as a search model. The H. insolens enzyme displays a high degree of structural similarity with its T. reeseiequivalent. The structure features both O- (α-linked mannose) and N-linked glycosylation and a hexa-co-ordinate Mg2+ ion. The active-site residues are located within the enclosed tunnel that is typical for cellobiohydrolase enzymes and which may permit a processive hydrolysis of the cellulose substrate. The close structural similarity between the two enzymes implies that kinetics and chain-end specificity experiments performed on the H. insolens enzyme are likely to be applicable to the homologous T. reesei enzyme. These cast doubt on the description of cellobiohydrolases as exo-enzymes since they demonstrated that Cel6A (CBH II) shows no requirement for non-reducing chain-ends, as had been presumed. There is no crystallographic evidence in the present structure to support a mechanism involving loop opening, yet preliminary modelling experiments suggest that the active-site tunnel of Cel6A (CBH II) is too narrow to permit entry of a fluorescenyl-derivatized substrate, known to be a viable substrate for this enzyme.Co-ordinates for the structure described in this paper have been deposited with the Brookhaven Protein Data Bank with accession code 1BVW.PDB.
Semiautonomous Medical Image Segmentation Using Seeded Cellular Automaton Plus Edge Detector (2012)

Segmentations of medical images are required in a number of medical applications such as quantitative analyses and patient-specific orthotics, yet accurate segmentation without significant user attention remains a challenge. This work presents a novel segmentation algorithm combining the region-growing Seeded Cellular Automata with a boundary term based on an edge-detected image. Both single processor and parallel processor implementations are developed and the algorithm is shown to be suitable for quick segmentations (2.2 s for voxel brain MRI) and interactive supervision (2–220 Hz). Furthermore, a method is described for generating appropriate edge-detected images without requiring additional user attention. Experiments demonstrate higher segmentation accuracy for the proposed algorithm compared with both Graphcut and Seeded Cellular Automata, particularly when provided minimal user attention.