gebhart/patrepeval huggingface dataset:
[Identification of crude oils in Bohai Sea by polycyclic aromatic hydrocarbon fingerprinting]. (2008)

Crude oils from different sources have quite different polycyclic aromatic hydrocarbon (PAH) distributions. Also, many PAH compounds are more resistant to weathering than their saturated counterparts (n-alkanes and isoprenoids) and volatile alkylbenzene compounds, thus PAils become one of the most valuable classes of hydrocarbons for oil identification using fingerprinting. A reliable, effective, and accurate gas chromatography/mass spectrometry (GC/MS) method for the differentiation and source identification of crude oils by the use of PAH compounds is described. PAll components of 6 crude oil samples from 5 different platforms in 4 different oil fields in Bohal Sea were analyzed by GC/MS. Using different methods, such as the comparisons of original fingerprinting, characteristic information, and diagnostic ratios of PAHs, 6 crude oil samples were identified completely, which showed distinctive characteristics of the same platform oils. Although distinction was diminutive, it can still be identified by GC/MS. PAHs could be used in weathering check of spilled oils in identification and to ensure the correctness of the identification.
Isolation of a Candidate Human Telomerase Catalytic Subunit Gene, Which Reveals Complex Splicing Patterns in Different Cell Types (1997)

Telomerase is a multicomponent reverse transcriptase enzyme that adds DNA repeats to the ends of chromosomes using its RNA component as a template for synthesis. Telomerase activity is detected in the germline as well as the majority of tumors and immortal cell lines, and at low levels in several types of normal cells. We have cloned a human gene homologous to a protein from Saccharomyces cerevisiae and Euplotes aediculatus that has reverse transcriptase motifs and is thought to be the catalytic subunit of telomerase in those species. This gene is present in the human genome as a single copy sequence with a dominant transcript of approximately 4 kb in a human colon cancer cell line, LIM1215. The cDNA sequence was determined using clones from a LIM1215 cDNA library and by RT-PCR, cRACE and 3'RACE on mRNA from the same source. We show that the gene is expressed in several normal tissues, telomerase-positive post-crisis (immortal) cell lines and various tumors but is not expressed in the majority of normal tissues analyzed, pre-crisis (non-immortal) cells and telomerase-negative immortal (ALT) cell lines. Multiple products were identified by RT-PCR using primers within the reverse transcriptase domain. Sequencing of these products suggests that they arise by alternative splicing. Strikingly, various tumors, cell lines and even normal tissues (colonic crypt and testis) showed considerable differences in the splicing patterns. Alternative splicing of the telomerase catalytic subunit transcript may be important for the regulation of telomerase activity and may give rise to proteins with different biochemical functions.
Contribution of respiratory acidosis to diaphragmatic fatigue at exercise (2002)

The factors that may modulate ventilatory muscle fatigue during exercise are controversial. In this study the contribution of acidosis to exercise-induced diaphragmatic fatigue was investigated, using measurements of the twitch mouth pressure response (tw,Pmo) to cervical magnetic stimulation. After learning sessions, 14 healthy subjects performed two cycling tests (at 60% of maximal aerobic power for 16 min), one while breathing spontaneously (mean minute ventilation (V'E) 67.9 L x min(-1)) and the other while hypoventilating voluntarily (mean V'E 53.8 L x min(-1)). Exercise was voluntarily set at a moderate power to avoid a fatiguing effect of exercise per se. As compared with spontaneous breathing (SB), voluntary hypoventilation (VHV) significantly increased mean carbon dioxide tension in arterial blood (Pa,CO2) (51 mmHg versus 41 mmHg) and significantly decreased arterial pH (7.28 versus 7.34). After 10 min of SB test, tw,Pmo was unchanged compared to the baseline value (19.1 versus 18.5 cmH2O) whereas tw,Pmo fell significantly as compared to baseline (17.1 versus 18.5 cmH2O) and to SB (17.1 versus 19.1 cmH2O) after the VHV test. The results of this study suggest that exposure to hypercapnia may impair respiratory muscle function. This impairment could be more clinically relevant in patients with chronic obstructive lung disease.
Plasmonic black gold by adiabatic nanofocusing and absorption of light in ultra-sharp convex grooves (2012)

Excitation of localized and delocalized surface plasmon resonances can be used for turning excellent reflectors of visible light, such as gold and silver, into efficient absorbers, whose wavelength, polarization or angular bandwidths are however necessarily limited owing to the resonant nature of surface plasmon excitations involved. Nonresonant absorption has so far been achieved by using combined nano- and micro-structural surface modifications and with composite materials involving metal nanoparticles embedded in dielectric layers. Here we realize nonresonant light absorption in a well-defined geometry by using ultra-sharp convex metal grooves via adiabatic nanofocusing of gap surface plasmon modes excited by scattering off subwavelength-sized wedges. We demonstrate experimentally that two-dimensional arrays of sharp convex grooves in gold ensure efficient (>87%) broadband (450-850 nm) absorption of unpolarized light, reaching an average level of 96%. Efficient absorption of visible light by nanostructured metal surfaces open new exciting perspectives within plasmonics, especially for thermophotovoltaics.
More ‘Malignant’ Than Cancer? Five-Year Survival Following a First Admission for Heart Failure (2001)

With the notable exception of lung cancer, heart failure is as 'malignant' as many common types of cancer and is associated with a comparable number of expected life-years lost.
A clinician's guide to ventilators: how they work and why they can fail. A classification system to make sense of available options. (1992)

To select a ventilator (or a ventilatory mode), consider the most basic characteristics: How is tidal volume generated (with a constant or nonconstant flow or pressure generator)? How does the ventilator trigger a changeover from exhalation to inhalation and cycle back to exhalation? How is tidal volume delivered to the patient (either directly from a power source or indirectly from an intermediate chamber)? What special functions are available? The answers to these questions will not only let you make the best selection but will also help you troubleshoot when a ventilator fails to function properly.
IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices (1999)

This paper describes a new software package, IMPALA, designed for the complementary procedure of comparing a single query sequence with a database of PSI-BLAST-generated PSSMs. We illustrate the use of IMPALA to search a database of PSSMs for protein folds, and one for protein domains involved in signal transduction. IMPALA's sensitivity to distant biological relationships is very similar to that of PSI-BLAST. However, IMPALA employs a more refined analysis of statistical significance and, unlike PSI-BLAST, guarantees the output of the optimal local alignment by using the rigorous Smith-Waterman algorithm. Also, it is considerably faster when run with a large database of PSSMs than is BLAST or PSI-BLAST when run against the complete non-redundant protein database.
Enzymatic barriers to peptide and protein absorption. (1988)

Continuing advances in biotechnology promise to provide a large number of peptides and proteins that would significantly expand the range of pharmaceuticals to treat diseases now poorly controlled. Even at this early stage, it is clear that the success of these entities as drugs of the future would depend, at least in part, on the success in overcoming the obstacles in their delivery. Chief among these are the ubiquitous enzymatic barriers. These include the site of administration, where the peptide is placed, the vascular endothelium that peptides must cross to enter the circulation, the blood that distributes the peptide to its target site, and the liver and kidneys where the peptide is metabolized and eliminated, respectively. The review examines: (1) the nature and efficiency of the enzymatic barriers in degrading peptides and proteins at various absorption sites, and (2) the strategies that can be used to perturb these barriers. These sites include the subcutaneous and intramuscular spaces and the intestinal, nasal, buccal, rectal, vaginal, and ocular surfaces.
Fast Mass Transport Through Sub-2-Nanometer Carbon Nanotubes (2006)

We report gas and water flow measurements through microfabricated membranes in which aligned carbon nanotubes with diameters of less than 2 nanometers serve as pores. The measured gas flow exceeds predictions of the Knudsen diffusion model by more than an order of magnitude. The measured water flow exceeds values calculated from continuum hydrodynamics models by more than three orders of magnitude and is comparable to flow rates extrapolated from molecular dynamics simulations. The gas and water permeabilities of these nanotube-based membranes are several orders of magnitude higher than those of commercial polycarbonate membranes, despite having pore sizes an order of magnitude smaller. These membranes enable fundamental studies of mass transport in confined environments, as well as more energy-efficient nanoscale filtration.
Minireview: The Wnt Signaling Pathway Effector TCF7L2 and Type 2 Diabetes Mellitus (2008)

Since the relationship between TCF7L2 (also known as TCF-4) polymorphisms and type 2 diabetes mellitus was identified in 2006, extensive genome-wide association examinations in different ethnic groups have further confirmed this relationship. As a component of the bipartite transcription factor beta-catenin/TCF, TCF7L2 is important in conveying Wnt signaling during embryonic development and in regulating gene expression during adulthood. Although we still do not know mechanistically how the polymorphisms within the intron regions of TCF7L2 affect the risk of type 2 diabetes, this transcriptional regulator was shown to be involved in stimulating the proliferation of pancreatic beta-cells and the production of the incretin hormone glucagon-like peptide-1 in intestinal endocrine L cells. In this review, we introduce background knowledge of TCF7L2 as a component of the Wnt signaling pathway, summarize recent findings demonstrating the association between TCF7L2 polymorphisms and the risk of type 2 diabetes, outline experimental evidence of the potential function of TCF7L2 in pancreatic and intestinal endocrine cells, and present our perspective views.
Interchromosomal recombination in the extremely radioresistant bacterium Deinococcus radiodurans (1995)

Deinococcus radiodurans and other members of the genus Deinococcus are remarkable for their extreme resistance to ionizing radiation and many other agents that damage DNA. We have recently shown that recombinational processes participate in interplasmidic repair following in vivo irradiation. We now present direct studies on interchromosomal recombination among chromosomes irradiated in vivo during stationary phase (four chromosomes per cell). Following an exposure to 1.75 Mrad (the dose required to achieve a survival of 37%, which degrades the cells' four chromosomes into about 500 fragments), we determined that there may be as many as 175 crossovers per chromosome (700 crossovers per nucleoid) undergoing repair. In addition, these studies suggest that many of the crossovers occurring during repair are nonreciprocal.
The successful experimental induction of necrotic enteritis in chickens by Clostridium perfringens: a critical review (2012)

Necrotic enteritis (NE) is one of the most important enteric diseases in poultry and is a high cost to the industry worldwide. It is caused by avian-specific, Necrotic Enteritis Beta toxin (NetB)-producing, strains of Clostridium perfringens that also possess in common other virulence-associated genes. In Europe the disease incidence has increased since the ban on in-feed "growth promoting" antibiotics. Because of this, many recent studies of NE have focused on finding different ways to control the disease, and on understanding its pathogenesis. Frustratingly, reproduction of the disease has proven impossible for some researchers. This review describes and discusses factors known to be important in reproducing the disease experimentally, as well as other considerations in reproducing the disease. The critical bacterial factor is the use of virulent, netB-positive, strains; virulence can be enhanced by using tpeL- positive strains and by the use of young rather than old broth cultures to increase toxin expression. Intestinal damaging factors, notably the use of concurrent or preceding coccidial infection, or administration of coccidial vaccines, combined with netB-positive C. perfringens administration, can also be used to induce NE. Nutritional factors, particularly feeding high percentage of cereals containing non-starch polysaccharides (NSP) (wheat, rye, and barley) enhance disease by increasing digesta viscosity, mucus production and bacterial growth. Animal proteins, especially fish meal, enhance C. perfringens proliferation and toxin production. Other factors are discussed that may affect outcome but for which evidence of their importance is lacking. The review compares the different challenge approaches; depending on the aim of particular studies, the different critical factors can be adjusted to affect the severity of the lesions induced. A standardized scoring system is proposed for international adoption based on gross rather than histopathological lesions; if universally adopted this will allow better comparison between studies done by different researchers. Also a scoring system is provided to assist decisions on humane euthanasia of sick birds.
Tumor Exosomes: Cellular Postmen of Cancer Diagnosis and Personalized Therapy (2016)

Nanosized (30-150 nm) extracellular vesicles 'exosomes' are secreted by cells for intercellular communication during normal and pathological conditions. Exosomes carry biomacromolecules from cell-of-origin and, therefore, represent molecular bioprint of the cell. Tumor-derived exosomes or TDEx modulate tumor microenvironment by transfer of macromolecules locally as well as at distant metastatic sites. Due to their biological stability, TDEx are rich source of biomarkers in cancer patients. TDEx focused cancer diagnosis allows liquid biopsy-based tumor typing and may facilitate therapy response monitoring by developing novel exosomes diagnostics. Therefore, efficient and specific capturing of exosomes for subsequent amplification of the biomessages; for example, DNA, RNA, miRNA can reinvent cancer diagnosis. Here, in this review, we discuss advancements in exosomes isolation strategies, presence of exosomes biomarkers and importance of TDEx in gauging tumor heterogeneity for their potential use in cancer diagnosis, therapy.
Molecular imaging with polymers (2012)

Polymers open up new possibilities in the field of molecular imaging, allowing sensitive and robust agents that can be imaged over long periods of time. This review highlights some recent advances in polymeric molecular imaging agents in both (pre)clinical and emerging applications.
Fabrication of Microcantilever with a Silicon Tip Prepared by Anodization (1998)

The fabrication process of a microcantilever with a silicon tip prepared by anodization for an atomic force microscope(AFM) is demonstrated. The silicon tip having a high aspect ratio can be prepared using preferential anodization of a silicon wafer with n / p junction. The microcantilever is fabricated by patterning a silicon nitride film deposited on the anodized wafer. The silicon tip is examined by observing the surface morphology of an anisotropically etched silicon step and the grains of a vacuum evaporated Au film.
An Introduction to Pectins: Structure and Properties (1986)

Pectin, a polysaccharide, is composed primarily of essentially linear polymers of D-galactopyranosyluronic acid units joined in α-D(1→4) glycosidic linkages; the polymer chains are esterified to various degrees with methanol. This regular structure is interrupted, however, with L-rhamnopyranosyl units and with side chains containing other neutral sugars. The polymer chains may also be partially acetylated. The most important physical property of pectin is its ability to form spreadable gels. Gel formation results when the polymer chains interact over a portion of their length to form a three-dimensional network. This aggregation of chains occurs through hydrogen bonding, divalent cation crossbridging, and/or hydrophobic interactions.
Prevention of Collagen-Induced Arthritis with an Antibody to gp39, the Ligand for CD40 (1993)

The ligand for the CD40 antigen is a 39-kilodalton protein, gp39, expressed on the surface of activated CD4+ T cells and is essential for thymus-dependent humoral immunity. The role of gp39-CD40 interactions in autoimmune disease was investigated in vivo with the use of an antibody that blocks their interactions (anti-gp39). Arthritis induced in mice by immunization with type II collagen was inhibited by anti-gp39. Anti-gp39 blocked the development of joint inflammation, serum antibody titers to collagen, the infiltration of inflammatory cells into the subsynovial tissue, and the erosion of cartilage and bone. Thus, interference with gp39-CD40 interactions may have therapeutic potential in the treatment of autoimmune disease.
Bacteriophytochromes: Phytochrome-Like Photoreceptors from Nonphotosynthetic Eubacteria (1999)

Phytochromes are a family of photoreceptors used by green plants to entrain their development to the light environment. The distribution of these chromoproteins has been expanded beyond photoautotrophs with the discovery of phytochrome-like proteins in the nonphotosynthetic eubacteria Deinococcus radiodurans and Pseudomonas aeruginosa. Like plant phytochromes, the D. radiodurans receptor covalently binds linear tetrapyrroles autocatalytically to generate a photochromic holoprotein. However, the attachment site is distinct, using a histidine to potentially form a Schiff base linkage. Sequence homology and mutational analysis suggest that D. radiodurans bacteriophytochrome functions as a light-regulated histidine kinase, which helps protect the bacterium from visible light.
Generation of Unidirectionally Propagated Action Potentials in a Peripheral Nerve by Brief Stimuli (1979)

Single, unidirectionally propagated action potentials can be elicited in peripheral nerves by electrical stimuli of short duration. Propagation in one direction is blocked anodically by means of a quasi-trapezoidal stimulus wave form and a modified tripolar electrode configuration. Propagation in the other direction proceeds unhindered. This technique may be applicable to collision blocking of motor nerves for neural prostheses.
TRANSFER OF ZONA-FREE MOUSE EGGS TO UTERINE FOSTER MOTHERS (1969)

Summary. When blastocysts from pregnant mice 3½ days p.c. were transferred to the uteri of synchronous pseudopregnant recipients, the time of onset of implantation (judged by the appearance of pontamine blue reactivity in the uterus) was not altered by removal of the zona pellucida. The competence of zona-free blastocysts to elicit the pontamine blue reaction was similar to that of control blastocysts. The low implantation rate of eight-cell embryos from donors 2½ days p.c., transferred to recipients 3½ days p.c., was not increased by previous removal of the zona. It was concluded that, in mice, the decidualizing stimulus from the blastocyst to the uterus stems neither from the zona itself, nor from cellular contact between the vitelline surface and the uterine epithelium. Removal of the zona by treatment with pronase reduced the viability of transferred blastocysts, so that by mid-gestation the proportion of zona-free blastocysts represented by live embryos was significantly below the control level.
Distinct Epidermal Growth Factor Receptor and KRAS Mutation Patterns in Non–Small Cell Lung Cancer Patients with Different Tobacco Exposure and Clinicopathologic Features (2006)

This study shows EGFR mutations are prevalent in lung adenocarcinoma and suggests that it plays an increasing oncogenic role with decreasing direct tobacco damage.
The Multiple-Tunnel Junction and Its Application to Single-Electron Memory and Logic Circuits (1995)

The multiple-tunnel junction (MTJ) produced by forming a side-gated constriction in δ-doped GaAs is demonstrated as a basic component of single electronics. A single-electron memory cell, in which one bit of information is represented by the excess or lack of a precise number of electrons, was fabricated and the operation was confirmed at liquid helium temperature. A new switching element, the variable-barrier MTJ, and a new circuit, the single-charge injection logic circuit, are proposed.
Duration of Survival in Patients with Myeloma Treated with Thalidomide (2008)

To the Editor: Two years ago, we reported that the incorporation of thalidomide into high-dose therapy for myeloma increased the frequency of complete remission but not the duration of remission and extended event-free survival but not overall survival.1 We now report that after a median follow-up of 8 years, 399 patients remain alive and 286 are event-free, for median durations of 9 years and 5 years, respectively. Although the overall difference in the 8-year survival estimates of 56% for 323 patients who were randomly assigned to the thalidomide group and 45% for 345 patients in the control group was not . . .
Biodegradation of Bombyx mori silk fibroin fibers and films (2003)

Abstract The in vitro biodegradation of Bombyx mori silk fibroin was studied by incubating fibers and films with proteolytic enzymes (collagenase type F, α‐chymotrypsin type I‐S, protease type XXI), for times ranging from 1 to 17 days. The changes in sample weight and degree of polymerization of silk fibers exposed to proteolytic attack were negligible. However, tensile properties were significantly affected, as shown by the drop of strength and elongation as a function of the degradation time. Upon incubation with proteolytic enzymes, silk films exhibited a noticeable decrease of sample weight and degree of polymerization, the extent of which depended on the type of enzyme, on the enzyme‐to‐substrate ratio, and on the degradation time. Protease was more aggressive than α‐chymotrypsin or collagenase. Film fragments resistant to enzymatic degradation were enriched in glycine and alanine. FT‐IR measurements showed that the degree of crystallinity of biodegraded films increased. Soluble degradation products of silk films consisted of a range of peptides widely differing in size, deriving from the amorphous sequences of the silk fibroin chains. Biodegraded fibers showed an increase of surface roughness, while films displayed surface cracks and cavities with internal voids separated by fiber‐like elements. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 91: 2383–2390, 2004