gebhart/patrepeval huggingface dataset:
The prognostic significance of the ratio of positive to total nodes in colorectal cancer (2008)

4045 Background: Patients with node positive colorectal cancer (CRC) have a grave prognosis. Current AJCC staging distinguishes between those with 1–3 positive lymph nodes (N1) and those with 4 or more (N2). We sought to determine whether the ratio of positive to total nodes examined (LNR) was a more powerful predictor of outcome than N staging. Methods: 2,636 patients diagnosed between January 1, 1994 to December 31, 2003 with stage III CRC from Region 5 of the California Cancer Registry were analyzed. LNR was stratified into quintiles of <0.19, 0.2–0.39, 0.4–0.59, 0.6–0.70 or 0.8–1.0. The major endpoint was actuarial 5-year disease specific survival (DSS). Significant differences in DSS between groups were determined by the log-rank test. A multivariate Cox proportional hazard regression was performed for all patients to determine whether N stage, LNR, number of lymph nodes examined, or number of positive lymph nodes were independent prognostic factors. Results: The median age was 71 with women making up 49.9% of the patients. 65% of the patients (n=1,717) had N1 disease; and 35% had N2 disease (n=919). 5 year DSS among N1 and N2 disease was 65% and 47%, respectively (p<0.0001). Within the N1 group, increasing LNR quintiles had worsening 5 year DSS of 71%, 63%, 59%, 52% and 50% (p<0.0001). Similarly for the N2 group, 5 year DSS worsened with increasing LNR quintiles: 74%, 53%, 52%, 43%, and 31% (p<0.0001). Absolute difference in DSS between the highest and lowest quintiles for N1 was 21%; and N2, 43%. Multivariate analysis revealed that the number of nodes examined (p=0.0116), number of positive lymph nodes (p=0.0002), N stage (p=0.0139) and LNR (p=0.017) were all predictors of DSS. Quintiles 4 (RR=1.39, 95% CI=1.0087–1.9253) and 5 (RR=1.72, 95% CI=1.2406–2.4004) were more powerful predictors of DSS than N stage (RR=1.2613, 95% CI=1.0478–1.5184) or number of positive lymph nodes (RR=1.0457, 95% CI=1.0223–1.0698). Conclusions: LNR along with number of lymph nodes examined and number of positive lymph nodes is a predictor of DSS in stage III patients. Furthermore, a LNR ≥ 0.6 (quintiles 4 and 5) is a stronger prognosticator than N stage or number of positive lymph nodes. No significant financial relationships to disclose.
Impact of Blood–Brain Barrier Integrity on Tumor Growth and Therapy Response in Brain Metastases (2016)

Our study provides the first direct evidence that nonpermeable brain micro- and macrometastases can effectively be targeted by a drug designed to cross the BBB. Small-molecule inhibitors with these optimized properties are promising agents in preventing or treating brain metastases in patients. Clin Cancer Res; 22(24); 6078-87. ©2016 AACRSee related commentary by Steeg et al., p. 5953.
Characterization of a prototype strain of hepatitis E virus. (1992)

A strain of hepatitis E virus (SAR-55) implicated in an epidemic of enterically transmitted non-A, non-B hepatitis, now called hepatitis E, was characterized extensively. Six cynomolgus monkeys (Macaca fascicularis) were infected with a strain of hepatitis E virus from Pakistan. Reverse transcription-polymerase chain reaction was used to determine the pattern of virus shedding in feces, bile, and serum relative to hepatitis and induction of specific antibodies. Virtually the entire genome of SAR-55 (7195 nucleotides) was sequenced. Comparison of the sequence of SAR-55 with that of a Burmese strain revealed a high level of homology except for one region encoding 100 amino acids of a putative nonstructural polyprotein. Identification of this region as hypervariable was obtained by partial sequencing of a third isolate of hepatitis E virus from Kirgizia.
Role of endothelin in the maintenance of blood pressure in conscious rats with chronic heart failure. Acute effects of the endothelin receptor antagonist Ro 47-0203 (bosentan). (1994)

Endothelin plays a role in the maintenance of blood pressure in CHF rats, as evidenced by the significant reduction in mean arterial pressure after oral administration of bosentan. Therefore, endothelin antagonists may be useful therapeutic agents in the treatment of CHF.
From Swimming to Walking with a Salamander Robot Driven by a Spinal Cord Model (2007)

The transition from aquatic to terrestrial locomotion was a key development in vertebrate evolution. We present a spinal cord model and its implementation in an amphibious salamander robot that demonstrates how a primitive neural circuit for swimming can be extended by phylogenetically more recent limb oscillatory centers to explain the ability of salamanders to switch between swimming and walking. The model suggests neural mechanisms for modulation of velocity, direction, and type of gait that are relevant for all tetrapods. It predicts that limb oscillatory centers have lower intrinsic frequencies than body oscillatory centers, and we present biological data supporting this.
Neurotransmitter Detection Using Corona Phase Molecular Recognition on Fluorescent Single-Walled Carbon Nanotube Sensors (2013)

Temporal and spatial changes in neurotransmitter concentrations are central to information processing in neural networks. Therefore, biosensors for neurotransmitters are essential tools for neuroscience. In this work, we applied a new technique, corona phase molecular recognition (CoPhMoRe), to identify adsorbed polymer phases on fluorescent single-walled carbon nanotubes (SWCNTs) that allow for the selective detection of specific neurotransmitters, including dopamine. We functionalized and suspended SWCNTs with a library of different polymers (n = 30) containing phospholipids, nucleic acids, and amphiphilic polymers to study how neurotransmitters modulate the resulting band gap, near-infrared (nIR) fluorescence of the SWCNT. We identified several corona phases that enable the selective detection of neurotransmitters. Catecholamines such as dopamine increased the fluorescence of specific single-stranded DNA- and RNA-wrapped SWCNTs by 58-80% upon addition of 100 μM dopamine depending on the SWCNT chirality (n,m). In solution, the limit of detection was 11 nM [K(d) = 433 nM for (GT)15 DNA-wrapped SWCNTs]. Mechanistic studies revealed that this turn-on response is due to an increase in fluorescence quantum yield and not covalent modification of the SWCNT or scavenging of reactive oxygen species. When immobilized on a surface, the fluorescence intensity of a single DNA- or RNA-wrapped SWCNT is enhanced by a factor of up to 5.39 ± 1.44, whereby fluorescence signals are reversible. Our findings indicate that certain DNA/RNA coronae act as conformational switches on SWCNTs, which reversibly modulate the SWCNT fluorescence. These findings suggest that our polymer-SWCNT constructs can act as fluorescent neurotransmitter sensors in the tissue-compatible nIR optical window, which may find applications in neuroscience.
The Micon system for computer design (1989)

A description is given of the microprocessor configurer system, or Micon, which was designed to provide support for computer hardware designers. The objective of Micon is to reduce the time required to construct a hardware system. The approach to achieving this objective rests on two points: capturing and disseminating design expertise in a format that actively assists designers, and providing a tool environment that supports all aspects of computer design. Artificial intelligence provides design synthesis and the acquisition of design expertise. Databases provide consistent views of data to all tools. Networking allows the system to efficiently share common resources, such as the database, across many users of the system. Micon is compared to related design systems, its architecture is described, examples of its use are given, and a set of experiments to test its viability is described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The role of glycosylation and phosphorylation in the expression of active human beta-glucuronidase (1993)

Phosphorylation of mannose residues on N-linked oligosaccharide side chains of lysosomal enzymes targets them to lysosomes. We used site-directed mutagenesis to observe the effect of eliminating selective glycosylation sites from human beta-glucuronidase on enzyme sorting. Expression studies allowed us to determine which of four potential sites were glycosylated, preferentially phosphorylated, and required for catalytic activity. All four sites of the human enzyme were glycosylated, whereas in the mouse and rat enzymes, only three of four sites are used. Sites 2 and 3 were preferentially phosphorylated. Elimination of sites 2 and 3 in combination markedly decreased sorting to lysosomes and increased enzyme secretion. Each of the four glycosylation sites could be eliminated individually without drastic reduction in catalytic activity. Activity was progressively lost as combinations of two, three, and four sites were eliminated. Wild-type enzyme produced in the presence of tunicamycin was also inactive, indicating that glycosylation is required for realization of enzyme activity. However, active enzyme could be deglycosylated with only minimal loss of activity. Mutant enzyme completely lacking glycosylation did not form tetramers. Partial restoration of tetramerization was achieved by the co-expression of normal rat enzyme, provided that the normal rat enzyme supplied at least two subunits to the tetramer.
Numerical analysis of eigenmodes and splice losses of thermally diffused expanded core fibers (1999)

Field distributions and far-field patterns (FFP's) of the eigenmodes of thermally diffused expanded core (TEC) fibers are clarified by numerical analysis. The spot size of the TEC fiber is estimated by using the FFP that can be measured more easily than the near-field pattern (NFP). Splice losses of two TEC fibers are analyzed numerically considering a single or composite effect of gap, offset, and tilt. The results are useful for estimating isolations of fiber-integrated optical isolators and insertion losses of other fiber-integrated type optical devices. Splice losses considering multiple reflection between two endfaces of the TEC fibers with gaps are also analyzed numerically. This is useful for the design of fiber-integrated tunable wavelength filters.
Light f ield head-mounted display with correct focus cue using micro structure array (2014)

A new type of light field display is proposed using a head-mounted display (HMD) and a micro structure array (MSA, lens array or pinhole array). Each rendering point emits abundant rays from different directions into the viewer's pupil, and at one time the dense light field is generated inside the exit pupil of the HMD through the eyepiece. Therefore, the proposed method not only solves the problem of accommodation and convergence conflict in a traditional HMD, but also drastically reduces the huge data in real three-dimensional (3D) display. To demonstrate the proposed method, a prototype is developed, which is capable of giving the observer a real perception of depth.
Introduction to Solid State Physics (1957)

Mathematical Introduction Acoustic Phonons Plasmons, Optical Phonons, and Polarization Waves Magnons Fermion Fields and the Hartree-Fock Approximation Many-body Techniques and the Electron Gas Polarons and the Electron-phonon Interaction Superconductivity Bloch Functions - General Properties Brillouin Zones and Crystal Symmetry Dynamics of Electrons in a Magnetic Field: de Haas-van Alphen Effect and Cyclotron Resonance Magnetoresistance Calculation of Energy Bands and Fermi Surfaces Semiconductor Crystals I: Energy Bands, Cyclotron Resonance, and Impurity States Semiconductor Crystals II: Optical Absorption and Excitons Electrodynamics of Metals Acoustic Attenuation in Metals Theory of Alloys Correlation Functions and Neutron Diffraction by Crystals Recoilless Emission Green's Functions - Application to Solid State Physics Appendix: Perturbation Theory and the Electron Gas Index.
Regulation of macrophage migration inhibitory factor by endogenous glucocorticoids in rat adjuvant-induced arthritis (2000)

These findings provide the first in vivo confirmation of the observation that endogenous glucocorticoids are involved in the regulation of MIF in a site of inflammation, and that local and systemic MIF production are differentially regulated in this setting. The reversal of disease in ADX rats by anti-MIF mAb suggests that balance between glucocorticoids and MIF may influence the expression of inflammatory disease.
Lung ventilation injures areas with discrete alveolar flooding, in a surface tension-dependent fashion (2014)

With proteinaceous-liquid flooding of discrete alveoli, a model of the edema pattern in the acute respiratory distress syndrome, lung inflation over expands aerated alveoli adjacent to flooded alveoli. Theoretical considerations suggest that the overexpansion may be proportional to surface tension, T. Yet recent evidence indicates proteinaceous edema liquid may not elevate T. Thus whether the overexpansion is injurious is not known. Here, working in the isolated, perfused rat lung, we quantify fluorescence movement from the vasculature to the alveolar liquid phase as a measure of overdistension injury to the alveolar-capillary barrier. We label the perfusate with fluorescence; micropuncture a surface alveolus and instill a controlled volume of nonfluorescent liquid to obtain a micropunctured-but-aerated region (control group) or a region with discrete alveolar flooding; image the region at a constant transpulmonary pressure of 5 cmH2O; apply five ventilation cycles with a positive end-expiratory pressure of 0-20 cmH2O and tidal volume of 6 or 12 ml/kg; return the lung to a constant transpulmonary pressure of 5 cmH2O; and image for an additional 10 min. In aerated areas, ventilation is not injurious. With discrete alveolar flooding, all ventilation protocols cause sustained injury. Greater positive end-expiratory pressure or tidal volume increases injury. Furthermore, we determine T and find injury increases with T. Inclusion of either plasma proteins or Survanta in the flooding liquid does not alter T or injury. Inclusion of 2.7-10% albumin and 1% Survanta together, however, lowers T and injury. Contrary to expectation, albumin inclusion in our model facilitates exogenous surfactant activity.
Antimicrobial Activity and Stability to Proteolysis of Small Linear Cationic Peptides with D‐Amino Acid Substitutions (2002)

Antimicrobial peptides contribute to innate host defense against a number of bacteria and fungal pathogens. Some of antimicrobial synthetic peptides were systemically administered in vivo; however, effective protection has so far not been obtained because the effective dose of peptides in vivo seems to be very high, often close to the toxic level against the host. Alternatively, peptides administered in vivo may be degraded by certain proteases present in serum. In this study, D-amino acids were substituted for the L-amino acids of antimicrobial peptides to circumvent these problems. Initially a peptide (L-peptide) rich in five arginine residues and consisting of an 11-amino acid peptide (residues 32-42) of human granulysin was synthesized. Subsequently, the L-amino acids of the 11-amino acid peptide were replaced partially (D-peptide) or wholly (AD-peptide) with D-amino acids. Activity and stability to proteolysis, in particular, in the serum of antimicrobial peptides with D-amino acid substitutions were examined. Peptides with D-amino acid substitutions were found to lyse bacteria as efficiently as their all-L-amino acid parent, L-peptide. In addition, the peptide composed of L-amino acids was susceptible to trypsin, whereas peptides containing D-amino acid substitutions were highly stable to trypsin treatment. Similarly, the peptide consisting of L-amino acids alone was also susceptible to fetal calf serum (FCS), however, protease inhibitors restored the lowered antimicrobial activity of the FCS-incubated peptide. Thus, D-amino acid substitutions can make antimicrobial peptides resistant to proteolysis, suggesting that the antimicrobial peptides consisting of D-amino acids are potential candidates for clinical therapeutic use.
Reaktionen aktiver Methylenverbindungen mit Aziden, V. Über ein α‐Diazo‐β‐keto‐sulfon (1965)

Abstract 2.3‐Dihydro‐thionaphthenon‐(3)‐1.1‐dioxid (III), für das eine ergiebige Synthese beschrieben wird, bildet mit p ‐Tosylazid das Hydrazon VIII. Beim Erwärmen in stark polaren, „basischen”︁ Lösungsmitteln wie Äthylenglykol, Dimethylformamid oder Dimethylsulfoxid entkuppelt VIII zu dem α‐Diazo‐β‐keto‐sulfon IX und III. Einige Verkochungs‐ und Azo‐Kupplungsreaktionen von IX mit trans ‐fixierten β‐Diketonen zu Azoverbindungen werden beschrieben.
Purification of rabbit bone inhibitor of collagenase (1981)

1. Rabbit bones in tissue culture synthesize an inhibitor of collagenase during the first 4 days of culture. 2. The inhibitor was purified by a combination of gel filtration, concanavalin A--Sepharose chromatography, ion-exchange chromatography and zinc-chelate affinity chromatography. 3. The purified inhibitor migrated as a single band on sodium dodecyl sulphate/polyacrylamide-gel electrophoresis and had a mol.wt. of 28000. 4. The inhibitor blocked the activity of the metalloproteinases collagenase, gelatinase, neutral proteinase III (proteoglycanase), human leucocyte collagenase and gelatinase, but not thermolysin or bacterial collagenase. The serine proteinases plasmin and trypsin were not inhibited. 5. The inhibitor interacted with purified rabbit bone collagenase with 1:1 stoichiometry. 6. The inhibitory activity was lost after incubation for 1 h at 90 degrees C, after treatment with trypsin (250 micrograms/ml) at 37 degrees C for 30 min and after reduction and alkylation.
Synthesis of Functionalized Cyclopentanes, Cyclohexanes and Cycloheptanes by a Silicon‐Induced Domino Reaction (1996)

Abstract 1,3‐Functionalized cyclopentanes, ‐hexanes and ‐heptanes are obtained by addition of lithiated silyldithioacetals 7 to epoxyhomoallyl tosylates 4–6 , The reaction involves a cascade of epoxide ring opening, of Brook 1,4‐rearrangement and tosylate substitution. The method is particularly suitable for the preparation of cyclopentanes, whereas cyclohexanes and ‐heptanes are formed in yields only up to 49%. Use of enantiomerically pure epoxides provides optically active cyclopentanes ( S )‐ 10b, d, 11a as well as oxetanes ( S )‐ 14a, b. Hydrolysis of the dithioacetal function leads to the corresponding ketones 12 , Cyclization of epoxide 24b gives an anellated cyclopentane 26 , the configuration of which was established by X‐ray structural analysis of dinitrobenzoate 27 . Use of epoxide 29b provides the anellated tetrahydrofuran 30 .
Ultrawideband radiation and pentylenetetrazol‐induced convulsions in rats (1999)

New non-ionizing pulsed systems using ultrawideband (UWB) require safety assessment before they can be used by either military or civilian communities. The development of directed energy weaponry intended for use against electronically vulnerable targets, as well as ground-probing radar systems, have used fast-rise-time high-peak-power electromagnetic pulses characteristic of UWB emitters. It has been postulated that these ultrashort pulses might produce electromagnetic transients resulting in tissue damage. Several challenges to this notion have been posed, however. One report found that rats exposed to UWB after receiving a convulsant drug tended toward longer latency to the onset of convulsions than the no-exposure group. Although not statistically significant, the presence of this trend prompted the present study. An ED99 dose of the convulsant pentylenetetrazol (PTZ) or saline was given just before UWB or sham exposure and resultant seizure activity was recorded. The data from the current study show no effect of UWB exposure on PTZ-induced seizure activity, thereby not supporting the tissue damage concerns, at least for the exposure parameters used here. Bioelectromagnetics 20:327–329, 1999. Published 1999 Wiley-Liss, Inc.
Protein adsorption to polymer particles: Role of surface properties (1987)

Adsorption isotherms of four plasma proteins (fibrinogen, IgG, human serum albumin, and bovine serum albumin) using four different types of small particles as substrates (siliconized glass, Teflon, polyvinylchloride, and Nylon-6,6) are reported. The suspending liquid medium was phosphate-buffered saline, with a surface tension higher than that of any of the proteins. In keeping with the thermodynamic expectations for these systems, protein adsorption decreases for all solids in sequence from fibrinogen (the most hydrophobic) to IgG, human serum albumin, and bovine serum albumin (the most hydrophilic). Furthermore, the extent of protein adsorption also decreases from the low surface tension (hydrophobic) to the higher surface tension solids, again as expected on thermodynamic grounds. There is one minor yet interesting exception to the thermodynamic pattern: In spite of the slightly lower surface tension of siliconized glass, the extent of protein adsorption is slightly higher to Teflon than to siliconized glass. This result is attributed to the theoretically well known phenomenon of "screening."
Ligation Overcomes Terminal Underrepresentation in Multiple Displacement Amplification of Linear DNA (2005)

The amount of DNA available for informative genomic studies is often limiting. Thus, several methods have been developed to achieve a whole genome amplification (WGA). Particu-larly promising is a variant, called multiple displacement amplification (MDA) (1,2), which exploits the high processivity of Φ29 phage DNA polymerase and suffers an amplifi-cation bias significantly lower than previous, PCR-based WGA (3).Even though MDA-DNA has been successfully used for many applica-tions (1,4–7), some problems have been reported. For example, sequences near the ends of linear chromosomes appear underrepresented after MDA (6,8,9). Both defective priming events and abortive chain terminations could contribute to this problem, which limits the applications of MDA and jeopardizes its use on short linear DNA (e.g., cDNA and degraded genomes from forensic, archeological, and fetal origin) (10). In these cases, the terminal underrepresentation would cause the loss of substantial information.We studied this problem using λ phage DNA (48.5 kb; Promega Biosciences, San Luis Obispo, CA, USA). MDA was performed using the Genomiphi
An amorphous Ti‐Si‐N diffusion barrier layer for cu interconnections (1995)

Abstract This paper discusses the amorphous Ti‐Si‐N diffusion barrier layer without crystalline grain boundaries. The Ti‐Si‐N layers were sputter‐deposited in Ar‐N 2 mixture gas using TiSi and TiSi 2 targets. In particular, films with a composition of Ti: Si: N = 1: 1: 1.4 were evaluated. It was confirmed that the films were amorphous and thermally stable. The stress of the films was low and compressive, where it was 0.28 GPa. The junction leakage current measurement indicated that the barrier characteristic was effective at 600°C. Therefore, it was concluded that the amorphous Ti‐Si‐N layer could be used as a barrier for Cu interconnections.