gebhart/patrepeval huggingface dataset:
Regulation of Protein Traffic in Polarized Epithelial Cells: The Polymeric Immunoglobulin Receptor Model (1995)

Most eukaryotic cells are spatially asymmetric or polarized. One of the most basic types of polarized cell organization found in multicellular animals is the epithelial cell (for review, see Mostov et al. 1992; Rodriguez-Boulan and Powell 1992; Mostov and Cardone 1995). Epithelial cells form sheets that line cavities, or they externally cover an organism. In this manner, these cells constitute the fundamental interface between the organism and the outside world. A simple epithelium is formed by a monolayer of cells. A circumferential tight junction divides the plasma membrane of each cell into two domains: The apical plasma membrane faces the lumen of the cavity, and the basolateral plasma membrane faces adjoining cells and the underlying basement membrane and connective tissue. These two domains of the plasma membrane differ in their protein and lipid compositions, reflecting the different functions served by the two surfaces in a polarized cell.
A comparison of tiled and overlapping windows (1986)

It is widely believed that overlapping windows are preferable to tiled (non-overlapping) ones, but there is very little research to support that belief. An analysis of the basic characteristics of windowing regimes predicts that there are, in fact, situations where overlapping windows are inferior to tiled. An experiment to test this prediction verified that there are indeed tasks and users for which tiled windows yield faster performance. This result suggests a need for closer study of the principles underlying windowing regimes, so that designers have a better understanding of the tradeoffs involved in using them.
Septicemia in Granulocytopenic Patients: A Shift in Bacterial Etiology (1992)

35 episodes of septicemia in 33 patients occurred among 269 consecutive patients with granulocytopenia (granulocyte cell count less than or equal to 0.5 x 10(9)/l) during the 7-year period 1982-1988. 59% of isolated bacteria were Gram-positive (Staphylococcus aureus, Staph. epidermidis, Streptococcus species and Pneumococcus) and 41% Gram-negative (Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Enterobacter, Acinetobacter and Citrobacter). Compared to the 7-year period 1975-1981, there was a decrease in the relative number of patients with Gram-negative septicemia. Thus, a shift from a predominating Gram-negative etiology in the 1975-1981 period to a predominating Gram-positive etiology in the 1982-1988 period was noted. In both periods the mortality rate was high in patients with Gram-negative septicemia, especially in patients with a Ps, aeruginosa infection.
Incidence and clinical significance of neutralizing antibodies in patients receiving recombinant interferon alfa-2a by intramuscular injection (1987)

More than 1600 patients with neoplastic disorders have received recombinant human interferon alfa-2a (Roferon-A, Hoffmann-La Roche, Nutley, NJ) as part of ongoing or completed clinical trials. In this report, the efficacy of interferon alfa-2a therapy was compared with the incidence of antibodies to this interferon in 617 patients who received the drug by intramuscular administration. Antibody measurements were performed using a highly sensitive enzyme immunoassay, and an interferon antiviral neutralization bioassay. Partial or complete remission occurred in 28% (43 of 152) of the antibody-positive patients, and in 24% (112 of 465) of the antibody-negative patients (P = 0.33). The highest incidence of antibody formation occurred among patients with renal cell carcinoma and acquired immune deficiency syndrome (AIDS)-related Kaposi's sarcoma (44% and 34%, respectively). Both the duration of treatment and length of survival were significantly longer for antibody-positive than for antibody-negative patients. No significant intergroup differences emerged for response rates or for time to onset or duration of therapeutic response. When results from the above assays were compared to those used for the detection of antibodies to recombinant interferon alfa-2b (Intron A, Schering-Plough Inc., Kenilworth, NJ), the immunoradiometric assay method was determined to be seriously deficient for determination of antibody incidence. This decreased assay sensitivity may account for the reportedly lower incidence of antibodies to recombinant alfa-2b interferon.
The Life and Work of Shoichiro Tsukita (2009)

We dedicate the 2008 Berlin conference and this collection of scientific manuscripts to the memory of our colleague Shoichiro Tsukita. His seminal scientific contributions and impact on the field of tight junctions is substantial. Shoichiro was a professor at Kyoto University and one the world's most influential biologists when he passed away on December 11, 2005 at the age of 52 from complications of pancreatic cancer. He was a pioneer in several areas of cell biology; most particularly he will be remembered as the founding father of the molecular study of tight junctions.
Transformation of Ag Nanocubes into Ag–Au Hollow Nanostructures with Enriched Ag Contents to Improve SERS Activity and Chemical Stability (2014)

We report a strategy to complement the galvanic replacement reaction between Ag nanocubes and HAuCl4 with co-reduction by ascorbic acid (AA) for the formation of Ag-Au hollow nanostructures with greatly enhanced SERS activity. Specifically, in the early stage of synthesis, the Ag nanocubes are sharpened at corners and edges because of the selective deposition of Au and Ag atoms at these sites. In the following steps, the pure Ag in the nanocubes is constantly converted into Ag(+) ions to generate voids owing to the galvanic reaction with HAuCl4, but these released Ag(+) ions are immediately reduced back to Ag atoms and are co-deposited with Au atoms onto the nanocube templates. We observe distinctive SERS properties for the Ag-Au hollow nanostructures at visible and near-infrared excitation wavelengths. When plasmon damping is eliminated by using an excitation wavelength of 785 nm, the SERS activity of the Ag-Au hollow nanostructures is 15- and 33-fold stronger than those of the original Ag nanocubes and the Ag-Au nanocages prepared by galvanic replacement without co-reduction, respectively. Additionally, Ag-Au hollow nanostructures embrace considerably improved stability in an oxidizing environment such as aqueous H2O2 solution. Collectively, our work suggests that the Ag-Au hollow nanostructures will find applications in SERS detection and imaging.
The scientist and engineer's guide to digital signal processing (1997)

In early 1980s, DSP was taught as a graduate level course in electrical engineering. A decade later, DSP had become a standart part of the ungraduate curriculum.
Phase I clinical and pharmacological study of liposome-entrapped cis-bis-neodecanoato-trans-R,R-1,2-diaminocyclohexane platinum(II). (1990)

cis-Bis-neodecanoato-trans-R,R-1,2-diaminocyclohexaneplatinum++ +(II) (NDDP) is a liposome dependent cisplatin analogue since the liposome carrier is required for its i.v. administration and for its biological activity. A Phase I study of liposome entrapped NDDP (L-NDDP) was performed using a single i.v. injection every 4 weeks. L-NDDP was prepared and characterized at M. D. Anderson Cancer Center. The maximum tolerated dose of L-NDDP was 312.5 mg/m2. The dose-limiting toxicity was myelosuppression, affecting all three blood cell lineages. The granulocyte nadir occurred on days 14-18, and the platelet nadir consistently earlier (days 11-12). The median day of recovery of blood cell counts was day 21 (range, 18-32). Other toxicities included grade 2 nausea and vomiting, fever consisting of a single temperature spike in most patients, grade 1 diarrhea after 60% of courses, and grade 1-2 malaise lasting for 5-10 days after the infusion in 73% of courses. Transient alanine aminotransferase elevations without clinical relevance were common. No signs of renal dysfunction or ototoxicity were observed. One patient with a preexisting peripheral neuropathy showed some progression of the neuropathy after a cumulative dose of 1605 mg/m2. Except for fever and transient liver dysfunction, no liposome related side effects were observed in spite of the high doses of lipid administered. The blood clearance of L-NDDP fits a two-compartment model at lower doses and a single-compartment model at the maximum tolerated dose, suggesting that saturation of the reticuloendothelial organs occurs at the maximum tolerated dose. Two minimal responses were observed. L-NDDP has a toxicity profile similar to that of carboplatin. Phase II studies to address the issue of how the therapeutic index of platinum compounds is affected by liposome entrapment are being planned.
DNA tumor virus oncogenes antagonize the cGAS-STING DNA-sensing pathway (2015)

Cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS) detects intracellular DNA and signals through the adapter protein STING to initiate the antiviral response to DNA viruses. Whether DNA viruses can prevent activation of the cGAS-STING pathway remains largely unknown. Here, we identify the oncogenes of the DNA tumor viruses, including E7 from human papillomavirus (HPV) and E1A from adenovirus, as potent and specific inhibitors of the cGAS-STING pathway. We show that the LXCXE motif of these oncoproteins, which is essential for blockade of the retinoblastoma tumor suppressor, is also important for antagonizing DNA sensing. E1A and E7 bind to STING, and silencing of these oncogenes in human tumor cells restores the cGAS-STING pathway. Our findings reveal a host-virus conflict that may have shaped the evolution of viral oncogenes.
A fully integrated low-noise 1-GHz frequency synthesizer design for mobile communication application (1997)

This paper describes a fully monolithic phase-locked loop (PLL) frequency synthesizer circuit implemented in a standard 0.8-/spl mu/m CMOS technology. To be immune to noise, all the circuits in the synthesizer use differential schemes with the digital parts designed by static logic. The experimental voltage controlled oscillator (VCO) has a center frequency of 800 MHz and a tuning range of /spl plusmn/25%. The measured frequency synthesizer performance has a frequency range from 700 MHz to 1 GHz with -80 dBc/Hz phase noise at a 100 kHz carrier offset. With an active area of 0.34 mm/sup 2/, the test chip consumes 125 mW at maximum frequency from a 5 V supply. The only external components are the supply decoupling capacitors and a passive filter.
Photochemical and Thermal Decomposition of 1-Pyrazolines (1974)

Quantum yields for photochemical nitrogen extrusion from seven 1-pyrazolines were found to range from 0.12 to 0.88 but 4-oxo-3,3,5,5-tetramethyl-1-pyrazoline (8) proved to be photochemically and thermally remarkably stable. 4-Isopropylidene-3,3,5,5-tetramethyl-1-pyrazoline (7) decomposed thermally with E a = 39.8 kcal mol −1 and ΔS ≠ = 0.7 e.u. The high stability of this compound contrasts with 4-methylene-1-pyrazoline (17).
Apolipoprotein E Status as a Predictor of the Development of Alzheimer's Disease in Memory-Impaired Individuals (1995)

These data suggest the following: (1) patients with mild cognitive impairment can be clinically defined, (2) many members of this group progress to Alzheimer's disease, and (3) APOE epsilon 4 allele status appears to be a strong predictor of clinical progression.
Dopamine-dependent changes in the functional connectivity between basal ganglia and cerebral cortex in humans (2002)

We test the hypothesis that interaction between the human basal ganglia and cerebral cortex involves activity in multiple functional circuits characterized by their frequency of oscillation, phase characteristics, dopamine dependency and topography. To this end we took recordings from macroelectrodes (MEs) inserted into the subthalamic nucleus (STN) in eight awake patients following functional neurosurgery for Parkinson's disease. An EEG was also recorded, as were the signals from MEs in the globus pallidus interna (GPi) in two of the cases. Coherence between EEG and ME potentials was apparent in three major frequency bands, 2-10 Hz, 10-30 Hz and 70-85 Hz. These rhythmic activities differed in their cortical topography, although coherence was always strongest over the midline. Coherence between EEG and ME potentials in the 70-85 Hz band was only recorded in patients treated with levodopa. Cortical activity phase led that in the basal ganglia in those oscillatory activities with frequencies <30 Hz. In contrast, STN and GPi phase led cortex in the 70-85 Hz band. The temporal differences in the way in which cortical activity led or lagged behind that in STN/GPi were similar, around 20 ms, regardless of the overall direction of information flow and frequency band. We conclude that the basal ganglia may receive multiple cortical inputs at frequencies <30 Hz and, in the presence of dopaminergic activity, produce a high frequency drive back to the cerebral cortex, in particular the supplementary motor area (SMA).
Simultaneous augmentation of hard and soft tissues for implant site preparation using recombinant human platelet-derived growth factor: a human case report. (2008)

This paper documents the treatment of a patient for whom a tissue engineering approach was used for both soft and hard tissue implant site development following the extraction of a failing maxillary left central incisor. The tooth had advanced pocketing and recurrent abscess formation secondary to failing endodontic treatment. Extraction revealed a lack of buccal plate as well as insufficient soft tissue for anterior esthetics. After extraction, the bony defect was filled with freeze-dried mineralized bone allograft mixed with recombinant human platelet-derived growth factor (rhPDGF), and a titanium-reinforced expanded polytetrafluoroethylene membrane was placed over it. The soft tissue deficiency was corrected with a pediculated connective tissue graft, and the graft bed was rinsed with rhPDGF. Seven months after surgery, the site was re-entered for implant placement. The grafted site was trephined for histologic analysis and an implant was placed. Subsequently, the implant osseointegrated and was restored. The radiographic and clinical results were acceptable. Histologic analysis revealed bone regeneration. Although this approach needs further investigation, this report emphasizes the potential for the use of rhPDGF for simultaneous soft and hard tissue implant site preparation.
Sources of Error in Lung Densitometry with CT (1999)

A change in a lung density parameter over time can actually be the result of tube replacement or changing blood density. A simple postprocessing technique can correct for these changes.
Statistical Methods (1993)

1. Data and statistics; 2. Probability and sampling distributions; 3. Principles of inference; 4. Inferences on a single population; 5. Inferences for two populations; 6. Inferences for two or more means; 7. Linear regression; 8. Multiple regression; 9. Linear models; 10. Factorial experiments; 11. Design of experiments;12. Categorical data; 13. Generalized linear models; 14. Nonparametric methods
Nanoelectromechanical systems (2005)

Nanoelectromechanical systems (NEMS) are drawing interest from both technical and scientific communities. These are electromechanical systems, much like microelectromechanical systems, mostly operated in their resonant modes with dimensions in the deep submicron. In this size regime, they come with extremely high fundamental resonance frequencies, diminished active masses,and tolerable force constants; the quality (Q) factors of resonance are in the range Q∼103–105—significantly higher than those of electrical resonant circuits. These attributes collectively make NEMS suitable for a multitude of technological applications such as ultrafast sensors, actuators, and signal processing components. Experimentally, NEMS are expected to open up investigations of phonon mediated mechanical processes and of the quantum behavior of mesoscopic mechanical systems. However, there still exist fundamental and technological challenges to NEMS optimization. In this review we shall provide a balanced introduction to NEMS by discussing the prospects and challenges in this rapidly developing field and outline an exciting emerging application, nanoelectromechanical mass detection.
Effect of renal sympathetic nerve stimulation on proximal water and sodium reabsorption. (1976)

The renal responses to sympathetic nerve stimulation were studied in saline-expanded rats. The left kidney was partially denervated by crushing the left greater splanchnic nerve. Then the distal portion of the nerve was stimulated with square wave pulses of 0.5 ms duration, voltage twice threshold, and 1 or 2 Hz frequency while monitoring the compound action potential. Fibers with conduction speeds of 13-17 m-s-1 and of 0.7-1 m-s-1 were identified. Only stimulation of the latter appeared to produce changes in renal Na and water excretion. Whole kidney and individual nephron studies were performed alternating control and nerve stimulation periods. Nerve stimulation produced approximately a 25% reduction of the left kidney urine volume and sodium excretion. Glomerular filtration rate and renal plasma flow remained unchanged. Right kidney Na and water excretion, glomerular filtration rate, and renal plasma flow remained constant. In the left kidney, during nerve stimulation, the tubular fluid to plasma inulin concentration ratio increased significantly in the late proximal tubule. We conclude that the antidiuresis and antinatriuresis seen during sympathetic nerve stimulation were caused by increased sodium and water reabsorption in the proximal tubule, probably mediated by the stimulation of slowly conducting unmyelinated fibers. These responses appeared to be unrelated to systemic or intrarenal hemodynamic changes.
An Accurate Finite-Difference Method for Higher Order Waveguide Modes (1968)

The study of new waveguide shapes requires an accurate knowledge of their higher order modes for bandwidth consideration, waveguide discontinuity analysis, and multimode launching and propagation studies. The finite-difference method solved by successive overrelaxation is a very accurate and general technique for dominant mode solution. The method makes minimum demand on computer store, the number of storage locations required being equal to the order of the matrix defining the system of linear equations used. Convergence criteria require that this matrix be positive semidefinite. For modes higher than the dominant, the method fails to converge as this condition is violated. Solution is obtained by redefining the problem such that the matrix is positive semidefinite for all modes. An algorithm is described which produces one row at a time of the new matrix, as required for successive overrelaxation, and thus reserves almost all computer store for the eigenvector. The eigenvector elements give field potentials at discrete points in the guide cross section. Iteration for higher order modes is successfully applied with all the computational benefits realized by previous finite-difference schemes for the dominant mode. Examples studied are the rectangular, circular, asymmetric ridge, and lunar guides. Results for higher order cutoff wave numbers are usually accurate to within 0.1 percent.
Association of the Pro12Ala Polymorphism in the PPAR-γ2 Gene With 3-Year Incidence of Type 2 Diabetes and Body Weight Change in the Finnish Diabetes Prevention Study (2002)

The association of the Pro12Ala polymorphism of the PPAR-gamma2 gene with the incidence of type 2 diabetes was investigated in 522 subjects with impaired glucose tolerance (IGT) participating in the Finnish Diabetes Prevention Study. Subjects were randomized to either an intensive diet and exercise group or a control group. By 3 years of intervention, the odds ratio of the development of type 2 diabetes for subjects with the Ala12 allele was 2.11-fold compared with that for subjects with the Pro12Pro genotype (95% CI 1.20-3.72). The risk for type 2 diabetes increased also in subjects who gained weight or belonged to the control group. In the intervention group, subjects with the Ala12Ala genotype lost more weight during the follow-up than subjects with other genotypes (Pro12Pro vs. Ala12Ala P = 0.043), and none of subjects with the Ala12Ala genotype developed type 2 diabetes in this group. In conclusion, the Ala12 allele may predispose to the development of type 2 diabetes in obese subjects with IGT. However, beneficial changes in diet, increases in physical activity, and weight loss may reverse, to some extent, the diabetogenic impact of the Ala12 allele, possibly due to an improved insulin sensitivity.
25 million flows later (2013)

In recent years, the Web witnessed a move towards sophis- ticated client-side functionality. This shift caused a signifi- cant increase in complexity of deployed JavaScript code and thus, a proportional growth in potential client-side vulnera- bilities, with DOM-based Cross-site Scripting being a high impact representative of such security issues. In this paper, we present a fully automated system to detect and validate DOM-based XSS vulnerabilities, consisting of a taint-aware JavaScript engine and corresponding DOM implementation as well as a context-sensitive exploit generation approach. Using these components, we conducted a large-scale analysis of the Alexa top 5000. In this study, we identified 6167 unique vulnerabilities distributed over 480 domains, show- ing that 9,6% of the examined sites carry at least one DOM- based XSS problem.
<title>Study of optical proximity effects using off-axis illumination with attenuated phase shift mask</title> (1995)

The global proximity effects of densed line, semi-isolated line are studied for conventional illumination, off-axis illumination, and finally off-axis illumination in combination with attenuated phase shift masks which have transmittance of 4% and 8%, respectively, by experiments and simulations. To analyze the behavior of proximity effects, the lithographic performances of the super resolution technique are investigated comparing the cross-sectional view of resist pattern profile, useful depth of focus, and the curves of linewidth vs. defocus for 0.30 micrometers , 0.35 micrometers , and 0.40 micrometers pattern size, respectively. The global proximity effect is quantitatively analyzed by fitting the curve for densed line and isolated line to 2nd order polynomials. Off- axis illumination with attenuated phase shift mask is very effective to minimize the proximity effects for the pattern size less than 0.40 micrometers , and have useful depth of focus of 1.0 micrometers for 0.30 micrometers patterns.
Functional importance of the A chain loop in relaxin and insulin. (1994)

Relaxin and insulin are disulfide homologues with divergent functions and antigenicity. We have synthesized human relaxin II and porcine insulin and several A chain loop variants of each and measured the effect of substitutions in vivo and in vitro. Substitution of IleA10 in insulin with glycine reduced the receptor binding ability by 2 orders of magnitude. Conversely, exchange of the glycine A14 residue in relaxin, which corresponds to the insulin position A10 for isoleucine, reduced the bio-activity and the receptor binding capacity of relaxin about 100-fold. Substitution of L-Ala in insulin as well as relaxin represented a compromise that allowed both hormones to recover about 30% of the native potency. X-ray analysis and computer-derived energy calculation confirm our receptor binding and biological potency studies, which suggest that the functional difference between derivatives and native hormones is based upon a structural change introduced into the A chain loop by substitution of the penultimate intrachain loop residue. In order to achieve a conformation that favors dynamic or passive interaction with the receptor, insulin and relaxin require a different A chain loop structure in spite of the striking overall similarity.