gebhart/patrepeval huggingface dataset:
Selective incorporation of isotopically labeled amino acids for identification of intact proteins on a proteome‐wide level (2001)

Abstract The post‐genomic era and increased demands for broad proteome measurements have greatly increased the needs for protein identification. We describe a strategy that uses accurate mass measurements and partial amino acid content information to unambiguously identify intact proteins, and show its initial application to the proteomes of Escherichia coli and Saccharomyces cerevisiae . Proteins were extracted from the organisms grown in minimal medium or minimal medium to which isotopically labeled leucine (Leu‐D 10 ) had been added. The two protein extracts were mixed and analyzed by capillary isoelectric focusing (CIEF) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICR). The incorporation of the isotopically labeled residue has no effect on the CIEF separation of proteins, and both isotopically labeled and unlabeled versions of specific proteins are observed within the same mass spectrum. The difference in the mass of the unlabeled and labeled proteins is used to determine the number of Leu residues present in a particular protein. Proteins can then often be unambiguously identified based on their accurately determined molecular mass and the additional constraint provided by number of Leu residues. The identities of proteins were further confirmed by repeating CIEF/FTICR measurements with samples that contain other isotopically labeled amino acid residues (e.g. His, Arg, Ile, Phe, Lys). A theoretical study of the amino acid composition (for a difference in the amino acid sequence) showed the constraints needed in order to identify the protein unambiguously. Additionally, the mass differences between the predicted and the experimental accurate mass measurement provide insights into the nature of simple post‐translational modifications. Copyright © 2001 John Wiley & Sons, Ltd.
Methanol intoxication. Comparison of peritoneal dialysis and hemodialysis treatment (1974)

A unique opportunity presented itself for reviewing and comparing the results of two different methods of dialytic therapy for the treatment of methanol (methyl alcohol) poisoning. The group that was treated with hemodialysis initially had a faster fall in serum methanol level, regained consciousness faster, had a shorter hospital stay, and, most importantly, had no residual effects when compared with the group treated with peritoneal dialysis. In this group, one patient died and another was permanently blinded. Therefore, we believe that hemodialysis, when available, is the initial treatment of choice in methanol poisoning and should be used concomitantly with alkaline therapy and the administration of alcohol (ethanol, ethyl alcohol).
Phosphonoacetic Acid-Resistant Herpes Simplex Virus Infection in Hairless Mice (1975)

Phosphonoacetic acid (PAA)-resistant type 1 herpes simplex virus population was isolated by repeated passage of the virus in the presence of this inhibitor. Hairless mice infected percutaneously with the inhibitor-resistant or the parental inhibitor-susceptible virus were treated intraperitoneally with PAA and 9-beta-d-arabinofuranosyl-adenine by using several different dosage schedules. Whereas 9-beta-d-arabinofuranosyl-adenine was effective both in the PAA-susceptible and PAA-resistant herpes simplex virus-induced skin infection, PAA suppressed only the infection induced by the parental PAA-susceptible virus.
Modeling wireless channel fading (2002)

We compare measured fading data with the popular Rayleigh model. Our results show that this model does not agree with the experimental data. As an alternative, we approximate the experimental data using autoregressive moving average (ARMA) models. To validate the models, we compare several characteristics of fading obtained analytically, by simulation, and from measured data.
In Silico Dynamic Molecular Interaction Networks for the Discovery of New Therapeutic Targets (2010)

Systems biology has emerged as a major trend in biological research during the past decade. As living organisms are described in more and more detail, it aims at filling the gap between understanding basic molecular processes and complex biological systems in which new properties often emerge from the combination of these elementary processes. This approach culminates in the development of computer-based mathematical models of physiological and pathophysiological processes. We review the state of the art in dynamic modelling, with emphasis on two complementary approaches: the modelling of small systems that is mostly developed by academic teams and aims at understanding generic biological properties, and the modelling of large systems that is mostly implemented by industrial companies and aims at the generation of new therapeutic strategies. We also provide an example of such large-scale modelling applied to the identification of drug targets for neurodegeneration.
Nonprofit law dictionary (1994)

The vocabulary of non-profit organizations may be difficult for non-profit managers to understand as so much of the activities of non-profits are defined by laws and regulations. Technical terms - such as UBIT (unrelated business income taxation), pooled income fund, and the Commerciality Doctrine - may mean something to lawyers and accountants practising in this area, but they may bewilder and intimidate the lay people running non-profit organizations This A-Z desktop reference defines basic legal and tax terms in plain English.
Hybrid Semiconducting Polymer Dot–Quantum Dot with Narrow-Band Emission, Near-Infrared Fluorescence, and High Brightness (2012)

This communication describes a new class of semiconducting polymer nanoparticle-quantum dot hybrid with high brightness, narrow emission, near-IR fluorescence, and excellent cellular targeting capability. Using this approach, we circumvented the current difficulty with obtaining narrow-band-emitting and near-IR-fluorescing semiconducting polymer nanoparticles while combining the advantages of both semiconducting polymer nanoparticles and quantum dots. We further demonstrated the use of this new class of hybrid nanomaterial for effective and specific cellular and subcellular labeling without any noticeable nonspecific binding. This hybrid nanomaterial is anticipated to find use in a variety of in vitro and in vivo biological applications.
An Improved Negative-Lens Field Expander for Patients With Concentric Field Constriction (1985)

<h3>To the Editor.</h3> —We have successfully evaluated an improved version of the negative-lens field expander recently described by Kozlowski et al<sup>1</sup>in theArchives. The improvement consists of an aperture drilled in the center of the lens, enabling the patient to fixate through it (Figure). The original device is an oversized negative-powered spectacle lens held at a fixed distance in front of the eye. It was successfully used to orient patients with tunnel vision in unknown surroundings. When these patients used the field expander, maximum predetermined field expansion was obtained at the cost of a proportionate decrease in visual acuity. This outcome limited the field expander's use to patients with good central visual acuity. Once patients used the lens to locate objects of interest, they had difficulties discerning the details, as the device produced a minification effect. Without the lens, however, patients had difficulties in locating landmarks because of
Aurilides B and C, Cancer Cell Toxins from a Papua New Guinea Collection of the Marine Cyanobacterium <i>Lyngbya </i><i>m</i><i>ajuscula</i> (2006)

Cytotoxicity-guided fractionation of a strain of the marine cyanobacterium Lyngbya majuscula collected from Papua New Guinea led to the isolation of aurilides B (1) and C (2). The planar structures of 1 and 2 were established by spectroscopic analysis, including HR-FABMS, 1D (1)H and (13)C NMR, and 2D COSY, HSQC, HSQC-TOCSY, and HMBC spectra. The absolute configuration was determined by spectroscopic analysis and chiral HPLC analysis of acid hydrolysates of 1 and 2. Both aurilides B and C showed in vitro cytotoxicity toward NCI-H460 human lung tumor and the neuro-2a mouse neuroblastoma cell lines, with LC(50) values between 0.01 and 0.13 microM. Aurilide B (1) was evaluated in the NCI 60 cell line panel and found to exhibit a high level of cytotoxicity (the mean panel GI(50) concentration was less than 10 nM) and to be particularly active against leukemia, renal, and prostate cancer cell lines.
Artemether for Severe Malaria: A Meta‐Analysis of Randomized Clinical Trials (1999)

The treatment of choice for severe malaria is quinine. However, a gradual progression of resistance to quinine has become a concern in parts of the world. Artemisinin-related compounds are a relatively new class of drugs. This meta-analysis assesses the evidence regarding the clinical effectiveness of artemether for severe malaria. Computerized literature searches identified all randomized clinical trials of artemether in comparison with quinine. Standardized data extraction was independently performed by both authors. Results of nine trials, entered in the meta-analysis, demonstrate the absence of a significant difference between artemether and quinine in terms of mortality rate (odds ratio [OR], 0.76; 95% confidence interval [CI], 0.50-1.14). Statistical pooling of data from trials in Southeast Asia showed a trend toward enhanced reduction of mortality (OR, 0.38; 95% CI, 0.14-1.02). These data demonstrate the equality of artemether and quinine for severe malaria and indicate a trend toward greater effectiveness of artemether in regions where there is recognized quinine resistance.
On Constrained Pin-Mapping for FPGA–PCB Codesign (2006)

Field-programmable gate arrays (FPGAs) are commonly used in board designs. The authors consider the constrained FPGA pin-mapping problem in the FPGA–printed circuit board (PCB) codesign process. Unlike all previous works, which only saw constrained FPGA pin mapping as an independent chip-level problem, they take into account the connectivity of the FPGA with other components on the PCB to minimize the occurrence of net crossover and the PCB wirelength when computing a pin mapping. They propose an efficient tool, the versatile input/output (VIO) mapper, to automatically generate a proper pin-mapping upfront during the FPGA–PCB codesign process. Their input/output (I/O) mapper has a high level of flexibility. It can handle the different kinds of complex restrictions found in different FPGA devices. And it allows the PCB designers to lock down, say, the pin assignments for some critical signals before generating the assignments for the rest of the signals. Their mapper is based on an elegant 0–1 integer linear program (ILP) formulation. They show that due to the effective control of the number of integer variables and the use of a strong formulation (instead of an alternative weak formulation), their ILP-based approach is highly efficient in practice. It runs much faster than the mapping tool in Altera's Quartus II tool suite. In addition, they experimentally showed that the industrial tool's mapping algorithm is very far from optimal. For many instances on which Quartus II failed, feasible I/O mappings were found using the VIO mapper.
Chiral Separations in Capillary Electrophoresis Using Human Serum Albumin as a Buffer Additive (1994)

This study examined the theory and mechanisms of chiral separations in capillary electrophoresis based on the use of proteins as buffer additives. Human serum albumin (HSA) was used as the model ligand; D,L-tryptophan and (R,S)-warfarin were used as the test analytes to be separated by this protein. Items examined in this work included the amount of HSA adsorbed to the capillary wall and the stability of this adsorbed protein layer. These were investigated by performing frontal analysis on the capillary with HSA and by injecting neutral markers through the capillary at different applied voltages before and after HSA treatment. The role of adsorbed HSA vs HSA in the buffer in determining the stereoselectivity of the CE system was also examined. Adsorbed HSA was the predominant agent involved in the separation of (R,S)-warfarin, while HSA in the buffer had the most significant effect in the resolution of D,L-tryptophan. Two distinct separation mechanisms were proposed to explain these differences. Good agreement was obtained between the results predicted by these mechanisms and the experimental data. Under optimized conditions, both pairs of enantiomers were separated with baseline resolution in less than 12 min.
Retrieving both the impedance contrast and background velocity; a global strategy for the seismic reflection problem (1989)

Abstract Recorded seismic reflection waveforms contain information as to the small-scale variations of impedance and the large-scale variations of velocity. This information can be retrieved by minimizing the misfit between the recorded waveforms and synthetic seismograms as a function of the model parameters. Because of the different physical characters of the velocity and the impedance, we update these parameters in an alternating fashion, which amounts to a relaxation approach to the minimization of the waveform misfit. As far as the impedance is concerned, this minimization can be performed efficiently using gradient algorithms. For the inversion for seismic velocities, gradient methods do not work nearly as well; therefore, we use different minimization methods for determining impedances and velocities. However, the determination of the impedance and the determination of the velocity are strongly coupled; relaxation is most effective when this coupling is as weak as possible. Weak coupling can be achieved partially by parameterizing the impedances not as a function of depth but as a function of traveltime. A nonlinear, nonlocal method is presented for determining the smooth reference velocity from seismic reflection data. This technique is applied both to synthetic seismograms and to real marine data. In both cases, the velocity information implicitly contained in the curvature of the reflection hyperbolas was fully retrieved using nonlinear waveform optimization. In this way, it is possible to reconstruct both the impedance contrast and the smooth reference velocity from band-limited seismic reflection data using a single waveform-fit criterion.
Low Power Pilot Aided Sub-sample Based Channel Estimation for Mmwave Cellular Systems (2019)

The fast temporal changes of a millimeter wave channel necessitate frequent estimation of the channel. Power reduction techniques for the channel estimation process for ultra-wideband 5G systems are highly desirable. High speed analog-to-digital converters for the wideband data conversion and high speed baseband processing of the Nyquist rate digital samples are the main contributors to high power consumption. This work utilizes the subsequence properties of Zadoff Chu sequences and presents a training based channel estimation algorithm that can operate at a fraction of the symbol rate and thus save power. The algorithm also provides a framework for tradeoff between channel estimation performance and computational complexity. This can allow a receiver to go into power saving mode during high signal to noise ratio channel estimation. Our analysis and simulation results show that our sub-Nyquist based approach achieves maximum likelihood performance at full rate sequence for a single path channel model.
Erythrocyte rosettes provide an analogue for Schiff base formation in specific T cell activation. (1990)

Human T cells spontaneously bind sheep E and this reflects physiologic interactions between specific adhesion molecules, principally T cell CD2, and the sheep equivalent of LFA-3. This interaction is important in T cell adhesion and in transmission of accessory activational signals. In this respect, E rosettes provide a partial analogue for T cell:accessory cell interaction and rosetting induces functional alterations in T cells. In studies of Ag-dependent T cell activation, we have obtained evidence that the formation of covalent Schiff bases between ligands on APC and T cell is an essential element. In our study, the specific chemical criteria defining Schiff base formation were applied to T cell E rosettes formed at room temperature, as follows: 1) Prior formation of Schiff bases on T cell epsilon-amino groups by glutaraldehyde inhibited E rosette formation. 2) Rosette formation was inhibited in the presence of exogenous lysine. 3) Reduction of constitutive T cell aldehydes by NaBH4 inhibited subsequent E rosette formation. In response to these chemical modifications of cellular ligands, T cell E rosette formation and T cell inductive interaction with APC were affected in the same way. 4) Oxidation of NaBH4-treated T cells by NaIO4 or galactose oxidase to regenerate cell-surface aldehydes on N-acetylneuraminic acid or galactose residues respectively, consistently restored E rosette formation. 5) Conversion of reversible Schiff bases to irreversible secondary amines by NaCNBH3 stabilized E rosettes against mechanical disruption. Together, these data demonstrate that E rosettes provide an analogue for the Schiff base-forming reactions that are essential in specific T cell activation.
Serum amyloid A (SAA3) produced by rabbit synovial fibroblasts treated with phorbol esters or interleukin 1 induces synthesis of collagenase and is neutralized with specific antiserum. (1991)

We report that nucleic acid sequence analysis of a full-length cDNA clone for a rabbit serum amyloid A (SAA)-like protein has identified this protein as more closely related to SAA3 than to SAA1. SAA3 induced collagenase synthesis in rabbit synovial fibroblasts, and immune IgG raised against this SAA protein abrogated the induction. Using antisera to immunoprecipitate biosynthetically labeled 3H-SAA and 3H-collagenase from culture medium, we compared the levels of SAA and collagenase synthesized by cultures of rabbit fibroblasts at early passage (passages 3-6) with those synthesized by late passage cells (passage 16). Comparatively high levels of both proteins were produced constitutively by fibroblasts at low passage. With increasing passage, levels of both proteins drop so that by passage 16, constitutive production of SAA and collagenase was only approximately 15-20% that of passage 3 cells. Cells at low passage could be readily stimulated with phorbol myristate acetate (PMA) or interleukin 1 (IL-1) to synthesize increased amounts of both SAA and collagenase. In passage 5 cells treated with PMA, we detected increased SAA mRNA by 1.5 h and collagenase mRNA by 5 h. However, older passage cells were more refractory to stimulation and required longer induction times. We suggest that SAA3 may be expressed by fibroblasts at sites of acute inflammation or injury, and that elevated levels of SAA3 may signify "activated" fibroblasts which are already producing increased amounts of collagenase constitutively and which are predisposed to further stimulation.
Micropapillary Variant of Transitional Cell Carcinoma of the Urinary Bladder Histologic Pattern Resembling Ovarian Papillary Serous Carcinoma (1994)

Eighteen cases of transitional cell carcinoma (TCC) of the urinary bladder containing a micropapillary component (MPC) (>90%, three cases; 50–90%, nine cases; <50%, six cases) are presented. The patients' mean age was 66.6 years (range, 47–81 years) with a male predominance (male-to-female ratio of 5:1). The MPC was part of the surface noninvasive TCC in 16 cases and part of the invasive portion of the TCC in all 18 cases. Eight patients had metastases, each with a predominant (≥50%) MPC in the metastases; local recurrence was documented in one case, and the tumor was locally invasive into pelvic structures in three cases. Histologically, the surface MPC comprised slender, delicate filiform processes or small papillary clusters of tumor cells, whereas the deep MPC was composed of infiltrating tight clusters of micropapillary aggregates that were often present within lacunae. Vascular-lymphatic invasion was consistently present in the micropapillary areas. The cytologic features of the MPC were those of grade 3 TCC. A concurrent TCC in situ was identified in 10 cases, noninvasive papillary TCC component in all cases, and glandular differentiation of the invasive TCC in five cases. The initial stage at presentation was usually high stage: one patient with stage A, nine with stage B, six with stage C, and two with stage D. Follow-up data (mean, 44.8 months; range, 6–96 months) indicated that four patients were alive with disease, seven patients were dead of disease, and there was no evidence of disease in seven patients. In five cases, DNA ploidy analyzed by static image analysis showed nondiploid indices within the micropapillary TCC component, and in three cases the DNA index of the MPC (noninvasive, invasive, or at metastatic site) exceeded the DNA index of the noninvasive papillary TCC. In conclusion, the presence of a MPC in TCC is associated with high-grade and high-stage TCC with a tendency to vascular invasion. Our data suggest that a surface MPC in bladder biopsy specimens is a poor prognostic histologic feature and, if the biopsy does not contain muscularis propria, deeper biopsies should be recommended to determine the presence of muscle invasion.
Development of a patient-specific dosimetry estimation system in nuclear medicine examination (2011)

The purpose of this study is to develop a patient-specific dosimetry estimation system in nuclear medicine examination using a SimSET-based Monte Carlo code. We added a dose deposition routine to store the deposited energy of the photons during their flights in SimSET and developed a user-friendly interface for reading PET and CT images. Dose calculated on ORNL phantom was used to validate the accuracy of this system. The S values for <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">99m</sup> Tc, <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">18</sup> F and <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">131</sup> I obtained by the system were compared to those from the MCNP4C code and OLINDA. The ratios of S values computed by this system to those obtained with OLINDA for various organs were ranged from 0.93 to 1.18, which are comparable to that obtained from MCNP4C code (0.94 to 1.20). The average ratios of S value were 0.99±0.04, 1.03±0.05, and 1.00±0.07 for isotopes <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">131</sup> I, <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">18</sup> F, and <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">99m</sup> Tc, respectively. The simulation time of SimSET was two times faster than MCNP4C's for various isotopes. A 3D dose calculation was also performed on a patient data set with PET/CT examination using this system. Results from the patient data showed that the estimated S values using this system differed slightly from those of OLINDA for ORNL phantom. In conclusion, this system can generate patient-specific dose distribution and display the isodose curves on top of the anatomic structure through a friendly graphic user interface. It may also provide a useful tool to establish an appropriate dose-reduction strategy to patients in nuclear medicine environments.