gebhart/patrepeval huggingface dataset:
Facile removal of high mannose structures prior to extracting complex type N‐glycans from de‐N‐glycosylated peptides retained by C18 solid phase to allow more efficient glycomic mapping (2013)

The relative amount of high mannose structures within an N-glycomic pool differs from one source to another, but quite often it predominates over the larger size complex type structures carrying biologically important glyco-epitopes. An efficient method to separate these two classes of N-glycans would significantly aid in detecting the lower abundant components by MS. Capitalizing on an initial observation that only high mannose type structures were recovered in the flow-through fraction when peptide-N-glycosidase F digested peptides were passed through a C18 cartridge in 0.1% formic acid, we demonstrated here that native complex type N-glycans can be retained by C18 cartridge and to be efficiently separated from both the smaller high mannose type structures, as well as de-N-glycosylated peptides by stepwise elution with increasing ACN concentration. The weak retention of the largely hydrophilic N-glycans on C18 resin is dependent not only on size but also increased by the presence of α6-fucosylation. This was shown by comparing the resulting N-glycomic profiles of the washed and low-ACN eluted fractions derived from both a human cancer cell line and an insect cell line.
Coherent population transfer beyond the adiabatic limit: Generalized matched pulses and higher-order trapping states (1999)

We show that the physical mechanism of population transfer in a three-level system with a closed loop of coherent couplings is not equivalent to an adiabatic rotation of the dark state of the Hamiltonian, but corresponds to a rotation of a higher-order trapping state in a generalized adiabatic basis. The concept of generalized adiabatic basis sets is used as a constructive tool to design pulse sequences for stimulated Raman adiabatic passage, which also give maximum population transfer under conditions when the usual condition of adiabaticty is only poorly fulfilled. Under certain conditions for the pulses (generalized matched pulses), there exists a higher-order trapping state, which is an exact constant of motion, and analytic solutions for the atomic dynamics can be derived.
Service Restoration in DG-Integrated Distribution Networks Using an Exact Convex OPF Model (2018)

The ever-increasing requirements for reliability and quality of supply suggest to enable the self-healing features of modern distribution networks. Within the context of Active Distribution Networks (ADNs), new, fast and efficient restoration strategies can be developed relying not only on switching devices to realize load transfer operation, but also on the contribution of Distributed Generators (DGs) while controlling their set points. In this paper, a global optimization method is proposed for the restoration problem in a DG-integrated distribution network. The objective is to restore a maximum of loads with a minimum number of switching operations. In order to check the technical constraints of the resulting configuration (ex., line current and bus voltage constraints), a recently published method for exact convex formulation of the OPF problem is incorporated making the restoration problem robust particularly in the case of high nodal injections. The proposed restoration model is formulated as a mixed-integer second-order cone programming (MISOCP) problem. Two test cases are used to quantify the DG effects on the quality of the restoration strategy and to demonstrate the feasibility of the identified solution in cases where general relaxation methods for OPF problem leads to inexact solutions.
Pediatric Spinal Neoplasms (1993)

Magnetic resonance imaging (MRI) is an accurate and noninvasive tool in the evaluation of children with spinal neoplasm. Localization and definition of site and extent of disease for treatment planning, the most important goals of neuroimaging in spinal neoplastic disease, have become more precise with MRI, because all spinal compartments can be seen without the need for subarachnoid puncture. Epidural and contiguous soft tissue disease, and associated vertebral abnormalities such as marrow replacement by metastatic processes, are readily confirmed during the same examination. In children, as in adults, gadolinium-diethylenetriaminepentaacetic acid aids in separating intramedullary neoplasms from associated edema or syrinx, and is essential in the evaluation of intradural-extramedullary spread of neoplasm. MRI is also useful in the exclusion of compressive lesions in children with systemic neoplasms and cord infarction or treatment-related transverse myelopathy.
VLSI reliability challenges: from device physics to wafer scale systems (1993)

The philosophical and practical differences between Japanese and US IC industries in regard to VLSI reliability, as well as recent research topics and new analysis methods such as wafer scale testing, are discussed. It is suggested that a new approach to VLSI reliability is needed in response to the paradigm shift being brought about by simple scaling limitations, increased process complexity and application of VLSI to advanced systems. An example of this shift is the movement from simple failure analysis by sampling the output of a manufacturing line to the building-in-reliability approach. To introduce and expand on the building-in reliability approach in VLSIs, the authors discuss the required deeper physical understanding of such important processes as hot-carrier effects, dielectrics and metallization.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
ChemInform Abstract: The Borosulfate Story Goes on — From Alkali and Oxonium Salts to Polyacids. (2014)

Abstract The crystal structures of (III), (V), and (VII)—(IX) are determined by single crystal XRD.
Simulation Methodology for Analysis of Substrate Noise Impact on Analog / RF Circuits Including Interconnect Resistance (2005)

The paper reports a novel simulation methodology for the analysis and prediction of substrate noise impact on analog/RF circuits taking into account the role of the parasitic resistance of the on-chip interconnect in the impact mechanism. This methodology allows investigation of the role of the separate devices (also parasitic devices) in the analog/RF circuit in the overall impact. In this way, it is revealed which devices have to be taken care of (shielding, topology change) to protect the circuit against substrate noise. The developed methodology is used to analyze the impact of substrate noise on a 3 GHz LC-tank voltage controlled oscillator (VCO) designed in a high-ohmic 0.18 /spl mu/m 1 PM6 CMOS technology. For this VCO (in the investigated frequency range from DC to 15 MHz) impact is mainly caused by resistive coupling of noise from the substrate to the non-ideal on-chip ground interconnect, resulting in analog ground bounce and frequency modulation. Hence, the presented test-case reveals the important role of the on-chip interconnect in the phenomenon of substrate noise impact.
Cardiovascular effect of intravenous lipid A in rabbits. (1987)

The in vivo cardiovascular effect of intravenous administration of monophosphoryl lipid A (mp-lipid A) and diphosphoryl lipid A (dp-lipid A) in awake New Zealand white rabbits was investigated. Observed changes were evaluated in comparison to a control group and an endotoxin-treated group. Rabbits given lipid A showed a significant depression in cardiac index (p less than .025), mean arterial pressure (p less than .025, dp-lipid A only), arterial carbon dioxide tension (p less than .025), and total leukocyte count (p less than .05) compared to controls. Animals receiving lipid A tended to respond overall in a manner closely matching that of the endotoxin group. Dosages of lipid A given were approximately 3.5 times larger than the endotoxin dosages with respect to actual number of molecules administered (1.25-2.0 times larger by mass). These results indicate that lipid A is active in producing the cardiovascular and leukopenic effects characteristic of experimental septic shock.
<i>cis‐/trans</i>‐Tris‐[2.1.1]‐σ‐homobenzenes; Synthesis and Stereochemistry of [<sub>σ</sub>2 + <sub>σ</sub>2 + <sub>σ</sub>2]‐Cycloreversions (1980)

Ring cleavage of the new cis-/trans-isomeric ketones (1) and (3) at 150 and 300°C leads via [σ2 + σ2 + σ2]-cycloreversion to the cyclodecatrienones (2) (100%) and (4) (88%) + (2) (5%), respectively. These reactions are impressive examples of the promotion of cooperative processes in tris-σ-homobenzenes.
Thrombotic Thrombocytopenic Purpura (1986)

Thrombotic thrombocytopenic purpura (TTP) is classically highlighted by a pentad of features: fever, hemolytic anemia, thrombocytopenia purpura, transient or permanent central nervous system signs, and renal disease. The antemortem diagnosis is reliant upon the multisystem clinical signs and symptoms in conjunction with severe hemolytic anemia and thrombocytopenia. Relapse is common within the first six months after initial presentation. Laboratory findings have been generally nonspecific per se, and antemortem tissue biopsy findings are frequently unrewarding. Recently, however, unusually large multimers of the Factor VIII:Ag molecule (von Willebrand protein) have been identified in the plasma of patients with TTP who have recovered from an acute attack. This observation is very important because it may lead to essential information on the nature of the inciting event in this devastating illness. The differential diagnosis includes several multisystem disease processes such as the hemolytic uremic syndrome, toxemia of pregnancy, systemic lupus erythematosus, subacute bacterial endocarditis, nonbacterial thrombotic endocarditis, immune thrombocytopenic purpura, and the postpartum renal failure syndrome. The hemolytic uremic syndrome, toxemia of pregnancy, and TTP may resemble each other, exhibit many overlapping features, and are probably related. The cause of TTP remains unknown; the overwhelming majority of cases occur in otherwise healthy people without any recognizable underlying illness. Since 1965 45 to 70% of patients survive, a significant improvement in contrast to the early 1900s when the mortality rate was greater than 90%. The most dramatic advance has been observed in therapeutics, namely the utilization of some mode of plasma therapy (either infusion alone or plasmapheresis followed by plasma infusion). Corticosteroids remain very important in the management of patients with TTP. Vincristine may be very helpful, but additional studies are needed. The efficacy of vinca alkaloids, chronic immunosuppressive therapy, and sple. nectomy remains undefined. At present there is very little, if any, evidence that antiplatelet agents, aspirin, and prostacyclin are beneficial to patients with TTP. Prompt diagnosis and vigorous aggressive therapy is critical for successful management of TTP patients.
On the Development of a Light Dosimetry Planning Tool for Photodynamic Therapy in Arbitrary Shaped Cavities: Initial Results (2020)

Previous dosimetric studies during photodynamic therapy (PDT) of superficial lesions within a cavity such as the nasopharynx, demonstrated significant intra- and interpatient variations in fluence rate build-up as a result of tissue surface re-emitted and reflected photons, which depends on the optical properties. This scattering effect affects the response to PDT. Recently, a meta-tetra(hydroxyphenyl)chlorin-mediated PDT study of malignancies in the paranasal sinuses after salvage surgery was initiated. These geometries are complex in shape, with spatially varying optical properties. Therefore, preplanning and in vivo dosimetry is required to ensure an effective fluence delivered to the tumor. For this purpose, two 3D light distribution models were developed: first, a simple empirical model that directly calculates the fluence rate at the cavity surface using a simple linear function that includes the scatter contribution as function of the light source to surface distance. And second, an analytical model based on Lambert's cosine law assuming a global diffuse reflectance constant. The models were evaluated by means of three 3D printed optical phantoms and one porcine tissue phantom. Predictive fluence rate distributions of both models are within ± 20% accurate and have the potential to determine the optimal source location and light source output power settings.
A novel uracil analog, 6-chloro-5-(2-propenyl)uracil, preferentially enhances growth inhibition and differentiation of myeloid leukemia cells induced by 1alpha,25-dihydroxyvitamin D3. (1998)

The novel uracil analog, 6-chloro-5-(2-propenyl)uracil (TI90), inhibited the growth of myeloid leukemia cells and induced morphologic and functional differentiation of the cells. Although TI90 was a weak inducer of differentiation, it greatly enhanced the growth inhibition and differentiation of the leukemia cells previously induced by 1alpha,25-dihydroxyvitamin D3 (VD3) or all-trans retinoic acid (ATRA). TI90 cooperated with VD3 much more effectively than with ATRA in inhibiting cell growth and inducing differentiation. It also decreased the effective concentration of VD3 to the 10(-10) M level. On the other hand, there was no significant synergy between VD3 and the other uracil analogs. TI90 did not affect VD3 metabolism or the number and affinity of VD3 receptors (VDR) in HL-60 cells. Signals from VD3 are predominantly mediated by VDR and the ligand-activated binding of VDR to vitamin D-responsive element (VDRE) as a heterodimer with the retinoid X receptor (RXR). According to the results of a gel shift assay, TI90 enhanced the intensity of the retarded band with synthetic VDRE oligomer in the presence of VD3, suggesting that TI90 increases the number of phosphorylated receptors by inhibiting phosphatase activity, and also stimulates the formation of a functional complex of VDR with RXR.
ChemInform Abstract: “MICELLAR” CATALYSIS IN THE AQUEOUS INTERMOLECULAR DIELS‐ALDER REACTION: RATE ACCELERATION AND ENHANCED SELECTIVITY (1983)

Abstract Die Diels‐Alder‐Reaktion zwischen dem ungesiittigten Aldehyd (I) und dem Dien (II) zu den isomeren Addukten.
Investigation of the Vertical Movement of an Isothermal Line at the Density Maximum in H2O and D2O (2008)

We studied the cooling of a column of water, primarily in a freezer, and analyzed the development and movement of an isothermal line at ~4 degC in H2O and ~11 degC in D2O. Our experiments show that the vertical velocity of the symmetrical isothermal line moving up the column of water is inversely proportional to the diameter of the column of water. It has a measured maximum velocity of 1.4 +/- 0.1 cm/min when the column diameter is 22 mm and decreases to 0.4 +/- 0.1 cm/min when the diameter is increased to 125 mm. The measurement of the velocity becomes increasingly difficult to obtain when the column diameter is less than 22 mm because of the lack of complete development of the isothermal line. The data and discussion presented in this paper raise serious questions to the claim of new phase transitions in water made by S. Esposito, et. al. 0704.1381
Raman-Based Feedback Control of the Enzymatic Hydrolysis of Lactose (2016)

The development of real-time monitoring and an improved control system was performed according to a process analytical technology initiative focusing on the benefits of the pharmaceutical industry. As an extension of the results of pioneering Raman-based closed-loop feedback control of crystallization and synthesis, a bioprocess, namely, the enzymatic hydrolysis of lactose, was investigated in this work. For this purpose, an effective control system was developed to maintain the lactose concentration at a level of 20 g/L. Real-time evaluation of Raman spectra was accomplished using classical least-squares (CLS) and partial least-squares (PLS) multivariate data analysis methods. Formation of oligosaccharides during the hydrolysis of lactose causes inaccuracy in the CLS evaluation, and thus, optimization of lactose hydrolysis was needed to decrease oligosaccharide formation. After optimization, control of lactose hydrolysis could be achieved. To improve real-time evaluation, the PLS method was used, resulting in better evaluation of spectra during control experiments.
Synthesis and some pharmacological properties of three new analogues of arginine-vasopressin modified in positions 1,2,4 and 9. (1990)

We have synthesized three new analogues of arginine-vasopressin (AVP) to determine some of the structural features that account for antagonistic potency. These analogues are as follows: 4-glutamic acid (gamma-N,N-diethylamide)-8-arginine-vasopressin (I), N,N-diethylamide 1-(1-mercaptocyclohexaneacetic acid)-2-0-methyltyrosine- 4-glutamic acid (gamma-N,N-diethylamide)-8-arginine-vasopressin (II) and 1-(1-mercaptocyclohexaneacetic acid)-2-0-methyltyrosine-4-glutamic acid (gamma-glycine amide)-8-arginine-vasopressin (III). Analogues II and III are weak and moderate antagonists of the vasopressor response to AVP, respectively. Analogue III only exhibits a weak anti-antidiuretic activity. Analogue I lacks antagonistic effects in both systems.
Globalization of electrical safety codes and standards (2003)

As the world economic markets become more global, the interface of electrical codes and standards among countries becomes a more complex issue. The issues that need to be addressed to create harmony are as complex as the backgrounds and cultures are different. The issues include the origins and purposes of the different codes and standards and how they are administered and used in the various countries. This paper discusses the similarities and differences among the world's safety codes and standards. It proposes strategies that could assist in developing positive harmonization.
Implementation of a Multiplex and Quantitative Proteomics Platform for Assessing Protein Lysates Using DNA-Barcoded Antibodies (2018)

Molecular analysis of tumors forms the basis for personalized cancer medicine and increasingly guides patient selection for targeted therapy. Future opportunities for personalized medicine are highlighted by the measurement of protein expression levels via immunohistochemistry, protein arrays, and other approaches; however, sample type, sample quantity, batch effects, and "time to result" are limiting factors for clinical application. Here, we present a development pipeline for a novel multiplexed DNA-labeled antibody platform which digitally quantifies protein expression from lysate samples. We implemented a rigorous validation process for each antibody and show that the platform is amenable to multiple protocols covering nitrocellulose and plate-based methods. Results are highly reproducible across technical and biological replicates, and there are no observed "batch effects" which are common for most multiplex molecular assays. Tests from basal and perturbed cancer cell lines indicate that this platform is comparable to orthogonal proteomic assays such as Reverse-Phase Protein Array, and applicable to measuring the pharmacodynamic effects of clinically-relevant cancer therapeutics. Furthermore, we demonstrate the potential clinical utility of the platform with protein profiling from breast cancer patient samples to identify molecular subtypes. Together, these findings highlight the potential of this platform for enhancing our understanding of cancer biology in a clinical translation setting.
Metabolomics in Toxicology: Preclinical and Clinical Applications (2010)

Metabolomics first burst into the toxicology arena approximately 10–12 years ago, experiencing rapid growth as a science in the intervening period (Fig. 1). Though metabolomics still trails the publication rates of its sister technologies, genomics and proteomics, it is closing the gap in terms of both the numbers of publications and the quality of those publications. One continuing source of confusion is differentiating the terms metabolomics, metabonomics, and metabolic profiling. Although metabonomics was the first term formally defined (Nicholson et al., 1999), the term metabolomics came into usage shortly thereafter (Fiehn, 2002). Metabolic profiling is used by some as a generic term to avoid confusion of the two aforementioned ‘‘omic’’ terms, but that phrase itself can be confused with the comprehensive metabolite analysis of xenobiotics, so it is debatable whether its use adds any clarity to the situation. Whatever the case, it is now clear that metabolomics is the term preferred by most practitioners (Fig. 1). Therefore, metabolomics will be used in this review with the understanding that it represents all three terms. For most people, the names can be used interchangeably, but the reader is still advised to utilize all three terms when performing literature searches. Now that we have determined what to call it, we need to define what it is. The literature is replete with fine-tuned definitions, but the most succinct definition still appears to be most appropriate, and that is that metabolomics is ‘‘the comprehensive and quantitative analysis of all metabolites’’ (Fiehn, 2001). Every word in that phrase could be subject to debate as no analytical technique can measure ‘‘all’’ metabolites and what exactly qualifies as a metabolite? Do dietaryderived metabolites qualify, what about gut flora–derived metabolites? Rather than wade into this academic argument, we will leave it to the reader to define metabolomics as he or she chooses. For the toxicologist, the important point is that a metabolomics approach has the potential to reveal novel biochemical sequelae of toxicant administration that can lead to mechanistic insights and identification of biomarkers of cause and/or effect. Furthermore, the technology has the potential to characterize models or disease states to provide biochemical bases for observed interactions with xenobiotics. Given the explosion of recent literature, this review will not revisit the origins of metabolomics to any extent but will focus on recent advances in the field. Although botanical, environmental, and nutritional applications of the technology have expanded with the field, there is now such a wealth of literature this review will not be able to cover those burgeoning areas of metabolomic research. After providing some historical perspective, this review focuses on the biomedical applications of metabolomic technology with emphasis on new analytical approaches, preclinical, and clinical applications of the technology, particularly those areas relevant to practicing toxicologists.