gebhart/patrepeval huggingface dataset:
Optimal model‐based design of the twin‐column CaptureSMB process improves capacity utilization and productivity in protein A affinity capture (2015)

Multi-column chromatographic processes have recently been developed for protein A affinity chromatography to efficiently capture monoclonal antibodies from cell culture supernatant. In this work, the novel twin-column CaptureSMB process was compared to a batch capture process with dual loading flow rate to identify performance gains. As a case study, the isolation of a monoclonal antibody with the Amsphere JWT-203 protein A resin was investigated. Using model based optimization, both processes were optimized and compared over a wide range of operating conditions. A trade-off between productivity and capacity utilization was found, and the resulting pareto-curves showed that CaptureSMB dominates batch, except at very low productivity values. With a feed titer of 1.2 mg mL(-1) , CaptureSMB could reach a productivity of up to 19.5 mg mL(-1) h(-1) experimentally, while maintaining relatively high capacity utilization of 63.8%. On the other hand, at maximum capacity utilization of 95.5%, a productivity of 10.2 mg mL(-1) h(-1) could be reached. This corresponds to a performance improvement with respect batch operation of about 25% in capacity utilization and 40% in productivity, for given yield and purity. CaptureSMB therefore offers a greatly increased performance over batch capture.
Purification and Characterization of Insulin, Glucagon, and Two Glucagon-Like Peptides with Insulin-Releasing Activity from the Pancreas of the Toad,Bufo marinus1 (1998)

Insulin and four peptides derived from the posttranslational processing of proglucagon have been isolated in pure form from the pancreas of the cane toad, Bufo marinus. Although Bufo insulin contains 9 amino acid substitutions, compared with human insulin, all those residues that are considered to be involved in receptor-binding and in dimer and hexamer formation have been conserved. Bufo insulin was, however, more potent (4-fold) than human insulin in inhibiting the binding of [125I-Tyr-A14] insulin to the soluble full-length recombinant human insulin receptor, which is probably a consequence of the substitution (Thr --> His) at position A-8. Bufo glucagon was isolated in two molecular forms: glucagon-29 shows only one amino acid substitution (Thr29 --> Ser), compared with human glucagon; and glucagon-36 comprises glucagon-29, extended from its C-terminus by Lys-Arg-Ser-Gly-Gly-Met-Ser. The human proglucagon gene contains one copy of glucagon-like peptide (GLP)-1, a potent insulin secretogogue, and one copy of GLP-2 that is devoid of insulin-releasing activity. In contrast, two proglucagon-derived peptides with 32- and 37-amino acid residues (GLP-32 and GLP-37), displaying greater structural similarity to human GLP-1 than to GLP-2, were isolated from Bufo pancreas. Both peptides produced concentration-dependent increases in insulin release from glucose-responsive rat insulinoma-derived BRIN-BD11 cells. The threshold concentrations producing a significant (P < 0.001) effect were 10(-8) M (GLP-32) and 10(-9) M (GLP-37), and the maximum increase in the rate of insulin release produced by 10(-6) M concentrations of both peptides was approximately 5-fold.
Abstract B38: In vivo genome editing and organoid transplantation models of colorectal cancer and metastasis (2018)

Abstract In vivo interrogation of the function of genes implicated in tumorigenesis is limited by the need to generate and cross germline mutant mice. Here we describe approaches to model colorectal cancer (CRC) and metastasis that rely on in situ gene editing and orthotopic organoid transplantation in mice without cancer-predisposing mutations. Autochthonous tumor formation is induced by CRISPR/Cas9-based editing of the Apc and Trp53 tumor suppressor genes in colon epithelial cells and by orthotopic transplantation of Apc-edited colon organoids. ApcΔ/Δ;KrasG12D/+;Trp53Δ/Δ (AKP) mouse colon organoids and human CRC organoids engraft in the distal colon and metastasize to the liver. Finally, we apply the orthotopic transplantation model to characterize the clonal dynamics of Lgr5+ stem cells and demonstrate sequential activation of an oncogene in established colon adenomas. These experimental systems enable rapid in vivo characterization of cancer-associated genes and reproduce the entire spectrum of tumor progression and metastasis. Citation Format: Jatin Roper, Tuomas Tammela, Naniye Malli Cetinbas, Adam Akkad, Ali Roghanian, Steffen Rickelt, Mohammad Almeqdadi, Katherine Wu, Matthias Oberli, Francisco Sánchez-Rivera, Yoona Park, Xu Liang, George Eng, Martin S. Taylor, Roxana Azimi, Dmitriy Kedrin, Rachit Neupane, Semir Beyaz, Ewa T. Sicinska, Yvelisse Suarez, James Yoo, Lillian Chen, Lawrence Zukerberg, Pekka Katajisto, Vikram Deshpande, Adam Bass, Philip N. Tsichlis, Jacqueline Lees, Robert Langer, Richard O. Hynes, Jianzhu Chen, Arjun J. Bhutkar, Tyler Jacks, Ömer H. Yilmaz. In vivo genome editing and organoid transplantation models of colorectal cancer and metastasis [abstract]. In: Proceedings of the AACR Special Conference: Advances in Modeling Cancer in Mice: Technology, Biology, and Beyond; 2017 Sep 24-27; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(10 Suppl):Abstract nr B38.
A Grading System for the Assessment of Risk of Extraprostatic Extension of Prostate Cancer at Multiparametric MRI (2019)

Purpose To evaluate MRI features associated with pathologically defined extraprostatic extension (EPE) of prostate cancer and to propose an MRI grading system for pathologic EPE. Materials and Methods In this prospective study, consecutive male study participants underwent preoperative 3.0-T MRI from June 2007 to March 2017 followed by robotic-assisted laparoscopic radical prostatectomy. An MRI-based EPE grading system was defined as follows: curvilinear contact length of 1.5 cm or capsular bulge and irregularity were grade 1, both features were grade 2, and frank capsular breach were grade 3. Multivariable logistic regression and decision curve analyses were performed to compare the MRI grade model and clinical parameters (prostate-specific antigen, Gleason score) for pathologic EPE prediction by using the area under the receiver operating characteristic curve (AUC) value. Results Among 553 study participants, the mean age was 60 years ± 8 (standard deviation); the median prostate-specific antigen value was 6.3 ng/mL. A total of 125 of 553 (22%) participants had pathologic EPE at radical prostatectomy. Detection of pathologic EPE, defined as number of pathologic EPEs divided by number of participants with individual MRI features, was as follows: curvilinear contact length, 88 of 208 (42%); capsular bulge and irregularity, 78 of 175 (45%); and EPE visible at MRI, 37 of 56 (66%). For MRI, grades 1, 2, and 3 for detection of pathologic EPE were 18 of 74 (24%), 39 of 102 (38%), and 37 of 56 (66%), respectively. Clinical features plus the MRI-based EPE grading system (prostate-specific antigen, International Society of Urological Pathology stage, MRI grade) predicted pathologic EPE better than did MRI grade alone (AUC, 0.81 vs 0.77, respectively; P < .001). Conclusion Higher MRI-based extraprostatic extension (EPE) grading categories were associated with a greater risk of pathologic EPE. Clinical features plus MRI grading had the highest diagnostic performance for prediction of pathologic EPE. © RSNA, 2019 Online supplemental material is available for this article. See also the editorial by Eberhardt in this issue.
Exciton–Exciton Annihilation in Mixed‐Phase Polyfluorene Films (2009)

Abstract Singlet–singlet annihilation is studied in polyfluorene (PFO) films containing different fractions of β ‐phase chains using time‐resolved fluorescence. On a timescale of &gt;15 ps after excitation, the results are fitted well by a time‐independent annihilation rate, which indicates that annihilation is controlled by 3D exciton diffusion. A time‐dependent annihilation rate is observed during the first 15 ps in the glassy phase and in the β ‐phase rich films, which can be explained by the slowdown of exciton diffusion after excitons reach low‐energy sites. The annihilation rate in the mixed‐phase films increases with increasing fraction of β ‐phase present, indicating enhanced exciton diffusion. The observed trend agrees well with a model of fully dispersed β ‐phase chromophores in the surrounding glassy phase with the exciton diffusion described using the line‐dipole approximation for an exciton wavefunction extending over 2.5 nm. The results indicate that glassy and β ‐phase chromophores are intimately mixed rather than clustered or phase‐separated.
Phonon Scattering and Thermal Conductivity in p‐Type Nanostructured PbTe‐BaTe Bulk Thermoelectric Materials (2012)

Abstract Transmission electron microscopy studies show that a PbTe‐BaTe bulk thermoelectric system represents the coexistence of solid solution and nanoscale BaTe precipitates. The observed significant reduction in the thermal conductivity is attributed to the enhanced phonon scattering by the combination of substitutional point defects in the solid solution and the presence of high spatial density of nanoscale precipitates. In order to differentiate the role of nanoscale precipitates and point defects in reducing lattice thermal conductivity, a modified Callaway model is proposed, which highlights the contribution of point defect scattering due to solid solution in addition to that of other relevant microstructural constituents. Calculations indicate that in addition to a 60% reduction in lattice thermal conductivity by nanostructures, point defects are responsible for about 20% more reduction and the remaining reduction is contributed by the collective of dislocation and strain scattering. These results underscore the need for tailoring integrated length‐scales for enhanced heat‐carrying phonon scattering in high performance thermoelectrics.
Hierarchical Modeling, Optimization, and Synthesis for System-Level Analog and RF Designs Small models, that represent the overall functioning of portions of large or complex circuits, can be generated by algorithms and used for system design and verification. (2007)

The paper describes the recent state of the art in hierarchy. This paper surveys recent advances in analog design tools that specifically deal with the hierarchical nature of practical analog and RF systems. We begin with a detailed survey of algorithmic techniques for automatically extracting a suitable nonlinear macromodel from a device-level circuit. Such techniques are critical to both verification and synthesis activities for complex systems. We then survey recent ideas in hierarchical synthesis for analog systems and focus in particular on numerical techniques for handling the large number of degrees of freedom in these designs and for exploring the space of performance tradeoffs early in the design process. Finally, we briefly touch on recent ideas for accommodating models of statistical manufacturing variations in these tools and flows.
Diabetic Retinopathy (2022)

Diabetes is a major public health problem associated with micro- and macrovascular complications, poor quality of life, and premature mortality. Diabetes is estimated to affect 415 million people worldwide in 2015 and is projected to increase to 642 million by 2040. The classical retinal microvascular signs of DR include presence of microaneurysms, hemorrhages, hard exudates, cotton-wool spots, intraretinal microvascular abnormalities, venous beading, and new vessels. Although diabetes prevalence is increasing worldwide, the brunt of the burden is borne by low- and middle-income countries, in particular, China and India, which together contribute 43% of diabetes cases globally. In 2012, Yau et al. estimated the global prevalence of DR in 2010 by pooling data from 35 studies across 16 countries, of which 13 were from developed countries and three from developing countries. Depending upon the stage of the diseases process, public health-based prevention strategies are classified into primary, secondary, and tertiary.
Modeling the Role of the Glymphatic Pathway and Cerebral Blood Vessel Properties in Alzheimer’s Disease Pathogenesis (2015)

Alzheimer's disease (AD) is the most common cause of dementia in the elderly, affecting over 10% population over the age of 65 years. Clinically, AD is described by the symptom set of short term memory loss and cognitive decline, changes in mentation and behavior, and eventually long-term memory deficit as the disease progresses. On imaging studies, significant atrophy with subsequent increase in ventricular volume have been observed. Pathology on post-mortem brain specimens demonstrates the classic findings of increased beta amyloid (Aβ) deposition and the presence of neurofibrillary tangles (NFTs) within affected neurons. Neuroinflammation, dysregulation of blood-brain barrier transport and clearance, deposition of Aβ in cerebral blood vessels, vascular risk factors such as atherosclerosis and diabetes, and the presence of the apolipoprotein E4 allele have all been identified as playing possible roles in AD pathogenesis. Recent research has demonstrated the importance of the glymphatic system in the clearance of Aβ from the brain via the perivascular space surrounding cerebral blood vessels. Given the variety of hypotheses that have been proposed for AD pathogenesis, an interconnected, multilayer model offers a unique opportunity to combine these ideas into a single unifying model. Results of this model demonstrate the importance of vessel stiffness and heart rate in maintaining adequate clearance of Aβ from the brain.
Study of the possibility of realization of a spin valve on the basis of superconductor/ferromagnet multilayers (2006)

Abstract The ways of realization of two different schemes of a spin valve for the superconducting current on the basis of the superconductor/ferromagnet proximity effect are studied. First, we have studied the superconducting proximity effect in the thin film system Fe/Cr/V/Cr/Fe where the Cr layers play the role of screening layers between the superconducting V‐layer and the strongly pair breaking Fe‐layers. Besides the new results concerning the magnetic phase transitions in the Cr layers we found the upper limit of the thickness of the screening Cr layers for operation a spin valve based on the Fe/V/Fe trilayer. Second, we studied the superconducting spin valve effect of a V‐layer coupled to an antiferromagnetic [Fe/V]‐superlattice. The parallel upper critical magnetic field exhibits an anomalous temperature dependence up to the ferromagnetic saturation field of the superlattice, indicating that the superconducting transition temperature T c decreases when rotating the relative magnetization directions of the sublattice from antiparallel to parallel. (© 2006 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Lattice Quantization With Side Information: Codes, Asymptotics, and Applications in Sensor Networks (2007)

In this paper, we consider the problem of rate/distortion with side information available only at the decoder. For the case of jointly Gaussian source X and side information Y, and mean-squared error distortion, Wyner proved in 1976 that the rate/distortion function for this problem is identical to the conditional rate/distortion function R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X|Y</sub> , assuming the side information Y is available at the encoder. In this paper we construct a structured class of asymptotically optimal quantizers for this problem: under the assumption of high correlation between source X and side information Y, we show there exist quantizers within our class whose performance comes arbitrarily close to Wyner's bound. As an application illustrating the relevance of the high-correlation asymptotics, we also explore the use of these quantizers in the context of a problem of data compression for sensor networks, in a setup involving a large number of devices collecting highly correlated measurements within a confined area. An important feature of our formulation is that, although the per-node throughput of the network tends to zero as network size increases, so does the amount of information generated by each transmitter. This is a situation likely to be encountered often in practice, which allows us to cast under new-and more "optimistic"-light some negative results on the transport capacity of large-scale wireless networks
Polarization Characteristics of Quantum-Dot Vertical-Cavity Surface-Emitting Laser With Light Injection (2010)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> This investigation explores experimentally the optical characteristics of long-wavelength quantum-dot vertical-cavity surface-emitting lasers (QD VCSELs). The InAs QD VCSEL, fabricated on a GaAs substrate, is grown by molecular beam epitaxy with fully doped distributed Bragg reflectors. The optical characteristics of QD VCSEL without and with light injection are studied in detail. The QD VCSEL has the potential to be used in all-optical signal processing systems. </para>
Studies on the vinyl polymerization photoinitiated by p‐benzoylperoxybenzoic acid tert‐butylester (1981)

Abstract p ‐Benzoylperoxybenzoic acid tert ‐butylester (BPE) undergoes an efficient photodecomposition producing cleavage of the peroxy bond. The excited triplet benzophenone carbonyl group of the perester is quenched by vinyl monomers (the degree of which depends on the type of monomer used) thus reducing the rate of decomposition of BPE when it is used as a photoinitiator. Radicals generated from the decomposition of BPE are highly efficient in initiating vinyl polymerization. The benzophenone‐containing end groups of the polymer chain can be estimated and the carbonyl function is useful for polymer modification.
FET-Like Silicon Sensor with a Porous Layer for NO2 Detection (2006)

A new porous silicon-based sensor for detection of low level NO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> concentrations (100 ppb) is presented. The sensor is an integrated p-channel JFET, provided with a porous adsorbing layer as sensing element. Adsorbed molecules by the porous silicon layer modulate the electrical current flowing through the crystalline p-channel below, in a similar way as the gate voltage in a FET. As a matter of fact, the device current increases as the NO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> concentration increases. The effect of different NO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> concentrations on the sensor current is investigated at different relative humidity levels and using ethanol as interfering gas. The sensor is highly selective for NO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2 </sub> with respect to ethanol. In fact, while 100 ppb of NO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> produce a significant current variation (more that one order of magnitude), exposure to 500 ppm of ethanol does not produce appreciable changes. The relative humidity shows a screen effect, that is the current variation decreases as the relative humidity increases
Differences in function and safety between Medicare Functional Classification Level-2 and -3 transfemoral amputees and influence of prosthetic knee joint control. (2009)

The functional differences between persons with amputation who are classified as Medicare Functional Classification Level (MFCL)-2 and -3 include the abilities to walk at various cadences and to negotiate environmental barriers outside the home. This study compared the effect of active microprocessor control and passive mechanical control of the prosthetic knee on function and safety in 17 subjects with transfemoral amputation (8 MFCL-2 and 9 MFCL-3). Assessed functional tasks included hill and stair descent, an attentional demand task, and an obstacle course. Self-reported measures included concentration, multitasking ability, and numbers of stumbles and falls. Active knee control was associated with significant improvements (p < 0.05) in hill and stair gait, speed (hills, obstacle course, and attentional demand task), and ability to multitask while walking for both cohorts. MFCL-2 subjects also reported a significant reduction (p < 0.01) in uncontrolled falls. Over the study, 50% of MFCL-2 subjects and 33% of MFCL-3 subjects transitioned to a higher MFCL. Results suggest that active knee control improves function and reduces the frequency of adverse events in a population that is at risk for falls. Use of active knee control may allow persons with amputation to expand their functional domain, transition to a higher MFCL, and access additional prosthetic options.
Compressive Coded Random Access for Massive MTC Traffic in 5G Systems (2017)

Massive MTC support is an important future market segment, but not yet efficiently supported in cellular systems. In this paper we follow-up on recent concepts combining advanced MAC protocols with Compressed Sensing (CS) based multiuser detection. Specifically, we introduce a concept for sparse joint activity, channel and data detection in the context of the Coded ALOHA (FDMA) protocol. We will argue that a simple sparse activity and data detection is not sufficient (as many papers do) because control resources are in the order of the data. In addition, we will improve on the performance of such protocols in terms of the reduction of resources required for the user activity, channel estimation and data detection. We will mathematically analyze the system accordingly and provide expressions for the capture probabilities of the underlying sparse multiuser detector. Finally, we will provide structured CS algorithms for the joint estimation scheme and evaluate its performance.
EVIDENCE THAT GLUCOCORTICOSTEROID-MEDIATED IMMUNOSUPPRESSIVE EFFECTS DO NOT INVOLVE ALTERING SECOND MESSENGER FUNCTION (1991)

The mechanism by which glucocorticosteroids (GCS) suppress proliferation of human peripheral blood mononuclear leukocytes (PBML) was investigated. Using the proliferative responses to immobilized anti-CD3 mAb or mitogens (PHA + PMA) as biological readouts, dexamethasone (DEX) and 6 alpha-methylprednisolone (6 alpha-MP) were shown to inhibit PBML proliferation in a concentration-dependent fashion. The mechanism by which GCS mediate immunosuppression did not involve interference with Ca2+ fluxes as: (1) DEX failed to block Ca2+ entry into anti-CD3 + PMA stimulated cells; and (2) Ca2+ ionophores (ionomycin and A23187) failed to circumfent DEX-mediated suppression. DEX also had no effect on protein kinase C (PKC) activity as: (1) inhibitors (H-7 and staurosporin) or stimulators (1,2-dihexanoyl-sn-glycerol [DiC6] and 1,2-dioctanoyl-rac-glycerol [DiC8]) of PKC did not prevent DEX-mediated suppression; (2) DEX did not affect the activation-induced upregulation of CD4 and CD8 expression, an indirect index of PKC activity; and (3) DEX did not alter the activation-associated translocation of PKC from cytosolic to membrane-bound compartments. This, in addition to previous results demonstrating that GCS directly inhibit cytokine gene transcription and that rII-1 + rIL-6 + rIFN-gamma completely abrogated GCS-mediated suppressive effects, further supports the notion that GCS exert their immunosuppressive effects through inhibition of cytokine gene expression.