gebhart/patrepeval huggingface dataset:
Deep tissue optical imaging of upconverting nanoparticles enabled by exploiting higher intrinsic quantum yield through use of millisecond single pulse excitation with high peak power (2013)

We have accomplished deep tissue optical imaging of upconverting nanoparticles at 800 nm, using millisecond single pulse excitation with high peak power. This is achieved by carefully choosing the pulse parameters, derived from time-resolved rate-equation analysis, which result in higher intrinsic quantum yield that is utilized by upconverting nanoparticles for generating this near infrared upconversion emission. The pulsed excitation approach thus promises previously unreachable imaging depths and shorter data acquisition times compared with continuous wave excitation, while simultaneously keeping the possible thermal side-effects of the excitation light moderate. These key results facilitate means to break through the general shallow depth limit of upconverting-nanoparticle-based fluorescence techniques, necessary for a range of biomedical applications, including diffuse optical imaging, photodynamic therapy and remote activation of biomolecules in deep tissues.
Oligomethylene‐Bridged Vitamin B12 Dimers (1995)

The reaction of the highly nucleophilic CoI form of vitamin B12 with 1,ω-dibromo-n-alkanes (ω ≥ 4) leads to oligomethylene-bridged B12 dimers in high yields. Use of 1,4-dibromobutane results in a dimer (shown schematically on the right), in which the two cobalamin moieties are tightly packed and coaxially linked through a tetramethylene chain, which is a synclinal conformation.
The effects of acylation stimulating protein supplementation VS antibody neutralization on energy expenditure in wildtype mice (2010)

In vitro, Anti-ASP effectively neutralized ASP stimulated fatty acid uptake. In vivo, Anti-ASP treatment increased whole body energy utilization while rASP increased energy storage. Therefore, ASP is a potent anabolic hormone that may also be a mediator of energy expenditure.
False-Accept/False-Reject Trade-offs in Biometric Authentication Systems (2018)

Biometric authentication systems, based on secret key generation, work as follows. In the enrollment stage, an individual provides a biometric signal that is mapped into a secret key and a helper message, the former being prepared to become available to the system at a later time (for authentication), and the latter is stored in a public database. When an authorized user requests authentication, claiming his/her identity as one of the subscribers, he/she has to provide a biometric signal again, and then the system, which retrieves also the helper message of the claimed subscriber, produces an estimate of the secret key, that is finally compared to the secret key of the claimed user. In case of a match, the authentication request is approved, otherwise, it is rejected. Evidently, there is an inherent tension between two desired, but conflicting, properties of the helper message encoder: on the one hand, the encoding should be informative enough concerning the identity of the real subscriber, in order to approve him/her in the authentication stage, but on the other hand, it should not be too informative, as otherwise, unauthorized imposters could easily fool the system and gain access. A good encoder should then trade off the two kinds of errors: the false reject (FR) error and the false accept (FA) error. In this work, we investigate trade-offs between the random coding FR error exponent and the best achievable FA error exponent. We compare two types of ensembles of codes: fixed-rate codes and variable-rate codes, and we show that the latter class of codes offers considerable improvement compared to the former. In doing this, we characterize the optimal rate functions for both types of codes. We also examine privacy leakage constraints for both fixed-rate codes and variable-rate codes.
CD138/syndecan-1: a useful immunohistochemical marker of normal and neoplastic plasma cells on routine trephine bone marrow biopsies. (1999)

Detection of abnormal numbers and/or distribution of bone marrow (BM) plasma cells (PCs) on trephine biopsies can be important in the differential diagnosis of multiple myeloma (MM) and other PC disorders. A variety of immunohistochemical markers can potentially improve the specificity and sensitivity of PC detection on routine histological sections obtained from trephine BM biopsies, but most of them are not completely satisfactory. In this study, we investigated whether the antibody CD138/B-B4, which is an optimal marker for PC detection on BM aspirates by flow cytometry, can be used successfully for the identification of PCs also on formalin-fixed, decalcified biopsies. A series of samples including normal BM [12], MM [65], monoclonal gammopathies of undetermined significance [44], and B-cell lymphoma of various types [94], including B-cell precursor lymphoblastic leukemia [9], lymphoplasmacytoid [17], immunoblastic [14], lymphocytic/CLL [23], hairy cell leukemia [4], large B-cell [8], mantle-cell [3], marginal zone [6] and follicular [10] lymphomas, have been investigated for CD138 expression using a sensitive immunohistochemical technique. Within the BM microenvironment, CD138 was characterized by excellent sensitivity and specificity. Virtually all normal and neoplastic PCs expressed clear-cut membrane CD138 immunostaining, whereas all other cell types did not. All cases of MM, including plasmablastic and leukemic cases, showed strong immunoreactivity. Conversely, all B-cell lymphomas, including all cases characterized by secretive features, lymphoplasmacytoid, and immunoblastic lymphomas, were completely negative. These results demonstrate that CD138 is a highly sensitive and specific marker that is useful for the rapid and precise localization of normal and neoplastic PCs on routine BM sections. In addition, because of its clear-cut cell membrane localization, CD138 can be used successfully in double-marker immunostaining reactions to evaluate precisely nuclear prognostic markers such as Ki67 and p53 in MMs.
The ESAT 2008 system for N-Best Dutch speech recognition benchmark (2009)

This paper describes the ESAT 2008 Broadcast News transcription system for the N-Best 2008 benchmark, developed in part for testing the recent SPRAAK Speech Recognition Toolkit. ESAT system was developed for the Southern Dutch Broadcast News subtask of N-Best using standard methods of modern speech recognition. A combination of improvements were made in commonly overlooked areas such as text normalization, pronunciation modeling, lexicon selection and morphological modeling, virtually solving the out-of-vocabulary (OOV) problem for Dutch by reducing OOV-rate to 0.06% on the N-Best development data and 0.23% on the evaluation data. Recognition experiments were run with several configurations comparing one-pass vs. two-pass decoding, high-order vs. low-order n-gram models, lexicon sizes and different types of morphological modeling. The system achieved 7.23% word error rate (WER) on the broadcast news development data and 20.3% on the much more difficult evaluation data of N-Best.
PnPP-19, a Synthetic and Nontoxic Peptide Designed from a Phoneutria nigriventer Toxin, Potentiates Erectile Function via NO/cGMP (2015)

PnPP-19 potentiates erection in vivo and ex vivo via the nitric oxide/cyclic guanosine monophosphate pathway. It does not affect sodium channels or rat hearts and shows no toxicity and low immunogenicity. These findings make it a promising candidate as a novel drug in the therapy of erectile dysfunction.
Natural Buffering of Groundwater Contaminants Related to Development in Fractured Rock (2013)

Abstract In rural areas of New England groundwater from fractured crystalline and sedimentary bedrock is a critical water resource. Increasingly, studies have shown that development occurring in rural areas is resulting in the impairment of water quality in fractured rock aquifers. The objective of this study was to evaluate the spatial and temporal variations in groundwater quality associated with development and evaluate the extent to which common groundwater contaminants associated with rural development may be naturally buffered. The study entailed a compilation and synthesis of over 2500 reports on domestic water quality that spanned a 30 year period. Focus was placed on the spatial distribution and temporal variations in sodium, chloride, iron, manganese, nitrate, and nitrite. Results indicate that despite significant levels of development, the amount of contamination to the bedrock has been minimal. Of the constituents examined, only the chloride concentration exhibits a systematic increase over time, but the level of chloride remained relatively low. The flux of chloride to the bedrock from deicing appears minimal despite the significant amounts of road salt used in the study area. Sodium concentrations in the bedrock remained relatively constant and appear to be buffered by ion exchange with calcium as suggested by the increase in hardness with time. Iron and manganese were present at relatively low levels but did not show any systematic trends over time. Nitrate and nitrite concentrations were very low and found to be inversely correlated with manganese and iron concentrations. This suggests that the presence of iron and manganese contribute to denitrification. This study indicated that both geochemical and biogeochemical processes are active buffering mechanisms that help shield the bedrock from contaminants associated with development.
Evidence that exposure of the telomere 3′ overhang sequence induces senescence (2003)

Normal human cells cease proliferation after a finite number of population doublings, a phenomenon termed replicative senescence. This process, first convincingly described by Hayflick and Moorhead [Hayflick, L. & Moorhead, P. S. (1961) Exp. Cell Res. 25, 595-621] for cultured human fibroblasts 40 years ago, is suggested to be a fundamental defense against cancer. Several events have been demonstrated to induce the senescent phenotype including telomere shortening, DNA damage, oxidative stress, and oncogenic stimulation. The molecular mechanisms underlying senescence are poorly understood. Here we report that a 1-week exposure to oligonucleotide homologous to the telomere 3'-overhang sequence TTAGGG (T-oligo) similarly specifically induces a senescent phenotype in cultured human fibroblasts, mimicking serial passage or ectopic expression of a dominant negative form of the telomeric repeat binding factor, TRF2(DN). We propose that exposure of the 3' overhang due to telomere loop disruption may occur with critical telomere shortening or extensive acute DNA damage and that the exposed TTAGGG tandem repeat sequence then triggers DNA-damage responses. We further demonstrate that these responses can be induced by treatment with oligonucleotides homologous to the overhang in the absence of telomere disruption, a phenomenon of potential therapeutic importance.
Electron traps in polyethylene due to water (2022)

Electron traps in polyethylene (PE) origin from water has been calculated using density functional theory. Atomistic structure has been simulated using molecular dynamics (MD) and used to calculate the electronic structure. Densities comparable with experimentally determined values are obtained. Both single water molecules and cluster of water molecules are considered. For a single water molecule both electron and hole states are within the bands from PE. The electron state is close to the conduction band minima (CBM) and may coincide with the CBM depending on the local atomic density. The absence of electron traps due to water is contradictory to previous simulation results but can be explained by atomic density and relaxation of conduction states of PE. Systems with 10 water molecules relaxed to two pentamers in the MD simulations. Calculation of trap levels of the pentamers result in trap levels in the order of 0.1-0.3 eV.
Stack, seal, evacuate, draw: a method for drawing hollow-core fiber stacks under positive and negative pressure (2022)

The two-stage stack and draw technique is an established method for fabricating microstructured fibers, including hollow-core fibers. A stack of glass elements of around a meter in length and centimeters in outer diameter forms the first stage preform, which is drawn into millimeter scale canes. The second stage preform is one of the canes, which is drawn, under active pressure, into microscopic fiber. Separately controlled pressure lines are connected to different holes or sets of holes in the cane to control the microstructure of the fiber being drawn, often relying on glues or other sealants to isolate the differently-pressured regions. We show that the selective fusion and collapse of the elements of the stack, before it is drawn to cane or fiber, allows the stack to be drawn directly under differential pressure without introducing a sealant. Three applications illustrate the advantages of this approach. First, we draw antiresonant hollow-core fiber directly from the stack without making a cane, allowing a significantly longer length of fiber to be drawn. Second, we fabricate canes under pressure, such that they are structurally more similar to the final fiber. Finally, we use the method to fabricate new types of microstructured resonators with a non-circular cross-section.
Validation of a New Lattice Physics Code GALAXY for PWRs (2010)

A new lattice physics and assembly calculation code GALAXY with the 172 energy-group ENDF/B-VII.0 library has been developed. GALAXY generates few group nuclear constants used in a new core simulator COSMO-S. The GALAXY code uses the many enhanced calculation method for more explicit treatment of neutronics characteristics. The outline of enhanced methods used in GALAXY and the qualification results are shown in this paper. From the qualifications in the continuous energy Monte Carlo benchmark, critical experiment analyses and post irradiation examination (PIE) analyses, GALAXY with the library was validated and the applicability of GALAXY to PWR nuclear design was confirmed.
ChemInform Abstract: Glycosyl Halides in Oligosaccharide Synthesis (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Titelei/Inhaltsverzeichnis (2017)

Mord an der Wirtschaftsuniversität: Als Lester Sternberg eines Morgens in die Arbeit kommt, ist nichts mehr so, wie es einmal war. Denn er steht unter dringendem Tatverdacht seinen Chef, Professor van Slyke, ermordet zu haben.
Size‐based separations as an important discriminator in development of proximity ligation assays for protein or organism detection (2010)

Proximity ligation is a powerful technique to measure minute concentrations of target protein with high specificity, and it has been demonstrated to be effective on a wide variety of protein targets. The proximity ligation assay (PLA) technique is shown to be compromised by the amplification of a nonspecific fluorescent product that is not indicative of protein presence, which was previously unidentified in a published procedure. This result illuminates the complexity of designing the optimal PLA and the possibility of using a size-based separation to increase the reliability of PLAs in general. Nucleic acid controls were developed to optimize the assay, which led to a novel end-point detection method that exploits microchip electrophoresis to size the products. This method provides a greater ability to distinguish a between the target protein's signal and noise in a PLA. The utility of the PLA is demonstrated by the detection of human pathogenic Escherichia coli O157:H7 bacteria, a pathogen at the root of many recent life-threatening food poisoning outbreaks. The results of the PLA show a detection limit of 100 E. coli O157:H7 cells with minimal cross-reactivity with gram positive control Staphylococcus aureus bacteria. The advantages of miniaturizing this process are the 100-fold reduction in volume, greatly reducing reagent requirements, and doubling of the thermocycling speed via noncontact infrared heating. This work, consequently, adds to the understanding of background fluorescence in PLAs, provides a method for evaluating nonspecific amplification, and shows that a qualitative PCR response indicative of the presence protein can be achieved with PLA.
Metabolic acclimation to excess light intensity in Chlamydomonas reinhardtii (2013)

There are several well-described acclimation responses to excess light in green algae but the effect on metabolism has not been thoroughly investigated. This study examines the metabolic changes during photoacclimation to high-light (HL) stress in Chlamydomonas reinhardtii using nuclear magnetic resonance and mass spectrometry. Using principal component analysis, a clear metabolic response to HL intensity was observed on global metabolite pools, with major changes in the levels of amino acids and related nitrogen metabolites. Amino acid pools increased during short-term photoacclimation, but were especially prominent in HL-acclimated cultures. Unexpectedly, we observed an increase in mitochondrial metabolism through downstream photorespiratory pathways. The expression of two genes encoding key enzymes in the photorespiratory pathway, glycolate dehydrogenase and malate synthase, were highly responsive to the HL stress. We propose that this pathway contributes to metabolite pools involved in nitrogen assimilation and may play a direct role in photoacclimation. Our results suggest that primary and secondary metabolism is highly pliable and plays a critical role in coping with the energetic imbalance during HL exposure and a necessary adjustment to support an increased growth rate that is an effective energy sink for the excess reducing power generated during HL stress.
Continuous infusion of vinblastine for advanced hormone-refractory prostate cancer. (1985)

Thirty-nine patients with metastatic prostate cancer refractory to hormonal manipulation were treated with vinblastine by continuous infusion. The dose was 1.5 mg/m2 daily for 5 days. A 21% response rate was obtained. Eight patients, two with visceral metastasis, one with nodal disease, and five with osseous metastasis achieved objective response. The median duration of response was 28 weeks. Myelosuppression was the major side effect: the median leukocyte count nadir was 2.8 X 10(3)/ml and the median platelet count nadir was 184 X 10(3)/ml.
Efficient high-dimensional variational data assimilation with machine-learned reduced-order models (2021)

Data assimilation (DA) in the geophysical sciences remains the cornerstone of robust forecasts from numerical models. Indeed, DA plays a crucial role in the quality of numerical weather prediction, and is a crucial building block that has allowed dramatic improvements in weather forecasting over the past few decades. DA is commonly framed in a variational setting, where one solves an optimization problem within a Bayesian formulation using raw model forecasts as a prior, and observations as likelihood. This leads to a DA objective function that needs to be minimized, where the decision variables are the initial conditions specified to the model. In traditional DA, the forward model is numerically and computationally expensive. Here we replace the forward model with a low-dimensional, data-driven, and differentiable emulator. Consequently, gradients of our DA objective function with respect to the decision variables are obtained rapidly via automatic differentiation. We demonstrate our approach by performing an emulator-assisted DA forecast of geopotential height. Our results indicate that emulator-assisted DA is faster than traditional equation-based DA forecasts by four orders of magnitude, allowing computations to be performed on a workstation rather than a dedicated high-performance computer. In addition, we describe accuracy benefits of emulator-assisted DA when compared to simply using the emulator for forecasting (i.e., without DA).
Specularity Gathers for Diffraction Imaging (2013)

Seismic diffraction imaging is recognized as a rapidly emerging technology with great potential to reduce exploration and production risks and increase recovery, for conventional reservoirs as well as unconventional resources such as shale gas. The idea behind diffraction imaging in a pre-stack migration framework is to apply a weight factor inside the migration loops, which attenuates events that satisfy Snell&apos;s law of specular reflection, while preserving diffractive events that do not satisfy Snell&apos;s law. Conceptually, it can be paraphrased as &apos;switching off reflectivity during migration&apos;. Here we present an approach, called specularity gathers, to construct the weight factor in a very efficient way, with applications on test models and the Eagle Ford shale play of South Texas. Specularity gather analysis proves to be a very useful tool to calibrate diffraction imaging, enabling the efficient construction of diffraction images and updates based on interpretation input. We expect that further development and deployment in the industry will be key in advancing diffraction imaging technology.
Cellular Volume and Matrix Stiffness Direct Stem Cell Behavior in a 3D Microniche (2018)

The central question addressed in this study is whether cells with different sizes have different responses to matrix stiffness. We used methacrylated hyaluronic acid (MeHA) hydrogels as the matrix to prepare an in vitro 3D microniche in which the single stem cell volume and matrix stiffness can be altered independently from each other. This simple approach enabled us to decouple the effects of matrix stiffness and cell volume in 3D microenvironments. Human mesenchymal stem cells (hMSCs) were cultured in individual 3D microniches with different volumes (2800, 3600, and 6000 μm<sup>3</sup>) and stiffnesses (5, 12, and 23 kPa). We demonstrated that cell volume affected the cellular response to matrix stiffness. When cells had an optimal volume, cells could form clear stress fibers and focal adhesions on soft, intermediate, or stiff matrix. In small cells, stress fiber formation and YAP/TAZ localization were not affected by stiffness. This study highlights the importance of considering cellular volume and substrate stiffness as important cues governing cell-matrix interactions.