gebhart/patrepeval huggingface dataset:
Amino Acid Turnover by Bovine Oocytes Provides an Index of Oocyte Developmental Competence In Vitro1 (2012)

Amino acid profiling has been used to distinguish between human embryos of differing developmental competence. We sought to determine whether amino acid profiling could be used to distinguish between metaphase II (MII) bovine oocytes with different developmental capabilities in vitro. Amino acid turnover was assayed during the final 6 h of in vitro maturation prior to oocytes undergoing individual fertilization in vitro. Following insemination, zygotes were immobilized in groups of 16 on the base of a Petri dish using Cell-Tak tissue adhesive to enable the developmental progress of each to be tracked to the blastocyst stage. Spent droplets of in vitro maturation medium were analyzed by high performance liquid chromatography, which revealed glutamine, arginine, and asparagine were depleted in the greatest quantities. Incompetent MII oocytes that failed to cleave by 72 h postfertilization depleted significantly more glutamine from (P = 0.0006) and released more alanine (P = 0.0001) into the medium than oocytes that cleaved. When cutoff values were selected for the turnover of alanine, arginine, glutamine, leucine, and tryptophan and modeled to predict fertilization and cleavage potential, oocytes that did not exceed the cutoff values for ≥2 of these key amino acids were more likely to cleave. The sensitivity, specificity, accuracy, and positive predictive value of this model were 60.5%, 76.8%, 63.5%, and 92.0%, respectively. Significant differences (P ≤ 0.015) in the consumption/production of alanine and glutamine were also observed when comparing uncleaved oocytes with those that produced blastocysts. The data show that noninvasive amino acid profiling can be used to measure oocyte developmental competence.
High Production Rate Synthesis of CdS Nanoparticles Using a Reverse Oscillatory Flow Method (2014)

A reverse oscillatory flow (ROF) mixing system is discussed having a reaction channel 460 μm high by 152 mm wide for high flow rate processing of nanoparticle (NP) chemistries. The ROF system is demonstrated to produce CdS nanoparticles at a production rate of 115.7 g/h with a coefficient of variation (CV) for particle size down to 19%. These production rates are substantially higher than those achieved using other microchannel mixers while maintaining comparable size distributions. Advantages of the ROF approach include the use of larger microchannels which make the reactor easier to fabricate and less vulnerable to clogging.
Molecular Imaging of TGFβ-Induced Smad2/3 Phosphorylation Reveals a Role for Receptor Tyrosine Kinases in Modulating TGFβ Signaling (2011)

The reporter is a dynamic, noninvasive imaging modality for monitoring TGFβ-induced Smad2 signaling in live cells and tumor xenografts. It has immense potential for identifying novel effectors of R-Smad phosphorylation, for validating drug-target interaction, and for studying TGFβ signaling in different metastasis models.
Choroidal Thickness in Macular Holes: A Case-Control Study (2015)

Choroidal thickness was significantly decreased in eyes with FTMH except at 2 mm temporal to the fovea and decreased in contralateral eyes with VMA in the nasal directions, suggesting an association between choroidal thinning and macular hole.
A Map Inference Approach Using Signal Processing from Crowd-sourced GPS Data (2021)

The amount of GPS data that can be collected is increasing tremendously, thanks to the increased popularity of Global Position System (GPS) devices (e.g., smartphones). This article aims to develop novel methods of converting crowd-sourced GPS traces into road topology maps. We explore map inference using a three-stage approach, which incorporates a novel Multi-source Variable Rate (MSVR) signal reconstruction mechanism. Unlike conventional map inference methods based on map graph theory, our approach, to the best of our knowledge, is the first use of estimation theory for map inference. In particular, our approach addresses the unique challenges of vehicular GPS data. This data is plentiful but suffers from noise in location and variable coverage of regions. This makes it difficult to differentiate between noise and sparsely covered regions when increasing coverage and reducing noise. Due to the asynchronous, variable sampling rate, and often under-sampled nature of the data, our MSVR approach can better handle inherent GPS errors, reconstruct road shapes more accurately, and better deal with variable GPS data density in empirical environments. We evaluated our method for map inference by comparing to Open Street Map maps as ground truth. We use the F-Measure, Precision, and Recall metrics to evaluate our method on Tsinghua University’s Beijing Taxi Dataset and Shanghai Jiao Tong University’s SUVnet Dataset. On these datasets, we obtained a mean&lt;?brk?&gt; F-Measure, Precision, and Recall of 0.7212, 0.9165, and 0.6021, respectively, outperforming a well-known method based on Kernel Density Estimation in terms of these evaluation metrics.
High-throughput creation and functional profiling of eukaryotic DNA sequence variant libraries using CRISPR/Cas9 (2017)

ABSTRACT Construction of genetic variant libraries with phenotypic measurement is central to advancing today’s functional genomics, and remains a grand challenge. Here, we introduce a Cas9-based approach for generating pools of mutants with defined genetic alterations (deletions, substitutions and insertions), along with methods for tracking their fitness en masse . We demonstrate the utility of our approach in performing focused analysis of hundreds of mutants of a single protein and in investigating the biological function of an entire family of poorly characterized genetic elements. Our platform allows fundamental biology questions to be investigated in a quick, easy and affordable manner.
Enhanced Image Reconstruction From Quarter Sampling Measurements Using An Adapted Very Deep Super Resolution Network (2020)

Quarter sampling is a novel sensor concept that enables the acquisition of higher resolution images without increasing the number of pixels. This is achieved by covering three quarters of each pixel of a low-resolution sensor such that only one quadrant of the sensor area of each pixel is sensitive to light. By randomly masking different parts, effectively a non-regular sampling of a higher resolution image is performed. Combining a properly designed mask and a high-quality reconstruction algorithm, a higher image quality can be achieved than using a low-resolution sensor and subsequent upsampling. For the latter case, the image quality can be enhanced using super resolution algorithms. Recently, algorithms based on machine learning such as the Very Deep Super Resolution network (VDSR) proofed to be successful for this task. In this work, we transfer the concepts of VDSR to the special case of quarter sampling. Besides adapting the network layout to take advantage of the case of quarter sampling, we introduce a novel data augmentation technique enabled by quarter sampling. Altogether, using the quarter sampling sensor, the image quality in terms of PSNR can be increased by + 0.67 dB for the Urban 100 dataset compared to using a low-resolution sensor with VDSR.
AKT Inhibitors Promote Cell Death in Cervical Cancer through Disruption of mTOR Signaling and Glucose Uptake (2014)

The mutational spectrum of the PI3K/AKT pathway in cervical cancer is complex. AKT inhibitors effectively block mTORC1/2, decrease glucose uptake, glycolysis, and decrease cell viability in vitro. These results suggest that AKT inhibitors may improve response to chemoradiation in cervical cancer.
Multiplex inhibitor screening and kinetic constant determinations for yeast hexokinase using mass spectrometry based assays (2003)

An electrospray ionization mass spectrometry based assay was developed for kinetic measurements and inhibitor screening of yeast hexokinase. There is considerable discrepancy in the literature as to the accuracy of kinetic data obtained for hexokinase. In the assay described herein, the product, glucose 6-phosphate was directly monitored by ion trap mass spectrometry and quantified using an internal standard, 2 deoxy-glucose 6-phosphate. The kinetic parameters, K(M) and V(max) for the two substrates were determined without using a coupling enzyme as is normally employed in the traditional spectrophotometric assay for systems lacking a chromophore. In addition, hexokinase was successfully immobilized onto an amino-link gel, and a mock library was screened against the immobilized enzyme for the identification of possible inhibitors. After comparing the mass spectra of the library before and after incubation, trehalose 6-phosphate, ADP, and oxidized glutathione were differentiated from other weak or non-inhibitors. Inhibition behavior of ADP with respect to ATP was further evaluated with the ESI-MS assay and the value of K(i) was determined. This ESI-MS assay was demonstrated to be both accurate and precise for determining kinetic constants and for identifying enzyme inhibitors.
Solution‐Processable Dithienothiophenoquinoid (DTTQ) Structures for Ambient‐Stable n‐Channel Organic Field Effect Transistors (2017)

A series of dialkylated dithienothiophenoquinoids ( DTTQ s), end‐functionalized with dicyanomethylene units and substituted with different alkyl chains, are synthesized and characterized. Facile one‐pot synthesis of the dialkylated DTT core is achieved, which enables the efficient realization of DTTQ s as n‐type active semiconductors for solution‐processable organic field effect transistors (OFETs). The molecular structure of hexyl substituted DTTQ‐6 is determined via single‐crystal X‐ray diffraction, revealing DTTQ is a very planar core. The DTTQ cores form a “zig‐zag” linking layer and the layers stack in a “face‐to‐face” arrangement. The very planar core structure, short core stacking distance (3.30 Å), short intermolecular SN distance (2.84 Å), and very low lying lowest unoccupied molecular orbital energy level of −4.2 eV suggest that DTTQ s should be excellent electron transport candidates. The physical and electrochemical properties as well as OFETs performance and thin film morphologies of these new DTTQ s are systematically studied. Using a solution‐shearing method, DTTQ‐11 exhibits n‐channel transport with the highest mobility of up to 0.45 cm 2 V −1 s −1 and a current ON/OFF ratio ( I ON /I OFF ) greater than 10 5 . As such, DTTQ‐11 has the highest electron mobility of any DTT‐based small molecule semiconductors yet discovered combined with excellent ambient stability. Within this family, carrier mobility magnitudes are correlated with the alkyl chain length of the side chain substituents of DTTQ s.
Antigen delivery using functionalized hydroxyapatite powder (2014)

Over the last few decades, the development of devices for controlled local delivery of antigens has attracted considerable interest. Different carrier devices such as viral, recombinant protein, inorganic and polymeric carriers are tested extensively. Inorganic micro particulate carriers are interesting due to their functionality, easier production and low cost. In particular calcium phosphate materials, such as hydroxyapatite (HA), composed of the same elements as bone, are interesting because of their biocompatibility and non-toxicity. These inorganic carriers however are still in pre-clinical assessment and extensive research is required with respect to the antigen loading capacity and cellular transfer efficiency. This study focusses on the increase of the loading of a model antigen, Bovine Serum Albumin (BSA), on the HA powder. \nOne way of enhancing the adsorption capacity of BSA on HA is achieved by functionalizing the HA powder with linker molecules that increase the interaction with BSA. Two amino-acid linker molecules, L-Arginine and L-Lysine, are selected to increase the BSA loading. In order to quantify this functionalization, an in-situ quantification of the amount of amino acid on the HA powder in solution is performed with Nuclear Magnetic Resonance (NMR) spectroscopy. Various NMR techniques that are already well-known in the context of nm sized colloidal semi-conductor quantumdots in organic solutions, [1] are now tested for these µm-sized HA particles in aqueous solution. Moreover, we found that HR-MAS, an NMR technique that so far was not used for this type of research, provides additional information on the system characteristics. This results in a full understanding of the interaction of the amino acid linker molecules with the HA surface.
Studies of Rhodium(II) Carboxylates as Potential Antitumor Agents (1974)

SummaryRhodium (II) acetate and rhodium (II) propionate were found to be antineoplastic agents. Both compounds inhibited DNA and RNA synthesis. The rhodium(II) propionate was also found to block de novo purine biosynthesis. Binding studies employing the carbon-14-labeled rhodium (II) acetate showed binding to DNA (poly A), and two proteins.
Towards an Edge Cloud Based Coordination Platform for Multi-User AR Applications Built on Open-Source SLAMs (2023)

Augmented Reality (AR) applications can reshape our society enabling novel ways of interactions and immersive experiences in many fields. However, multi-user and collaborative AR applications pose several challenges. The expected user experience requires accurate position and orientation information for each device and precise synchronization of the respective coordinate systems in real-time. Unlike mobile phones or AR glasses running on battery with constrained resource capacity, cloud and edge platforms can provide the computing power for the core functions under the hood. In this paper, we propose a novel edge cloud based platform for multi-user AR applications realizing an essential coordination service among the users. The latency critical, computation intensive Simultaneous Localization And Mapping (SLAM) function is offloaded from the device to the edge cloud infrastructure. Our solution is built on open-source SLAM libraries and the Robot Operating System (ROS). Our contribution is threefold. First, we propose an extensible, edge cloud based AR architecture. Second, we develop a proof-of-concept prototype supporting multiple devices. Third, a dedicated measurement methodology is described and the overall performance of the system is evaluated via real experiments.
Molecular design of reactive microgels (1996)

Abstract Structure and properties of microgels prepared by emulsion copolymerization depend on the composition and concentration of the monomers at the reaction sites, on the reactivity ratios and on the solubility of the comonomers in water. By separate and joint solubilization of 1,4‐divinyl benzene and various comonomers of different solubility it could be shown, that the diffusion control of the copolymerization rate is favoured by crosslinking, by a high concentration of an oil‐soluble initiator and of the emulsifier and by a low solubility of the comonomer in water.
Effect of enzymatic crosslinking on the handling properties of dough as a function of NaCl levels for CWRS varieties, Pembina and Harvest (2019)

The effects of transglutaminase (TG) and glucose oxidase (GO) on the handling properties of model bread dough were examined at both normal (2% wt. by flour) and reduced (1% wt.) sodium chloride (NaCl) levels using two Canada Western Red Spring (CWRS) cultivars; Pembina and Harvest. The reduction of NaCl level had negative effects on dough rheology and stickiness, however, the inclusion of GO (0.001 and 0.01% by flour weight) or TG (only at the 0.5% by flour weight inclusion) was able to improve dough strength and reduce stickiness. GO appeared to be more effective than TG (at 0.01%) at equivalent concentrations for improving dough-handling properties. Flour cultivar had significant effects; Harvest flour (weaker) was more impacted by salt reduction and enzyme inclusion compared to Pembina flour (stronger). Crosslinking assays showed significant differences in glutenin macropolymer (GMP) content in dough prepared with GO, and dough prepared with different flours. Additionally, significantly fewer free thiol groups were found in dough produced with GO compared to dough without any enzymes and those with TG. GO appears to have potential for use as a bread improver to reduce stickiness and improve the strength of bread dough produced at lower salt concentrations, especially for dough prepared with weaker flour cultivars.
Community pharmacy interventions for health promotion: effects on professional practice and health outcomes (2014)

Health-promotion interventions in the community pharmacy context probably improve pharmacy workers' behaviour and probably have a slight beneficial effect on health-related behaviour, intermediate clinical outcomes, and quality of life for pharmacy users. Such interventions are likely to be cost-effective and the effects are seen across a range of clinical conditions and health-related behaviours. Nevertheless the magnitude of the effects varies between conditions, and more effective interventions might be developed if greater consideration were given to the theoretical basis of the intervention and mechanisms for effecting behaviour change.
EGF/TGF-alpha and progesterone in urine of ovarian cancer patients. (1995)

EGF/TGF-alpha and progesterone were measured in the urine of 74 ovarian carcinoma patients, 21 postmenopausal women with non-gynecological disseminated cancer, 20 premenopausal and 20 postmenopausal controls. Radically operated women excreted significantly less EGF/TGF-alpha into urine than women with residual tumour mass. The patients who died from ovarian carcinoma had significantly higher concentrations of growth factor in urine than patients who were alive and disease-free at follow-up. The highest urinary concentrations were found in the premenopausal control group and among women with non-ovarian malignancies. A significant correlation between concentrations of progesterone and EGF/TGF-alpha in urine was noted.
Sensitivity optimization of a rhodopsin-based fluorescent voltage indicator (2023)

The ability to optically image cellular transmembrane voltages at millisecond-timescale resolutions can offer unprecedented insight into the function of living brains in behaving animals. Here, we present a point mutation that increases the sensitivity of Ace2 opsin-based voltage indicators. We use the mutation to develop Voltron2, an improved chemigeneic voltage indicator that has a 65% higher sensitivity to single APs and 3-fold higher sensitivity to subthreshold potentials than Voltron. Voltron2 retained the sub-millisecond kinetics and photostability of its predecessor, although with lower baseline fluorescence. In multiple in vitro and in vivo comparisons with its predecessor across multiple species, we found Voltron2 to be more sensitive to APs and subthreshold fluctuations. Finally, we used Voltron2 to study and evaluate the possible mechanisms of interneuron synchronization in the mouse hippocampus. Overall, we have discovered a generalizable mutation that significantly increases the sensitivity of Ace2 rhodopsin-based sensors, improving their voltage reporting capability.
Systematic Evaluation of the Metabolic to Mitogenic Potency Ratio for B10-Substituted Insulin Analogues (2012)

Several B10-substituted insulin analogues devoid of disproportionate increases in mitogenic compared to metabolic potencies were identified. In the present study, receptor binding affinity rather than insulin receptor off-rate appears to be the major determinant of both metabolic and mitogenic potency. Our results also suggest that the increased mitogenic potency is attributable to both insulin and IGF-I receptor activation.
Leveraging Possibilistic Beliefs in Unrestricted Combinatorial Auctions (2016)

In unrestricted combinatorial auctions, we put forward a mechanism that guarantees a meaningful revenue benchmark based on the possibilistic beliefs that the players have about each other’s valuations. In essence, the mechanism guarantees, within a factor of two, the maximum revenue that the “best informed player” would be sure to obtain if he/she were to sell the goods to his/her opponents via take-it-or-leave-it offers. Our mechanism is probabilistic and of an extensive form. It relies on a new solution concept, for analyzing extensive-form games of incomplete information, which assumes only mutual belief of rationality. Moreover, our mechanism enjoys several novel properties with respect to privacy, computation and collusion.
Annotation of Hox cluster and Hox cofactor genes in the Asian citrus psyllid, Diaphorina citri, reveals novel features (2022)

Hox genes and their cofactors are essential developmental genes specifying regional identity in animals. Hox genes have a conserved arrangement in clusters in the same order in which they specify identity along the anterior-posterior axis. A few insect species have breaks in the cluster, but these are exceptions. We annotated the 10 Hox genes of the Asian citrus psyllid <i>Diaphorina citri</i>, and found a split in its Hox cluster between the <i>Deformed</i> and <i>Sex combs reduced</i> genes - the first time a break at this position has been observed in an insect Hox cluster. We also annotated <i>D. citri</i> orthologs of the Hox cofactor genes <i>homothorax, PKNOX</i> and <i>extradenticle</i> and found an additional copy of <i>extradenticle</i> in <i>D. citri</i> that appears to be a retrogene. Expression data and sequence conservation suggest that the <i>extradenticle</i> retrogene may have retained the original <i>extradenticle</i> function and allowed divergence of the parental <i>extradenticle</i> gene.
Highly Conducting Lyotropic Liquid Crystalline Mesophases of Pluronics (P65, P85, P103, and P123) and Hydrated Lithium Salts (LiCl and LiNO3) (2014)

Demand for ionically conducting materials, as membranes and electrodes, is one of the driving forces of current research in chemistry, physics, and engineering. The lithium ion is a key element of these materials, and its assembly into nanostructures and mesophases is important for the membrane and electrode technologies. In this investigation, we show that hydrated lithium salts (such as LiCl·xH2O and LiNO3·xH2O, x is as low as 1.5 and 3.0, respectively) and pluronics (triblock copolymer such as PX where X is 65, 85, 103, and 123) form lyotropic liquid crystalline mesophases (LLCM), denoted as LiY·xH2O-PX-n (Y is Cl(-) or NO3(-), and n is the salt/PX mole ratio). The structure of the mesophase is hexagonal over a broad salt concentration and transforms to a cubic mesophase and then to disordered gel phase with an increasing salt content of the mixtures. The mesophases are unstable at low salt contents and undergo a phase separation into pure pluronics and salt-rich LLCMs. The salt content of the ordered mesophase can be as high as 30 mole ratio for each pluronic, which is a record high for any known salted phases. The mesophases also display high ac ionic conductivities, reaching up to 21 mS/cm at room temperature (RT), and are sensitive to the water content. These mesophases can be useful as ion-conducting membranes and can be used as media for the synthesis of lithium-containing nanoporous materials.
Efficient and programmable ethernet switching with a NoC-enhanced FPGA (2014)

Communications systems make heavy use of FPGAs; their programmability allows system designers to keep up with emerging protocols and their high-speed transceivers enable high bandwidth designs. While FPGAs are extensively used for packet parsing, inspection and classification, they have seen less use as the switch fabric between network ports. However, recent work has proposed embedding a network-on-chip (NoC) as a new "hard" resource on FPGAs and we show that by properly leveraging such a NoC one can create a very efficient yet still highly programmable network switch.