gebhart/patrepeval huggingface dataset:
Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions (2019)

Charting a temporal path in gene networks requires linking early transcription factor (TF)-triggered events to downstream effects. We scale-up a cell-based TF-perturbation assay to identify direct regulated targets of 33 nitrogen (N)-early response TFs encompassing 88% of N-responsive Arabidopsis genes. We uncover a duality where each TF is an inducer and repressor, and in vitro cis-motifs are typically specific to regulation directionality. Validated TF-targets (71,836) are used to refine precision of a time-inferred root network, connecting 145 N-responsive TFs and 311 targets. These data are used to chart network paths from direct TF<sub>1</sub>-regulated targets identified in cells to indirect targets responding only in planta via Network Walking. We uncover network paths from TGA1 and CRF4 to direct TF<sub>2</sub> targets, which in turn regulate 76% and 87% of TF<sub>1</sub> indirect targets in planta, respectively. These results have implications for N-use and the approach can reveal temporal networks for any biological system.
AC electrophoresis of microdroplets in anisotropic liquids: transport, assembling and reaction (2013)

We describe the realization and controlled transport of water-based microreactors dispersed in a nematic liquid crystal and transported by application of an alternating electric field through the mechanism of induced charge electrophoresis. We characterize the propulsion speed of these microreactors in terms of droplet size, strength and frequency of the applied field and show how to use them to transport microscale colloidal cargoes and coalesce water miscible chemicals. Controlled motion of microdoplets in anisotropic fluids is a rich field of research which unveils new perspectives in the transport of water miscible chemicals or drugs.
Fluorescence guided intraluminal endoscopy in the gastrointestinal tract: A systematic review (2020)

The use of fluorescence endoscopy is a promising method adding diagnostic value in the detection of neoplasia, adenomas, and assessment of tumor invasion within the gastrointestinal tract. More studies are needed to utilize the feasibility of fluorescence endoscopy compared with other endoscopic methods.
Challenges in industrial fermentation technology research (2014)

Industrial fermentation processes are increasingly popular, and are considered an important technological asset for reducing our dependence on chemicals and products produced from fossil fuels. However, despite their increasing popularity, fermentation processes have not yet reached the same maturity as traditional chemical processes, particularly when it comes to using engineering tools such as mathematical models and optimization techniques. This perspective starts with a brief overview of these engineering tools. However, the main focus is on a description of some of the most important engineering challenges: scaling up and scaling down fermentation processes, the influence of morphology on broth rheology and mass transfer, and establishing novel sensors to measure and control insightful process parameters. The greatest emphasis is on the challenges posed by filamentous fungi, because of their wide applications as cell factories and therefore their relevance in a White Biotechnology context. Computational fluid dynamics (CFD) is introduced as a promising tool that can be used to support the scaling up and scaling down of bioreactors, and for studying mixing and the potential occurrence of gradients in a tank.
Isochronous services in home multimedia networks (2003)

The paper discusses the isochronous services provided in Whitecap/sup TM/ networks. The Whitecap is based on a micro-cell (subnet) architecture. The Whitecap architecture is designed to efficiently communicate multimedia data from one device to another. In Whitecap networks, each subnet consists of a master device and several client devices. Whitecap inherently supports heterogeneous client devices like the ones found in a home environment. The number of simultaneous clients serviced depends on the available bandwidth and the bandwidth requirement of the client device. Some of the common data types requiring isochronous services are voice, audio and video. Whitecap architecture guarantees these data types the required bandwidth and throughput services through Quality of service (Qos) negotiations. Some of the supported features are dynamic bandwidth negotiations, guaranteed bandwidth, guaranteed limit on latencies, different levels of error protection and retransmission rate. Negotiations can occur any number of times throughout the period of the connection. For best performance, audio and video compressions are optionally provided within the layers of this architecture.
Chemical reactivity of aromatic hydrocarbons and operational degradation of organic light-emitting diodes (2010)

We report the study of the chemical reactivity of representative hydrocarbon organic light-emitting diode (OLED) materials—fully aromatic derivatives of anthracene and tetracene in the OLED environment. In addition to the participation in free-radical chemistry initiated by homolytic bond dissociation reactions of arylamines, the hydrocarbons appear to initiate and undergo dehydrogenation reactions following the electronic excitation caused by the recombination of charge carriers or by the absorption of a photon. A chemical product of the intramolecular dehydrogenation reaction, cyclization, was identified in photoexcited films of representative anthracene derivative and detected in electrically degraded OLEDs utilizing this material in the emissive layer. Other analogous intra- and intermolecular dehydrogenation reactions initiated by the excited states of hydrocarbons are also expected to occur in operating OLEDs. The stepwise transfers of hydrogen atoms or ions to neighboring molecules are likely to yield, at least in part, neutral or ionic forms of performance-damaging species—nonradiative recombination centers and luminescence quenchers. A comparison of the luminescence losses and quantities of the identified degradation product in OLEDs and photoexcited films suggests that the dehydrogenation mechanism plays a minor but not negligible part in the operational degradation of modern OLEDs utilizing hydrocarbons as emissive layer hosts.
Extensions and Concluding Remarks (2015)

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The Design of KIVIEW: An Object-Oriented Browser. (1988)

KIVIEW is an object-oriented browsing interface to databases. The underlying internal model is a semantic network, defined via a collection of triplet facts which are governed by a small set of integrity requirements. KIVIEW's only ezternal structure is a display, called uiew, that presents all the information that is pertinent to a given object. KIVIEW features two kinds of activity, called nawgation and manipulation. Navigation is an exploration activity wherein the user repeatedly displays new views of objects that are referenced in current views. To speed up repetitive navigational tasks, which otherwise could become very tedious, viewa inay be eynchronized: the user sets up several viewa, linked in cr tree-like structure, so that when the information displayed in the root view is modified, the contents of the other views change automatically. Manipulation is a processing activity wherein the user operates on existing views to create new virtual views. Manipulation is interleaved with navigation to assemble information located while browsing into reeulte of browsing sessions. Using convenient graphic tools, these two activities are integrated into a single tool, which is flexible and effective, yet simple to use. This work waa supported in part by the European Communitiee under ESPRIT project 1117; the work of Motro was also supported by NSF Grant No. IRE8609912 and by an Amoco Foundation Engineering Faculty Grant; the work of Tarantino waa also supported by ENIDATA. 107 108 EXPERT DATABASE SYSTEMS
Extending Policy Languages for Expressing the Self-Adaptation of Web Services (2020)

With the growing demand on Web Services, self-adaptation in the highly-dynamic environment is becoming a key capability of service-based systems. As a solution for Web services to provide added value and high QoS, combining self-* and policies allows reducing management complexity and effectively drives adaptation. Also, providers must participate in the self-adaptation process as they are aware of the capabilities of their offered services and exceptions that may occur. Despite the important role of service providers, existing approaches did not address this major issue. Thus, the description of self-adaptive Web services must not be limited to functional and QoS data. To address these issues, we extend the WS-Policy framework to represent capabilities and requirements of self-* Web services. We also extend UDDI in order to store and manage service policies, as the current UDDI model does not offer these capabilities. Finally, we propose an ECA-based planning mechanism to specify decision making in the self-adaptation process.
The microbiota–gut–brain axis in gastrointestinal disorders: stressed bugs, stressed brain or both? (2014)

The gut-brain axis is the bidirectional communication between the gut and the brain, which occurs through multiple pathways that include hormonal, neural and immune mediators. The signals along this axis can originate in the gut, the brain or both, with the objective of maintaining normal gut function and appropriate behaviour. In recent years, the study of gut microbiota has become one of the most important areas in biomedical research. Attention has focused on the role of gut microbiota in determining normal gut physiology and immunity and, more recently, on its role as modulator of host behaviour ('microbiota-gut-brain axis'). We therefore review the literature on the role of gut microbiota in gut homeostasis and link it with mechanisms that could influence behaviour. We discuss the association of dysbiosis with disease, with particular focus on functional bowel disorders and their relationship to psychological stress. This is of particular interest because exposure to stressors has long been known to increase susceptibility to and severity of gastrointestinal diseases.
MIMO Capacity for Spatial Channel Model Scenarios (2007)

The capacity of Multiple Input Multiple Output (MIMO) systems has received much attention in recent years. In this paper, we analyse the capacity of MIMO systems for the 3GPP-3GPP2 Spatial Channel Model (SCM). We examine the impact of number of antennas, inter-element distance and mutual coupling, assuming both waterfilling and uniform transmit power allocation schemes, for different SCM scenarios.We also compare the simulation results with prior measurement results. The comparison provides insight into the accuracy of MIMO capacity predictions using SCM model.
Fusion: Managing Healthcare Records at Cloud Scale (2012)

An experimental open, cloud-based platform for large-scale, low-cost delivery of healthcare applications enables broader use of patient-centric management of electronic health records and facilitates the secure and seamless sharing of EHRs among stakeholders within a healthcare system.
[A synthetic peptide-based immunoenzyme test system for the joint detection of human retrovirus (HTLV-1 and HIV-1) antibodies]. (1993)

The study was made to develop an immunodiagnostic test system based on synthetic peptides able to detect in the same assay the total concentration of heterospecific antibodies against human retroviruses HTLV-1 and HIV-1. Three panels of reference-sera contained antibodies to HTLV-1 (70 specimens), HIV-1 (50 and 16 specimens) and 4 synthetic peptides corresponding to protein fragments p19 gag and gp46 env HTLV-1, gp120 and gp41 env HIV-1. Immune reactivity of the peptides with reference sera was measured in the immunoassay. It is established that relevant peptides mimic immunodominant B-epitopes of structural proteins HTLV-1 and HIV-1 and are recognized specifically by relevant antiviral antibodies. The enzyme immunoassay test system has been designed using a peptide combination in a single antigen complex. The system showed high diagnostic sensitivity.
Think Locally, Act Globally: Federated Learning with Local and Global Representations (2020)

Federated learning is a method of training models on private data distributed over multiple devices. To keep device data private, the global model is trained by only communicating parameters and updates which poses scalability challenges for large models. To this end, we propose a new federated learning algorithm that jointly learns compact local representations on each device and a global model across all devices. As a result, the global model can be smaller since it only operates on local representations, reducing the number of communicated parameters. Theoretically, we provide a generalization analysis which shows that a combination of local and global models reduces both variance in the data as well as variance across device distributions. Empirically, we demonstrate that local models enable communication-efficient training while retaining performance. We also evaluate on the task of personalized mood prediction from real-world mobile data where privacy is key. Finally, local models handle heterogeneous data from new devices, and learn fair representations that obfuscate protected attributes such as race, age, and gender.
<i>HPP1</i> : A transmembrane protein-encoding gene commonly methylated in colorectal polyps and cancers (2000)

Adenomas are the precursors of most colorectal cancers. Hyperplastic polyps have been linked to the subset of colorectal cancers showing DNA microsatellite instability, but little is known of their underlying genetic etiology. Using a strategy that isolates differentially methylated sequences from hyperplastic polyps and normal mucosa, we identified a 370-bp sequence containing the 5' untranslated region and the first exon of a gene that we have called HPP1. Rapid amplification of cDNA ends was used to isolate HPP1 from normal mucosa. Using reverse transcription-PCR, HPP1 was expressed in 28 of 30 (93%) normal colonic samples but in only seven of 30 (23%) colorectal cancers (P < 0.001). The 5' region of HPP1 included a CpG island containing 49 CpG sites, of which 96% were found to be methylated by bisulfite sequencing of DNA from colonic tumor samples. By COBRA analysis, methylation was detected in six of nine (66%) adenomas, 17 of 27 (63%) hyperplastic polyps, and 46 of 55 (84%) colorectal cancers. There was an inverse relationship between methylation level and mRNA expression in cancers (r = -0.67; P < 0.001), and 5-aza-2-deoxycytidine treatment restored HPP1 expression in two colorectal cancer cell lines. In situ hybridization of HPP1 indicated that expression occurs in epithelial and stromal elements in normal mucosa but is silenced in both cell types in early colonic neoplasia. HPP1 is predicted to encode a transmembrane protein containing follistatin and epidermal growth factor-like domains. Silencing of HPP1 by methylation may increase the probability of neoplastic transformation.
A Cell-Intrinsic Role for <i>Mst1</i> in Regulating Thymocyte Egress (2009)

The MST1 kinase was recently identified as playing an essential role in the promotion of lymphocyte polarization and adhesion stimulated by chemokines and TCR signaling. However, the physiological relevance of the Mst1 pathway in thymocyte development is not completely understood. In this study, we analyzed the effect of Mst1 disruption on thymocyte development and migration. Mst1-deficient (Mst1(-/-)) mice displayed an accumulation of mature thymocytes in the thymus, a dramatic reduction of lymphocytes in blood and peripheral lymphoid tissues, and a decrease of homing ability to peripheral lymph nodes. Mst1(-/-) thymocytes were impaired in chemotactic response to chemokines, such as CCL19, but not to sphingosine-1-phosphate. Further analyses of Mst1(-/-) mice revealed a severe impairment in the egress of mature T cells from the thymus. T lineage-specific knockout of the Mst1 gene demonstrates a cell-intrinsic role for Mst1 in regulating T cell development. Our study indicates that Mst1 is crucial in controlling lymphocyte chemotaxis and thymocyte emigration.
The Thermographic Phosphor Labkit (2015)

The thermographic phosphor (TGP) Labkit is a flexible instrument for students beyond the first year and is also a useful laboratory tool for physics and research and development. It aids in teaching and demonstrating a number of useful concepts and skills. Students will learn important aspects of optical physics and spectroscopy. By producing fluorescence and measuring its characteristics versus temperature, students will become familiar with atomic energy levels, lifetimes, radiative and non-radiative transitions, spectral bands and linewidth, spectral distribution, and absorption. In addition, measurements involve optics, electro-optics, and electronic instrumentation. The Labkit contains an ultraviolet light emitting diode of 365 nm that illuminates a thin phosphor layer. The phosphor adheres to a copper plate in intimate contact with a Peltier heater/cooler that covers 0 to 100 C. A thermocouple attaches to the copper plate to monitor temperature. The Labkit allows for controlling the pulse duration of the LED and the rate of repetition. Representative signals from 10 to 55 C are presented and the resulting well behaved lifetime versus temperature plot. Results of separate measurements at 10 C indicate repeatability. Detector linearity is demonstrated over a factor of eight in detector gain. Practice and familiarity with common laboratory and industry tools such as thermocouples, Peltier devices, and photomultiplier detectors also contribute to the educational objectives. Finally, in the course of exercising the instrument, the student will learn the practical skill of temperature measurement and control.
Study of Sustainability and Scalability in the Cp*Rh(III)-Catalyzed Direct C–H Amidation with 1,4,2-Dioxazol-5-ones (2015)

The practical aspects of Cp*Rh(III)-catalyzed direct C–H amidation with 1,4,2-dioxazol-5-ones were investigated on the operational safety, use of green solvent, and scalability. Differential scanning calorimeter (DSC) measurement showed that 3-phenyl-1,4,2-dioxazol-5-one is thermally stable while benzoyl azide, a conventionally employed precursor of acyl nitrene, rapidly decomposes to isocyanate. It was confirmed that the replacement of acyl azide with 1,4,2-dioxazol-5-one brings not only high reactivity but also improvement in safety. In respect to a green process development, functional group tolerant Cp*Rh(III) catalyst exhibited high reactivity in ethyl acetate, successfully replacing 1,2-dichloroethane solvent used in the original report. Upon the validation on safety and environmental concerns, scalability was also tested. Two different types of arenes bearing pyridyl and oxime directing groups showed excellent conversions on tens of gram scale reactions, and single recrystallization gave desired products with high yields and purity.
The Significance of Meaning: Why Do Over 90% of Behavioral Neuroscience Results Fail to Translate to Humans, and What Can We Do to Fix It? (2014)

The vast majority of drugs entering human trials fail. This problem (called "attrition") is widely recognized as a public health crisis, and has been discussed openly for the last two decades. Multiple recent reviews argue that animals may be just too different physiologically, anatomically, and psychologically from humans to be able to predict human outcomes, essentially questioning the justification of basic biomedical research in animals. This review argues instead that the philosophy and practice of experimental design and analysis is so different in basic animal work and human clinical trials that an animal experiment (as currently conducted) cannot reasonably predict the outcome of a human trial. Thus, attrition does reflect a lack of predictive validity of animal experiments, but it would be a tragic mistake to conclude that animal models cannot show predictive validity. A variety of contributing factors to poor validity are reviewed. The need to adopt methods and models that are highly specific (i.e., which can identify true negative results) in order to complement the current preponderance of highly sensitive methods (which are prone to false positive results) is emphasized. Concepts in biomarker-based medicine are offered as a potential solution, and changes in the use of animal models required to embrace a translational biomarker-based approach are outlined. In essence, this review advocates a fundamental shift, where we treat every aspect of an animal experiment that we can as if it was a clinical trial in a human population. However, it is unrealistic to expect researchers to adopt a new methodology that cannot be empirically justified until a successful human trial. "Validation with known failures" is proposed as a solution. Thus new methods or models can be compared against existing ones using a drug that has translated (a known positive) and one that has failed (a known negative). Current methods should incorrectly identify both as effective, but a more specific method should identify the negative compound correctly. By using a library of known failures we can thereby empirically test the impact of suggested solutions such as enrichment, controlled heterogenization, biomarker-based models, or reverse-translated measures.
Formation of Tectocapsules by Assembly and Cross-linking of Poly(divinylbenzene-<i>a</i><i>lt</i>-maleic anhydride) Spheres at the Oil−Water Interface (2003)

Novel tectocapsules were prepared by interfacial assembly and covalent cross-linking of poly(divinylbenzene-alt-maleic anhydride) microspheres at the oil−water interface. Dispersions of the anhydride-functional microspheres in a range of organic core solvents, including xylene and propyl acetate and their mixtures, were in turn suspended in a continuous aqueous phase. Addition of polyethylenimines with number average molecular weights ranging from about 200 to about 100 000 to the aqueous phase led to the formation of up to 200 μm diameter tectocapsules, having walls comprised of cross-linked microspheres. The effects of microsphere loading, composition and solubility parameter of the core solvents, type of amine, and rate of amine addition on wall morphology are discussed.
Calcium Carbonate Crystallization in the Presence of Biopolymers (2006)

The influence on calcium carbonate crystallization of a series of biopolymers that contain carboxylic acid or sulfate functional groups was studied using pH and turbidity measurements, optical microscopy, and scanning electron microscopy. Without biopolymer, single calcite (104) rhombohedra were formed. In the presence of nongelling biopolymers (xanthan and gellan) in the conditions used, (104) rhombohedra formed aggregates that were “stack-like”, but in the presence of gelling biopolymers (pectin, κ-carrageenan, and sodium alginate) the aggregates were “rosette-like”. The “rosettes” were proposed to form by the nucleation of calcite on a gelled microparticle template to form a hollow shell. Low methoxy (LM) pectin was particularly effective at directing the growth of calcite rosettes and led to aggregates of radially aligned crystals. The influence of biopolymer concentration on calcite crystallization was studied for LM pectin and κ-carrageenan. In the former case, an increasingly favorable influence of the pectin molecules on the surface energy of calcite nuclei was proposed to result in an enhanced propensity for nucleation, until the pectin concentration was so high that all of the calcium was sequestered. In the latter case, an increase in calcium binding with increasing κ-carrageenan concentration decreased the solution supersaturation and hence decreased the propensity for calcite formation.