gebhart/patrepeval huggingface dataset:
Microbial and Processing Criteria for Production of Probiotics: A Review (2006)

The use of probiotics has become widely accepted as a natural means to promote health for both humans and animals. Today, probiotics are used as health supplements in food and feeds and they are replacing the use of antibiotic growth promotors or chemical supplements. Under the right conditions the claims made for probiotic preparations can be realized. The development of suitable technology for probiotic production, taking into account and stability, is a key area of research for industrial production. Production of probiotics should be based on the microbial criteria, and the ability to withstand stress during processing and storage of products is important. Thermophilic/thermotolerant probiotics are of great interest in this area as they can have all the desired characteristics. This review makes an overview of probiotic selection studies including new technologies for isolation/identification, adhesion and immune response. The importance of multistrain cultures is also stressed. The development of suitable probiotics in food and feed needs good proof of their efficacy and function in order to be accepted as a valuable product.
The design and implementation of architectural components for the integration of the IP multimedia subsystem and wireless sensor networks (2010)

The IP multimedia subsystem is becoming the de facto standard for IP-based multimedia services, while wireless sensor networks are gaining in popularity due to their ability to capture a rich set of contextual information. Integrating the sensing capabilities of WSNs in the IMS can open the door to a wide range of context-aware applications in areas such as wireless healthcare and pervasive gaming. We have previously proposed a presence-based architecture for WSN/IMS integration. This architecture relies on two key components: a WSN/IMS gateway acting as an interworking unit between WSNs and the IMS; and an extended presence server serving as a context information management node in the core network. In this article we focus on the design and implementation of these two components. Furthermore, two applications (a pervasive game and a personalized call control application) are used to concretely show how new applications can be developed using our architecture. Performance has also been evaluated. Several important findings were made in the course of this work; one is that the IMS integration with a large and evolving variety of WSNs may be a never-ending endeavor - the gateway requiring constant upgrading due to the lack of standard APIs for the interaction with sensors produced by different vendors. Another finding is that while the introduction of context as an application building block in the IMS ensures the availability of additional contextual information in the network and enables fast and easy development of context-aware applications, the lack of mature IMS application development toolkits remains a roadblock.
Influence of C4 null genes on infection with human immunodeficiency virus (1988)

The hypothesis that complement is important in the host response to human immunodeficiency virus (HIV) was tested. Complement C4 and Bf allotypes were determined in 26 patients who fulfilled the diagnostic criteria for persistent generalised lymphadenopathy due to HIV, 72 homosexuals who were negative for antibody to HIV, and 185 control subjects drawn from the local population. HLA-A, B, and DR were also typed and the phenotypes examined for the presence of supratypes and C4BQ0. Eleven patients (42%) had C4B null alleles compared with only 13 (18%) homosexuals who were negative for antibody and 28 (15%) controls. From estimates of gene frequencies the difference between the patients with lymphadenopathy and the controls was significant after conservative correction. In the patients only a minority (six) of the C4B null alleles were contained within ancestral haplotypes. Together with the fact that C4 null alleles result in partial deficiency of C4, this finding suggests that products of complement genes are important in infection with HIV or its consequences, or both. A role is proposed for complement and Fc receptors.
Demonstration of 20 Gbit/s all-optical logic XORin integrated SOA-based interferometric wavelength converter (2000)

The results of optical logic exclusive-OR (XOR) at up to 20 Gbit/s in an integrated SOA-based Mach-Zehnder interferometer are presented. For the first time, to the knowledge of the authors, BER measurements are demonstrated on 10 Gbit/s optical logic XOR, with zero penalty. In addition, for the first time, 20 Gbit/s all-optical XOR, with an integrated device that allows simple, stable and efficient operation, is demonstrated.
Experiments with large ensembles for segmentation and classification of cervical cancer biopsy images (2014)

To classify cervical cells as normal or cancer, the histological image must be segmented. After segmentation mean nuclear volume can be used to distinguish between normal and cancer cells. Due to the rapid reproduction of cancer cells, they have higher mean nuclear volume than typical normal cells. We propose a large ensemble of segmentations which separate normal and cancer cases based on the single feature of mean nuclear volume. Four basic segmentors with different parameters generate the segmentations. The mean nuclear volume is extracted from the segmentations. The dataset used for this paper contained multiple images from 30 normal and 32 cancer patients. Hematoxylin and eosin (H&E) was used to stain archival tissue sections from the normal cervix and cervical cancers. Results show it is possible to predict class with greater than 84% accuracy.
Acoustic Echo Cancellation Using a Vector-Space-Based Adaptive Filtering Algorithm (2015)

A novel vector-space-based adaptive filtering (VAF) algorithm for acoustic echo cancellation (AEC) is presented. The proposed VAF algorithm can be divided into two phases: offline and online. In the offline phase, VAF constructs a vector space to incorporate the prior knowledge of adaptive filter coefficients from a wide range of different channel characteristics. Then, in the online phase, a mapping function is derived to estimate the adaptive filter for the testing condition using the constructed vector space. By using the vector space, VAF can effectively and efficiently estimate the parameters of the adaptive filter for the unknown testing condition. The experimental results for three designed AEC tasks demonstrate that VAF provides notably faster convergence rates compared to conventional adaptive filtering methods.
Deep3D: Fully Automatic 2D-to-3D Video Conversion with Deep Convolutional Neural Networks (2016)

As 3D movie viewing becomes mainstream and Virtual Reality (VR) market emerges, the demand for 3D contents is growing rapidly. Producing 3D videos, however, remains challenging. In this paper we propose to use deep neural networks for automatically converting 2D videos and images to stereoscopic 3D format. In contrast to previous automatic 2D-to-3D conversion algorithms, which have separate stages and need ground truth depth map as supervision, our approach is trained end-to-end directly on stereo pairs extracted from 3D movies. This novel training scheme makes it possible to exploit orders of magnitude more data and significantly increases performance. Indeed, Deep3D outperforms baselines in both quantitative and human subject evaluations.
A Little Common Sense is a Dangerous Thing: The Inherent Inconsistency Between KSR and Current Official Notice Policy (2012)

[Excerpt] “The question of whether an invention is an obvious variation of existing technology is one that has troubled courts for decades. From its roots in nineteenth century case law to the recent Supreme Court decision KSR v. Teleflex, Inc., the doctrine of obviousness has waxed and waned—moving through a variety of judicially-created tests to a current state that is still far from perspicuous. This paper will examine obviousness through a particular lens: the U.S. Patent and Trademark Office (“USPTO,” “PTO”) tool known as “official notice”—the practice of declaring a patent application’s claims unpatentable as obvious based on undocumented reasoning, such as the common sense or common knowledge of a person having ordinary skill in the art to which the application pertains. After KSR, using unsubstantiated common sense-based rationales for rejecting patent claims is considered a completely valid practice. However, a line of obviousness cases, including one from the United States Supreme Court, stands for the polar opposite position—that declaring a patent invalid as obvious without underlying prior art support does not comport with the standards of the Administrative Procedure Act. Unfortunately, this contradiction leaves patent practitioners and the federal district courts to reconcile diametrically opposed holdings, especially when a case involves official notice. Part II of this paper will give a brief history of general obviousness jurisprudence up to the Supreme Court’s KSR decision in 2007. Next, Part III will introduce the reader to the obviousness inquiry through the eyes of a USPTO examiner by presenting a hypothetical patent application scenario and defining various terms of art. Part IV will introduce the concept of formal official notice at the USPTO, including an examination of the official agency guidelines for the practice, and will present a judicial history of official notice. Part V will return to KSR, presenting more recent Federal Circuit obviousness cases and introducing the problems that the current jurisprudence brings about. Finally, Part VI will conclude with potential solutions to the issue, arguing that the judiciary should hold the USPTO to task in providing evidence that an invention is in fact obvious.”
Optimal Parallel Scheduling of Gaussian Elimination DAG's (1983)

A parallel algorithm for Gaussian elimination (GE) is described, which solves a linear system of size n using m ≤ n parallel processors and a shared random access memory. Converting the serial GE algorithm to parallel form involves scheduling its computation DAG (directed acyclic graph) on m processors. A lower bound for schedule length is established for dense GE DAG's and it is proved that the proposed algorithm produces schedules which achieve these bounds. Finally, both the construction and execution of the schedule are incorporated into a single concurrent program which is shown to run in optimal time.
Biosynthesis of Silver Nanoparticles using <i>Olea europaea</i> Leaves Extract and its Antibacterial Activity (2013)

This paper reports a rapid and ecofriendly green method for the synthesis of silver nonoparticles from silver nitrate solution using <i>O</i><i>lea europaea</i> leaves extract. Effect of <i>Olea europaea</i> leaves extract, silver nitrate concentration, reaction time and temperature on reaction rate were investigated. The synthesized silver nanoparticles (AgNPS) were characterized with scanning electron microscopy (SEM), X-ray diffraction (XRD), atomic absorption spectroscopy (AAS) and fourier infrared spectroscopy (FT-IR). UV-vis spectra gave surface plasmon resonance (SPR) at 430 nm. This reveals the reduction of silver ions (Ag<SUP>+</SUP>) to silver (Ag<SUP>o</SUP>) which indicates the formation of silver nanoparticles (AgNPs). The antibacterial activity of green synthesized AgNPs showed effective inhibitory activity against water borne pathogens <i>Listeria monocytogenes, Shigella and Staphylococcus aureus.</i> This reveals that silver nanoparticles could provide a safer alternative to conventional antimicrobial and antibacterial agents.
Automated Lip Reading Technique for Password Authentication (2012)

As technology is starting to conquer every strata of the society, the war for protecting confidential data from being intercepted is growing intense by the hour. Biometric-security stands out as the most secure form of authentication in high security zones such as defense, space missions and research head-quarters. Today, forms of password-protection range from facerecognition to retina -scan. Here, we develop a system for recognizing and converting lip movement of an individual into a recognized pattern which is set as a password for the system using image-processing. This system is also a break-through for providing people with motor-disabilities a robust and easy way of protecting their data. By capturing and tracing the successive movement of lips during speech, the corresponding word can be detected. The captured images are represented as points on a two-dimensional flat manifold that enables us to efficiently define the pronunciation of each word and thereby analyze or synthesize the motion of the lips. The motion of lips helps us track the word syllable-by-syllable. With multiple levels of image processing, it becomes possible to set the matching parameters to a very close value, hence not allowing any bruteforce or other infamous hacking techniques to break into the user's system. This lip reading technique also serves applications in areas where communication via direct speech is not possible.
Robust AAV Genotyping Based on Genetic Distances in Rep Gene That Are Maintained by Ubiquitous Recombination (2022)

Adeno-associated viruses (AAVs) are a convenient tool for gene therapy delivery. According to the current classification, they are divided into the species AAV A and AAV B within the genus Dependoparvovirus. Historically AAVs were also subdivided on the intraspecies level into 13 serotypes, which differ in tissue tropism and targeted gene delivery capacity. Serotype, however, is not a universal taxonomic category, and their assignment is not always robust. Cross-reactivity has been shown, indicating that classification could not rely on the results of serological tests alone. Moreover, since the isolation of AAV4, all subsequent AAVs were subdivided into serotypes based primarily on genetic differences and phylogenetic reconstructions. An increased interest in the use of AAV as a gene delivery tool justifies the need to improve the existing classification. Here, we suggest genotype-based AAV classification below the species level based on the <i>rep</i> gene. A robust threshold was established as 10% nt differences within the 1248 nt genome fragment, with 4 distinct AAV genotypes identified. This distinct sub-species structure is maintained by ubiquitous recombination within, but not between, <i>rep</i> genes of the suggested genotypes.
The Use of a Dual Dye Photometric Calibration Method to Identify Possible Sample Dilution from an Automated Multichannel Liquid-handling System (2006)

A significant difference between the reported volumes delivered by a fluid-filled automated liquid-handling system with eight stainless steel fixed tips was observed when a gravimetric method and a dual dye photometric method were used to measure delivered volumes between 20 and 200 μL. A series of experiments, using the default pipetting parameters, was performed which demonstrated that the difference in the reported volume was due to a dilution effect by the system liquid of the liquid handler and did not indicate an error in the delivered volumes. This dilution effect led to a decrease in the reported volume by the dual dye method, which alerted the user to the problem of sample dilution. In contrast, the gravimetric method provided the expected volume, and therefore did not alert the user to the problem. Without optimization of pipetting parameters, the dilution issue can be significant, because the resultant change in the concentration of the compound(s) of interest in the sample could lead to an unidentified error in the sample assay.
Development of a data warehouse for non-operational data in power utilities (2006)

Power engineers are concerned about the operational data, which would enable the real time monitoring, and control of the power system. However the non-operational data retrievable from the system has a potential to reveal useful information regarding the health of the system and infrastructural flaws in the system. The non-operational data consists of records or logs of multiple events such as series of faults, power fluctuations, disturbances and lightning strikes. The paper describes the concept of data warehousing of non-operational data for a power utility. The value of analyzing non-operational data is elaborated. The identification and sources of non-operational data is established and the methods of collecting the data are elaborated. The user groups who would benefit from the non-operational data are identified. The concept of a data warehouse and the steps involved in the implementation are discussed. Finally, the establishment of a functional data path to transfer the SCADA data to the warehouse is discussed in detail and the retrieval of data is also demonstrated
Argo: an integrative, interactive, text mining-based workbench supporting curation (2012)

Curation of biomedical literature is often supported by the automatic analysis of textual content that generally involves a sequence of individual processing components. Text mining (TM) has been used to enhance the process of manual biocuration, but has been focused on specific databases and tasks rather than an environment integrating TM tools into the curation pipeline, catering for a variety of tasks, types of information and applications. Processing components usually come from different sources and often lack interoperability. The well established Unstructured Information Management Architecture is a framework that addresses interoperability by defining common data structures and interfaces. However, most of the efforts are targeted towards software developers and are not suitable for curators, or are otherwise inconvenient to use on a higher level of abstraction. To overcome these issues we introduce Argo, an interoperable, integrative, interactive and collaborative system for text analysis with a convenient graphic user interface to ease the development of processing workflows and boost productivity in labour-intensive manual curation. Robust, scalable text analytics follow a modular approach, adopting component modules for distinct levels of text analysis. The user interface is available entirely through a web browser that saves the user from going through often complicated and platform-dependent installation procedures. Argo comes with a predefined set of processing components commonly used in text analysis, while giving the users the ability to deposit their own components. The system accommodates various areas and levels of user expertise, from TM and computational linguistics to ontology-based curation. One of the key functionalities of Argo is its ability to seamlessly incorporate user-interactive components, such as manual annotation editors, into otherwise completely automatic pipelines. As a use case, we demonstrate the functionality of an in-built manual annotation editor that is well suited for in-text corpus annotation tasks. DATABASE URL: http://www.nactem.ac.uk/Argo.
PIAS3 Suppresses NF-κB-mediated Transcription by Interacting with the p65/RelA Subunit (2004)

Nuclear factor-kappaB (NF-kappaB) is a transcription factor critical for key cellular processes, including immune response, apoptosis, and cell cycle progression. A yeast two-hybrid screening, using the Rel homology domain (RHD) of the p65 subunit (RelA) of NF-kappaB as bait, led to the isolation of PIAS3, previously identified as a specific inhibitor of STAT3. We show that PIAS3 can directly associate with p65 using an in vitro pull-down and in vivo coimmunoprecipitation assays. When overexpressed, PIAS3 inhibits NF-kappaB-dependent transcription induced by treatment with tumor necrosis factor alpha (TNF-alpha) or interleukin-1beta or by overexpression of TNF family receptors such as RANK, TNFR1, and CD30 or signal transducers of TNF receptor-associated factors (TRAFs), including TRAF2, TRAF5, and TRAF6. Downregulation of PIAS3 by RNA interference reverses its effect on TNF-alpha-mediated NF-kappaB activation. We found that an N-terminal region of PIAS3 is necessary for both the interaction with p65 and the transcriptional suppression activity. In addition, we found that an LXXLL coregulator signature motif located within the N-terminal region of PIAS3 is the minimal requirement for the interaction with p65. Furthermore, we demonstrate that PIAS3 interferes with p65 binding to the CBP coactivator, thereby resulting in a decreased NF-kappaB-dependent transcription. Taken together, these data suggest that PIAS3 may function in vivo as a modulator in suppressing the transcriptional activity of p65.
Histocompatibility Antigens in Alzheimer’s Disease (1981)

A preliminary study of Alzheimer's disease showed an apparent excess of the antigen A2 in patients who presented the disease before the age of 60, whereas those with onset after 64 showed different frequencies of the antigens A1 and A3 when compared with the local population. There was no abnormality in the distribution of B locus antigens. The findings are briefly discussed.
Reusable Schedule Design and Execution Framework for Autonomous Mission Management in Space (2021)

Aerospace mission autonomy can improve mission capabilities, reduce the burden on ground operators, and prevent mission failure when encountering unexpected situations. However, autonomy comes at the cost of additional complexity for design, development, and testing. This research presents an autonomous mission framework to bridge the gap between existing aerospace mission systems and emerging autonomous paradigms. Traditional aerospace missions without custom autonomy solutions generally follow rigid schedules, and tasks are executed during specified time windows. For these types of scenarios, the only task constraint is the current time. Our proposed framework, called the Schedule Manager, expands on this concept by adding additional constraint checks such as conflict, priority, and resource constraints. Through the design and upload of task schedules, constraint tables, and contingency schedules, the benefits of autonomy can be achieved without deviating significantly from the standard, thereby simplifying the adoption, integration, and safety analysis process. This framework was integrated and tested with NASA’s core Flight System and 42 spacecraft simulator, and run on development boards comparable to flight hardware.
Preserving Fluid Sheets with Adaptively Sampled Anisotropic Particles (2012)

This paper presents a particle-based model for preserving fluid sheets of animated liquids with an adaptively sampled Fluid-Implicit-Particle (FLIP) method. In our method, we preserve fluid sheets by filling the breaking sheets with particle splitting in the thin regions, and by collapsing them in the deep water. To identify the critically thin parts, we compute the anisotropy of the particle neighborhoods, and use this information as a resampling criterion to reconstruct thin liquid surfaces. Unlike previous approaches, our method does not suffer from diffusive surfaces or complex remeshing operations, and robustly handles topology changes with the use of a meshless representation. We extend the underlying FLIP model with an anisotropic position correction to improve the particle spacing, and adaptive sampling to efficiently perform simulations of larger volumes. Due to the Lagrangian nature of our method, it can be easily implemented and efficiently parallelized. The results show that our method can produce visually complex liquid animations with thin structures and vivid motions.