gebhart/patrepeval huggingface dataset:
Somatic mosaicism in Wiskott–Aldrich syndrome suggests<i>in vivo</i>reversion by a DNA slippage mechanism (2001)

Somatic mosaicism caused by in vivo reversion of inherited mutations has been described in several human genetic disorders. Back mutations resulting in restoration of wild-type sequences and second-site mutations leading to compensatory changes have been shown in mosaic individuals. In most cases, however, the precise genetic mechanisms underlying the reversion events have remained unclear, except for the few instances where crossing over or gene conversion have been demonstrated. Here, we report a patient affected with Wiskott--Aldrich syndrome (WAS) caused by a 6-bp insertion (ACGAGG) in the WAS protein gene, which abrogates protein expression. Somatic mosaicism was documented in this patient whose majority of T lymphocytes expressed nearly normal levels of WAS protein. These lymphocytes were found to lack the deleterious mutation and showed a selective growth advantage in vivo. Analysis of the sequence surrounding the mutation site showed that the 6-bp insertion followed a tandem repeat of the same six nucleotides. These findings strongly suggest that DNA polymerase slippage was the cause of the original germ-line insertion mutation in this family and that the same mechanism was responsible for its deletion in one of the propositus T cell progenitors, thus leading to reversion mosaicism.
An Increased Percentage of Long Amyloid β Protein Secreted by Familial Amyloid β Protein Precursor (βApp <sub>717</sub> ) Mutants (1994)

Normal processing of the amyloid beta protein precursor (beta APP) results in secretion of a soluble 4-kilodalton protein essentially identical to the amyloid beta protein (A beta) that forms insoluble fibrillar deposits in Alzheimer's disease. Human neuroblastoma (M17) cells transfected with constructs expressing wild-type beta APP or the beta APP717 mutants linked to familial Alzheimer's disease were compared by (i) isolation of metabolically labeled 4-kilodalton A beta from conditioned medium, digestion with cyanogen bromide, and analysis of the carboxyl-terminal peptides released, or (ii) analysis of the A beta in conditioned medium with sandwich enzyme-linked immunosorbent assays that discriminate A beta 1-40 from the longer A beta 1-42. Both methods demonstrated that the 4-kilodalton A beta released from wild-type beta APP is primarily but not exclusively A beta 1-40. The beta APP717 mutations, which are located three residues carboxyl to A beta 43, consistently caused a 1.5- to 1.9-fold increase in the percentage of longer A beta generated. Long A beta (for example, A beta 1-42) forms insoluble amyloid fibrils more rapidly than A beta 1-40. Thus, the beta APP717 mutants may cause Alzheimer's disease because they secrete increased amounts of long A beta, thereby fostering amyloid deposition.
Transposed FIR filter structure with time-varying coefficients for digital data resampling (2000)

A new time-domain derivation is presented for interpolation and decimation by a fractional factor U/D. Though it is well known that such a filter can be implemented using a direct-form I, FIR filter with time-varying coefficients, a novel time-varying alternative, using a transposed filter structure, is described. Time-varying filters are especially important for implementation on a digital signal processor. The new time-varying structure has the advantage of reduced buffer memory for downscaling, or increased parallelism for high-speed upscaling, compared to the conventional time-varying structure.
Preforming of a Fuselage C-Shaped Frame Manufactured by Resin Transfer Molding (2013)

<div class="section abstract"><div class="htmlview paragraph">The need for efficient manufacturing approaches has emerged with the increasing usage of composites for structural components in commercial aviation. Resin Transfer Molding (RTM), a process where a fiber preform is injected with resin into a closed tool, can achieve high fiber content required for structural components as well as improved dimensional accuracy since all surfaces are controlled by a tool surface.</div><div class="htmlview paragraph">Moreover, RTM is well suited for parts that can be standardized throughout the aircraft, such as a fuselage frames and stringers. The objective of this investigation is to develop a preforming approach for a C-Shaped Fuselage frame. Two approaches are proposed: tri-axial braiding and hand lay-up of Non-Crimp Fabrics. The fiber architecture of the basic materials as well as the complete preforms is explained. The necessary preforming operations are detailed. The quality control measurement of fiber orientation and thickness are presented. A relation between the fabric lay-up angle, the fabric construction and the potential defects is drawn. The fiber architecture of the molded part is reported. The fiber volume content and void content of C-Shaped frames are measured using the acid digestion method. The outcome of this study can be applied to the fabrication of aircraft frames.</div></div>
Co-designing the failure analysis and monitoring of large-scale systems (2008)

Large-scale distributed systems provide the backbone for numerous distributed applications and online services. These systems span over a multitude of computing nodes located at different geographical locations connected together via wide-area networks and overlays. A major concern with such systems is their susceptibility to failures leading to downtime of services and hence high monetary/business costs. In this paper, we argue that to understand failures in such a system, we need to co-design monitoring system with the failure analysis system. Unlike existing monitoring systems which are not designed specifically for failure analysis, we advocate a new way to design a monitoring system with the goal of uncovering causes of failures. Similarly the failure analysis techniques themselves need to go beyond simple statistical analysis of failure events in isolation to serve as an effective tool. Towards this end, we provide a discussion of some guiding principles for the co-design of monitoring and failure analysis systems for planetary scale systems.
A genetic algorithm for the design space exploration of datapaths during high-level synthesis (2006)

High-level synthesis is comprised of interdependent tasks such as scheduling, allocation, and module selection. For today's very large-scale integration (VLSI) designs, the cost of solving the combined scheduling, allocation, and module selection problem by exhaustive search is prohibitive. However, to meet design objectives, an extensive design space exploration is often critical to obtaining superior designs. We present a framework for efficient design space exploration during high-level synthesis of datapaths for data-dominated applications. The framework uses a genetic algorithm (GA) to concurrently perform scheduling and allocation with the aim of finding schedules and module combinations that lead to superior designs while considering user-specified latency and area constraints. The GA uses a multichromosome representation to encode datapath schedules and module allocations and efficient heuristics to minimize functional and storage area costs, while minimizing circuit latencies. The framework provides the flexibility to perform resource-constrained scheduling, time-constrained scheduling, or a combination of the two, using a simple and fast list-scheduling technique. A graded penalty function is used as an objective function in evaluating the quality of designs to enable the GA to quickly reach areas of the search space where designs meeting user specified criteria are most likely to be found. Since GAs are population-based search heuristics, a unique feature of our framework is its ability to offer a large number of alternative datapath designs, all of which meet design specifications but differ in module, register, and interconnect configurations. Many experiments on well-known benchmarks show the effectiveness of our approach.
Local multi sectoral collaboration : preventing premature mortality among the working-age population of Ukraine (2007)

Ukraine’s population fell between 1991 and 2007 from 52 million to 46.2 million; at this rate, its 2050 population will be 36.2 million. Rich in natural resources, Ukraine is losing the working-age people who make its resources valuabl. However, much of the disease burden is amenable, and with proper intervention and a well-functioning preventative and curative health system, the crisis could be averted. This report presents the results of research that had two objectives : (i) To reveal oblast- and city-level understanding among certain stakeholders of the causes of working - age mortality and strategies to address it and (ii) To determine the extent to which collaboration is practiced at these levels, what methods of collaboration are used and what challenges prevent collaboration from being effective. Six oblasts were identified for the study, assuring diversity in several respects: Ivan-Frankivsk and Ternopil oblasts in western Ukraine; Mykolaiv Oblast in the southeast; and Dnipropetrovsk, Cherkassy and Poltava in the east. Known stakeholders in each oblast were interviewed between December 2008 and May 2009 to glean not only their comments but also their contacts in each oblast who might participate in focus group discussions. These two data collection methods garnered the opinions of nearly 60 representatives of the public and private sectors, oblast and city government levels, and the medical, labor, education or environment, and traffic or police “spheres.” (For clarity, these four sectors are referred to here as spheres to distinguish this category from that of the public and private sectors.) After these discussions, the grounded theory approach was used to analyze comments and develop themes.
Objective Video Quality Assessment Based on Neural Networks (2016)

Image/Video Quality Assessment (IQA/VQA) plays a significant role in image and video processing, as it can directly predict the impact of distortions on the video in the quality of experience (QoE) of the user. For this propose, in this paper, it is presented a new method for objective video quality assessment using an artificial neural network to predict the subjective evaluation of the video as if it were observed by a human user. The network was trained using degradation indicators extracted from the VQEG Phase I video database, which describe the level of distortion suffered by the original video under spatial and temporal scopes. The proposed method obtained an excellent correlation with the subjective scores over this same database.
A current-mode folding/interpolating CMOS analog to quaternary converter using binary to quaternary encoding block (2003)

A current-mode folding and interpolating analog to quaternary digital converter (AQC) with binary to quaternary encoder has been proposed in this paper. A current-mode three-level folding amplifier has been employed to reduce the number of reference current sources and a low impedance current-mode approach is adopted. A voltage level converter circuit has been proposed not only to encode the binary output signal to the quaternary output signal, but also to enable the proposed AQC to be applied as a starting point device of the quaternary logic. Fast settling time and low power consumption of the AQC are achieved by utilising the proposed architecture. The simulation results of the designed 4 digit AQC show a sampling rate of 14 MHz and a power dissipation of 150 mW with a single power supply of 3.3 V for a double poly four metal standard CMOS 0.35 /spl mu/m n-well technology.
Measured feedback-induced intensity noise for 1.3 µm DFB laser diodes (1989)

An experimental set-up has been described, allowing for reliable relative intensity noise (RIN) measurements for a wide feedback range. It could be verified experimentally for DFB lasers that the transition to the coherence collapic regime occurs at significantly larger feedback levels, if the laser is operated at larger optical powers. Furthermore, it has been noted that a large coupling strength κL in DFB lasers is beneficial for improved stability against optical feedback.
Cloud-based Livestock Monitoring System Using RFID and Blockchain Technology (2020)

Food security and quality has become an increasingly concerned issue around the world. Recent food falsification cases have caused vast public health risk and economic damage while eroding consumers’ trust. Ever more prevalent is the danger of infectious disease among livestock that may cause serious economic damage while adding uncertainty to the world’s food supply. Animal-human transmitted diseases infect humans and are the culprits for the 2003 SARS, 2009 H1N1 Avian Flu, and 2019 Coronavirus outbreaks. Livestock monitoring is a promising approach in disease warning, authenticating food supply chain and tracking sources of contamination in the production cycle. One way of addressing the traceability issue and ensuring accountability is by utilizing blockchain technology as a ledger. This paper proposes a novel method to apply blockchain technology to ensure traceability and authenticity in the livestock supply chain, hence making the livestock farming process more scientific and trustworthy.
Induction of drug‐metabolizing enzymes in human pancreatic cancer and chronic pancreatitis (1993)

Chronic pancreatitis and pancreatic cancer have both been linked with occupational exposure to organic chemicals. These chemicals are known to be metabolized within the liver by the cytochrome P-450 family of enzymes, and indeed are able to induce levels of these enzymes as evidence of their interaction. The purpose of this study was therefore to see if these enzyme systems were altered in chronic pancreatitis and pancreatic cancer. Immunocytochemistry of four phase I drug-metabolizing enzymes (cytochromes P-450 IIIA1, P-450 IIE, P-450 IA2, and NADPH cytochrome P-450 oxido-reductase) and one phase II enzyme [glutathione S-transferase (GST) 5-5] was therefore performed on pancreas and/or liver biopsy samples from organ donors and compared with patients with chronic pancreatitis or pancreatic cancer. In samples from donor subjects, the types and levels of drug-metabolizing enzymes in hepatocytes were similar to those seen in pancreatic acinar cells. In material from patients with chronic pancreatitis or pancreatic cancer, cytochrome P-450 enzyme levels were greater in both the liver and the pancreas than those seen in the donor group, while GST levels were unchanged. Islets of Langerhans showed high levels of P-450 IA2 in the donor group, with clear induction of P-450 IIIA1 and NADPH cytochrome P-450 oxidoreductase in patients with chronic pancreatitis but not in the pancreatic cancer group. Levels of GST 5-5 were also induced in the islets. The present findings raise the possibility of an aetiological relationship between elevated levels of drug-metabolizing enzymes and the subsequent development of disease.
Women’s Experiences with Oral and Vaginal Pre-Exposure Prophylaxis: The VOICE-C Qualitative Study in Johannesburg, South Africa (2014)

Personal acknowledgment of product nonuse was challenging. This qualitative inquiry highlighted key influences at all SEF levels that shaped women's perceptions of trial participation and experiences with investigational products. Whether these impacted women's behaviors and may have contributed to ineffective trial results warrants further investigation.
Trypsin Purification by<i>p</i>-Aminobenzamidine Immobilized on Macroporous Chitosan Membranes (1998)

Membranes with suitable mechanical properties, chemical stability, and macroporosity which have a selectivity for trypsin were prepared by coupling a ligand (p-aminobenzamidine) to cross-linked chitosan membranes via a spacer (succinic acid). The chitosan membranes were cross-linked with ethylene glycol diglycidyl ether in order to avoid their dissolution in acidic media. The cross-linked chitosan membranes were then covalently coupled with succinic anhydride, at ambient temperature, to obtain hydrophilic spacers with carboxyl terminals. The amino groups of the chitosan membranes which have not reacted with the succinic anhydride were blocked with acetic anhydride to avoid the nonspecific interactions. Finally the ligand p-aminobenzamidine (PAB) was incorporated via the coupling between the carboxyl groups of the succinic acid and the amino groups of PAB, using 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide (EDAC) as the activating agent. A PAB density of 2.7 × 10-3 mol/g of chitosan was achieved. Since the PAB−chitosan membranes have a much higher affinity toward trypsin than toward chymotrypsin, they have been employed for the purification of crude trypsin solutions. A purification factor > 7, a specific activity > 9500 BAEE units/mg, and activity yields between 60 and 80% were obtained. These results suggest that the PAB−chitosan affinity membrane can be efficient for trypsin purification.
Large-Scale Phosphorylation Analysis of α-Factor-Arrested <i>Saccharomyces cerevisiae</i> (2007)

Protein phosphorylation is essential for numerous cellular processes. Large-scale profiling of phosphoproteins continues to enhance the depth and speed at which we understand these processes. The development of effective phosphoprotein and peptide enrichment techniques and improvements to mass spectrometric instrumentation have intensified phosphoproteomic research in recent years, leading to unprecedented achievements. Here, we describe a large-scale phosphorylation analysis of alpha-factor-arrested yeast. Using a multidimensional separation strategy involving preparative SDS-PAGE for prefractionation, in-gel digestion with trypsin, and immobilized metal affinity chromatography (IMAC) enrichment of phosphopeptides, followed by LC-MS/MS analysis employing a hybrid LTQ-Orbitrap mass spectrometer, we were able to catalog a substantial portion of the phosphoproteins present in yeast whole-cell lysate. This analysis yielded the confident identification of 2288 nonredundant phosphorylation sites from 985 proteins. The ambiguity score (Ascore) algorithm was utilized to determine the certainty of site localization for the entire data set. In addition, the size of the data set permitted extraction of known and novel kinase motifs using the Motif-X algorithm. Finally, a large number of members of the pheromone signaling pathway were found as phosphoproteins and are discussed.
The plaque‐inhibiting capacity of 11 antibacterial compounds (1970)

The plaque inhibiting effect in vivo of 11 antibacterial agents was compared with their antibacterial activity against salivary bacteria in vitro. The in vivo effect was tested for 4 days in a human model with a supplement of sucrose in the diet. The antibacterial activity of the compounds, which were chosen from different main groups of disinfectants (alcohols, iodophores, dyes, quaternary ammonium bases, amidines, guanidines) were tested in four in vitro systems. No correlation was evident between the in vivo and in vitro effects. Chlorhexidine gluconate and ‐acetate proved most effective in vivo , whereas several other substances equally or more effective against salivary bacteria in vitro , exhibited no effect in vivo. It is concluded that other factors than the antibacterial properties are important in plaque inhibition in vivo.
Chromatography (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChromatographyGunter. Zweig and Joseph. ShermaCite this: Anal. Chem. 1974, 46, 5, 73–94Publication Date (Print):April 1, 1974Publication History Published online1 May 2002Published inissue 1 April 1974https://pubs.acs.org/doi/10.1021/ac60341a015https://doi.org/10.1021/ac60341a015research-articleACS PublicationsRequest reuse permissionsArticle Views378Altmetric-Citations4LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A method for the blind separation of sources for use as the first stage of a neonatal seizure detection system (2005)

A method is proposed for automatically choosing independent components (ICs) of interest from neonatal EEG data, with the aim of using them in further analysis to detect seizures. This procedure greatly reduces the amount of information which needs to be processed in the seizure detection system, and reduces the effect of noise and artefacts on its performance. The fast ICA algorithm is used to generate the ICs, and the complexity of each IC is examined to determine those of interest. The singular value fraction (SVF) measure is used to reduce the number of sources containing artefacts chosen. In the best case, the 12 channel EEG used in these tests is reduced to 2 or 3 sources of interest. In every case, at least 3 sources were removed that consisted of noise.
Engineering Living Functional Materials (2015)

Natural materials, such as bone, integrate living cells composed of organic molecules together with inorganic components. This enables combinations of functionalities, such as mechanical strength and the ability to regenerate and remodel, which are not present in existing synthetic materials. Taking a cue from nature, we propose that engineered 'living functional materials' and 'living materials synthesis platforms' that incorporate both living systems and inorganic components could transform the performance and the manufacturing of materials. As a proof-of-concept, we recently demonstrated that synthetic gene circuits in Escherichia coli enabled biofilms to be both a functional material in its own right and a materials-synthesis platform. To demonstrate the former, we engineered E. coli biofilms into a chemical-inducer-responsive electrical switch. To demonstrate the latter, we engineered E. coli biofilms to dynamically organize biotic-abiotic materials across multiple length scales, template gold nanorods, gold nanowires, and metal/semiconductor heterostructures, and synthesize semiconductor nanoparticles (Chen, A. Y. et al. (2014) Synthesis and patterning of tunable multiscale materials with engineered cells. Nat. Mater. 13, 515-523.). Thus, tools from synthetic biology, such as those for artificial gene regulation, can be used to engineer the spatiotemporal characteristics of living systems and to interface living systems with inorganic materials. Such hybrids can possess novel properties enabled by living cells while retaining desirable functionalities of inorganic systems. These systems, as living functional materials and as living materials foundries, would provide a radically different paradigm of materials performance and synthesis-materials possessing multifunctional, self-healing, adaptable, and evolvable properties that are created and organized in a distributed, bottom-up, autonomously assembled, and environmentally sustainable manner.