gebhart/patrepeval huggingface dataset:
Role of myocyte-specific enhancer-binding factor (MEF-2) in transcriptional regulation of the alpha-cardiac myosin heavy chain gene. (1993)

The intergenic region between the mouse alpha-cardiac myosin heavy chain and beta-myosin heavy chain genes has previously been shown to direct expression of the bacterial chloramphenicol acetyltransferase reporter gene in transgenic mice in a tissue-specific manner. Sequence analyses located a putative myocyte-specific enhancer-binding factor (MEF-2) site situated in the regulatory region of this gene proximal to the start site of transcription. The role of this element in directing the cardiac compartment-specific expression of the transgene was assessed. The polymerase chain reaction was used to perform substitution mutagenesis of the MEF-2 binding site, and lack of MEF-2 binding was confirmed by gel retardation assays. The resultant construct was used to generate transgenic mice. Surprisingly, transgene expression was not down-regulated, but was significantly increased in the hearts of the MEF-2 mutant mice. In addition, cardiac-specific expression of the transgene was perturbed with significant levels of ectopic expression occurring in the aorta.
A Novel Subtilisin-like Protease Gene from Arabidopsis thaliana is Expressed at Sites of Lateral Root Emergence (1999)

Differential screening of a cDNA library for mRNA species that specifically accumulate during auxin-induced lateral root formation in Arabidopsis thaliana led to the isolation of the AIR3 cDNA clone. The corresponding single copy gene consists of 10 exons which encode a protein that possesses all the characteristics of subtilisin-like proteases. The promoter of the AIR3 gene was fused to the gusA (beta-glucuronidase) reporter gene and introduced into Arabidopsis. Expression was almost completely restricted to the outer layers of the parental root at sites of lateral root emergence and could be observed even before protrusion of the newly formed root tip. In the presence of external auxin, GUS activity was visible throughout the parts of the root that are competent for lateral root formation. By digesting structural proteins in the extracellular matrix of cells located above sites of lateral root formation, AIR3 might weaken cell-to-cell connections and thus facilitate lateral root emergence.
The Interaction of 0.15- to 1.0-Mev Neutrons with U-238, U-235, and Pu-239 (1957)

The differential elastic scattering, total elastic scattering, and elastic transport cross sections for U238, U235, and Pu239 for 0.5- and 1.0-Mev neutrons are presented. The nonelastic reaction cross sections are given for these three materials for neutron energies of 0.25, 0.5, and 1.0 Mev and in addition for U238 for 0.15-Mev neutrons. The inelastic scattering cross sections for the excitation of the two lowest levels in U238 are also presented for neutron energies of 0.15, 0.25, and 0.5 Mev.
Performance of a Single Assay for Both Type III and Type VI TMPRSS2:ERG Fusions in Noninvasive Prediction of Prostate Biopsy Outcome (2008)

Although each test appears to have diagnostic value, PSA plus DRE plus type III and type VI TMPRSS2:ERG provided the best diagnostic performance in EPS specimens.
Methods of Determining the Distensibility of Blood Vessels (1966)

Methods of calculating the characteristic transmission parameters of arterial segments, which are very short compared to the wavelength, are presented. If the reflection coefficient is known (e.g., as with complete occlusion) two simultaneous measurements of pressure or flow suffice (Method I). If this is not known, as is generally the case, three measurements must be made (Method II). In either case, provided great attention is paid to the static and dynamic calibrations of the instruments, the results obtained are wholly reasonable and allow an estimation of vessel distensibility, and also a closer examination of the usefulness of various transmission-line hypotheses.
Video network traffic and quality comparison of VP8 and H.264 SVC (2010)

Google has recently released the video compression format VP8 to the open source community. This new compression format competes against the existing H.264 video standard developed by the ITU-T Video Coding Experts Group (VCEG) in collaboration with the ISO/IEC Moving Picture Experts Group (MPEG). This paper compares these two video coding standards in terms of video bit rate-distortion (quality) performance and the video network traffic variability with different long video sequences. We find that VP8 presently does not fulfill its promise to achieve twice the quality at half the bandwidth compared to H.264. The rate-distortion (RD) performance of VP8 is rather slightly below the RD performance of H.264. On the positive side, in contrast to H.264, VP8 has no license fees.
Biochemical and Molecular Characterization of AtPAP26, a Vacuolar Purple Acid Phosphatase Up-Regulated in Phosphate-Deprived Arabidopsis Suspension Cells and Seedlings (2006)

A vacuolar acid phosphatase (APase) that accumulates during phosphate (Pi) starvation of Arabidopsis (Arabidopsis thaliana) suspension cells was purified to homogeneity. The final preparation is a purple APase (PAP), as it exhibited a pink color in solution (A(max) = 520 nm). It exists as a 100-kD homodimer composed of 55-kD glycosylated subunits that cross-reacted with an anti-(tomato intracellular PAP)-IgG. BLAST analysis of its 23-amino acid N-terminal sequence revealed that this PAP is encoded by At5g34850 (AtPAP26; one of 29 PAP genes in Arabidopsis) and that a 30-amino acid signal peptide is cleaved from the AtPAP26 preprotein during its translocation into the vacuole. AtPAP26 displays much stronger sequence similarity to orthologs from other plants than to other Arabidopsis PAPs. AtPAP26 exhibited optimal activity at pH 5.6 and broad substrate selectivity. The 5-fold increase in APase activity that occurred in Pi-deprived cells was paralleled by a similar increase in the amount of a 55-kD anti-(tomato PAP or AtPAP26)-IgG immunoreactive polypeptide and a >30-fold reduction in intracellular free Pi concentration. Semiquantitative reverse transcription-PCR indicated that Pi-sufficient, Pi-starved, and Pi-resupplied cells contain similar amounts of AtPAP26 transcripts. Thus, transcriptional controls appear to exert little influence on AtPAP26 levels, relative to translational and/or proteolytic controls. APase activity and AtPAP26 protein levels were also up-regulated in shoots and roots of Pi-deprived Arabidopsis seedlings. We hypothesize that AtPAP26 recycles Pi from intracellular P metabolites in Pi-starved Arabidopsis. As AtPAP26 also exhibited alkaline peroxidase activity, a potential additional role in the metabolism of reactive oxygen species is discussed.
Glucocorticoid Insensitivity in Virally Infected Airway Epithelial Cells Is Dependent on Transforming Growth Factor-β Activity (2017)

Asthma and chronic obstructive pulmonary disease (COPD) exacerbations are commonly associated with respiratory syncytial virus (RSV), rhinovirus (RV) and influenza A virus (IAV) infection. The ensuing airway inflammation is resistant to the anti-inflammatory actions of glucocorticoids (GCs). Viral infection elicits transforming growth factor-β (TGF-β) activity, a growth factor we have previously shown to impair GC action in human airway epithelial cells through the activation of activin-like kinase 5 (ALK5), the type 1 receptor of TGF-β. In the current study, we examine the contribution of TGF-β activity to the GC-resistance caused by viral infection. We demonstrate that viral infection of human bronchial epithelial cells with RSV, RV or IAV impairs GC anti-inflammatory action. Poly(I:C), a synthetic analog of double-stranded RNA, also impairs GC activity. Both viral infection and poly(I:C) increase TGF-β expression and activity. Importantly, the GC impairment was attenuated by the selective ALK5 (TGFβRI) inhibitor, SB431542 and prevented by the therapeutic agent, tranilast, which reduced TGF-β activity associated with viral infection. This study shows for the first time that viral-induced glucocorticoid-insensitivity is partially mediated by activation of endogenous TGF-β.
Movement of potexviruses requires species-specific interactions among the cognate triple gene block proteins, as revealed by a trans-complementation assay based on the bamboo mosaic virus satellite RNA-mediated expression system (2006)

The intra- and intercellular transport of potexviruses require interactions among viral RNA, coat protein and elements of the triple gene block proteins (TGBps). In this study, the requirement of bamboo mosaic virus (BaMV) TGBps for movement functions and the compatibilities with those of two potexviruses, Potato virus X (PVX) and Foxtail mosaic virus (FoMV), were examined using a satellite RNA-mediated trans-complementation assay system. Single or multiple TGBps of BaMV, PVX and FoMV were expressed from BaMV satellite RNA (satBaMV RNA) vectors to complement the functions of green fluorescent protein-tagged, movement-defective BaMV with mutation(s) in the matching gene(s). It was found that individual BaMV TGBps expressed from the satellite vector could function normally in trans, whereas bi-gene BaMV TGBp constructs in which the expression of TGBp3 might be impaired and individual TGBp genes from PVX or FoMV could not complement the movement functions of the defective helper viruses. Furthermore, alterations of the ratio among TGBps by ectopic expression of individual components of TGBps from satBaMV RNA vectors did not affect the cell-to-cell movement capabilities of wild-type BaMV significantly. The results indicate that species-specific interactions among movement proteins are obligatory for the cell-to-cell movement of BaMV and possibly other potexviruses.
Multi-site fMRI analysis using privacy-preserving federated learning and domain adaptation: ABIDE results (2020)

Deep learning models have shown their advantage in many different tasks, including neuroimage analysis. However, to effectively train a high-quality deep learning model, the aggregation of a significant amount of patient information is required. The time and cost for acquisition and annotation in assembling, for example, large fMRI datasets make it difficult to acquire large numbers at a single site. However, due to the need to protect the privacy of patient data, it is hard to assemble a central database from multiple institutions. Federated learning allows for population-level models to be trained without centralizing entities' data by transmitting the global model to local entities, training the model locally, and then averaging the gradients or weights in the global model. However, some studies suggest that private information can be recovered from the model gradients or weights. In this work, we address the problem of multi-site fMRI classification with a privacy-preserving strategy. To solve the problem, we propose a federated learning approach, where a decentralized iterative optimization algorithm is implemented and shared local model weights are altered by a randomization mechanism. Considering the systemic differences of fMRI distributions from different sites, we further propose two domain adaptation methods in this federated learning formulation. We investigate various practical aspects of federated model optimization and compare federated learning with alternative training strategies. Overall, our results demonstrate that it is promising to utilize multi-site data without data sharing to boost neuroimage analysis performance and find reliable disease-related biomarkers. Our proposed pipeline can be generalized to other privacy-sensitive medical data analysis problems. Our code is publicly available at: https://github.com/xxlya/Fed_ABIDE/.
EUV Binary Phase Gratings: Fabrication and Application to Diffractive Optics (2005)

Diffractive optics play an important role in a variety of fields such as astronomy, microscopy, and lithography.For the extreme ultraviolet (EUV) region of the spectrum they have been difficult to make due to the extremely precise control required of their surface structure.We have developed a robust fabrication technique that achieves the required topographic control through the deposition of a thin film of Si on a Cr etch stop.We have fabricated binary phase gratings using this approach that have an efficiency of 80% of the theoretical maximum.The technique is applicable to any type of binary phase optical element.
DeepTrain: A Programmable Embedded Platform for Training Deep Neural Networks (2018)

This paper presents, DeepTrain, an embedded platform for high-performance and energy-efficient training of deep neural network (DNN). The key architectural concept of DeepTrain is to develop a spatially homogeneous computing (and memory) fabric with temporally heterogeneous programmable data flows to optimize memory mapping and data reuse during different phases of training operation.The DeepTrain is demonstrated as an in-memory accelerator integrated in the logic layer of a 3-D memory module. A programming model and supporting architecture utilizes the flexible data flow to efficiently accelerate training of various types of DNNs. The cycle level simulation and synthesized design in 15 nm FinFET shows power efficiency of 500 GFLOPS/W, and almost similar throughput for a wide range of DNNs, including convolutional, recurrent, and mixed (CNN+RNN) networks.
Measurement of Oxygen radicals in plasma by laser-induced fluorescence spectroscopy(LIFS). (1999)

We have demonstrated the measurement of two-photon laser-induced fluorescence to monitor atom concentrations in a magnetized sheet plasma with vertical gas flow system. The Oxygen atomic radicals were detected by exciting O atoms at 226nm and detecting fluorescence at 845nm.
Functional characterization of pectin methylesterase inhibitor (PMEI) in wheat (2010)

Pectin, one of the main components of plant cell wall, is deesterified by the pectin methylesterase (PME). PME activity is regulated by inhibitor proteins known as the pectin methylesterase inhibitor (PMEI), which plays a key role in wounding, osmotic stress, senescence and seed development. However, the role of PMEI in many plant species still remains to be elucidated, especially in wheat. To facilitate the expression analysis of the TaPMEI gene, RT-PCR was performed using leaf, stem and root tissues that were treated with exogeneous application of phytohormones and abiotic stresses. High transcription was detected in salicylic acid (SA) and hydrogen peroxide treatments. To elucidate the subcellular localization of the TaPMEI protein, the TaPMEI:GFP fusion construct was transformed into onion epidermal cells by particle bombardment. The fluorescence signal was exclusively detected in the cell wall. Using an enzyme assay, we confirmed that PME was completely inhibited by TaPMEI. These results indicated that TaPMEI was involved in inhibition of pectin methylesterification and may play a role in the plant defense mechanism via cell wall fortification.
Detection and quantitation of normal and variant haemoglobins: an analytical review (2004)

As well as six 'normal' haemoglobins that occur at various stages of development, more than 800 abnormal or variant haemoglobins have been described. Many of these variant haemoglobins have no significant clinical consequences apart from causing confusion to clinicians and in laboratories; however, some of the variant haemoglobins result in major morbidity or mortality. The laboratory challenge is to detect these clinically significant haemoglobins and to identify them with sufficient accuracy for clinical purposes, as well as to quantitate both these and the 'normal' haemoglobins. The techniques used to detect and quantitate these haemoglobins in routine service laboratories are discussed in detail. Methods used by referral laboratories, such as mass spectrometry and DNA analysis, are briefly discussed. Haemoglobin analysis is most often undertaken as part of neonatal, antenatal or pre-anaesthetic screening; these programmes are reviewed, together with possible changes to neonatal screening and antenatal screening that may occur as part of the NHS National Plan.
Polycrystalline diamond device processing (2002)

1 The authors describe processes developed for the fabrication of accelerometers, flow sensors, and microchannel cooling structures, using selectively deposited films and silicon micromachining. The diamond films were grown using an ASTeX high-pressure microwave chemical vapor deposition reactor at 950+/-25 degrees C with a growth rate of approximately 1 mu m/h. It was found that polycrystalline diamond films can be used to fabricate various microstructures. A technique for doping diamond films is shown to lower the resistance of the as-grown films.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Towards a network pattern language for complex systems (2005)

The development and use of complex systems models can involve many common problems, problems that are solved again and again by di#erent researchers with various backgrounds and experience. The application of the software engineering patterns paradigm to complex systems modeling will enable capture of the wisdom of the network modeling community in such a way that proven solutions to recurring challenges can be identified and tailored to the specific problem at hand. The use of networks for simulation and analysis are two areas of complex systems modeling that stand to benefit from the patterns approach. The use of networks to guide thinking, as analytic tools and as visualizations is ubiquitous in the field of complex systems.
Managing Health Services: How Administrative Data and Population-Based Analyses Can Focus the Agenda (1998)

University-based researchers in Manitoba, Canada, have used administrative data routinely collected as part of the national health insurance plan to design an integrated database and population-based health information system. This information system is proving useful to policymakers for providing answers to such questions as: which populations need more physician services? Which need fewer? Are high-risk populations poorly served or do they have poor health outcomes despite being well served? Does high utilization represent overuse or utilization related to high need? More specifically, this system provides decision-makers with the capability to make critical comparisons across regions and subregions of residents' health status, socioeconomic risk characteristics, and use of hospitals, nursing homes, and physicians. The system permits analyses of demographic changes, expenditure patterns, and hospital performance in relation to the population served. The integrated database has also facilitated outcomes research across hospitals and counties, utilization review within a single hospital, and longitudinal research on health reform. A particularly interesting application to planning physician supply and distribution is discussed. The discussion highlights the strengths of integrated population-based information in analyzing the health care system and raising important questions about the relationship between health care and health.
Temperature determines the pattern of anaerobic microbial dechlorination of Aroclor 1260 primed by 2,3,4,6-tetrachlorobiphenyl in Woods Pond sediment (1997)

Reductive dechlorination of the Aroclor 1260 residue in Woods Pond (Lenox, Mass.) sediment samples was investigated for a year at incubation temperatures from 4 to 66 degrees C. Sediment slurries were incubated anaerobically with and without 2,3,4,6-tetrachlorobiphenyl (2346-CB; 350 microM) as a primer for dechlorination of the Aroclor 1260 residue. Dechlorination of the Aroclor residue occurred only in live samples primed with 2346-CB and only at 8 to 34 degrees C and 50 to 60 degrees C. The extent and pattern of polychlorinated biphenyl (PCB) dechlorination were temperature dependent. At 8 to 34 degrees C, the dechlorination resulted in 28 to 65% decreases of the hexathrough nonachlorobiphenyls and corresponding increases in the tri- and tetrachlorobiphenyls. At 12 to 30 degrees C, 30 to 40% of the hexa- through nonachlorobiphenyls were dechlorinated in just 3 months. The optimal temperature for overall chlorine removal was 20 to 27 degrees C. We observed four different microbial dechlorination processes with different but partially overlapping temperature ranges, i.e., Process N (flanked meta dechlorination) at 8 to 30 degrees C, Process P (flanked para dechlorination) at 12 to 34 degrees C, Process LP (unflanked para dechlorination) at 18 to 30 degrees C, and Process T (a very restricted meta dechlorination of specific hepta- and octachlorobiphenyls) at 50 to 60 degrees C. These temperature ranges should aid in the development of strategies for the enrichment and isolation of the microorganisms responsible for each dechlorination process. The incubation temperature determined the relative dominance of the four PCB dechlorination processes and the extent and products of dechlorination. Hence, understanding the effects of temperature on PCB dechlorination at contaminated sites should assist in predicting the environmental fate of PCBs or planning bioremediation strategies at those sites.
Adaptive Priority Routing with Ack_Mechanism for DTN networks (2009)

In Disruption Tolerant Networks, simply flooding packet scheme has a major drawback in terms of network congestion. This paper proposes a new routing algorithm, called Adaptive Priority Routing with Ack_mechanism (APRA). APRA arranges the forwarding sequence and the dropping sequence based on their assigned priority. The priority is determined by the TTL, Delivery Predictability, and Replication Density. Meanwhile APRA has an ACK list exchange mechanism that is used to purge the redundant messages. An extensive simulation of APRA using various scenarios was carried out and its performance was compared to well known DTN routing protocols: Epidemic Routing, Randomized Routing and Spray-and-Wait Routing. Our results show that APRA outperforms them in all scenarios in terms of packet delay and delivery.
Control of size and shape of micelles, of flow properties, and of pH-values in aqueous CTAB-solutions via photoreactions of solubilizates (2007)

“New Trends in Colliod Science” contains the proceedings of the foundation meeting of the European Colloid and Interface Society (ECIS), October 1–3, 1986. Representatives from the major European groups working in this field contributed to the conference. The volume contains an up-to-date account of present developments in Colloid Science. The contributions cover a wide scope of subjects, and provide encouragement that structures and transport processes in dense colloidal systems can be understood on basic principles. The main subjects are include: phase diagrams of new surfactant systems microemulsions and their applications vesicles and bilayers transport properties of colloidal systems.