gebhart/patrepeval huggingface dataset:
Changes in viral protein function that accompany retroviral endogenization (2007)

Endogenous retroviruses (ERVs) are the remnants of ancient retroviral infections of germ cells and have been maintained in whole or part as heritable genomic elements. The last known endogenization events occurred several million years ago, and therefore stepwise analysis of retroviral endogenization has not been possible. A unique opportunity to study this process became available when a full-length ERV isolated from koalas (KoRV) was shown to have integrated into their germ line within the past 100 years. Even though KoRV shares 78% nucleotide identity with the exogenous and highly infectious gibbon ape leukemia virus (GALV), the infectivity of KoRV, like that of other ERVs, is substantially lower than that of GALV. Differences in the protein coding regions of KoRV that distinguish it from GALV were introduced into the GALV genome, and their functional consequences were assessed. We identified a KoRV gagpol L domain mutation as well as five residues present in the KoRV envelope (env) that, when substituted for the corresponding residues of GALV, resulted in vectors exhibiting substantially reduced titers similar to those observed with KoRV vectors. In addition, KoRV env protein lacks an intact CETTG motif that we have identified as invariant among highly infectious gammaretroviruses. Disruption of this motif in GALV results in vectors with reduced syncytia forming capabilities. Functional assessment of specific sequences that contribute to KoRV's attenuation from a highly infectious GALV-like progenitor virus has allowed the identification of specific modifications in the KoRV genome that correlate with its endogenization.
Evidence of Activity-Specific, Radial Organization of Mitotic Chromosomes in Drosophila (2011)

The organization and the mechanisms of condensation of mitotic chromosomes remain unsolved despite many decades of efforts. The lack of resolution, tight compaction, and the absence of function-specific chromatin labels have been the key technical obstacles. The correlation between DNA sequence composition and its contribution to the chromosome-scale structure has been suggested before; it is unclear though if all DNA sequences equally participate in intra- or inter-chromatin or DNA-protein interactions that lead to formation of mitotic chromosomes and if their mitotic positions are reproduced radially. Using high-resolution fluorescence microscopy of live or minimally perturbed, fixed chromosomes in Drosophila embryonic cultures or tissues expressing MSL3-GFP fusion protein, we studied positioning of specific MSL3-binding sites. Actively transcribed, dosage compensated Drosophila genes are distributed along the euchromatic arm of the male X chromosome. Several novel features of mitotic chromosomes have been observed. MSL3-GFP is always found at the periphery of mitotic chromosomes, suggesting that active, dosage compensated genes are also found at the periphery of mitotic chromosomes. Furthermore, radial distribution of chromatin loci on mitotic chromosomes was found to be correlated with their functional activity as judged by core histone modifications. Histone modifications specific to active chromatin were found peripheral with respect to silent chromatin. MSL3-GFP-labeled chromatin loci become peripheral starting in late prophase. In early prophase, dosage compensated chromatin regions traverse the entire width of chromosomes. These findings suggest large-scale internal rearrangements within chromosomes during the prophase condensation step, arguing against consecutive coiling models. Our results suggest that the organization of mitotic chromosomes is reproducible not only longitudinally, as demonstrated by chromosome-specific banding patterns, but also radially. Specific MSL3-binding sites, the majority of which have been demonstrated earlier to be dosage compensated DNA sequences, located on the X chromosomes, and actively transcribed in interphase, are positioned at the periphery of mitotic chromosomes. This potentially describes a connection between the DNA/protein content of chromatin loci and their contribution to mitotic chromosome structure. Live high-resolution observations of consecutive condensation states in MSL3-GFP expressing cells could provide additional details regarding the condensation mechanisms.
The impact of different methods of DNA extraction on microbial community measures of BALF samples based on metagenomic data. (2016)

A microbial DNA extraction method with pretreatment of depletion of host nucleic acid by Benzonase can enable a higher yield of microbial DNA from samples with a higher fraction of host cells to be obtained. The lower airways of patients with IIP without airway infection were inhabited by a great number of bacterium.
Time-resolved catch and release of an optical pulse from a dynamic photonic crystal nanocavity (2011)

We perform time-domain measurements of the interaction between light and silicon photonic crystal nanocavities under dynamic Q factor control. Time-resolved evidence of optical pulse capture and release on demand is demonstrated and compared for samples with dynamic Q ranges from ~3,000 to 26,000 and from 18,500 to 48,000. Observing the energy behaviour in response to dynamic control provides insight not available with time-integrated measurements into factors influencing device performance such as carrier absorption and pulse capture efficiency.
Improvement of blast-free mining technique for placers in permafrost zone (2016)

A critical analysis of the technical and economic indicators of systems and equipment used in underground mining of placers in the north-east of Russia suggests that the existing technologies have practically exhausted their capabilities. It is required to science-based evaluate and introduce blast-free mining technologies on the ground of studies and application of high-performance mining machines and mechanisms improving efficiency and safety of mining operations. The article describes the experimental results obtained in a placer mine in Yakutia in the course of permafrost drivage by roadheader GPKS equipped with a cutting head with a 55 kW capacity drive and with a percussion body having an impact energy of 1.7 kJ. The rate of penetration is about 1 m/h, the working speed is 3&ndash;4 m per shift at the operation factor of 0.5, which is almost three times higher than the drivage using drillingand-blasting. For the development of Solur diamond fi eld and the similar placer deposits, it is offered to apply room-andpillar method with backfilling and using roadheaders and self-propelled equipment. The research has allowed evaluation of the basic conceptual principles of underground placer mining in the permafrost zone.
Sign Language Recognition via Deformable 3D Convolutions and Modulated Graph Convolutional Networks (2023)

Automatic sign language recognition (SLR) remains challenging, especially when employing RGB video alone (i.e., with no depth or special glove-based input) and under a signer-independent (SI) framework, due to inter-personal signing variation. In this paper, we address SI isolated SLR from RGB video, proposing an innovative deep-learning framework that leverages multi-modal appearanceand skeleton-based information. Specifically, we propose three components for the first time in SLR: (i) a modified version of the ResNet2+1D network to capture signing appearance information, where spatial and temporal convolutions are substituted by their deformable counterparts, accomplishing both prevalent spatial modeling potential and motion-aware modeling adaptability; (ii) a novel spatio-temporal graph convolutional network (ST-GCN) that integrates a GCN variant, involving weight and affinity modulation for modeling diverse correlations between different body joints beyond the physical human skeleton structure, followed by a self-attention layer and a temporal convolution; and (iii) the “PIXIE” 3D human pose and shape regressor to generate 3D joint-rotation parameterization used for ST-GCN graph construction. Both appearance- and skeleton-based streams are ensembled in the proposed system and evaluated on two datasets of isolated signs, one in Turkish and one in Greek. Our system outperforms the state-of-the-art on the second set, yielding 53% relative error rate reduction (2.45% absolute), while it performs on par with the best reported system on the first.
Abstract 520: Peptide and SiRNA Modulation of HSP20 Influences Vasoreactivity (2014)

Subarachnoid hemorrhages affect 30,000 people each year and accounts for between 1-7% of all strokes. Nearly 85% of the time that the hemorrhage occurs, it is due to a cerebral aneurysm that leads to delayed vasospasm and stroke. Traditional vasodilators cannot be used because they will cause systemic hypotension leaving an unmet clinical need. HSPB1 is a small heat shock related protein that modulates vasorelaxation, is downregulated in vasospastic vessels, and represents a potential therapeutic modality for the treatment of SAH-induced vasospasm. siRNA against HSPB1 that was encapsulated with a diblock copolymer to enhance uptake, or Rat aortic smooth muscle was tested with a HSPB1 phospho-peptide (HSPB1-p) +/- a polyplex delivery system (polyplexHSPB1). Intracellular calcium was measured concurrently with force using a Fluoroplex sysem. Knockdown of HSPB1 inhibited sodium nitroprusside (SNP)-induced relaxation of rat aorta. In conclusion, HSP20 modulates calcium independent relaxation of vascular smooth muscle and HSPB1-p may represent a novel therapeutic for vasospasm. Tissue treated with HSPB1-p or polyplex HSPB1-p had a dose dependent inhibition of contraction. The polyplex inhibited contraction at a lower dose of HSPB1-p than peptide alone with complete inhibition of contraction at 500 μM). Complete inhibition of contraction occurred without inhibition of increases in intracellular calcium concentrations ([Ca 2+ ] i ).
The role of new eudesmane-type sesquiterpenoid and known eudesmane derivatives from the red alga Laurencia obtusa as potential antifungal–antitumour agents (2015)

A new eudesmane sesquiterpenoid, eudesma-4(15),7-diene-5,11-diol (1) along with the known trinor-sesquiterene, teuhetenone (2), and a seco-eudesmane sesquiterpene, chabrolidione B (3), have been isolated from the Red Sea red alga Laurencia obtusa. The chemical structures were elucidated on the basis of extensive spectroscopic analysis. The antifungal and cytotoxic activities of the isolated metabolites were tested against several fungi, yeast and human mammary carcinoma cell line (MCF-7). Compounds 1 and 3 showed a much better activity [minimum inhibitory concentration (MIC): 2.9 μM] than that of amphotericin B (MIC: 4.6 μM). Interestingly, compound 2, the least active antifungal compound, retained the high anticancer activity against MCF-7 (22 μM) in comparison with cisplatin (59 μM), which was determined by employing lactate dehydrogenase assay. Compounds 1-3 are recorded here for the first time from algal flora. The chemotaxonomic importance of the isolated metabolites was discussed.
Feasibility study of an FM-CW SAR system (2001)

There is an increasing interest in low-cost, high-resolution imaging radar systems to be operated from small and maybe even unmanned platforms. Existing imaging systems are generally too heavy for small platforms, or too expensive in day-to-day use to be applied in small-scale civil applications. Combining the compactness of FM-CW radar systems and the high azimuth resolution of SAR systems, an FM-CW SAR sensor could be of interest for small-scale applications. The feasibility of FM-CW SAR in the field of airborne earth observation is being investigated in a new research project. The research activities will concentrate on two main subjects: the system design and the development of special SAR processing algorithms, which take the characteristics of FM-CW radar signals into account. A demonstrator, based on commercially available components, will be built. This demonstrator should prove the feasibility of FM-CW SAR systems and provide test <data to validate the processing algorithms. From the system models can be concluded that, using off-the-shelf technology, the performance of the demonstrator will be limited. This is not considered a problem since the demonstrator is used just to show the feasibility of FM-CW SAR. Main difficultics are the phase noise, especially for larger ranges, the low clutter-to-noise ratio, and the possible azimuth ambiguities.
Rho-Kinase Is an Important Therapeutic Target in Cardiovascular Medicine (2005)

Rho-kinase has been identified as one of the effectors of the small GTP-binding protein Rho. Accumulating evidence has demonstrated that Rho/Rho-kinase pathway plays an important role in various cellular functions, not only in vascular smooth muscle cell (VSMC) contraction but also in actin cytoskeleton organization, cell adhesion and motility, cytokinesis, and gene expressions, all of which may be involved in the pathogenesis of cardiovascular disease. At molecular level, Rho-kinase upregulates various molecules that accelerate inflammation/oxidative stress, thrombus formation, and fibrosis, whereas it downregulates endothelial nitric oxide synthase. The expression of Rho-kinase itself is mediated by protein kinase C/NF-kappaB pathway with an inhibitory and stimulatory modulation by estrogen and nicotine, respectively. At cellular level, Rho-kinase mediates VSMC hypercontraction, stimulates VSMC proliferation and migration, and enhances inflammatory cell motility. In animal studies, Rho-kinase has been shown to be substantially involved in the pathogenesis of vasospasm, arteriosclerosis, ischemia/reperfusion injury, hypertension, pulmonary hypertension, stroke and heart failure, and to enhance central sympathetic nerve activity. Finally, in clinical studies, fasudil, a Rho-kinase inhibitor, is effective for the treatment of a wide range of cardiovascular disease, including cerebral and coronary vasospasm, angina, hypertension, pulmonary hypertension, and heart failure, with a reasonable safety. Thus, Rho-kinase is an important therapeutic target in cardiovascular medicine.
Abstract 9201: Association Between Remnant Cholesterol, High-Sensitivity C-reactive Protein, and Risk of Atherosclerotic Cardiovascular Disease Events in the Multi-ethnic Study of Atherosclerosis (MESA) (2021)

Background: Elevated remnant-like particle (RLP)-cholesterol (RLP-C) and high-sensitivity C-reactive protein (hsCRP) are each associated with atherosclerotic cardiovascular disease (ASCVD) individually. Whether a serum marker of systemic inflammation modifies RLP-C associated ASCVD risk is unknown. The purpose of this study was to evaluate the interplay of nuclear magnetic resonance (NMR)-derived RLP-C and hsCRP and their association with ASCVD risk in the Multi-Ethnic Study of Atherosclerosis (MESA). Methods: Lipoprotein particles were measured using NMR spectroscopic analysis among MESA participants. RLP-C includes very-low-density lipoprotein (VLDL)-cholesterol and intermediate-density lipoprotein (IDL)-cholesterol. Four groups were created as follows: Group 1: RLP-C ≤ median (≤29.14 mg/dL) and hsCRP &lt; 2 mg/dL; Group 2: RLP-C ≤ median (≤29.14 mg/dL) and hsCRP≥ 2 mg/dL; Group 3: RLP-C &gt; median (&gt;29.14 mg/dL) and hsCRP level &lt; 2 mg/dL; and Group 4: RLP-C &gt; median (&gt;29.14 mg/dL) and hsCRP level ≥ 2 mg/dL. Kaplan-Meier survival curves and multivariable adjusted Cox proportional hazard models were used to examine the relationship between RLP-C and hsCRP with incident ASCVD. Results: A total of 6,720 MESA participants (mean age 62.2 y, SD 10.2, 53% female) who had baseline NMR-derived RLP-C and hsCRP measurements were included. At a median follow-up of 15.6 years, a total of 1,032 ASCVD events were observed. In the fully adjusted model, compared to those in the reference group (Group 1), participants in Group 2, Group 3, and Group 4 demonstrated a 24% (95%CI, 1.02 - 1.50), 22% (1.01 - 1.46), and 47% (1.22 - 1.77) increased risk of incident ASCVD events, respectively (p &lt;0.001). Conclusion: We found an independent association of NMR-derived RLP-C and hsCRP with incident ASCVD in an ethnically and geographically diverse population. Notably, the combination of increased RLP-C and hsCRP was associated with a markedly increased risk of future ASCVD events.
9. Springing the Floor for a Different Kind of Dance (2020)

Edmond, Fischer, Romary, and Tasovac begin this chapter by exploring what infrastructure means in different contexts before going on to consider ‘digital infrastructure’ as not only a tool that needs to be built but also understood. They examine practices and theories in an attempt to define infrastructure for the arts and humanities in the digital age: firstly, considering infrastructure as knowledge spaces; secondly, considering why the arts and humanities need research infrastructure and; thirdly, establishing why a community approach should be adopted and what baseline requirements should be met. They focus on the case study of DARIA ERIC and its dual hierarchical and marketplace structure to optimise knowledge sharing and in-flow from within its community. They argue that infrastructures today not only represent a different model for supporting knowledge creation but are also developing new models for creating knowledge. They conclude that DARIAH ERIC harnesses the best of two communities — research infrastructures as originally conceived of in the sciences, as well as the arts and humanities research base.
Energy-aware video coding of multiple views via workload balancing (2011)

Video coding and compression reduce the storage space and/or the bandwidth required to transmit video. Multiview video systems make use of more than one camera to describe a scene and therefore demand more computing resources and energy consumption to compress and transmit video data. In this paper, we present an energy management framework for multiview systems that combines the two major video coding and compression paradigms: Predictive and Distributed Video Coding (PVC and DVC). The paradigms generally assume that the decoder (in PVC) and the encoder (in DVC) are resource constrained devices. However, there are a growing number of applications where resources are constrained at both encoder and decoder. Such scenarios cannot be handled due to the imbalance in PVC/DVC and demand a more flexible paradigm. In the proposed framework, video coding that combines PVC and DVC is used to balance multiview video coding workload between the video encoder and decoder in a way that maximizes system lifetime. Simulation results show that the proposed method can obtain a lifetime percentage increase of 58% and 30% on average and maintain video quality when compared to strict PVC and DVC systems respectively.
Examining the relationship between law libraries and democracy in transitional states — a case study of the republic of Rwanda (2014)

Democracy is now recognized as the preferred form of governance in the world. With its rise from the foundation of the United States and growth throughout the world, most recently with the fall of the Soviet Union, democratic governance is the cornerstone for the majority of governments worldwide. Three key elements emerge as essential to democratic governance: transparency, accessibility, and accountability. A democratic government must be transparent in that it allows citizens and active civil society participants to see into the halls of government. It must allow access to laws—and preferably the lawmaking process—to grant citizens an opportunity to scrutinize government actions. Finally, there must be a mechanism for citizens to hold government actors accountable for these actions, if necessary.&#13;\n&#13;\nWith these processes in mind, lawmakers, scholars and development professionals for decades have sought to define what institutions can best support transparency, accessibility, and accountability in government. One of these institutions—libraries—has gained support among information professionals and governance expertise alike as ideal for supporting the access principle of democratic government. Focusing on access, public libraries have long been held as institutions that have a wide-reaching effect on providing information to citizens regardless of socio-economic status, and are well-suited to promote accessibility and therefore democracy. Little has been written, however, about the important relationship between law libraries and democracy. These special libraries serve a similar but more narrowly defined mission in the democratic sphere: providing access specifically to that information necessary for scrutiny of government action.&#13;\n&#13;\nEspecially in developing democracies—those states transitioning from an authoritarian to democratic form of government—law libraries can play a significant role to promote and uphold the access principle of democracy. Law libraries collect precisely the information necessary to scrutinize government actors: records of lawmaking, administrative rules and decisions, government reports, and of course the laws themselves. In addition to the general public, law libraries also serve constituent groups important to governance, such as lawyers, judges, and lawmakers. Providing competent collections and research assistance for these groups strengthens good governance in its own ways as well.&#13;\n&#13;\nThis thesis seeks to clarify the relationship between libraries and democracy, and how it specifically supports the access principle of democratic governance. It particularly seeks to highlight this relationship between law libraries and democracy, and that role in developing and transitional states. Finally, it applies this analysis to a field investigation conducted in the Republic of Rwanda in June 2013, which sought to understand the role of law libraries in the developing democratic state.
Increased Expression of Axogenesis-Related Genes and Mossy Fibre Length in Dentate Granule Cells from Adult HuD Overexpressor Mice (2011)

The neuronal RNA-binding protein HuD plays a critical role in the post-transcriptional regulation of short-lived mRNAs during the initial establishment and remodelling of neural connections. We have generated transgenic mice overexpressing this protein (HuD-Tg) in adult DGCs (dentate granule cells) and shown that their mossy fibres contain high levels of GAP-43 (growth-associated protein 43) and exhibit distinct morphological and electrophysiological properties. To investigate the basis for these changes and identify other molecular targets of HuD, DGCs from HuD-Tg and control mice were collected by LCM (laser capture microscopy) and RNAs analysed using DNA microarrays. Results show that 216 known mRNAs transcripts and 63 ESTs (expressed sequence tags) are significantly up-regulated in DGCs from these transgenic mice. Analyses of the 3'-UTRs (3'-untranslated regions) of these transcripts revealed an increased number of HuD-binding sites and the presence of several known instability-conferring sequences. Among these, the mRNA for TTR (transthyretin) shows the highest level of up-regulation, as confirmed by qRT-PCR (quantitative reverse transcription-PCR) and ISH (in situ hybridization). GO (gene ontology) analyses of up-regulated transcripts revealed a large over-representation of genes associated with neural development and axogenesis. In correlation with these gene expression changes, we found an increased length of the infrapyramidal mossy fibre bundle in HuD-Tg mice. These results support the notion that HuD stabilizes a number of developmentally regulated mRNAs in DGCs, resulting in increased axonal elongation.