gebhart/patrepeval huggingface dataset:
Adiponectin Induces A20 Expression in Adipose Tissue to Confer Metabolic Benefit (2014)

Obesity is a major risk factor for metabolic disease, with white adipose tissue (WAT) inflammation emerging as a key underlying pathology. We detail that mice lacking Reverbα exhibit enhanced fat storage without the predicted increased WAT inflammation or loss of insulin sensitivity. In contrast to most animal models of obesity and obese human patients, Reverbα(-/-) mice exhibit elevated serum adiponectin levels and increased adiponectin secretion from WAT explants in vitro, highlighting a potential anti-inflammatory role of this adipokine in hypertrophic WAT. Indeed, adiponectin was found to suppress primary macrophage responses to lipopolysaccharide and proinflammatory fatty acids, and this suppression depended on glycogen synthase kinase 3β activation and induction of A20. Attenuated inflammatory responses in Reverbα(-/-) WAT depots were associated with tonic elevation of A20 protein and ex vivo shown to depend on A20. We also demonstrate that adipose A20 expression in obese human subjects exhibits a negative correlation with measures of insulin sensitivity. Furthermore, bariatric surgery-induced weight loss was accompanied by enhanced WAT A20 expression, which is positively correlated with increased serum adiponectin and improved metabolic and inflammatory markers, including C-reactive protein. The findings identify A20 as a mediator of adiponectin anti-inflammatory action in WAT and a potential target for mitigating obesity-related pathology.
An HTM-based update-side synchronization for RCU on NUMA systems (2020)

Read-copy update (RCU) can provide ideal scalability for read-mostly workloads, but some believe that it provides only poor performance for updates. This belief is due to the lack of RCU-centric update synchronization mechanisms. RCU instead works with a range of update-side mechanisms, such as locking. In fact, many developers embrace simplicity by using global locking. Logging, hardware transactional memory, or fine-grained locking can provide better scalability, but each of these approaches has limitations, such as imposing overhead on readers or poor scalability on non-uniform memory access (NUMA) systems, mainly due to their lack of NUMA-aware design principles.
Approaching zero thermal emissivity in thermophotovoltaic cells (2021)

A thermophotovoltaic (TPV) cell is specially designed to minimize the absorption of radiation below its lowest bandgap. This ensures that the unused power is returned to the hot thermal emitter, which keeps it from being wasted. This approach is termed photon recycling because the energy is recycled until it is emitted at a high enough frequency to be efficiently converted. To facilitate this process, we recently created a cell architecture that has a thin air layer behind the light-absorbing semiconductor. The resulting air-bridge cell (ABC) reflects back almost all of the low-energy photons. In this talk, I will discuss the development of an InGaAs ABC that achieved a record-high peak conversion efficiency of 32% and our recent efforts to improve performance.
Feasibility of an EMCCD-Based Beta Imaging Probe for Radioguided Surgery (2006)

We report on initial results of our new intraoperative probe, capable of functioning in real time with high spatial resolution and high sensitivity. This probe is based on a combination of two novel technologies, an electron multiplying charge coupled device (EMCCD) bonded to a microcolumnar CsI(Tl) scintillator via a flexible fiberoptic. Our data demonstrates that the probe can be used with such beta-emitting radiolabels as /sup 18/F, /sup 131/I, and /sup 32/P. The basic design of the probe and its evaluation using standard clinical phantoms is presented. Also, the operational data obtained on swine models is included to demonstrate the probe's efficacy in practical procedures.
Trend analysis of COVID-19 mis/disinformation narratives (Preprint) (2022)

<sec> <title>BACKGROUND</title> To tackle the COVID-19 infodemic, we selected as relevant for the analysis 42,410 articles from 460 unverified sources, that is, sources that were indicated by fact checkers and other disinformation experts as frequently spreading mis/disinformation, covering the period from 1 January 2020 to 31 December 2021. </sec> <sec> <title>OBJECTIVE</title> To identify the main narratives of COVID-19 mis/disinformation, develop a codebook, automate the process by training a classifier, and analyse the spread of narratives over time and across countries. </sec> <sec> <title>METHODS</title> Articles were retrieved with a customised version of the Europe Media Monitor (EMM) processing chain providing a stream of text items. Keyword-based categorisation, entity detection, including geolocation, sentiment analysis and machine translation were used to enrich the text items. Clustering was carried out with two different algorithms using titles and initial part of the article's text (teaser text). A training set was annotated according to a multi-level codebook for COVID-19 mis/disinformation. A Transformer-based model was developed to classify all text items according to the codebook. </sec> <sec> <title>RESULTS</title> We set up a process for classifying narratives of COVID-19 mis/disinformation in near real-time. The system relies on a multi-level codebook and a Transformer-based model. In the period from 1 January 2020 to 31 December 2021, we identified 12 supernarratives that evolved over time. With the availability of COVID-19 vaccines, a rise in anti-vax content occurred. </sec> <sec> <title>CONCLUSIONS</title> We established a process that allows for daily monitoring of COVID-19 mis/disinformation. The experience gathered over the first two years of the pandemic will be useful to analyse mis/disinformation on other topics, such as climate change, migration, and geopolitical developments. </sec>
A Signaling Pathway for Stimulation of Na+ Uptake Induced by Angiotensin II in Primary Cultured Rabbit Renal Proximal Tubule Cells. (1999)

The aim of the present study was to examine the signaling pathways for a low dose of angiotensin II (ANG II) on Na+ uptake of primary cultured rabbit renal proximal tubule cells (PTCs) in hormonally defined serum-free medium. The results were as follows; ANG II (10(-11) M) stimulated the proliferation of PTCs. 10(-11) M ANG II stimulated Na+ uptake by 20%, whereas 10(-9) M ANG II inhibited it by 20% (p < 0.05). The stimulatory effect of 10(-11) M ANG II on Na+ uptake was inhibited by amiloride (10(-3) M) and by losartan (ANG II receptor subtype 1 antagonist, 10(-8) M) but not by PD123319 (ANG II receptor subtype 2 antagonist, 10(-8) M). Pertussis toxin (PTX, 50 ng/ml) prevented the ANG II-induced stimulation of Na+ uptake (p < 0.01). 8-Bromoadenosine 3', 5'-cyclic monophosphate (8-Br-cAMP, 10(-6) M) did not affect Na+ uptake. SQ 22536 (adenylate cyclase inhibitor, 10(-6) M) also did not change the ANG II-induced stimulation of Na+ uptake. ANG II did not stimulate cAMP production. In contrast, 12-O-tetradecanoylphorbol-13-acetate (TPA, 0.01 ng/ml) produced significant increase in Na+ uptake. When ANG II and TPA were added together to the PTCs, there was no additive effect on Na+ uptake. Staurosporine (calcium-dependant protein kinase C inhibitor, 10(-6) M) led to a complete inhibition of ANG II-induced stimulation of Na+ uptake. ANG II-treatment resulted in a 26% increase in total protein kinase C (PKC) activity. However, 10(-11) M ANG II did not change [Ca2+]i mobilization and [3H]-AA release while 10(-9) M ANG II increased both of them. In conclusion, the PTX-sensitive PKC pathway may be the main signaling cascade in the stimulatory effects of low dose of ANG II (10(-11) M) on Na+ uptake in the primary cultured rabbit renal proximal tubule cells in hormonally defined serum-free medium.
RNA Scaffolds for Minihelix-Based Aminoacyl Transfer: Design of “Transpeptizymes” (2000)

Abstract Some evidence and considerations suggest that RNA minihelices based on the acceptor-TΨC stem-loop of tRNAs are the historical, more ancient part of the tRNA structure. These minihelices are substrates for aminoacylation by tRNA synthetases. In the transition from the RNA world to the theatre of proteins, aminoacyl minihelices may have had a role in early systems of peptide synthesis. Such systems would require bringing together aminoacyl groups into close proximity in order for peptide bonds to form. Here we report the design of RNA scaffolds based on pieces of the structure of the P4-P6 domain of the Tetrahymena ribozyme. RNA minihelices were incorporated into these scaffolds and the resulting RNAs could be enzymatically aminoacylated. The RNA scaffolds containing the minihelix-like pieces associated spontaneously to create the presumptive P4-P6 structure and thereby bring together the substrates for aminoacylation. Thus, peptide synthesis with associating RNA scaffolds that contain minihelix-like motifs appears plausible.
CAD Model Assembly Hierarchy Reorganization for Application in Virtual Assembly: A Hybrid Approach Using the CAD System and a Visualization Tool (2003)

The hierarchy of assembly components in a CAD assembly model is rarely a true representation of the sequence of assembly of these components during manufacturing. Thus, any assembly planning or evaluation software system needs to re-order and re-group the various components of the CAD assembly model to reflect the sequence of component assembly. Although all parametric CAD systems allow reorganization of the assembly tree, it is a difficult and timeconsuming process due to the relationships and constraints between the various components. We propose an alternative hybrid method that couples the CAD system and a visualization tool that supports reorganization, while preserving data, to allow fast and easy rearranging of the assembly hierarchy. Also, after the reorganization, polygonal representations of the new sub-assemblies are created and the original constraints are also transformed in a consistent manner. As a next logical step, we compare the time required to rearrange the assembly hierarchy using both methods — the CAD system alone and the hybrid system. A statistical analysis using three treatment factors indicates that if the number of components is more than 15, then it is more efficient to use the hybrid method over the CAD system. The overarching goal was to allow fast and efficient creation of different assembly hierarchies to allow the corresponding assembly sequences to be verified in a virtual assembly application that derives its models and constraints from the assembly hierarchy in the CAD system. We have implemented the method to allow the successful reorganization and virtual assembly verification of many industry models, some with several hundred components, provided by various industry partners.
Endolysosomolytically Active pH‐Sensitive Polymeric Nanotechnology (2010)

This chapter contains sections titled: Site - Specific Nanotherapeutics Destabilization of Endolysosomal Compartments Endolysosomolytic Polymeric Nanocarriers Conclusion Acknowledgments References
Mycobacterium tuberculosis Rv3406 Is a Type II Alkyl Sulfatase Capable of Sulfate Scavenging (2013)

The genome of Mycobacterium tuberculosis (Mtb) encodes nine putative sulfatases, none of which have a known function or substrate. Here, we characterize Mtb's single putative type II sulfatase, Rv3406, as a non-heme iron (II) and α-ketoglutarate-dependent dioxygenase that catalyzes the oxidation and subsequent cleavage of alkyl sulfate esters. Rv3406 was identified based on its homology to the alkyl sulfatase AtsK from Pseudomonas putida. Using an in vitro biochemical assay, we confirmed that Rv3406 is a sulfatase with a preference for alkyl sulfate substrates similar to those processed by AtsK. We determined the crystal structure of the apo Rv3406 sulfatase at 2.5 Å. The active site residues of Rv3406 and AtsK are essentially superimposable, suggesting that the two sulfatases share the same catalytic mechanism. Finally, we generated an Rv3406 mutant (Δrv3406) in Mtb to study the sulfatase's role in sulfate scavenging. The Δrv3406 strain did not replicate in minimal media with 2-ethyl hexyl sulfate as the sole sulfur source, in contrast to wild type Mtb or the complemented strain. We conclude that Rv3406 is an iron and α-ketoglutarate-dependent sulfate ester dioxygenase that has unique substrate specificity that is likely distinct from other Mtb sulfatases.
Mitosis-related phosphorylation of the eukaryotic translation suppressor 4E-BP1 and its interaction with eukaryotic translation initiation factor 4E (eIF4E) (2019)

Eukaryotic translation initiation factor 4E (eIF4E)-binding protein 1 (4E-BP1) inhibits cap-dependent translation in eukaryotes by competing with eIF4G for an interaction with eIF4E. Phosphorylation at Ser-83 of 4E-BP1 occurs during mitosis through the activity of cyclin-dependent kinase 1 (CDK1)/cyclin B rather than through canonical mTOR kinase activity. Here, we investigated the interaction of eIF4E with 4E-BP1 or eIF4G during interphase and mitosis. We observed that 4E-BP1 and eIF4G bind eIF4E at similar levels during interphase and mitosis. The most highly phosphorylated mitotic 4E-BP1 isoform (δ) did not interact with eIF4E, whereas a distinct 4E-BP1 phospho-isoform, EB-γ, phosphorylated at Thr-70, Ser-83, and Ser-101, bound to eIF4E during mitosis. Two-dimensional gel electrophoretic analysis corroborated the identity of the phosphorylation marks on the eIF4E-bound 4E-BP1 isoforms and uncovered a population of phosphorylated 4E-BP1 molecules lacking Thr-37/Thr-46-priming phosphorylation. Moreover, proximity ligation assays for phospho-4E-BP1 and eIF4E revealed different <i>in situ</i> interactions during interphase and mitosis. The eIF4E:eIF4G interaction was not inhibited but rather increased in mitotic cells, consistent with active translation initiation during mitosis. Phosphodefective substitution of 4E-BP1 at Ser-83 did not change global translation or individual mRNA translation profiles as measured by single-cell nascent protein synthesis and eIF4G RNA immunoprecipitation sequencing. Mitotic 5'-terminal oligopyrimidine RNA translation was active and, unlike interphase translation, resistant to mTOR inhibition. Our findings reveal the phosphorylation profiles of 4E-BP1 isoforms and their interactions with eIF4E throughout the cell cycle and indicate that 4E-BP1 does not specifically inhibit translation initiation during mitosis.
Influence of plasminogen activator inhibitor type 1 on choroidal neovascularization (2001)

High levels of the plasminogen activators, but also their inhibitor, plasminogen activator inhibitor 1 (PAI-1), have been documented in neovascularization of severe ocular pathologies such as diabetic retinopathy or age-related macular degeneration (AMD). AMD is the primary cause of irreversible photoreceptors loss, and current therapies are limited. PAI-1 has recently been shown to be essential for tumoral angiogenesis. We report here that deficient PAI-1 expression in mice prevented the development of subretinal choroidal angiogenesis induced by laser photocoagulation. When systemic and local PAI-1 expression was achieved by intravenous injection of a replication-defective adenoviral vector expressing human PAI-1 cDNA, the wild-type pattern of choroidal angiogenesis was restored. These observations demonstrate the proangiogenic activity of PAI-1 not only in tumoral models, but also in choroidal experimental neovascularization sharing similarities with human AMD. They identify therefore PAI-1 as a potential target for therapeutic ocular anti-angiogenic strategies.
-Therapy with ursodeoxycholic acid in primary biliary cirrhosis in pregnancy-. (1996)

Pregnancy is very uncommon in patients with primary biliary cirrhosis (PBC) and only few reports exist about pregnancy and PBC. However, no data are available on therapy and potential risks of treatment with ursodeoxycholic acid (UDCA) in PBC, especially in the first trimester of pregnancy. Furthermore, it is not known, whether UDCA is secreted into the breast milk during lactation. We report a 41 year old patient with the diagnosis of PBC stage III, who had been treated with UDCA (750 mg/day) for three years. At the time of diagnosis of pregnancy (5th gestational week), UDCA was withdrawn. Within nine days, severe pruritus developed, alkaline phosphatase and gamma-glutamyltransferase increased. UDCA was administered again (750 mg/day). The pruritus disappeared completely within one week. Liver enzymes decreased to baseline values and remained stable throughout the remainder of the pregnancy. No drug-related side effects were observed. Caesarean section for placental insufficiency unrelated to PBC was performed at the 34th week of pregnancy. The newborn thrived normally during a follow-up period of six months. When the patient's breast milk was analyzed by high pressure liquid chromatography, cholic acid, deoxycholic acid and lithocholic acid, but not UDCA were detected in trace amounts. It is concluded that UDCA therapy in PBC may be continued in the early pregnancy and during the breast feeding period. UDCA may be effective for the prevention of cholestasis in PBC during pregnancy.
The Building Component Library: An Online Repository to Facilitate Building Energy Model Creation (2012)

Powerful and affordable computing has made detailed whole-building energy simulations a reality. These simulations require complicated energy models that comprise thousands of inputs ranging from weather data to system component performances. The accuracy and integrity of these data are critical to the accuracy of the predicted performance. Although detailed information is paramount to ensure valid models, recreating the information for each new building model is an arduous task. A vehicle that facilitates input data reuse is vital to minimizing the effort required to adequately model buildings. This paper describes the Building Component Library, the U.S. Department of Energy’s comprehensive online searchable library of energy modeling building blocks and descriptive metadata. Novice users and seasoned practitioners can use the freely available and uniquely identifiable components to create energy models and cite the sources of input data, which will increase the credibility and reproducibility of their simulations.
A cluster approach to spatio-temporal channel estimation (2002)

In a severe multipath environment the antenna receives multiple copies of the same transmitted signal. To solve for all waves is difficult if possible at all. In this paper we use the approach of grouping the spatio-temporal reflections into clusters. We study how the aperture and bandwidth affects the cluster resolution using experimental data. The measurements were obtained by transmitting linear FM (chirp) signals of 150 MHz bandwidth, in the 1800 MHz band. An antenna array of 16 elements was used as a receiver.
In Vivo Dissection of theHelicobacter pyloriFur Regulatory Circuit by Genome-Wide Location Analysis (2006)

Iron homeostasis is particularly important in pathogenic bacteria, which need to compete with the host for this essential cofactor. In Helicobacter pylori, a causative agent of several gastric pathologies, iron uptake and storage genes are regulated at the transcriptional level by the ferric uptake regulator Fur. The regulatory circuit of Fur has recently come under focus because of an intimate interlink with a broader regulatory network governing metal homeostasis, acidic response, and virulence. To dissect the Fur regulatory circuit and identify in vivo targets of regulation, we developed a genome-wide location analysis protocol which allowed the identification of 200 genomic loci bound by Fur as well as the investigation of the binding efficiency of the protein to these loci in response to iron. Comparative analysis with transcriptomes of wild-type and fur deletion mutant strains allowed the distinction between targets associated with Fur regulation and genes indirectly influenced by the fur mutation. The Fur regulon includes 59 genes, 25 of which appear to be positively regulated. A case study conducted by primer extension analysis of two oppositely regulated genes, hpn2 and flaB, suggests that negative regulation as well as positive regulation occurs at the transcriptional level. Furthermore, the results revealed the existence of 13 Fur targeted loci within polycistronic operons, which were associated with transcript deregulation in the fur mutant strain. This study provides a systematic insight of Fur regulation at the genome-wide level in H. pylori and points to regulatory functions extending beyond the classical Fur repression paradigm.
Human–Machine Haptic Interface Design Using Stochastic Resonance Methods (2005)

A study was conducted with haptic (forces produced on a human via mechanical systems) interfaces and how they may interact with an operator to improve tracking performance. What differs from traditional approaches is that a certain amount of random noise (in a haptic sense) was inserted into the human-machine loop. It was observed that the tracking performance of the operator benefitted from this interaction.
How Many Samples are Needed to Estimate a Convolutional or Recurrent Neural Network? (2018)

It is widely believed that the practical success of Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNNs) owes to the fact that CNNs and RNNs use a more compact parametric representation than their Fully-Connected Neural Network (FNN) counterparts, and consequently require fewer training examples to accurately estimate their parameters. We initiate the study of rigorously characterizing the sample-complexity of estimating CNNs and RNNs. We show that the sample-complexity to learn CNNs and RNNs scales linearly with their intrinsic dimension and this sample-complexity is much smaller than for their FNN counterparts. For both CNNs and RNNs, we also present lower bounds showing our sample complexities are tight up to logarithmic factors. Our main technical tools for deriving these results are a localized empirical process analysis and a new technical lemma characterizing the convolutional and recurrent structure. We believe that these tools may inspire further developments in understanding CNNs and RNNs.
Relationship between CD38 expression on peripheral blood T‐cells and monocytes, and response to antiretroviral therapy: A one‐year longitudinal study of a cohort of chronically infected ART‐naive HIV‐1+ patients (2006)

Combined quantitative measurement of CD38 expression on PB monocytes, and CD8+ and CD4+ T-cells is a more useful tool for monitoring HIV-1+ patients under ART, rather than quantitation of CD38 expression on PB CD8+ T-lymphocytes alone.