gebhart/patrepeval huggingface dataset:
HHQ and PQS, two Pseudomonas aeruginosa quorum‐sensing molecules, down‐regulate the innate immune responses through the nuclear factor‐κB pathway (2009)

To explore whether bacterial secreted 4-hydroxy-2-alkylquinolines (HAQs) can regulate host innate immune responses, we used the extracts of bacterial culture supernatants from a wild-type (PA14) and two mutants of Pseudomonas aeruginosa that have defects in making HAQs. Surprisingly, the extract of supernatants from the P. aeruginosa pqsA mutant that does not make HAQs showed strong stimulating activity for the production of innate cytokines such as tumour necrosis factor-alpha and interleukin-6 in the J774A.1 mouse monocyte/macrophage cell line, whereas the extract from the wild-type did not. The addition of 4-hydroxy-2-heptylquinoline (HHQ) or 2-heptyl-3,4-dihydroxyquinoline (PQS, Pseudomonas quinolone signal) to mammalian cell culture media abolished this stimulating activity of the extracts of supernatants from the pqsA mutant on the expression of innate cytokines in J774A.1 cells and in the primary bronchoalveolar lavage cells from C57BL/6 mice, suggesting that HHQ and PQS can suppress the host innate immune responses. The pqsA mutant showed reduced dissemination in the lung tissue compared with the wild-type strain in a mouse in vivo intranasal infection model, suggesting that HHQ and PQS may play a role in the pathogenicity of P. aeruginosa. HHQ and PQS reduced the nuclear factor-kappaB (NF-kappaB) binding to its binding sites and the expression of NF-kappaB target genes, and PQS delayed inhibitor of kappaB degradation, indicating that the effect of HHQ and PQS was mediated through the NF-kappaB pathway. Our results suggest that HHQ and PQS produced by P. aeruginosa actively suppress host innate immune responses.
Score informed audio source separation using constrained nonnegative matrix factorization and score synthesis (2013)

In this paper we present a new method for musical audio source separation, using the information from the musical score to supervise the decomposition process. An original framework using nonnegative matrix factorization (NMF) is presented, where the components are initially learnt on synthetic signals with temporal and harmonic constraints. A new dataset of multitrack recordings with manually aligned MIDI scores is created (TRIOS), and we compare our separation results with other methods from the literature using the BSS EVAL and PEASS evaluation toolboxes. The results show a general improvement of the BSS EVAL metrics for the various instrumental configurations used.
Oxidative modifications of cerebral transthyretin are associated with multiple sclerosis (2013)

Transthyretin (TTR) is a homotetrameric protein of the CNS that plays a role of as the major thyroxine (T4) carrier from blood to cerebrospinal fluid (CSF). T4 physiologically helps oligodendrocyte precursor cells to turn into myelinating oligodendrocytes, enhancing remyelination after myelin sheet damage. We investigated post-translational oxidative modifications of serum and CSF TTR in multiple sclerosis subjects, highlighting high levels of S-sulfhydration and S-sulfonation of cysteine in position ten only in the cerebral TTR, which correlate with an anomalous TTR protein folding as well as with disease duration. Moreover, we found low levels of free T4 in CSF of multiple sclerosis patients, suggestive of a potential role of these modifications in T4 transport into the brain.
Stress granules in neurodegeneration – lessons learnt from TAR DNA binding protein of 43 kDa and fused in sarcoma (2013)

Stress granules (SGs) are cytoplasmic foci that rapidly form when cells are exposed to stress. They transiently store mRNAs encoding house-keeping proteins and allow the selective translation of stress-response proteins (e.g. heat shock proteins). Besides mRNA, SGs contain RNA-binding proteins, such as T cell internal antigen-1 and poly(A)-binding protein 1, which can serve as characteristic SG marker proteins. Recently, some of these SG marker proteins were found to label pathological TAR DNA binding protein of 43 kDa (TDP-43)- or fused in sarcoma (FUS)-positive cytoplasmic inclusions in patients with amyotrophic lateral sclerosis and frontotemporal lobar degeneration. In addition, protein aggregates in other neurodegenerative diseases (e.g. tau inclusions in Alzheimer's disease) show a co-localization with T cell internal antigen-1 as well. Moreover, several RNA-binding proteins that are commonly found in SGs have been genetically linked to neurodegeneration. This suggests that SGs might play an important role in the pathogenesis of these proteinopathies, either by acting as a seed for pathological inclusions, by mediating translational repression or by trapping essential RNA-binding proteins, or by a combination of these mechanisms. This minireview gives an overview of the general biology of SGs and highlights the recently identified connection of SGs with TDP-43, FUS and other proteins involved in neurodegenerative diseases. We propose that pathological inclusions containing RNA-binding proteins, such as TDP-43 and FUS, might arise from SGs and discuss how SGs might contribute to neurodegeneration via toxic gain or loss-of-function mechanisms.
Formulas for the solutions of quadratic equations overGF(2^m)(Corresp.) (1982)

There are several known approaches to solving quadratic equations over GF <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">(2^{m})</tex> . Here the approach to solving the equations is different from the known approaches in that the solutions are presented in terms of the parameters of the equations. The formulas for solving the quadratic equations are also used to solve the equations of degrees three and four. The results can be combined with other known techniques to solve equations of higher degrees.
Microstructure and Mechanical Properties of Reticulated Titanium Scrolls (2011)

Abstract Reticulated titanium scrolls are produced by printing titanium hydride lattices composed of two orthogonal layers of ink filaments, which are then rolled into cylinders and reduced to titanium upon partial vacuum sintering. The resulting three‐dimensional titanium scrolls contain a hierarchical pore size distribution composed of macroporosity between patterned filaments and micropores within each filament. These reticulated architectures exhibit an attractive combination of stiffness, strength, and ductility when tested in uniaxial compression.
Comparison of the biology of Down syndrome (DS) acute lymphoblastic leukemia (ALL) and non-DS ALL: Children’s Oncology Group (COG) study P9900 (2008)

10003 Background: DS ALL is a heterogeneous disorder with inferior survival compared to non-DS. Controversy exists regarding the relative frequencies of sentinel cytogenetic lesions in children with DS and ALL. Methods: COG P9900 was a laboratory classification study for ALL therapeutic trials from 12/99 to 2/05. Flow cytometry for DNA index; molecular testing for TEL-AML1, E2A-PBX1, BCR-ABL and FISH testing for trisomies 4 and 10 and for MLL rearrangements were done centrally for risk group stratification in a prospective manner to assign continuing treatment. Results: Eighty of 2811 (3%) consecutively enrolled eligible B-precursor ALL patients (pts) had DS. Age > or < than 10 years of age, gender, presenting white blood cell count (WBC) and NCI risk group were similar between ALL patients with/without DS. However, the genetic lesions present in DS-ALL patients and the event-free survival (EFS) and overall survival (OS) differed from those of non-DS patients. No BCR/ABL or MLL translocations were found in the DS pts. TEL-AML1 fusion was present in 2.5% (2/80) of DS-ALL pts vs. 24% (651/2710) (p<0.0001) of non-DS-ALL pts. Trisomies of chromosomes 4 and 10 were present in 7.7% (6/78) of DS-ALL pts vs. 24% (643/2689) (p=0.0004) of non-DS-ALL pts. Five-year EFS and OS were inferior in pts with DS-ALL; 70% vs. 76% (p=0.078), and 86% vs. 90% (p=0.0333). However, when pts with MLL, BCR/ABL, TEL-AML 1 and trisomies 4 and 10 were excluded, the EFS and OS for both groups were equivalent with EFS for DS 68% vs. 70% for non-DS (p=0.8174), and OS for DS 87% vs. 85% for non-DS (p=0.8519). Conclusions: The inferior outcome of patients with ALL and DS is related to a much lower incidence of favorable genetic features (TEL- AML 1 and trisomies of chromosomes 4 and 10). Further investigation into the distinct pathogenesis of DS ALL is warranted to improve treatment response. No significant financial relationships to disclose.
T-cell proliferation to subinfectious SIV correlates with lack of infection after challenge of macaques (1994)

The inability to productively infect macaques previously exposed to subinfectious doses of SIV suggests that a T-cell-mediated response may confer long-term protection against infection, and that AIDS vaccines should be designed to optimize the cellular arm of the immune response.
Progressive Tau Accumulation in Alzheimer Disease: 2-Year Follow-up Study (2019)

Tau PET enables in vivo visualization and quantitation of tau accumulation in Alzheimer disease (AD). In cross-sectional tau PET studies, tau burden reflects disease severity and phenotypic variation. We investigated longitudinal changes in cortical tau accumulation and their association with cognitive decline in patients with AD. <b>Methods:</b> We enrolled 107 participants (45 amyloid-β-negative cognitively unimpaired [CU-], 7 amyloid-β-positive cognitively unimpaired [CU+], 31 with prodromal AD [mild cognitive impairment; MCI+], and 24 with AD dementia [DEM+]) who completed 2 baseline PET scans (<sup>18</sup>F-flortaucipir and <sup>18</sup>F-florbetaben), MRI, and neuropsychologic tests. All participants underwent the same assessments after 2 y. After correcting for partial-volume effect, we created SUV ratio (SUVR) images. By using a linear mixed-effect model, we investigated the changes in SUVR across time within each group. We also investigated a correlation between the progression of tau accumulation and cognitive decline. <b>Results:</b> In contrast to no change in global cortical SUVR in the CU- and CU+ groups during the 2-y period, global cortical SUVR increased by 0.06 (2.9%) in the MCI+ group and 0.19 (8.0%) in the DEM+ group at follow-up. The MCI+ group was associated with additional tau accumulation predominantly in the medial and inferior temporal cortices, whereas the DEM+ group showed increases in the lateral temporal cortex. Progressive tau accumulation occurred in the diffuse cortical areas in the MCI+ patients who developed dementia and the DEM+ patients who showed deterioration of global cognition, whereas there was only a small increase of additional tau accumulation in the lateral temporal cortex in those who did not show worsening of cognition. Deterioration of global cognition and language functions was associated with progression of diffuse tau accumulation in the association neocortex. <b>Conclusion:</b> Progressive tau accumulation occurs in prodromal AD and DEM patients in the cortical areas at different levels of tau accumulation. Progression of cognitive dysfunction may be related to the additional tau accumulation in regions of higher Braak stage. <sup>18</sup>F-flortaucipir PET is an imaging biomarker for monitoring the progression of AD.
Experimental Posterolateral Lumbar Spinal Fusion With a Demineralized Bone Matrix Gel (1998)

Demineralized bone matrix was effective as a graft extender when used in up to a 3:1 ratio with autograft in a rabbit posterolateral spine fusion model. When less than the standard volume of autograft was used, the addition of demineralized bone matrix gel lead to fusion success rates comparable to those of the standard amount of autograft alone. However, demineralized bone matrix did not increase the frequency of successful fusion when added to the standard amount of autograft.
Observing reorientation dynamics with Time-Resolved fluorescence and molecular dynamics in varying periodic boundary conditions (2021)

This work presents a combined study of time-resolved fluorescence spectroscopy and all-atom molecular dynamics simulation to investigate periodic boundary conditions' and water models' influence on the orientation dynamics and translational and rotational diffusion of peptides in solution. We have characterized the effects of solvent box size and water model choice on the dynamics of two peptide systems, NATA and WK5. Computationally, translational, and rotational diffusion and internal fluctuations are investigated through all-atom molecular dynamics simulation with two water models and different box sizes. These results are compared with time-resolved fluorescence anisotropy decay (FAD) measurements. The associated time constant and orientation dynamics from FAD measurement along the <sup>1</sup>L<sub>b</sub> axis provided baseline data to validate molecular dynamics simulation. The modeling results show that diffusion rates vary roughly in inverse proportion to water model viscosity, as one would expect. Corrections for finite box size are significant for translational diffusion and insignificant for rotational diffusion. This study also finds that internal dynamics described by autocorrelation functions and kinetic network models are relatively insensitive to both box size and water model properties. Our observation suggests that different peptide properties respond differently to a change in simulation conditions.Communicated by Ramaswamy H. Sarma.
Effects of breed and slaughter weight on longissimus muscle biochemical traits and sensory quality in pigs (1998)

International audience
Q-switched Nd:YAG laser: rhytid improvement by non-ablative dermal remodeling (2000)

The Q-switched Nd:YAG laser may be used for the non-ablative treatment of facial rhytids.
D-4F reduces EO6 immunoreactivity, SREBP-1c mRNA levels, and renal inflammation in LDL receptor-null mice fed a Western diet (2007)

LDL receptor-null (LDLR(-/-)) mice on a Western diet (WD) develop endothelial dysfunction and atherosclerosis, which are improved by the apolipoprotein A-I (apoA-I) mimetic peptide D-4F. Focusing on the kidney, LDLR(-/-)mice were fed a WD with D-4F or the inactive control peptide scrambled D-4F (ScD-4F) added to their drinking water. The control mice (ScD-4F) developed glomerular changes, increased immunostaining for MCP-1/CCL2 chemokine, increased macrophage CD68 and F4/80 antigens, and increased oxidized phospholipids recognized by the EO6 monoclonal antibody in both glomerular and tublo-interstitial areas. All of these parameters were significantly reduced by D-4F treatment, approaching levels found in wild-type C57BL/6J or LDLR(-/-) mice fed a chow diet. Sterol-regulatory element binding protein-1c (SREBP-1c) mRNA levels and triglyceride levels were elevated in the kidneys of the control mice (ScD-4F) fed the WD compared with C57BL/6J and LDLR(-/-) mice on chow (P < 0.001 and P < 0.001, respectively) and compared with D-4F-treated mice on the WD (P < 0.01). There was no significant difference in plasma lipids, lipoproteins, glucose, blood pressure, or renal apoB levels between D-4F- and ScD-4F-treated mice. We conclude that D-4F reduced renal oxidized phospholipids, resulting in lower expression of SREBP-1c, which, in turn, resulted in lower triglyceride content and reduced renal inflammation.
A Bayesian multitaper method for nonstationary data with application to EEG analysis (2017)

Nonparametric spectral analysis using overlapping sliding windows is among the most widely used techniques in analyzing nonstationary time series. Although sliding window analysis is convenient to implement, the resulting estimates are sensitive to the subjective choice of window length and overlap extent and additionally lack precise statistical interpretation. In this paper, we propose a spectral estimator by explicitly modeling the spectral dynamics through combining the multitaper method with state-space models in a Bayesian estimation framework. The states are efficiently estimated using an instance of the Expectation-Maximization algorithm, from which the spectral estimates and their confidence intervals are constructed. We apply our proposed algorithm to synthetic data as well as real data from human EEG recordings, revealing significant improvements in spectral resolution and noise rejection.
Pr/Ba cation-disordered perovskite Pr<sub>2/3</sub>Ba<sub>1/3</sub>CoO<sub>3−δ</sub> as a new bifunctional electrocatalyst for oxygen reduction and oxygen evolution reactions (2018)

Electrocatalysts for oxygen evolution reaction (OER) and oxygen reduction reaction (ORR) play an important role in renewable energy source technologies, typically including metal-air batteries, fuel cells and water splitting devices. Therefore, the development of bifunctional catalysts for OER and ORR is of great importance to enhance the performance of these devices. Herein, we present a Pr/Ba cation-disordered perovskite Pr2/3Ba1/3CoO3−δ, as a novel bifunctional catalyst for OER and ORR. Here δ is the content of oxygen vacancies. Rietveld refinement of the X-ray powder diffraction data of Pr2/3Ba1/3CoO2.98 was successfully performed by a single phase with an orthorhombic Pnma Pr/Ba cation-disordered perovskite-type structure. The bond valence sum of Co cation, 3.11 and thermogravimetric measurements suggested the coexistence of Co3+, Co4+, Pr3+ and Pr4+ cations in the bulk Pr2/3Ba1/3CoO2.98. The X-ray photoemission spectroscopy of Pr2/3Ba1/3CoO2.98 indicated the coexistence of these four cations at the sample surface, which would improve the electrocatalysis. The electrical conductivity σ of Pr/Ba cation-disordered perovskite Pr2/3Ba1/3CoO3−δ was higher than that of Pr/Ba cation-ordered layered perovskite PrBaCo2O6−δ. The σ of Pr2/3Ba1/3CoO3−δ and PrBaCo2O6−δ decreased with an increase of temperature. The concentration of oxygen vacancies δ of Pr2/3Ba1/3CoO3−δ increased with increasing temperature. Electrochemical measurements of the Pr/Ba cation-disordered perovskite Pr2/3Ba1/3CoO2.98 indicated higher OER and ORR catalytic activities, compared to the Pr/Ba cation-ordered layered perovskite PrBaCo2O6−δ. The Pr2/3Ba1/3CoO2.98 exhibited higher bifunctional electrocatalytic activities compared with many bifunctional catalysts in the literature. These results highlight the Pr/Ba cation-disordered perovskite-type Pr2/3Ba1/3CoO3−δ as a promising bifunctional catalyst for renewable energy applications.
Intermittent Bictegravir/Emtricitabine/Tenofovir Alafenamide Treatment Maintains High Level of Viral Suppression in Virally Suppressed People Living with HIV (2023)

In this observational study, we aimed to evaluate whether bictegravir/emtricitabine/tenofovir alafenamide (B/F/TAF) administered 5 or 4 days a week is able to maintain viral suppression in people living with HIV (PLHIV). We enrolled 85 patients who initiated intermittent B/F/TAF between 28 November 2018 and 30 July 2020: median (IQR) age 52 years (46-59), duration of virological suppression 9 years (3-13), CD4 633/mm<sup>3</sup> (461-781). Median follow-up was 101 weeks (82-111). The virological success rate (no virological failure [VF]: confirmed plasma viral load [pVL] ≥ 50 copies/mL, or single pVL ≥ 200 copies/mL, or ≥50 copies/mL with ART change) was 100% (95%CI 95.8-100) and the strategy success rate (pVL < 50 copies/mL with no ART regimen change) was 92.9% (95%CI 85.3-97.4) at W48. Two VF occurred at W49 and W70, in 2 patients self-reporting poor compliance. No resistance mutation emerged at time of VF. Eight patients presented strategy discontinuation for adverse events. There was no significant change in the CD4 count, residual viraemia rate, neither body weight during follow-up, but a slight increase in CD4/CD8 ratio (<i>p</i> = 0.02). In conclusion, our findings suggest that B/F/TAF administered 5 or 4 days a week could maintain the control of HIV replication in virologically suppressed PLHIV while reducing cumulative exposition of ART.
Spatially- and Temporally-resolved Multi-parameter Interferometric Rayleigh Scattering (2011)

A novel approach to simultaneously measure the translational temperature, bulk velocity, and density in gases by collecting, referencing, and analyzing nanosecond time-scale Rayleigh scattered light from molecules is described. A narrow-band pulsed laser source is used to probe two largely separated measurement locations, one of which is used for reference. The elastically scattered photons containing information from both measurement locations are collected at the same time and analyzed spectrally using a planar Fabry - Perot interferometer. A practical means of referencing the measurement of velocity using the laser frequency, and the density and temperature using the information from the reference measurement location maintained at constant properties is described. To demonstrate the technique single-shot spectra of elastic scattered light are obtained in a near zero velocity H2-air Hencken burner flame and simultaneously in an N2-filled gas cell. A simplified Gaussian distribution model to the scattered light spectra is used to obtain the flame properties. Corrections to this model are applied at lower gas temperatures when the simplified Gaussian approximation is no longer suitable. The near-zero measured velocity as a function of the measured flame temperature, and a comparison of the measured flame density and temperature with the perfect gas law are presented.
ChemInform Abstract: Studies on Structurally Simple Butenolides. Part 5. Reactions of Protoanemonin with Piperidine and C‐Nucleophiles. (1986)

Abstract Reaction of protoanemonin (I) with piperidine gives (II)‐(IV).
Cladistic Representation of Reticulate Evolution (1975)

Cladistic Representation of Reticulate Evolution Get access P. H. A. Sneath P. H. A. Sneath M.R.C. Microbial Systematics Research Unit, University of LeicesterLEI 7RH, England Search for other works by this author on: Oxford Academic PubMed Google Scholar Systematic Biology, Volume 24, Issue 3, September 1975, Pages 360–368, https://doi.org/10.1093/sysbio/24.3.360 Published: 01 September 1975
An Encephalitozoon cuniculi Ortholog of the RNA Polymerase II Carboxyl-Terminal Domain (CTD) Serine Phosphatase Fcp1 (2004)

Fcp1 is an essential protein serine phosphatase that dephosphorylates Ser2 or Ser5 of the RNA polymerase II carboxyl-terminal domain (CTD) heptad repeat Y(1)S(2)P(3)T(4)S(5)P(6)S(7). The CTD of the microsporidian parasite Encephalitozoon cuniculi consists of 15 heptad repeats, which approximates the minimal CTD length requirement for cell viability in yeast. Here we show that E. cuniculi encodes a minimized 411-aa Fcp1-like protein (EcFcp1), which consists of a DxDx(T/V) phosphatase domain and a BRCA1 carboxyl terminus (BRCT) domain but lacks the large N- and C-terminal domains found in fungal and metazoan Fcp1 enzymes. Nonetheless, EcFcp1 can function in lieu of Saccharomyces cerevisiae Fcp1 to sustain yeast cell growth. Recombinant EcFcp1 is a monomeric enzyme with intrinsic phosphatase activity against nonspecific (p-nitrophenyl phosphate) and specific (CTD-PO(4)) substrates. EcFcp1 dephosphorylates CTD positions Ser2 and Ser5 with similar efficacy in vitro. We exploit synthetic CTD Ser2-PO(4) and Ser5-PO(4) peptides to define minimized substrates for EcFcp1 and to illuminate the importance of CTD primary structure in Ser2 and Ser5 phosphatase activity.