gebhart/patrepeval huggingface dataset:
Inhibition of HIV-1 Replication and Activation of RNase L by Phosphorothioate/Phosphodiester 2′,5′-Oligoadenylate Derivatives (1995)

2',5'-Oligoadenylate (2-5A) derivatives have been designed to act distal to the human immunodeficiency virus-1 (HIV-1)-induced blockade in the 2-5A synthetase/RNase L antiviral pathway. Stereochemical modification of individual internucleotide linkages of the 2-5A molecule was accomplished by phosphoramidite and phosphotriester chemical syntheses. Phosphorothioate/phosphodiester trimer and tetramer 2-5A derivatives revealed differences in the stereodynamics of activation of RNase L and inhibition of HIV-1 replication. The first and second internucleotide linkages are critical for activation of recombinant, human RNase L; A(Rp)ApA, A(Sp)ApA and ApA(Rp)A are agonists (IC50 = 2 x 10(-7), 2 x 10(-6) and 8 x 10(-6) M); ApA(Sp)A is an antagonist. The second and third internucleotide linkages are crucial for activation of murine RNase L; ApA(Rp)A, ApA(Rp)ApA, and ApApA(Rp)A are agonists (IC50 = 5 x 10(-7) M); ApA(Sp)A, ApA(Sp)ApA, and ApApA(Sp)A are antagonists. Inhibition of HIV-1-induced syncytia formation by the phosphorothioate/phosphodiester derivatives is specific for derivatives with substitution at the 2',3'-terminus. ApA(Rp)A, ApA(Sp)A, ApApA(Rp)A, and ApApA(Sp)A are potent inhibitors of HIV-1-induced syncytia formation (80-, 10-, 40-, and 15-fold more inhibitory, respectively, than solvent control). HIV-1 infection results in enhanced uptake and accumulation of ApA(Rp)A and ApA(Sp)A (7- and 10-fold, respectively). These stereochemically modified 2-5A derivatives are taken up preferentially by HIV-1-infected cells and show promise in anti-HIV-1 chemotherapy.
Ordering of a Nanoconfined Water Network around Zinc Ions Induces High Proton Conductivity in Layered Titanate (2022)

We demonstrated that the chemical intercalation of Zn2+ ions within the interlayer space of the structure of a disordered layered titanate results in a drastic increase of the room-temperature bulk proton conductivity from 8.11 × 10–5 S m–1 for the pristine to 3.7 × 10–2 S m–1 for Zn-titanate. Because of the crystallographic disordered nature of these compounds, we combined different techniques to establish the structural-transport relationships. The pair distribution function revealed that upon chemical insertion of Zn2+, the local lepidocrocite arrangement is maintained, providing a suitable model to investigate the effect of chemically intercalated ions on the transport properties and dynamics within the interlayer space. Broadband dielectric spectroscopy (50 to 1010 Hz) enabled establishing that Zn2+ inclusion promotes proton-hopping by self-dissociation of H2O molecules yielding high proton mobility. Using Zn–K edge extended X-ray absorption fine structure and chemical analyses (EDX, TGA, 1H NMR), Zn2+ ions were shown to be stabilized by ZnCl2(H2O) complexes within the interlayer space. Such complexes induce an increase of the H-bonding strength as evidenced by 1H NMR, yielding a fast proton motion. Molecular dynamics simulations highlighted proton transfer between water molecules from the structural interlayer and bonded to Zn2+ ions. The increasing interactions between these water molecules favor proton transfer at the origin of the fast bulk proton conductivity, which was assigned to a Grotthuss-type mechanism taking place at a long-range order. This work provides a better understanding of how ion–water interactions mediated ionic transport and opens perspectives into the design of ionic conductors that can be used in energy-storage applications.
Preparation of high‐fructose syrup from the tubers of the Jerusalem artichoke (Helianthus tuberosusL.) (1979)

Fructose has recently received much attention due to renewed interest in natural sweeteners. In addition, fructose has some advantages to sucrose in sweetness, solubility, viscosity, and dental health characteristics. Fructose is deposited as storage fructans of the inulin (beta-1,2) type in tubers and rhizomes of the Compositae family. The utilization of the Jerusalem artichoke (Helianthus tuberosus) tuber as a source of fructose syrup is discussed. This plant has the potential to produce more sugar per acre than corn or sugar beets. In addition, the artichoke has higher frost resistance and lower heat unit requirements than corn and is somewhat more tolerant to low moisture conditions than sugar beets. A high quality fructose syrup can be produced from artichoke tubers. The extraction step was found to be particularly important since development of adverse colors and flavors must be prevented. The fructans may be acid or enzyme hydrolyzed but the latter method gave a higher quality syrup. Ion-exchange resins and activated charcoal were effective in removing coloring and flavoring materials, and also reduced other noncarbohydrate constituents. Since the enzymatic hydrolysis of the fructans is an attractive alternative to acid hydrolysis, a process was developed for producing and purifying a special beta-fructofuranosidase (inulase) from Saccharomyces fragilis. Inulase has a much higher specificity for fructans than commerically available beta-fructofuranosidase (invertase).
Glucagon regulation of gluconeogenesis and ketogenesis in periportal and perivenous rat hepatocytes. Heterogeneity of hormone action and of the mitochondrial redox state (1988)

Hepatocytes isolated from the periportal or perivenous zones of livers of fed rats were used to study the long-term (14 h) and short-term (2 h) effects of glucagon on gluconeogenesis and ketogenesis. Long-term culture with glucagon (100 nM) resulted in a greater increase (P less than 0.01) in gluconeogenesis in periportal than in perivenous cells (93 +/- 16 versus 30 +/- 14 nmol/h per mg of protein; 72% versus 30% increase), but short-term incubation (2 h) with glucagon resulted in similar stimulation in the two cell populations. Rates of ketogenesis (acetoacetate and D-3-hydroxybutyrate production) were not significantly higher in periportal cells cultured without glucagon, compared with perivenous cells. However, after long-term culture with glucagon, the periportal cells had a significantly higher rate of ketogenesis (from either palmitate or octanoate as substrate), but a lower 3-hydroxybutyrate/acetoacetate production ratio, suggesting a more oxidized mitochondrial NADH/NAD+ redox state despite the higher rate of beta-oxidation. Periportal hepatocytes had a higher activity of carnitine palmitoyltransferase but a lower activity of citrate synthase than did perivenous cells. These findings suggest that: (i) glucagon elicits greater long-term stimulation of gluconeogenesis in periportal than in perivenous hepatocytes maintained in culture; (ii) after culture with glucagon, the rates of ketogenesis and the mitochondrial redox state differ in periportal and perivenous hepatocytes.
Expression Conditional GAN for Facial Expression-to-Expression Translation (2019)

In this paper, we focus on the facial expression translation task and propose a novel Expression Conditional GAN (ECGAN) which can learn the mapping from one image domain to another one based on an additional expression attribute. The proposed ECGAN is a generic framework and is applicable to different expression generation tasks where specific facial expression can be easily controlled by the conditional attribute label. Besides, we introduce a novel face mask loss to reduce the influence of background changing. Moreover, we propose an entire framework for facial expression generation and recognition in the wild, which consists of two modules, i.e., generation and recognition. Finally, we evaluate our framework on several public face datasets in which the subjects have different races, illumination, occlusion, pose, color, content and background conditions. Even though these datasets are very diverse, both the qualitative and quantitative results demonstrate that our approach is able to generate facial expressions accurately and robustly.
Oxidative Addition of Phosphorus Ylides to Ru3(CO)12 (1990)

The Ru3C-cluster 1 with a C-bonded phosphane ligand is the final product of the reaction of Ph3PCH2 with Ru3(CO)12. This cluster could be structurally characterized, as also could a phosphonio enolate isolated as intermediate. The formation of 1 completes the use of all methane H-atoms in the sequence CH4 → CH3I → CH2 = PPh3 → 1.
Mixed-Norm Multi-Objective Robust Controller Applied to a Very Flexible Aircraft (2016)

A mixed-norm multi-objective robust controller is designed and integrated with a very flexible aircraft. Due to the aircraft high level of flexibility, the aircraft’s aeroservoelastic equations of motion are extremely nonlinear. In a very flexible aircraft, even slight deviation of flight conditions from their nominal values can highly affect the vehicle’s stability. A control architecture is proposed to minimize the adverse effects of trim velocity variation on the stability and performance of the closed-loop system. The linear matrix inequalities technique is used to express the control design process as a convex optimization problem. The performance of the designed controller when applied to a very flexible aircraft trimmed at various cruise velocities is evaluated and compared with a non-robust H2 controller. I.
Efficient Sampling of Bacterial Signal Transduction for Detection of Pulse-Amplitude Modulated Molecular Signals (2015)

The sampling of the bacterial signal transduction is investigated for molecular communication (MC). It is assumed that the finite-duration amplitude modulated, i.e., pulse-amplitude modulated (PAM), concentration of a certain type of molecule is used for information transmission. The bacterial signaling pathway is modified to transduce the input molecules to the output signal, i.e., produce green fluorescent protein (GFP). The bacterial signal transduction is composed of a set of biochemical reactions which impose randomness on the response. Therefore, the input-output relation, the timing issues, and the noise effects for the bacteria response are characterized based on both analytical and experimental observations. Sampling schemes for the raw bacteria response are proposed based on the total response duration, the peak value, the ramp-up slope, and the ramp-down slope. Each sampling scheme is shown to be providing a one-to-one and monotonic function of the input. The sampling based on the ramp-up slope is shown to be statistically favorable for the detection of PAM molecular signals. Accordingly, the time interval selection and non-coherent sampling are studied for the efficient calculation of the ramp-up slope from the raw bacteria response. This work provides a basis for the sampling of the raw bacteria response and enables accurate detection of PAM molecular signals via bacterial response for MC and sensing applications.
Skeletal Muscle Dysfunction and Metabolic Abnormalities in Individuals with Familial Partial Lipodystrophy Is Associated with Diminished Mitochondrial Fatty Acid Oxidation (2018)

Background: Familial Partial Lipodystrophy, Dunnigan variety (FPLD) is characterized by post-natal fat loss leading to severe insulin resistance. Affected individuals also display striking skeletal muscle hypertrophy, but there is limited information on muscle function and energy metabolism. We therefore systematically investigated muscle and mitochondrial function in 6 individuals with FPLD and 6 matched controls. Methods: Body composition and intramyocellular lipid content (IMCL) were assessed by DEXA and magnetic resonance spectroscopy, respectively. Maximal voluntary strength and fatigue were assessed for both recumbent leg press and seated chest press. Vastus lateralis muscle biopsies were obtained prior to and following a high fat (40%) mixed-meal. Oxygen consumption in isolated mitochondria was measured using substrates supporting carbohydrate or lipid-based respiration. Insulin Sensitivity Index (SI) was calculated by minimal modelling. Results: Individuals with FPLD had significantly lower SI, lower body fat content, and higher lean mass. Peak leg press and chest press force were not different, but FPLD individuals had earlier fatigue during chest press (number of repetitions: 15 ± 0.6 vs. 20 ± 0.3, p = 0.01). They also had a 50-60% decrease in state 3 respiration measured using substrates supporting lipid-based respiration (p = 0.04). Further, mitochondrial oxidative capacity showed a strong correlation with muscle fatigue (r = 0.76, p = 0.003), and inversely correlated with fasting and post-prandial lipemia and measures of insulin resistance. Conclusion: Individuals with FPLD have higher lean body mass and lower insulin sensitivity. Despite preserved peak muscle strength, they demonstrated earlier muscle fatigue. Decreased mitochondrial fatty acid oxidative capacity, likely related to elevated IMCL, may contribute to muscular and metabolic abnormalities. Disclosure V. Simha: None. I.R. Lanza: None. N. LeBrasseur: None. K. Klaus: None. J. Port: None. M.C. Laurenti: Other Relationship; Self; GlySens Incorporated. C. Cobelli: Research Support; Self; Sanofi-Aventis. Advisory Panel; Self; Novo Nordisk Inc.. K. Nair: None.
Leukocytosis as prognostic indicator of major injury. (2010)

WBC count is not a useful addition as a diagnostic indicator of major trauma in our study population.
How to Get the Most Out of Two Phosphorus Chemistries. Studies on H‐Phosphonates. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Arterial Inflammation Detected With 18F‐Fluorodeoxyglucose–Positron Emission Tomography in Rheumatoid Arthritis (2017)

Traditional CV risk factors and RA disease characteristics (rheumatoid nodules and the Disease Activity Score in 28 joints using the C-reactive protein level in anti-CCP antibody-positive individuals) were independently associated with ascending aortic FDG uptake in RA patients without clinical CVD.
Power allocation for the downlink of nonregenerative cooperative multi-user MIMO communication system (2010)

Amplify-and-forward (AF) is one of the most popular and simple approaches to transmit information over a cooperative multi-input multi-output (MIMO) relay channel. In this paper, we propose three novel power allocation methods for the downlink of cooperative multi-user MIMO AF system, which are designed to maximize the weighted sum-rate (WSR) of the cooperative system, by considering two different levels of channel state information (CSI). We design efficient precoding algorithms at the relay by assuming that either only the receive CSI or both receive and transmit CSI is available at the relay. Results show the performance improvement that our schemes can achieve in terms of sum-rate and WSR metrics.
Integration of Heterogeneous Semistructured Data Models in the Canonical One (1999)

To provide for interoperability of heterogeneous information objects it is required to establish a global, uniform view of the underlying digital collections and services. An information model is needed which is able to express uniformly the structure and semantics of heterogeneous data collections as well as the available services. Usually the mediator&amp;apos;s layer is introduced to provide the users with the metainformation uniformly characterizing content of the underlying collections and with the canonical information model applied for definition of such metainformation and for querying integrated world of digital collections. The paper focuses on the canonical model intended for homogeneous representation of various semistructured and hybrid data models that have been developed recently with orientation on the data contained in Web sites. The paper provides a short overview of several representative semistructured and hybrid data models. The canonical information model (based on the SY...
Pro-inflammatory polarization primes Macrophages to transition into a distinct M2-like phenotype in response to IL-4 (2021)

Tissue repair is largely regulated by diverse Mϕ populations whose functions are timing- and context-dependent. The early phase of healing is dominated by pro-inflammatory Mϕs, also known as M1, followed by the emergence of a distinct and diverse population that is collectively referred to as M2. The extent of the diversity of the M2 population is unknown. M2 Mϕs may originate directly from circulating monocytes or from phenotypic switching of pre-existing M1 Mϕs within the site of injury. The differences between these groups are poorly understood, but have major implications for understanding and treating pathologies characterized by deficient M2 activation, such as chronic wounds, which also exhibit diminished M1 Mϕ behavior. This study investigated the influence of prior M1 activation on human Mϕ polarization to an M2 phenotype in response to IL-4 treatment in vitro. Compared to unactivated (M0) Mϕs, M1 Mϕs up-regulated several receptors that promote the M2 phenotype, including the primary receptor for IL-4. M1 Mϕs also up-regulated M2 markers in response to lower doses of IL-4, including doses as low as 10 pg/mL, and accelerated STAT6 phosphorylation. However, M1 activation appeared to also change the Mϕ response to treatment with IL-4, generating an M2-like phenotype with a distinct gene and protein expression signature compared to M2 Mϕs prepared directly from M0 Mϕs. Functionally, compared to M0-derived M2 Mϕs, M1-derived M2 Mϕs demonstrated increased migratory response to SDF-1α, and conditioned media from these Mϕs promoted increased migration of endothelial cells in transwell assays, although other common Mϕ-associated functions such as phagocytosis were not affected by prior polarization state. In summary, M1 polarization appears to prime Mϕs to transition into a distinct M2 phenotype in response to IL4, which leads to increased expression of some genes and proteins and decreased expression of others, as well as functional differences. Together, these findings indicate the importance of prior M1 activation in regulating subsequent M2 behavior, and suggest that correcting M1 behavior may be a therapeutic target in dysfunctional M2 activation.
Transcriptional mapping of the amplified region encoding the dihydrofolate reductase-thymidylate synthase of Leishmania major reveals a high density of transcripts, including overlapping and antisense RNAs. (1989)

We have examined the transcriptional organization of the R region of the protozoan parasite Leishmania major. This region encodes the bifunctional enzyme dihydrofolate reductase-thymidylate synthase (DHFR-TS) and is frequently amplified as a 30-kilobase (kb) extrachromosomal circular DNA in methotrexate-resistant lines. Northern (RNA) blot analysis shows that the R region encodes at least 10 stable cytoplasmic polysomal poly(A)+ RNAs, ranging in size from 1.7 to 13 kb and including the 3.2-kb DHFR-TS mRNA. Transcriptional mapping reveals that these RNAs are closely spaced and collectively cover more than 95% of the 30-kb amplified R region. The organization is complex, including several overlapping RNAs 3' of DHFR-TS and two examples of antisense RNAs 5' of DHFR-TS. The R region RNAs can be grouped into two empirical domains, with eight contiguous RNAs transcribed in the same direction as that of DHFR-TS and two contiguous RNAs transcribed in the orientation opposite to that of DHFR-TS. The two 5'-most RNAs of the DHFR-TS-containing domain overlap the RNAs transcribed from the opposite strand. These data are relevant to models of transcription, including recent studies suggesting polycistronic transcription in trypanosomatids. The abundance of R region RNAs increases uniformly 10- to 15-fold in the amplified R1000-3 line relative to the wild type, and no new RNAs were observed. This suggests that all elements required in cis for DHFR-TS expression are contained within the 30-kb circular DNA. Quantitative analysis reveals that the steady-state DHFR-TS mRNA and protein levels are not growth phase regulated, unlike the monofunctional mouse DHFR. DHFR-TS is developmentally regulated, however, declining about fivefold in lesion amastigotes relative to promastigotes.
Adsorption and Dissociation of O2 on Pt−Co and Pt−Fe Alloys (2004)

Self-consistent periodic density functional theory calculations (GGA-PW91) have been performed to study the adsorption of O and O(2) and the dissociation of O(2) on the (111) facets of ordered Pt(3)Co and Pt(3)Fe alloys and on monolayer Pt skins covering these two alloys. Results are compared with those obtained on two Pt(111) surfaces, one at the equilibrium lattice constant and the other laterally compressed by 2% to match the strain in the Pt alloys. The absolute magnitudes of the binding energies of O and O(2) follow the same order in the two alloy systems: Pt skin < compressed Pt(111) < Pt(111) < Pt(3)Co(111) or Pt(3)Fe(111). The reduced activity of the compressed Pt(111) and Pt skins for oxygen can be rationalized as being due to the shifting of the d-band center increasingly away from the Fermi level. We propose that an alleviation of poisoning by O and enhanced rates for reactions involving O may be some of the reasons why Pt skins are more active for the oxygen reduction reaction in low-temperature fuel cells. Finally, a linear correlation between the transition-state and final-state energies of O(2) dissociation on monometallic and bimetallic surfaces is revealed, pointing to a simple way to screen for improved cathode catalysts.
Multi-Layered Maps of Neuropil with Segmentation-Guided Contrastive Learning (2022)

Abstract Maps of the nervous system that identify individual cells along with their type, subcellular components, and connectivity have the potential to reveal fundamental organizational principles of neural circuits. Volumetric nanometer-resolution imaging of brain tissue provides the raw data needed to build such maps, but inferring all the relevant cellular and subcellular annotation layers is challenging. Here, we present Segmentation-Guided Contrastive Learning of Representations (“SegCLR”), a self-supervised machine learning technique that produces highly informative representations of cells directly from 3d electron microscope imagery and segmentations. When applied to volumes of human and mouse cerebral cortex, SegCLR enabled the classification of cellular subcompartments (axon, dendrite, soma, astrocytic process) with 4,000-fold less labeled data compared to fully supervised approaches. Surprisingly, SegCLR also enabled inference of cell types (neurons, glia, and subtypes of each) from fragments with lengths as small as 10 micrometers, a task that can be difficult for humans to perform and whose feasibility greatly enhances the utility of imaging portions of brains in which many neuron fragments terminate at a volume boundary. These predictions were further augmented via Gaussian process uncertainty estimation to enable analyses restricted to high confidence subsets of the data. Finally, SegCLR enabled detailed exploration of layer-5 pyramidal cell subtypes and automated large-scale statistical analysis of upstream and downstream synaptic partners in mouse visual cortex.
ICME Observations During the Ulysses Fast Latitude Scan (2003)

Between November 2000 and October 2001 the Ulysses spacecraft performed a fast traversal of the heliospheric latitudes between 80°S and 80°N, a period close to the activity maximum of the current solar cycle. This paper provides an overview of the Ulysses observations of the transient solar wind structures associated with coronal mass ejections (ICMEs) during this period. Compared to the previous Ulysses fast latitude scan near solar minimum in 1995, many more ICME related signatures were observed in the present data set. Events were encountered spread over the full latitude range between 80°S and 80°N. Those at high northern latitudes, where fast solar wind from a northern polar coronal hole had become re‐established, were of the over‐expanding type first identified in Ulysses data at mid‐latitudes near solar minimum. The signatures of these events and their latitude dependence are discussed and some ongoing and possible future studies with this data set are described.