gebhart/patrepeval huggingface dataset:
Immunity in Society: Diverse Solutions to Common Problems (2012)

Understanding how organisms fight infection has been a central focus of scientific research and medicine for the past couple of centuries, and a perennial object of trial and error by humans trying to mitigate the burden of disease. Vaccination success relies upon the exposure of susceptible individuals to pathogen constituents that do not cause (excessive) pathology and that elicit specific immune memory. Mass vaccination allows us to study how immunity operates at the group level; denser populations are more prone to transmitting disease between individuals, but once a critical proportion of the population becomes immune, "herd immunity" emerges. In social species, the combination of behavioural control of infection--e.g., segregation of sick individuals, disposal of the dead, quality assessment of food and water--and aggregation of immune individuals can protect non-immune members from disease. While immune specificity and memory are well understood to underpin immunisation in vertebrates, it has been somewhat surprising to find similar phenomena in invertebrates, which lack the vertebrate molecular mechanisms deemed necessary for immunisation. Indeed, reports showing alternative forms of immune memory are accumulating in invertebrates. In this issue of PLoS Biology, Konrad et al. present an example of fungus-specific immune responses in social ants that lead to the active immunisation of nestmates by infected individuals. These findings join others in showing how organisms evolved diverse mechanisms that fulfil common functions, namely the discrimination between pathogens, the transfer of immunity between related individuals, and the group-level benefits of immunisation.
OPA1 Mutation and Late‐Onset Cardiomyopathy: Mitochondrial Dysfunction and mtDNA Instability (2012)

OPA1 mutation leads to deficiency in antioxidant transcripts, increased reactive oxygen species, mitochondrial dysfunction, and late-onset cardiomyopathy.
Proactive or Reactive Routing: A Unified Analytical Framework in MANETs (2008)

We present a mathematical framework for the performance evaluation of proactive and reactive routing protocols operating in mobile ad hoc networks (MANETs). The model captures the functionality of the routing protocols together with the characterization of the performance of the medium access control protocol (MAC). It reveals the interplay between the protocol functionality and network parameters, and provides new insight on the relative benefits of proactive and on-demand routing in MANETS. The analytical results are corroborated with results obtained using discrete-event simulations.
Capacity Regions and Optimal Power Allocation for Groupwise Multiuser Detection (2005)

In this paper, optimal power allocation and capacity regions are derived for GSIC (groupwise successive interference cancellation) systems operating in multipath fading channels, under imperfect channel estimation conditions. It is shown that the impact of channel estimation errors on the system capacity is two-fold: it affects the receivers' performance within a group of users, as well as the cancellation performance (through cancellation errors). An iterative power allocation algorithm is derived, based on which it can be shown that the total required received power is minimized when the groups are ordered according to their cancellation errors, and the first detected group has the smallest cancellation error. Performace/complexity tradeoff issues are also discussed by directly comparing the system capacity for different implementations: GSIC with linear minimum-mean-square error (LMMSE) receivers within the detection groups, GSIC with matched filter receivers, multicode LMMSE systems, and simple all matched filter receivers systems.
Biologically Inspired Nanofibers for Use in Translational Bioanalytical Systems (2014)

Electrospun nanofiber mats are characterized by large surface-area-to-volume ratios, high porosities, and a diverse range of chemical functionalities. Although electrospun nanofibers have been used successfully to increase the immobilization efficiency of biorecognition elements and improve the sensitivity of biosensors, the full potential of nanofiber-based biosensing has not yet been realized. Therefore, this review presents novel electrospun nanofiber chemistries developed in fields such as tissue engineering and drug delivery that have direct application within the field of biosensing. Specifically, this review focuses on fibers that directly encapsulate biological additives that serve as immobilization matrices for biological species and that are used to create biomimetic scaffolds. Biosensors that incorporate these nanofibers are presented, along with potential future biosensing applications such as the development of cell culture and in vivo sensors.
Hemodynamic and clinical response to transseptal mitral valve‐in‐valve and valve‐in‐ring (2019)

Despite baseline differences in valvular disease, TMVR leads to significant hemodynamic and clinical improvement in both stenotic and regurgitant prosthetic mitral valve disease. In both cohorts, TMVR reduced intracardiac pressures to similar postprocedural levels, but pressures remained supranormal. This outcome suggests a multifactorial process defines the pathophysiology of patients undergoing TMVR, including contributions from prosthetic degeneration, changes in left atrial compliance, and diastolic dysfunction, and highlights the need to consider such factors in patient evaluation and treatment.
Simulation of sonic logging for deviated wells in anisotropic formations (2013)

Interpretation of sonic logging data acquired in environments with complex anisotropy is a difficult problem attracting attention of researchers and oil industry. In order to better understand physics of wave propagation in highly anisotropic medium and be able explaining observations from field data there is a need for fast and accurate numerical modeling capability. To address such challenge, we developed an efficient and accurate numerical algorithm for the simulation of sonic logging experiments in highly anisotropic formation. The basis of the approach is a heterogeneous spectral element method implemented on multi-GPU applied to acoustic-elastic wave equation. The approach was designed to simulate wave propagation in 3D arbitrary anisotropic elastic media with attenuation for a constant quality factor via standard linear solid using the tau-method. Due to the use of an unstructured grid, the spectral element algorithm enables handling tools in a fluid-filled borehole with surrounding geological models of high complexity. Several examples of log simulations for deviated wells in VTI formations for monopole, dipole, and quadrupole source symmetries and their comparison with real field data will be presented in this paper. Discussion regarding complex wave propagation will be developed in view of these simulations and real data.
The <scp>MerR</scp>‐family regulator <scp>NmlR</scp> is involved in the defense against oxidative stress in <i>Streptococcus pneumoniae</i> (2022)

Abstract Streptococcus pneumoniae has to cope with the strong oxidant hypochlorous acid (HOCl), during host–pathogen interactions. Thus, we analyzed the global gene expression profile of S. pneumoniae D39 towards HOCl stress. In the RNA‐seq transcriptome, the NmlR, SifR, CtsR, HrcA, SczA and CopY regulons and the etrx1‐ccdA1‐msrAB2 operon were most strongly induced under HOCl stress, which participate in the oxidative, electrophile and metal stress response in S. pneumoniae . The MerR‐family regulator NmlR harbors a conserved Cys52 and controls the alcohol dehydrogenase‐encoding adhC gene under carbonyl and NO stress. We demonstrated that NmlR senses also HOCl stress to activate transcription of the nmlR‐adhC operon. HOCl‐induced transcription of adhC required Cys52 of NmlR in vivo. Using mass spectrometry, NmlR was shown to be oxidized to intersubunit disulfides or S ‐glutathionylated under oxidative stress in vitro. A broccoli‐FLAP‐based assay further showed that both NmlR disulfides significantly increased transcription initiation at the nmlR promoter by RNAP in vitro, which depends on Cys52. Phenotype analyses revealed that NmlR functions in the defense against oxidative stress and promotes survival of S. pneumoniae during macrophage infections . In conclusion, NmlR was characterized as HOCl‐sensing transcriptional regulator, which activates transcription of adhC under oxidative stress by thiol switches in S. pneumoniae .
Accurate acoustic measurements in gases under difficult conditions (1991)

Accurate measurements of the speed of sound in gases are often made using metal resonators with small transducers that perturb the resonance frequencies in minor and predictable ways. We extend this method to gases that may be corrosive and to high temperatures by using remote transducers coupled to a resonator by acoustic waveguides. Thin metal diaphragms separate the waveguides from the resonator. Thus, only metal parts come into contact with the test gas. In the present apparatus, any gas compatible with gold and stainless steel can be studied.
Promoter prediction (2005)

Abstract We review current solutions for computer‐based prediction of promoters. We comment on useful biological signals, implemented technology, end‐user information, and achieved performances. Finally, we present a forecast of future trends in this field.
Ayurveda and Yoga in the Management of Epilepsy (2017)

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Influenza H7N9 and H9N2 Viruses: Coexistence in Poultry Linked to Human H7N9 Infection and Genome Characteristics (2014)

Our results suggest that avian influenza A virus of the H9N2 subtype likely made a recent contribution to the evolution of the H7N9 virus, a novel reassortant avian influenza virus A subtype, and continues to do so. The finding helps shed light on how the H7N9 virus emerged, spread, and transmitted to humans. It is of considerable interest for assessing the risk of the possible emergence of novel reassortant viruses with enhanced transmissibility to humans.
Optimization of partial discharge detection in high voltage cables based on advanced signal processing techniques (2012)

In this paper we approach the challenges of partial discharges (PD) detection in high voltage cables using signal processing techniques based on time frequency methods combined with Recurrence Plot Analysis (RPA) and high order spectrum analysis (HOSA). Detection of PD poses many problems in terms of speed of calculation, selection criteria and multitude of causes which lead to the occurrence of PD. In order to overcome these drawbacks, we have developed an algorithm which uses the spectrogram to perform a fast detection of parts from the signal which are susceptible of PD activity. The second stage calculates for each zone a detection curve using the HOSA concept of bispectrum and RPA. The latter has been applied in many non-linear systems in order to characterize the process on the basis of the recurrence matrix obtained from a time series given by the system.
Faculty Opinions recommendation of Undulating changes in human plasma proteome profiles across the lifespan. (2019)

Aging is a predominant risk factor for numerous chronic diseases that limit healthspan 1 .Mechanisms of aging are thus increasingly recognized as potential therapeutic targets.Blood from young mice reverses aspects of aging and disease across multiple tissues 2-10 , which supports a Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.
Transient EPR studies of Photosystem I containing non-native quinones (2001)

The quinone acceptors in both type I and type II reaction centres play a pivotal role in light induced photosynthetic electron transfer. Although, the quinones found in the various reaction centres are structurally similar, the rates of electron transfer and nature of the subsequent acceptors vary greatly. The relationship between the properties of the quinone binding-site, the structure of the quinone and the rates of electron transfer are still not well understood. Transient EPR data for the forward and back reaction kinetics will be presented for Photosystem I, in which the native phylloquinone has been replaced by a series of foreign quinones. Our results suggest that the ability of quinones to function in the electron transport chain is governed primarily by their midpoint potentials. We find that the less negative the midpoint potential of a given quinone is the slower the forward electron transfer rate. The back reaction from the iron sulphur centres is also influenced by the presence of a foreign quinone in the A1 site clearly showing that the back reaction from FA/FB proceeds via A1. In contrast to the forward rate, the back reaction rate increases as the midpoint potential of the quinone becomes less negative. The EPR data also suggest that naphthoquinone derivatives bind more strongly to the A1 site than benzoquinone derivatives do. This observation is can be understood as a result of differences in the proposed p-stacking arrangement between PsaA-W697 (PsaB-W677) and phylloquinone.
CONFORMATION-SPECIFIC INFRARED AND ULTRAVIOLET SPECTROSCOPY OF COLD [YAPAA+H]+ AND [YGPAA+H]+ IONS: A STEREOCHEMICAL "TWIST" ON THE β-HAIRPIN TURN (2017)

Incorporation of the unnatural D-proline ($^{D}$P) stereoisomer into a polypeptide sequence is a typical strategy to encourage formation of $beta$-hairpin loops because natural sequences are often unstructured in solution. Using conformation-specific IR and UV spectroscopy of cold (10 K) gas-phase ions, we probe the inherent conformational preferences of the $^{D}$P and $^{L}$P diastereomers in the protonated peptide [YAPAA+H]$^{+}$, where only intramolecular interactions are possible. Consistent with the solution phase studies, one of the conformers of [YADPAA+H]$^{+}$ is folded into a charge-stabilized $beta$-hairpin turn. However, a second predominant conformer family containing two sequential $gamma$-turns is also identified, with similar energetic stability. A single conformational isomer of the $^{L}$P diastereomer, [YALPAA+H]$^{+}$, is found and assigned to a structure that is not the anticipated “mirror image” $beta$-turn. Instead, the $^{L}$P stereo center promotes a cis alanine-proline amide bond. The assigned structures contain clues that the preference of the $^{D}$P diastereomer to support a trans-amide bond and the proclivity of $^{L}$P for a cis-amide bond is sterically driven and can be reversed by substituting glycine for alanine in position 2, forming [YGLPAA+H]$^{+}$. These results provide a basis for understanding the residue-specific and stereo-specific alterations in the potential energy surface that underlie these changing preferences, providing insights to the origin of $beta$-hairpin formation.
Structural Control of Endoplasmic Reticulum-associated Degradation (2003)

The endoplasmic reticulum (ER) quality control pathway destroys misfolded and unassembled proteins in the ER. Most substrates of this ER-associated degradation (ERAD) pathway are constitutively targeted for destruction through recognition of poorly understood structural hallmarks of misfolding. However, the normal yeast ER membrane protein 3-hydroxy-3-methylglutaryl-CoA reductase (Hmg2p) undergoes ERAD that is physiologically regulated by sterol pathway signals. We have proposed that Hmg2p ERAD occurs by a regulated transition to an ERAD quality control substrate. Consistent with this, we had previously shown that Hmg2p is strongly stabilized by chemical chaperones such as glycerol, which stabilize misfolded proteins. To understand the features of Hmg2p that permit regulated ERAD, we have thoroughly characterized the effects of chemical chaperones on Hmg2p. These agents caused a reversible, immediate, direct change in Hmg2p degradation consistent with an effect on Hmg2p structure. We devised an in vitro limited proteolysis assay of Hmg2p in its native membranes. In vitro, chemical chaperones caused a dramatic, rapid change in Hmg2p structure to a less accessible form. As in the living cell, the in vitro action of chemical chaperones was highly specific for Hmg2p and completely reversible. To evaluate the physiological relevance of this model behavior, we used the limited proteolysis assay to examine the effects of changing in vivo degradation signals on Hmg2p structure. We found that changes similar to those observed with chemical chaperones were brought about by alteration of natural degradation signal. Thus, Hmg2p can undergo significant, reversible structural changes that are relevant to the physiological control of Hmg2p ERAD. These findings support the idea that Hmg2p regulation is brought about by regulated alteration of folding state. Considering the ubiquitous nature of quality control pathways in biology, it may be that this strategy of regulation is widespread.
Asymptomatic Osteonecrosis (2004)

Currently, there is no consensus regarding the treatment of precollapse osteonecrosis, particularly for asymptomatic osteonecrosis. With approximately 10,000 to 20,000 new cases of osteonecrosis a year, no single surgeon or center has the kind of experience that is able to address the most important questions concerning this disease. The literature strongly documents that symptoms of osteonecrosis will progress. Although the literature also supports the progression of asymptomatic osteonecrosis to symptomatic osteonecrosis on to collapse, that support is less convincing. Progression is proportional to lesion size, with small lesions (< 15% of femoral head involvement by volume) unlikely to progress. Although the results of core decompression have been somewhat controversial, the weight of the literature supports both the efficacy and safety of the procedure. The decision to treat osteonecrosis with core decompression is primarily based upon lesion size and stage of disease and does not necessarily depend on whether the patient is symptomatic. As large lesions (> 30% of the femoral head) are less likely to be successfully treated by core decompression and small lesions (< 15% of the femoral head) are less likely to progress, asymptomatic lesions within these ranges can be observed. The literature supports the position that moderately sized lesions (15-30% of the femoral head) should be treated by core decompression (with or without bone grafting).
Concurrent ankle-assisted movement, biofeedback, and proprioceptive stimulation reduces lower limb motor impairment and improves gait in persons with stroke (2022)

Impairment-oriented training using a robotic device capable of applying assisted movement, biofeedback, and proprioceptive stimulation significantly reduces LL impairment and improves gait in moderately-to-severely impaired PwS.
P4–316: Aβ derivative vaccine does not cause brain microhemorrhages in Tg2576 mice and its effectiveness is age–dependent (2006)

Immunotherapy for AD targeting Aβ remains promising despite the setbacks in the initial clinical trial that may have been related to T–cell–mediated encephalitis. Prior to these side effects, we advocated that vaccination with Aβ derivatives that are non–toxic and preferentially elicit a Th2 immune response is likely to be safer for human use. In addition, for enhanced safety, adjuvants that induce a humoral response, such as alum, should be used. Another potential side effect of this type of therapy is cerebral bleeding which has been observed following passive immunization. This phenomenon has not been assessed in active immunization studies. To determine: 1) if our Aβ derivatives are effective when combined with alum; 2) whether our approach produces hemorrhages; 3) whether the efficacy of our vaccine is age–dependent. Tg2576 mice and wild–type littermates (n=66) were immunized with soluble, non–toxic Aβ derivative, K6Aβ1–30–NH2in alum adjuvant, starting at 11– and 19 months. This adjuvant is approved for humans and promotes humoral immunity. Mice went through various sensorimotor and cognitive tests at 22–24 months, and their brains were subsequently analyzed for amyloid burden and associated pathology including microhemorrhages. Treatment initiated at 11 months reduced cortical plaque burden by 31% (p<0.05), total brain Aβ40 levels by 30% (p=0.03), Aβ42 by 37% (p=0.02), but soluble Aβ levels remained unaltered. This effect was associated with cognitive improvements in both the radial arm maze and the Hebb–Williams maze. In contrast, treatment initiated at 19 months was not immunogenic, did not reduce plaque burden or improve cognition. In various sensorimotor tasks, Tg mice differed from their wild–type littermates but treatment effect was not observed, indicating that the therapy specifically improves cognition. Cerebral microhemorrhages were observed in the Tg mice but the immunotherapy did not increase the bleeding in contrast to previous Aβ antibody studies. These findings indicate that our Aβ derivative in alum adjuvant is effective when therapy is started early in the disease process and it may be safer than passive immunotherapy because this approach does not cause microhemorrhages.
Type-based flow analysis and context-free language reachability (2008)

We present a novel approach to computing the context-sensitive flow of values through procedures and data structures. Our approach combines and extends techniques from two seemingly disparate areas: polymorphic subtyping and interprocedural dataflow analysis based on context-free language reachability. The resulting technique offers several advantages over previous approaches: it works directly on higher-order programs; provides demand-driven interprocedural queries; and improves the asymptotic complexity of a known algorithm based on polymorphic subtyping from O ( n 8 ) to O ( n 3 ) for computing all queries. For intra-procedural flow restricted to equivalence classes, our algorithm yields linear inter-procedural flow queries.
Supplementary Figures S1-S7 from &lt;i&gt;miR-634&lt;/i&gt; Activates the Mitochondrial Apoptosis Pathway and Enhances Chemotherapy-Induced Cytotoxicity (2023)

&lt;p&gt;Supplementary Figures S1-S7. Effect of miR-634 overexpression in normal fibroblasts and LCLs (S1); Effect of NRF2 inhibition by specific siRNA transfection (S2); Simultaneous down-regulation of target genes by 7 siRNAs (S3); Expression analysis of miR-634 and target proteins in normal fibroblasts and LCLs (S4); Establishment of CDDP-resistant ESCC cell line and expression analysis of miR-634 and target proteins (S5); Changes in body weights of 6 mice in PBS group (S6); Expression analysis of miR-634 in ESCC samples (S7).&lt;/p&gt;
Diffraction-grating beam splitter, interferometric-lithography nanopatterning with a multilongitudinal-mode diode laser (2021)

Large-area, oblique-incidence interferometric nanopatterning using a low-cost multilongitudinal-mode diode laser as the source and a spin-on-glass based diffraction-phase-mask grating beam splitter is demonstrated. The phase mask is engineered to have only two equal intensity orders (0th and −1st), dramatically simplifying the optical arrangement and decreasing the propagation distance between the beam splitter and the sample. The low-cost, high-power (150 mW) TEM00 405-nm diode laser operates with a large number of longitudinal modes, resulting in an impractical mask-to-sample-gap proximity requirement. A dual-grating-mask, achromatic interferometric scheme is introduced to extend this gap dimension to easily accessible scales. Uniform nanopatterns with a periodicity of 600 nm were fabricated over a 1 cm diameter area using this multimode diode laser. This technique is scalable and has the potential for large-area nanopatterning applications.