gebhart/patrepeval huggingface dataset:
Transcriptional profile in afferent lymph cells following vaccination with liposomes incorporating CpG (2014)

Vaccine formulations incorporating innate immune stimulants are highly immunogenic; however, the biological signals that originate in the peripheral tissues at the site of injection and are transmitted to the local lymph node to induce immunity remain unclear. By directly cannulating the ovine afferent lymphatic vessels, we have previously shown that it takes 72 hr for mature antigen-loaded dendritic cells and monocytes to appear within afferent lymph following injection of a liposomal formulation containing the Toll-like receptor ligand CpG. In this present study, we characterize the global transcriptional signatures at this time-point in ovine afferent lymph cells as they migrate from the injection site into the lymphatics following vaccination with a liposome antigen formulation incorporating CpG. We show that at 72 hr post vaccination, liposomes alone induce no changes in gene expression and inflammatory profiles within afferent lymph; however, the incorporation of CpG drives interferon, antiviral and cytotoxic gene programmes. This study also measures the expression of key genes within individual cell types in afferent lymph. Antiviral gene signatures are most prominent in lymphocytes, which may play a significant and unexpected role in sustaining the immune response to vaccination at the site of injection. These findings provide a comprehensive analysis of the in vivo immunological pathways that connect the injection site with the local draining lymph node following vaccination.
Impaired sense of agency and associated confidence in psychosis (2022)

The Sense of Agency (SoA), our sensation of control over our actions, is a fundamental mechanism for delineating the Self from the environment and others. SoA arises from implicit processing of sensorimotor signals as well as explicit higher-level judgments. Psychosis patients suffer from difficulties in the sense of control over their actions and accurate demarcation of the Self. Moreover, it is unclear if they have metacognitive insight into their aberrant abilities. In this pre-registered study, we examined SoA and its associated confidence judgments using an embodied virtual reality paradigm in psychosis patients and controls. Our results show that psychosis patients not only have a severely reduced ability for discriminating their actions but they also do not show proper metacognitive insight into this deficit. Furthermore, an exploratory analysis revealed that the SoA capacities allow for high levels of accuracy in clinical classification of psychosis. These results indicate that SoA and its metacognition are core aspects of the psychotic state and provide possible venues for understanding the underlying mechanisms of psychosis, that may be leveraged for novel clinical purposes.
Vaccine development to preventStaphylococcus aureussurgical-site infections (2017)

There is an unmet medical need for novel S. aureus SSI prevention measures. Advances in understanding of S. aureus SSI pathophysiology could lead to the development of effective and safe prophylactic multiple-antigen vaccines to prevent S. aureus SSI.
Prerequisites for the Antitumor Vaccine-Like Effect of Chemotherapy and Radiotherapy (2011)

For a long time, anticancer therapies were believed to work (and hence convey a therapeutic benefit) either by killing cancer cells or by inducing a permanent arrest in their cell cycle (senescence). In both scenarios, the efficacy of anticancer regimens was thought to depend on cancer cell-intrinsic features only. More recently, the importance of the tumor microenvironment (including stromal and immune cells) has been recognized, along with the development of therapies that function by modulating tumor cell-extrinsic pathways. In particular, it has been shown that some chemotherapeutic and radiotherapeutic regimens trigger cancer cell death while stimulating an active immune response against the tumor. Such an immunogenic cell death relies on the coordinated emission of specific signals from dying cancer cells and their perception by the host immune system. The resulting tumor-specific immune response is critical for the eradication of tumor cells that may survive therapy. In this review, we discuss the molecular mechanisms that underlie the vaccine-like effects of some chemotherapeutic and radiotherapeutic regimens, with particular attention to the signaling pathways and genetic elements that constitute the prerequisites for immunogenic anticancer therapy.
Reagentless pH-stat for Microliter Fluid Specimens (2008)

pH-stating is a common technique for monitoring kinetics of various biochemical reactions that involve the generation of hydrogen or hydroxyl ions. In this work, we describe a reagentless electrochemical micro-pH-stat where the titrant of acid or base is produced by water electrolysis on the rotating sample system (RSS) platform. RSS originated from the authors' laboratory as a convective platform to support different analytical techniques in microliter-sized samples. As water electrolysis induces no volume change and the current that generates the reagent can be precisely measured even at low levels, very small samples in the microliter range become accessible for pH-stating: a reduction of more than an order of magnitude in specimen size relative to the most sensitive conventional methods. Nearly 100% current efficiency has been achieved with this system using a 250 microm Pt minidisc working electrode for electrolysis. The developed micro-pH-stat has been validated by the determination of the activity of erythrocyte acetylcholinesterase as a function of substrate concentration and pH. The optimal pH and activity profile obtained are in good agreement with those determined with standard techniques. The micro-pH-stat has the potential for applications for enzyme assays, reagentless pH control, acidity/alkalinity, and buffer capacity measurements in very small samples of biomedical and environmental origin.
P1‐167: Structural Basis of Unique Selectivity of Aducanumab for Oligomeric Forms of Amyloid‐β (2016)

There has been a renewed interest in immunotherapy targeting Aβ peptide for treatment of Alzheimer’s disease (AD) with the intriguing Phase 1b findings showing aducanumab significantly reduces amyloid in patients’ brains. Hypotheses being investigated for positive clinical data are the preferred epitope and selectivity for toxic Aβ aggregates. Aducanumab (BIIB037) is a human monoclonal antibody derived from a healthy donor cohort of elderly subjects lacking signs of cognitive impairment, which is in advanced clinical testing for treatment of AD. Aducanumab is unique among amyloid-targeted antibodies for its exquisite selectivity for both soluble oligomeric and insoluble fibrillar aggregates of Aβ found in brain β-amyloid plaques. To gain further insight into the epitope conformation and selectivity for Aβ aggregates, we investigated the structural details of amino-terminal epitope in Aβ using X-ray crystallography of aducanumab Fab:Aβ complex. Biochemical validation of critical interface residues was confirmed using standard ELISA and PepSpot binding assays. Here we report the crystal structure of a recombinant Fab fragment of aducanumab in complex with Aβ1-11 peptide solved at 2.5Å resolution. The N-terminus of Aβ is bound to aducanumab in an extended conformation with the binding interface composed primarily of Phe 4 and His 6 of Aβ. Comparison with other N-terminal Aβ targeting antibodies reveals that aducanumab has an exceptionally compact epitope, which contributes to its selectivity and high avidity for Aβ oligomers and fibrils, including aggregates composed of N-truncated Aβ variants, without targeting physiologic Aβ monomers. In silico Rosetta-based interface and antibody–flexible Aβ docking analysis further highlight aducanumab’s distinct biophysical interaction with the Aβ monomer that further corroborates its selectivity for Aβ oligomers. Aducanumab selectively targets pathologic Aβ conformations displayed by oligomeric and fibrillary aggregates. Our results provide the structural basis for this unique binding profile that differentiates aducanumab from other N-terminal specific antibodies, both in the conformation and orientation of the bound Aβ peptide, as well as the molecular details that comprise the antibody-peptide interface.
Mobile TV with Long Time Interleaving and Fast Zapping (2012)

The main challenge for provisioning of Mobile TV services is to overcome long burst errors as are often found in mobile reception conditions. Long time interleaving can be implemented by means of Application Layer FEC (AL-FEC) to increase the time diversity of the signal and thereby its robustness against burst errors. The main obstacle of long time interleaving for streaming services is the increase in service tune-in time, which significantly decreases the Quality of Experience (QoE) of end users. That is why today's Mobile TV systems are provisioned in a way to minimize the time interleaving length to provide an acceptable tune-in time, though the service robustness would significantly benefit from a longer interleaving length. This paper presents a new way of service provisioning that marries fast zapping and long time interleaving by combining Layer-Aware FEC and layered media codecs with unequal time interleaving and an appropriate transmission scheduling. The effect of the proposed scheme on the QoE as well as the service tune-in time is analyzed. Simulation results within a Gilbert-Elliot channel report the benefit of the proposed scheme, which for the first time enables broadcast services with fast tune-in and at the same time long time interleaving.
Tape erase bands measured by MFM compared to MR head cross erase band responses (1996)

The erase bands written on tape by heads with CoZrTa and permalloy poles were compared by using MFM techniques and by measuring MR head responses as the heads were moved in the cross track direction. Measurements were made under conditions of both the top and bottom poles trailing, as well as for two different overwrite frequencies (2f and 4f). From both methods, it was found that the erase band is more dependent on which pole is trailing, than on the write head pole materials. In all cases, the top pole trailing (TPT) case yields narrower erase bands than the bottom pole trailing (BPT) case. The boundaries of the erase band become less distinct when the overwrite frequency increases. The phase difference between adjacent tracks does not play a big role in the case of BPT, but does matter in the case of TPT. The cross erase band profile demonstrates that the transport system is stable enough, and that this method to measure the erase band is feasible in the presence of tape motion.
Protective Effect of Anthocyanin-Enriched Polyphenols from Hibiscus syriacus L. (Malvaceae) against Ultraviolet B-Induced Damage (2021)

Anthocyanin-enriched polyphenols from the flower petals of <i>H. syriacus</i> L. (Malvaceae, AHs) possess anti-septic shock, anti-oxidant, and anti-melanogenic properties. However, whether AHs positively or negatively regulate ultraviolet B (UVB)-mediated photoaging and photodamage remains unclear. This study aims to investigate the protective effect of AHs against UVB-induced damage. We examined the photoprotective effects of AHs on UVB-induced apoptosis, endoplasmic reticulum (ER) stress, and mitochondrial reactive oxygen species (mtROS). AHs prevented UVB irradiation-induced apoptosis of HaCaT keratinocytes by inhibiting caspase activation and ROS production. Moreover, AHs restored the survival rate and the hatchability of UVB-irradiated zebrafish larvae without any abnormalities. Furthermore, AHs inhibited UVB-induced ER stress, resulting in a decrease in mtROS production via the stabilization of the mitochondrial membrane potential. Our results indicate that AHs inhibit UVB-induced apoptosis by downregulating total cytosolic ROof cytosolic CaS and ER-mediated mitoROS production in both HaCaT keratinocytes and zebrafish larvae. These findings provide evidence for the applications of AHs to protect skin from UVB-induced photodamage.
Reversed interface effects in amorphous FeZr/AlZr multilayers (2014)

We report an anomalous enhancement of the critical temperature $({T}_{\mathrm{c}})$ when the thickness $(d)$ of the magnetic layer is decreased from 60 to 20 \AA{} in amorphous FeZr/AlZr multilayers. Further reduction of the thickness causes a decrease of ${T}_{\mathrm{c}}$, as expected by finite-size scaling, while the magnetic moment decreases monotonically for all values of $d$. The increase of the critical temperature is attributed to a reversed interface effect where local changes in the nearest-neighbor distance and coordination number gives a higher effective magnetic coupling at the interfaces compared to the interior of the layer. We have successfully described the results within a model where such interface effects are combined with finite-size scaling.
Does Smoking Status Influence Health-Related Quality of Life Outcome Measures in Patients Undergoing ACDF? (2019)

Whereas nonsmokers had higher function and lower pain than former or current smokers preoperatively, smoking status overall was not found to be an independent predictor of outcome scores after ACDF. This supports the notion that smoking status alone should not deter patients from undergoing ACDF for cervical degenerative pathology.
Low Heat Input Welding for Thin Steel Fabrication (2006)

As thinner members are used in marine construction, the use of conventional joining techniques results in significant angular and buckling distortion due to the inherent high heat input with these processes. Several low heat input alternatives, including laser beam, gas metal arc, and hybrid laser arc welding, are explored. The paper focuses on process development, real time distortion measurements, and implementation of these processes.
Use of an Isopropyl Ester Moiety as a Sulfonic Acid Protecting Group in a Greatly Improved Synthesis of an Arylsulfonic Acid‐Based Follicle Stimulating Hormone Antagonist. (2002)

Abstract For Abstract see ChemInform Abstract in Full Text.
The role of seasonal grass pollen on childhood asthma emergency department presentations (2012)

This is the first study to establish a clear relationship between increased risk of childhood asthma ED attendance and levels of ambient grass pollen below 20 grains/m(3) , independent of any impact of thunderstorm-associated asthma. These findings have important implications for patient care, such as asthma management programs that notify the general public regarding periods of high grass pollen exposure, as well as defining the timing of initiation of pollen immunotherapy.
Catalytic glycerol conversion into 1,2-propanediol in absence of added hydrogen (2008)

Conversion of glycerol into high yields of 1,2-propanediol in absence of added hydrogen is possible with Pt impregnated NaY zeolite characterized by extra-zeolitic metal particles combined with zeolite Brønsted acidity.
Robust wavenumber and dispersion calibration for Fourier-domain optical coherence tomography (2018)

Many Fourier-domain optical coherence tomography (FD-OCT) systems sample the interference fringes with a non-uniform wavenumber (k) interval, introducing a chirp to the signal that depends on the path length difference underlying each fringe. A dispersion imbalance between sample and reference arms also generates a chirp in the fringe signal which, in contrast, is independent of depth. Fringe interpolation to obtain a signal linear in k and compensate dispersion imbalance is critical to achieving bandwidth-limited axial resolution. In this work, we propose an optimization-based algorithm to perform robust and automated calibration of FD-OCT systems, recovering both the interpolation function and the dispersion imbalance. Our technique relies on the fact that the unique function that correctly linearizes the fringe data in k space produces a depth-independent chirp. The calibration procedure requires experimental data corresponding to a single reflector at various depth locations, which can easily be obtained by acquiring data while moving a sample mirror in depth. We have tested both spectral domain OCT and swept source OCT systems with various nonlinearities. Results indicate that the proposed calibration method has excellent performance on a wide range of data sets and enables nearly constant resolution at all imaging depths. An implementation of the algorithm is available online.
High-order tensor flow processing using integrated photonic circuits (2021)

Tensor analytics lays mathematical basis for the prosperous promotion of multiway signal processing. To increase computing throughput, mainstream processors transform tensor convolutions to matrix multiplications to enhance parallelism of computing. However, such order-reducing transformation produces data duplicates and consumes additional memory. Here, we demonstrate an integrated photonic tensor flow processor without tensor-matrix transformation, which outputs the convolved tensor as the input tensor 'flows' through the processor. The hybrid manipulation of optical dimensions of wavelength, time, and space enables the direct representation and processing of high-order tensors in optical domain. In the proof-of-concept experiment, processing of multi-channel images and videos is accomplished at the frequency of 20 GHz. A convolutional neural network is demonstrated on the processor, which achieves an accuracy of 97.9 percent on action recognition.
CSL controls telomere maintenance and genome stability in human dermal fibroblasts (2019)

Genomic instability is a hallmark of cancer. Whether it also occurs in Cancer Associated Fibroblasts (CAFs) remains to be carefully investigated. Loss of CSL/RBP-Jκ, the effector of canonical NOTCH signaling with intrinsic transcription repressive function, causes conversion of dermal fibroblasts into CAFs. Here, we find that CSL down-modulation triggers DNA damage, telomere loss and chromosome end fusions that also occur in skin Squamous Cell Carcinoma (SCC)-associated CAFs, in which CSL is decreased. Separately from its role in transcription, we show that CSL is part of a multiprotein telomere protective complex, binding directly and with high affinity to telomeric DNA as well as to UPF1 and Ku70/Ku80 proteins and being required for their telomere association. Taken together, the findings point to a central role of CSL in telomere homeostasis with important implications for genomic instability of cancer stromal cells and beyond.
EMT and MET as paradigms for cell fate switching (2011)

Cell fate determination is a major unsolved problem in cell and developmental biology. The discovery of reprogramming by pluripotent factors offers a rational system to investigate the molecular mechanisms associated with cell fate decisions. The idea that reprogramming of fibroblasts starts with a mesenchymal-epithelial transition (MET) suggests that the process is perhaps a reversal of epithelial to mesenchymal transition (EMT) found frequently during early embryogenesis. As such, we believe that investigations into MET-EMT may yield detailed molecular insights into cell fate decisions, not only for the switching between epithelial and mesenchymal cells, but also other cell types.
Exploring Human Interaction and Diet Effects on the Behavior of Dogs in a Public Animal Shelter (2002)

This study examined the effects of 2 manipulations--a brief, regular period of human contact and diet--on the behavior of dogs confined in a public animal shelter. A behavioral battery designed to assess reactions to novel situations, and a test of responsiveness to an unfamiliar human were administered both prior to (pretest) and immediately following (posttest) the 8-week intervention period. Overall, the regular periods of increased human contact together with a diet that contained augmented levels of digestible protein, fat, calories, and animal-derived ingredients reduced signs of behavioral reactivity from pretest to posttest. In some cases, the comparison diet appeared more effective, but only for dogs receiving minimal human interaction. The results indicate that a combination of human interaction and high quality diet may positively affect the behavior of dogs in animal shelters.
Studies of the Surface Treatment and Sizing of Carbon Fiber Surfaces on the Mechanical Properties of Composites Containing Carbon Fibers (1996)

Carbon fiber reinforced composites are materials where carbon fibers are used to reinforce a matrix to produce a light and strong material with important applications in the aerospace industry. There are many aspects of the preparation of these materials that would benefit from a study which combines the research of groups involved in the production, testing and analysis of these materials, and studies of the basic surface chemistry involved. This final reports presents the results of a project that has developed a collaboration between groups in all three of the major research universities in the State of Kansas, and promises to lead to a collaborative program that covers the major aspects of composite development and application. Sherwood has provided initial fiber surface treatment and sizing together with fiber and composite surface analysis; Lease, Tomblin and Wang have worked together toward the goal of preparing pre-preg and fabrication of laminated panels; Locke has developed computational models to evaluate the effect of surface treatment (and chemistry) on mechanical properties; Lease, Tomblin and Wang have worked together to perform all necessary mechanical testing. The research has been focused on materials that would benefit the High Speed Civil Transport (HSCT) program. The group has visited Dr. Howard Maars and his colleagues at NASA Langley, and has focused their studies on the NASA requirements discussed in this meeting. An important development, requested by NASA scientists, has been the acquisition and study of K3B as a matrix material for the composites. The project has led to the successful acquisition and surface analysis of K3B, together with the successful deposition of this material onto surface oxidized carbon fibers. Mechanical testing, modelling and the construction of composite preparation equipment has been achieved during the grant period.
Fabrication of Nanodispersed Pt–Sn/SBA-16 Catalysts and Their Catalytic Applications (2006)

Abstract Monodispersed bimetallic Pt–Sn/SBA-16 catalysts prepared by coimpregnation technique and microwave-drying method showed enhanced catalytic activities for selective dehydrogenation of n-dodecane to its corresponding mono-olefins and preferential oxidation (PROX) of CO in the presence of excess H2.
Enhanced thermoelectric properties of n-type NbCoSn half-Heusler by improving phase purity (2016)

Here we report the thermoelectric properties of NbCoSn-based n-type half-Heuslers (HHs) that were obtained through arc melting, ball milling, and hot pressing process. With 10% Sb substitution at the Sn site, we obtained enhanced n-type properties with a maximum power factor reaching ∼35 μW cm−1 K−2 and figure of merit (ZT) value ∼0.6 in NbCoSn0.9Sb0.1. The ZT is doubled compared to the previous report. In addition, the specific power cost ($ W−1) is decreased by ∼68% comparing to HfNiSn-based n-type HH because of the elimination of Hf.