gebhart/patrepeval huggingface dataset:
Purification and Characterization of Protein Nanotubes Assembled from a Single Bacterial Microcompartment Shell Subunit (2015)

Bacterial microcompartment (BMC) nanotubes are isolated and characterized for the first time. RmmH, a component of the Mycobacterium smegmatis BMC shell, self-assembles into protein nanotubes when expressed in Escherichia coli or by concentrating purified RmmH in vitro. BMC nanotubes offer a new biomaterial and spatial architecture that may be genetically or chemically modified and used as a molecular scaffold. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Her2 expression in gastroesophageal cancer (GEC) FFPE tissue using mass spectrometry (MS) and correlation with <i>HER2</i> gene amplification. (2015)

82 Background: HER2+ GEC derived benefit from trastuzumab. Her2 IHC is semi-quantitative, subjective, and sensitive to antigen instability; HER2 FISH is laborious, expensive, and subjective. False positivity/negativity have been described. Also, these are low throughput assays; there is known molecular heterogeneity, with several putative biomarkers, and only scarce tissue to assess for each. We sought to evaluate the association of Her2 MS expression with HER2 FISH, along with other markers within the ‘GEC-plex’. Methods: We utilized a previously described unique Her2 peptide and quantification method (Hembrough et al J Clin Oncol 32,2014(suppl 3;abstr17)). The assay was run on 27 cell lines, in parallel with HER2:CEP17 FISH. Her2 expression thresholds were established for HER2 amplification using ROC curves. We adjusted for Her3, Egfr, and Met MS expression levels and sample HER2:CEP17 ratio heterogeneity in a multiple linear regression model. The model/cut-offs were then validated prospectively on GEC tissues (n=142). Results: Her2 MS on cell lines revealed concordance with FISH (HER2:CEP17) ratio (R 2 =0.75), which improved by adjusting for Her3 MS, Egfr MS, Met MS and HER2:CEP17 heterogeneity (R 2 &gt;0.98), with significant interactions. IHC correlation with HER2:CEP17 ratio was poor (R 2 =0.12). A wide range of expression was noted within IHC3+ patients (&lt;150-24671amol/ug). Her2 MS expression (&gt;150 amol/ug) was seen in 72.9% (102/142) of tissues (range &lt;150-24671amol/ug); 9.9% (14/142) had Her2 &gt; 750 amol/ug - all were HER2 FISH amplified. 6/142 (4%) cases &lt;500 amol/ug were clinically ‘HER2amplified’. IHC/FISH results for cases with 550-750 amol/ug demonstrated an ‘equivocal’ zone, not unlike ‘IHC 2+’, but less frequent (8/142, 5.6% vs 46/142 32.4%). Conclusions: The MS HER2 assay can be multiplexed with other GEC biomarkers. A robust model was developed that showed strong correlation of Her2 MS with HER2:CEP17 ratio, particularly when adjusting for covariates Egfr MS, Met MS, Her3 MS, and HER2 FISH heterogeneity. Future analysis will assess the established model as a tool for better prediction of therapeutic benefit from anti-Her2 therapy compared to current methods.
THERMALLY INDUCED DEFLECTION OF MICROJETS (2008)

Deflection of a microjet as it passes through an asymmetrically heated orifice is investigated experimentally and with thermofluidic CFD modeling. Concentric and stacked deflection heater designs are studied, with orifice ranging from 6−8 ∝m in diameter and 1.4−5 ∝m in length. Concentric heater devices produced a higher absolute deflection, with maximum deflections of 1ϒ observed at 15−20 mW average steady-state deflection power and shorter orifice lengths. The deflection direction for both designs changed sign depending on the orifice length and heater dimensions, which can be understood as a transition from viscous to solid-liquid surface energy forces dominating the microjet deflection.
Evaluation of Varicella-Zoster Immune Globulin: Protection of Immunosuppressed Children after Household Exposure to Varicella (1983)

Varicella-zoster immune globulin (VZIG), an immunoglobulin prepared from normal donor plasma selected for high titer of antibody to varicella-zoster virus (VZV), and zoster immune globulin (ZIG), prepared from the plasma of donors convalescing from herpes zoster, were compared in a double-blind, randomized clinical trial to determine their relative efficacy in protecting immunosuppressed children from severe varicella. VZV infection occurred in 49 (60.4%) of 81 recipients of VZIG and in 57 (68.6%) of 83 recipients of ZIG. These rates and the clinical severity of varicella were not significantly different; however, the subclinical infection rate was significantly higher in ZIG recipients (31.3% vs. 16.0%). This difference was accounted for by a subgroup of patients receiving immunosuppressive therapy for nonneoplastic diseases. Doubling the dose of VZIG administered reduced the rate of subclinical infection. These data indicate that VZIG can be used to protect immunosuppressed children from severe chicken pox.
Synbiotic Effect of Bifidobacterium lactis CNCM I-3446 and Bovine Milk-Derived Oligosaccharides on Infant Gut Microbiota (2020)

This study demonstrated the strong synbiotic effect of BMOS and <i>B. lactis</i> on the infant gut microbiota, and suggests a strategy to improve its effectiveness in an otherwise low-<i>Bifidobacterium</i> microbiota.
Biochemical and Structural Insights into Enzymatic Depolymerization of Polylactic Acid and Other Polyesters by Microbial Carboxylesterases (2016)

Polylactic acid (PLA) is a biodegradable polyester derived from renewable resources, which is a leading candidate for the replacement of traditional petroleum-based polymers. Since the global production of PLA is quickly growing, there is an urgent need for the development of efficient recycling technologies, which will produce lactic acid instead of CO2 as the final product. After screening 90 purified microbial α/β-hydrolases, we identified hydrolytic activity against emulsified PLA in two uncharacterized proteins, ABO2449 from Alcanivorax borkumensis and RPA1511 from Rhodopseudomonas palustris. Both enzymes were also active against emulsified polycaprolactone and other polyesters as well as against soluble α-naphthyl and p-nitrophenyl monoesters. In addition, both ABO2449 and RPA1511 catalyzed complete or extensive hydrolysis of solid PLA with the production of lactic acid monomers, dimers, and larger oligomers as products. The crystal structure of RPA1511 was determined at 2.2 Å resolution and revealed a classical α/β-hydrolase fold with a wide-open active site containing a molecule of polyethylene glycol bound near the catalytic triad Ser114-His270-Asp242. Site-directed mutagenesis of both proteins demonstrated that the catalytic triad residues are important for the hydrolysis of both monoester and polyester substrates. We also identified several residues in RPA1511 (Gln172, Leu212, Met215, Trp218, and Leu220) and ABO2449 (Phe38 and Leu152), which were not essential for activity against soluble monoesters but were found to be critical for the hydrolysis of PLA. Our results indicate that microbial carboxyl esterases can efficiently hydrolyze various polyesters making them attractive biocatalysts for plastics depolymerization and recycling.
Subterahertz Emission at Strong REB-Plasma Interaction in Multimirror Trap GOL-3 (2011)

Investigation results for electromagnetic radiation emission induced by strong Langmuir turbulence driven by a microsecond relativistic electron beam are presented. The radiation is associated with a plasmon-plasmon merging process, which generates photons at a double plasma frequency in the range of few hundreds GHz. An original radiometric system for radiation spectrum and power measurements is described.
Event Localization in Bulk Organic Scintillators Using Direct Reconstruction. (2016)

Abstract not provided.
P19-56 LB. Priming with SOCS-1 silenced Dendritic cells induces robust HIV-specific CTL response in a novel HLA-A2 transgenic humanized mouse model (2009)

Results Targeted silencing of SOCS-1 in human DCs a) enhanced their cytokine responses to LPS and stimulated a strong mixed lymphocyte reaction in vitro, b) elicited a strong primary in vitro response to HLA-A2-restricted Melan-A/ MART-1 and HIV Gag SL9 epitope in naive CD8+ T cells from healthy donors and c) increased the HIV gag-specific cytokine response in CD8 T cells from seropositive subjects. More importantly, in HLA-A2 transgenic NOD/ SCID-iL2rγ-/mice reconstituted with CD34 HSC from HLA-A2 donors, injection of SOCS-1 silenced DCs pulsed with HIV A2-restricted gag peptides, but not the irrelevant flu peptide, gave rise to a robust HIV specific CD8 T cell response which protected effectively against lethal challenge with recombinant HIV Gag-vaccinia.
Diffusion SLAM: Localizing Diffusion Sources From Samples Taken by Location-Unaware Mobile Sensors (2021)

We consider diffusion fields induced by multiple localised and instantaneous sources. We assume a mobile sensor samples the field, uniformly along a piecewise linear trajectory, which is unknown. The problem we address is the estimation of the amplitudes and locations of the diffusion sources, as well as of the trajectory of the sensor. We first propose a method for diffusion source localisation and trajectory mapping (D-SLAM) in 2D, where we assume the activation times of the sources are known and the evolution of the diffusion field over time is negligible. The reconstruction method we propose maps the measurements obtained using the mobile sensor to a sequence of generalised field samples. From these generalised samples, we can then retrieve the locations of the sources as well as the trajectory of the sensor (up to a 2D orthogonal geometric transformation). We then relax these assumptions and show that we can perform D-SLAM also in the case of unknown activation times, from samples of a time-varying field, as well as in 3D spaces. Finally, simulation results on both synthetic and real data further validate the proposed framework.
Layer-by-layer ultraviolet assisted extrusion-based (UAE) bioprinting of hydrogel constructs with high aspect ratio for soft tissue engineering applications (2019)

One of the major challenges in the field of soft tissue engineering using bioprinting is fabricating complex tissue constructs with desired structure integrity and mechanical property. To accomplish such requirements, most of the reported works incorporated reinforcement materials such as poly(ϵ-caprolactone) (PCL) polymer within the 3D bioprinted constructs. Although this approach has made some progress in constructing soft tissue-engineered scaffolds, the mechanical compliance mismatch and long degradation period are not ideal for soft tissue engineering. Herein, we present a facile bioprinting strategy that combines the rapid extrusion-based bioprinting technique with an in-built ultraviolet (UV) curing system to facilitate the layer-by-layer UV curing of bioprinted photo-curable GelMA-based hydrogels to achieve soft yet stable cell-laden constructs with high aspect ratio for soft tissue engineering. GelMA is supplemented with a viscosity enhancer (gellan gum) to improve the bio-ink printability and shape fidelity while maintaining the biocompatibility before crosslinking via a layer-by-layer UV curing process. This approach could eventually fabricate soft tissue constructs with high aspect ratio (length to diameter) of ≥ 5. The effects of UV source on printing resolution and cell viability were also studied. As a proof-of-concept, small building units (3D lattice and tubular constructs) with high aspect ratio are fabricated. Furthermore, we have also demonstrated the ability to perform multi-material printing of tissue constructs with high aspect ratio along both the longitudinal and transverse directions for potential applications in tissue engineering of soft tissues. This layer-by-layer ultraviolet assisted extrusion-based (UAE) Bioprinting may provide a novel strategy to develop soft tissue constructs with desirable structure integrity.
Recent results of pulmonary arterial angioplasty: the differences between proximal and distal lesions (2005)

Our findings indicate the need to distinguish, and to consider, the important differences in technical issues and outcomes, when performing dilations at proximal as opposed to distal sites. Although angioplasty is effective therapy for pulmonary arterial stenosis, a subset of vessels, more often distal, remain resistant to conventional techniques.
Raman spectral shift versus strain and composition in GeSn layers with 6%–15% Sn content (2017)

GeSn alloys are the subject of intense research activities as these group IV semiconductors present direct bandgap behaviors for high Sn contents. Today, the control of strain becomes an important challenge to improve GeSn devices. Strain micro-measurements are usually performed by Raman spectroscopy. However, different relationships linking the Raman spectral shifts to the built-in strain can be found in the literature. They were deduced from studies on low Sn content GeSn layers (i.e., xSn &amp;lt; 8%) or on GeSiSn layers. In this work, we have calibrated the GeSn Raman relationship for really high Sn content GeSn binaries (6 &amp;lt; xSn &amp;lt; 15%). We have used fully strained GeSn layers and fully relaxed GeSn under-etched microstructures to clearly differentiate the contributions of strain and chemical composition on the Ge-Ge Raman spectral shift. We have shown that the GeSn Raman-strain coefficient for high Sn contents is higher compared with that for pure Ge.
Effect of chemically defined growth medium components on characteristics of bacterial inclusion bodies (2020)

Abstract BACKGROUND Inactive aggregated protein deposits formed during fermentation of recombinant bacteria – inclusion bodies (IBs) – continue to be a significant source of active proteins. Understanding how the microenvironment, in particular growth medium, affects the quality and quantity of the IBs would be desirable for optimal production of proteins. In this study, we explore the effect of various chemically defined media components on IBs using a variety of analytical techniques. Expression of a biotherapeutic, ranibizumab, has been chosen as a case study. RESULTS A repertoire of nutrients, including but not limited to carbon and nitrogen source, vitamins, cofactors, buffering agents and minerals, were examined. Sucrose, biotin, pantothenate, glutathione, K 2 HPO 4 , K 2 SO 4 , cyanocobalamin and CaSO 4 were shortlisted based on experimentation. A design of experiments (DOE) study was performed to identify optimal concentrations of and interactions between these nutrients. Higher concentrations of sucrose, biotin and pantothenate, and lower concentrations of cyanocobalamin, CaSO 4 and glutathione, resulted in larger IBs and greater product expression. Further, K 2 HPO 4 and K 2 SO 4 concentrations did not seem to have a meaningful impact on product formation. CONCLUSIONS Medium composition affects size and quality of IBs. The size of IBs exhibits a positive correlation with the quantity of product expressed, as well as the purity of the product, but does not correlate with the total amount of host cell proteins produced. IB size could be used as a key process attribute during bioreactor optimization, and the otherwise difficult task of measuring product concentration in the fermentation broth could be avoided. © 2020 Society of Chemical Industry
C-Reactive Protein, Interleukin-6, and Vascular Recurrence After Stroke: An Individual Participant Data Meta-Analysis (2023)

Blood markers of inflammation were independently associated with vascular recurrence after stroke, strengthening the rationale for randomized trials of anti-inflammatory therapies for secondary prevention after ischemic stroke/TIA.
Potential of genotype VII Newcastle disease viruses to cause differential infections in chickens and ducks (2018)

Newcastle disease (ND), caused by ND virus (NDV), is one of the most infectious and economically important diseases of the poultry industry worldwide. While infections are reported in a wide range of avian species, the pathogenicity of chicken-origin virulent NDV isolates in ducks remains elusive. In this study, two NDV strains were isolated and biologically and genetically characterized from an outbreak in chickens and apparently healthy ducks. Pathogenicity assessment indices, including the mean death time (MDT), intracerebral pathogenicity index (ICPI) and cleavage motifs in the fusion (F) protein, indicated that both isolates were velogenic in nature. While these isolates carried pathogenic characteristics, interestingly they showed differential pathogenicity in ducks. The chicken-origin isolate caused high (70%) mortality, whereas the duck-origin virus resulted in low (20%) mortality in 4-week-old ducks. Intriguingly, both isolates showed comparable disease pathologies in chickens. Full-genome sequence analysis showed that the virus genome contains 15 192 nucleotides and carried features that are characteristic of velogenic strains of NDV. A phylogenetic analysis revealed that both isolates clustered in class II and genotype VII. However, there were several mutations in the functionally important regions of the fusion (F) and haemagglutinin-neuraminidase (HN) proteins, which may be responsible for the differential pathogenicity of these viruses in ducks. In summary, these results suggest that NDV strains with the same genotype show differential pathogenicity in chickens and ducks. Furthermore, chicken-origin virulent NDVs are more pathogenic for ducks than duck-origin viruses. These findings propose a role for chickens in the evolution of viral pathogenicity and the potential genetic resistance of ducks to poultry viruses.
Dynamic Involvement of Real World Objects in the IoT: A Consensus-Based Cooperation Approach (2017)

A significant role in the Internet of Things (IoT) will be taken by mobile and low-cost unstable devices, which autonomously self-organize and introduce highly dynamic and heterogeneous scenarios for the deployment of distributed applications. This entails the devices to cooperate to dynamically find the suitable combination of their involvement so as to improve the system reliability while following the changes in their status. Focusing on the above scenario, we propose a distributed algorithm for resources allocation that is run by devices that can perform the same task required by the applications, allowing for a flexible and dynamic binding of the requested services with the physical IoT devices. It is based on a consensus approach, which maximizes the lifetime of groups of nodes involved and ensures the fulfillment of the requested Quality of Information (QoI) requirements. Experiments have been conducted with real devices, showing an improvement of device lifetime of more than 20 % , with respect to a uniform distribution of tasks.
Immunoengineering (2018)

Biomaterials have been developed with the aim of transplanting them into the human body as substitutes for dysfunctioning and/or defective tissues; the biggest challenge in the development of such biomaterials has been the action of the immune system that eliminates foreign objects. Therefore, the first generation of biomaterials was developed under the concept of immune evasion. However, biomaterials capable of treating and preventing diseases by regulating immune mechanisms have been developed owing to the improved understanding of immunological mechanisms in molecular biology and to the accumulation of knowledge on biomaterial design in recent years. This section focuses on the background of three types of biomaterials (immunoevasive, immune-activation, and immunosuppressive biomaterials) and provides a few examples of their applications.
Preparation of 5-Heteroaryl Substituted 1-(4-Fluorophenyl)-1<i>H</i>-indoles via Palladium-Catalyzed Negishi and Stille Cross-Coupling Reactions (2002)

Palladium-catalyzed Negishi cross-coupling of 5-1-(4-fluorophenyl)indolylzinc chloride with N-methyl-halopyrazoles, bromopyridines and bromopyrimidines in gram scale gave the corresponding cross-coupled products in 38-85% yield.
Determinants for the Occurrence of Acute Exacerbation of Hepatitis B Virus Infection in Chinese Patients after HBeAg Seroclearance (2005)

This study was performed to determine the factors for predicting the occurrence of acute exacerbation of hepatitis B virus infection in HBeAg-negative patients. Two hundred and sixteen patients with known times of HBeAg seroclearance were recruited. Liver biochemistry and virologic markers were monitored. Precore and core promoter mutations were determined by a line probe assay. The median age at HBeAg seroclearance was 34.5 years. The median follow-up duration was 26.4 months. Fifty-six (27.9%) patients had acute exacerbations. By Cox regression analysis, male gender, older age, and core promoter mutations at the time of HBeAg seroclearance were independently associated with the occurrence of acute exacerbation after HBeAg seroclearance (P = 0.025, 0.018, and 0.001, respectively). Fourteen (7.0%) patients had HBeAg seroreversion within a median follow-up period of 11.6 months after HBeAg seroclearance. By Cox regression analysis, older age at HBeAg seroclearance was independently associated with the chance of HBeAg seroreversion (P = 0.01). We concluded that male patients with core promoter mutations and delayed HBeAg seroclearance had a higher cumulative chance of acute exacerbation in the HBeAg-negative phase. Patients with delayed HBeAg seroclearance had a higher frequency of HBeAg seroreversion.
Multi-Band, Wide-Beam, Circularly Polarized, Crossed, Asymmetrically Barbed Dipole Antennas for GPS Applications (2013)

This communication presents a multi-band, circularly polarized (CP), wide beamwidth, highly efficient antenna for use in global positioning systems (GPS). The primary radiating elements are two crossed printed dipoles, which incorporate a 90° phase delay line realized with a vacant-quarter printed ring to produce the CP radiation and broadband impedance matching. To achieve multiple resonances, each dipole arm is divided into four branches with different lengths, and a printed inductor with a barbed end is inserted in each branch to reduce the radiator size. An inverted, pyramidal, cavity-backed reflector is incorporated with the crossed dipoles to produce a unidirectional radiation pattern with a wide 3-dB axial ratio (AR) beamwidth and a high front-to-back ratio. The multi-band antennas have broad impedance matching and 3-dB AR bandwidths, which cover the GPS L1-L5 bands.
Cholesterol Lowering Modulates T Cell Function In Vivo and In Vitro (2014)

Our results show that lipid lowering reduces T cell proliferation and function, supporting the notion that lipid lowering modulates T cell function in vivo and in vitro.