gebhart/patrepeval huggingface dataset:
Recombinant Dimeric IgA Antibodies as Tumor-Specific Agents. (2010)

Abstract Abstract 1488 Dimeric IgA antibodies contribute significantly to the humoral part of the mucosal immune system. However, their potential as immunotherapeutic agent has hardly been explored. Here, we describe the production, purification and functional evaluation of recombinant dimeric IgA, exemplarily directed against the epidermal growth factor receptor (EGF-R). Human J-chain-containing IgA was produced under serum-free conditions by transfecting non-adherent CHO-K1 cells expressing EGF-R specific monomeric IgA with a vector coding for the His-tagged human J-chain. For purification of J-chain-containing dimeric IgA two different affinity (anti-human-kappa and anti-His-tag) and one size exclusion chromatography were combined, resulting in a homogenous preparation of highly pure IgA dimers, as determined by gel electrophoresis under denaturing and native conditions using silver stain, Coomassie blue or Western blots for protein detection, respectively. Functional studies demonstrated dimeric IgA (dIgA) to be at least as effective as monomeric IgA (mIgA) in triggering ADCC of A431 tumor cells by isolated monocytes (EC50 0.35 and 0.30 μg/ml for mIgA and dIgA, 0.23 μg/ml for the corresponding IgG1; maximal killing 51.2 vs 43.3 vs 56.3 %), by isolated PMN (EC50 0.96, 1.20 and 0.8 μg/ml for mIgA, dIgA and IgG1; maximal killing 52.6 vs 50.6 vs 19.9 %) and in human whole blood assays (EC50 0.32 and 0.32 μg/ml for mIgA and dIgA; maximal killing 7.9 vs 12.5 %; IgG1: maximal killing 0.7 %, EC50 not determinable). Importantly, dimeric IgA was more effective in F(ab)-mediated mechanisms: inhibition of binding of FITC-labelled EGF to A431 cells by dimeric IgA was achieved at significantly lower concentrations than by monomeric IgA (EC50 7.1 vs 18.1 μg/ml, respectively). In addition, growth of EGF-R expressing DiFi colon carcinoma cells was inhibited at significantly lower concentrations by dimeric than by monomeric IgA (EC50 1.6 vs 3.7 μg/ml). Both IgA isoforms and their IgG1 variant were similarly effective in triggering apoptosis of DiFi cells, as analyzed by PARP cleavage. Furthermore, only dimeric but not monomeric IgA or IgG was directionally transported by the polymeric immunoglobulin receptor (pIgR) through an epithelial cell monolayer, as analyzed by an experimental transcytosis assay with polarized MDCK cells stably transfected with human pIgR. Together, these studies demonstrate that recombinant dimeric IgA antibodies recruit a distinct repertoire of effector functions compared to monomeric IgA or IgG1 antibodies, trigger important biological functions and constitute an interesting antibody format for future tumor therapies. Disclosures: van de Winkel: Genmab: Employment, Membership on an entity's Board of Directors or advisory committees. Valerius:Genmab: Consultancy, Research Funding.
Time-Resolved Raman Spectroscopy of Polaron Formation in a Polymer Photocatalyst (2021)

Polymer photocatalysts are a synthetically diverse class of materials that can be used for the production of solar fuels such as H<sub>2</sub>, but the underlying mechanisms by which they operate are poorly understood. Time-resolved vibrational spectroscopy provides a powerful structure-specific probe of photogenerated species. Here we report the use of time-resolved resonance Raman (TR<sup>3</sup>) spectroscopy to study the formation of polaron pairs and electron polarons in one of the most active linear polymer photocatalysts for H<sub>2</sub> production, poly(dibenzo[<i>b</i>,<i>d</i>]thiophene sulfone), P10. We identify that polaron-pair formation prior to thermalization of the initially generated excited states is an important pathway for the generation of long-lived photoelectrons.
Design, Theoretical, and Experimental Investigation of Tensile-Strained Germanium Quantum-Well Laser Structure (2021)

Strain and band gap engineered epitaxial germanium (ε-Ge) quantum-well (QW) laser structures were investigated on GaAs substrates theoretically and experimentally for the first time. In this design, we exploit the ability of an InGaAs layer to simultaneously provide tensile strain in Ge (0.7–1.96%) and sufficient optical and carrier confinement. The direct band-to-band gain, threshold current density (Jth), and loss mechanisms that dominate in the ε-Ge QW laser structure were calculated using first-principles-based 30-band k·p electronic structure theory, at injected carrier concentrations from 3 × 1018 to 9 × 1019 cm–3. The higher strain in the ε-Ge QW increases the gain at higher wavelengths; however, a decreasing thickness is required by higher strain due to critical layer thickness for avoiding strain relaxation. In addition, we predict that a Jth of 300 A/cm2 can be reduced to <10 A/cm2 by increasing strain from 0.2% to 1.96% in ε-Ge lasing media. The measured room-temperature photoluminescence spectroscopy demonstrated direct band gap optical emission, from the conduction band at the Γ-valley to heavy-hole (0.6609 eV) from 1.6% tensile-strained Ge/In0.24Ga0.76As heterostructure grown by molecular beam epitaxy, is in agreement with the value calculated using 30-band k·p theory. The detailed plan-view transmission electron microscopic (TEM) analysis of 0.7% and 1.2% tensile-strained ε-Ge/InGaAs structures exhibited well-controlled dislocations within each ε-Ge layer. The measured dislocation density is below 4 × 106 cm–2 for the 1.2% ε-Ge layer, which is an upper bound, suggesting the superior ε-Ge material quality. Structural analysis of the experimentally realistic 1.95% biaxially strained In0.28Ga0.72As/13 nm ε-Ge/In0.28Ga0.72As QW structure demonstrated a strained Ge/In0.28Ga0.72As heterointerface with minimal relaxation using X-ray and cross-sectional TEM analysis. Therefore, our monolithic integration of a strained Ge QW laser structure on GaAs and ultimately the transfer of the process to the Si substrate via an InGa(Al)As/III–V buffer architecture would provide a significant step toward photonic technology based on strained Ge on a Si platform.
Endothelial Dysfunction and Microvascular Complications in Type 1 Diabetes Mellitus (2008)

We examined whether alterations in vascular endothelial function and early structural changes in atherosclerosis are associated with microvascular complications in patients with type 1 diabetes mellitus (DM). Flow-mediated dilation (FMD) of the brachial artery and carotid intima-media thickness (IMT) measurement were performed in 70 young adults (aged 19 to 35 yr), 48 with type 1 DM, and 22 normal controls. Patients with diabetes had a lower peak FMD response (7.8+/-3.9 vs. 11.1+/-1.9%, p<0.001) and increased IMT (0.51+/-0.10 vs. 0.42+/-0.07 mm, p<0.001) compared with controls. Twenty (41.7%) of the patients had microvascular complications including neuropathy, nephropathy, or retinopathy. In these complicated diabetic patients, we found a lower FMD response (6.1+/-2.5 vs. 9.9+/-3.5%, p=0.001) compared with diabetics without microvascular complications. The presence of microvascular complications was also associated with older age and longer duration of the disease. However, no differences were observed in IMT, body size, blood pressure, HbA1c, C-reactive protein, low-density lipoprotein or high-density lipoprotein cholesterol levels between complicated and non-complicated patients. Endothelial dysfunction and early structural atherosclerotic changes are common manifestations in type 1 DM, and endothelial dysfunction is thought to be an early event in the atherosclerotic process and important in the pathogenesis of microvascular complications.
(Invited) Tribute to Prof. Zempachi Ogumi : In Operando Studies and in Situ Techniques for Li-Ion and Lithium Metal Polymer Batteries (2016)

Prof. Ogumi is one the leading pioneers of lithium-ion technology in Japan and worldwide. His research studies on battery materials include LiCoO 2 , graphite, and highly oriented pyrolytic graphite (HOPG), Much of his research involved in situ techniques that utilized X-ray, Raman spectroscopy and atomic force spectroscopy (AFM) to investigate the SEI (passivation layer) and lithium intercalation in graphite and HOPG in propylene carbonate (PC)- and ethylene carbonate (EC)-based electrolytes. In this presentation, we will show data and video movies that were obtained during studies of lithium-ion and solid-state batteries using various In operando studies and in situ techniques involving scanning electron microscopy (SEM), transmission electron microscopy (TEM), Raman spectroscopy, X-ray diffraction and ultraviolet-visible absorption spectroscopy (UV-vis). These in situ studies are helpful to understand the mechanisms for volume expansion of anodes consisting of lithium metal (20 %), graphite (10 %) and LTO (0 %). Another example that will be discussed is the dimensional changes of the anode, cathode and electrolyte that occur during charge/discharge. The mechanism of lithium dendrite formation was also studied, and details will be discussed in this presentation. [Don’t know what is meant by Bleand and deleted because I‘m not sure it is needed.] Lithium/solid polymer electrolyte (SPE)/sulfur cells were studied by two in situ techniques: SEM and UV-vis. During the operation of the cell, extensive polysulfide dissolution in the solid polymer electrolyte (cross-linked polyethylene oxide) leads to the formation of a catholyte. A clear micrograph was obtained of the thick passivation layer on the sulfur-rich anode and the decreased SPE thickness during cycling confirmed the failure mechanism; the capacity decays by reducing the amount of active material, which contributes to a charge inhibiting mechanism called polysulfide shuttle. The formation of elemental sulfur is clearly visible in real time during the charge process beyond 2.3 V. The non-destructive UV-vis also shows the characteristic absorption peaks that evolve with cycling, demonstrating the accumulation of various polysulfide species, and the predominant formation of S 4 2- and of S 6 2- during discharge and charge, respectively. This finding implies that the charge and discharge reactions are not completely reversible and proceed along different pathways.
Memristor-based pattern recognition for image processing: an adaptive coded aperture imaging and sensing opportunity (2010)

Adaptive coded aperture (diffraction) sensing, an emerging technology enabling real-time, wide-area IR/visible sensing and imaging, could benefit from new high performance biologically inspired image processing architectures. The memristor, a novel two terminal passive device can enable significantly powerful biologically inspired processing architectures. This device was first theorized by Dr. Leon Chua in 1971. In 2008, HP Labs successfully fabricated the first memristor devices. Due to its unique properties, the memristor can be used to implement neuromorphic functions as its dynamics closely model those of a synapse, and can thus be utilized in biologically inspired processing architectures. This paper uses existing device models to determine how device parameters can be tuned for the memristor to be used in neuromorphic circuit design. Specifically, the relation between the different models and the number of states the device can hold are examined.
Ergodic Fading MIMO Dirty Paper and Broadcast Channels: Capacity Bounds and Lattice Strategies (2017)

A multiple-input multiple-output (MIMO) version of the dirty paper channel is studied, where the channel input and the dirt experience the same fading process, and the fading channel state is known at the receiver. This represents settings where signal and interference sources are co-located, such as in the broadcast channel. First, a variant of Costa's dirty paper coding is presented, whose achievable rates are within a constant gap to capacity for all signal and dirt powers. In addition, a lattice coding and decoding scheme is proposed, whose decision regions are independent of the channel realizations. Under Rayleigh fading, the gap to capacity of the lattice coding scheme vanishes with the number of receive antennas, even at finite Signal-to-Noise Ratio (SNR). Thus, although the capacity of the fading dirty paper channel remains unknown, this paper shows it is not far from its dirt-free counterpart. The insights from the dirty paper channel directly lead to transmission strategies for the two-user MIMO broadcast channel, where the transmitter emits a superposition of desired and undesired (dirt) signals with respect to each receiver. The performance of the lattice coding scheme is analyzed under different fading dynamics for the two users, showing that high-dimensional lattices achieve rates close to capacity.
ChemInform Abstract: SYNTHESES AND DIFFERENTIATING ACTION OF VITAMIN D ENDOPEROXIDES. SINGLET OXYGEN ADDUCTS OF VITAMIN D DERIVATIVES IN HUMAN MYELOID LEUKEMIA CELLS (HL‐60) (1985)

Abstract Die Vitamin D‐Derivate (I) ergeben bei der Photooxidation die Endoperoxide (II).
Association of lack of uridine monophophosphate kinase expression in tumor samples from colorectal cancer patients with clinical resistance to 5-Fluorouracil (2004)

Proc Amer Assoc Cancer Res, Volume 45, 2004

2962 

Despite the fact that 5-fluorouracil (5FU) has been used to treat colorectal cancer for 4 decades, the mechanisms of acquired resistance to this drug in patients is fragmentary, due to lack of tumor samples from patients after relapse from treatment and lack of sensitive assays of relevant enzymes. Short term exposure of HCT-8 colon carcinoma cells to repeated fixed doses of 5FU in vitro resulted in resistance related to this drugs effect on RNA synthesis, while prolonged exposures to low doses of the drug produced resistance related to its effect on thymidylate synthase (Aschele et.al.Cancer Res. 52: 1855-1864.1992). An early study suggested that UMP Kinase, required for the conversion of 5FU to its diphosphate nucleotide, was associated with resistance to this drug in a mouse tumor (Reichard et.al.Cancer Res. 22: 235-243.1962). The recent cloning of the cDNA for this gene has allowed us to develop a sensitive real-time PCR assay to quantitate its expression in tumor cell lines and in patient samples. We show that the HCT-8 cell line resistant to short term exposure to 5FU, has decreased levels of UMP kinase mRNA as determined by Northern blotting, quantitative RT-PCR as well as decreased UMP kinase enzyme activity. There was no change in the Km for UMP between the resistant and the parental cell lines while the Vmax showed a 37% decrease. Restoration of UMP kinase protein by transfection restored 5FU sensitivity to the resistant cells. Importantly, we demonstrate that 7 of 19 tumor samples from hepatic metastasis from patients clinically resistant to “pulse” 5FU regimens, have decreased expression of this enzyme, as compared to 1 of 10 tumor samples of patients not previously treated. The implications are that these patients may still be sensitive to continuous exposure regimens of 5FU (or capecitabine) or 5-fluorodeoxyuridine.
Genetic evidence of susceptible wildlife in SARS-CoV-2 positive samples at the Huanan Wholesale Seafood Market, Wuhan: Analysis and interpretation of data released by the Chinese Center for Disease Control (2023)

Report:<br> Genetic evidence of susceptible wildlife in SARS-CoV-2 positive samples at the Huanan Wholesale Seafood Market, Wuhan: <br> Analysis and interpretation of data released by the Chinese Center for Disease Control
Sequential Therapy with Saratin, Bevacizumab and Ilomastat to Prolong Bleb Function following Glaucoma Filtration Surgery in a Rabbit Model (2015)

To determine if sequential treatment with Bevacizumab (Avastin), a monoclonal, VEGF antibody that blocks angiogenesis; Saratin, a 12 kD polypeptide with anti-inflammatory and anti-thrombotic properties; and Ilomastat, a matrix metalloproteinase (MMP) inhibitor, prolongs bleb life following glaucoma filtration surgery (GFS) in a rabbit model. Thirty-two New Zealand White rabbits (eight rabbits per group) underwent GFS in the left eye. Group 1 received a perioperative injection of both Saratin and Bevacizumab, and later, subconjuctival injections of Ilomastat on days 8 and 15. Group 2 received only Saratin perioperatively, and also received Ilomastat injections on days 8 and 15. Group 3, the negative control, received a single perioperative injection of Balanced Saline Solution (BSS) along with post-operative BSS injections on days 8 and 15. Group 4, the positive control, received topical treatment with Mitomycin-C (MMC) at the time of surgery with no further treatment. Blebs were evaluated by an observer masked to treatment every third day. Histology was obtained on two eyes in each group on post-op day twelve as well as all eyes following bleb failure. Eyes in group 1 had a mean bleb survival time of 29 ± 2.7 days, whereas those in group 2 that received the experimental treatment without Bevacizumab had a mean survival time of 25.5 ± 2.7 days. An ANOVA test showed that the Saratin/Ilomastat/Bevacizumab group demonstrated a significant prolongation of bleb survival compared to the BSS control-mean survival time of 19.7 ±2.7 days-(p = 0.0252) and was not significantly different from the MMC positive control group (p = 0.4238)-mean survival time of 32.5 ± 3.3. From tissue histology at day 12, the four different groups showed marked differences in the cellularity and capsule fibrosis. The MMC eyes showed minimal cellularity, were avascular and had minimal fibrous tissue. BSS group showed high cellularity, moderate to high fibrosis, and thicker and more defined capsules than either of the treatment groups and the positive control. Both the Saratin/Ilomastat/Bevacizumab and Saratin/Ilomastat only eyes showed moderate cellularity with minimal fibrosis, with less cellularity and fibrosis present in the triple treatment group. Sequential therapy with multiple agents, including Bevacizumab, prolonged bleb function following GFS in the rabbit model and were significantly better than the negative BSS control. The experimental group did not show the same surface tissue histological thinning and side effects associated with MMC treatment.
Aryl−Csp3 Bond Rotation Barriers of 2-Aryl Perhydropyrrolo[3,4-c]pyrrole-1,3-diones (2009)

The static and dynamic features of 2-aryl perhydropyrrolo[3,4-c]pyrrole-1,3-diones bearing N-acyl substituents have been assessed with the aid of crystal structures and VT NMR spectra. Rotation barriers for the aryl-Csp(3) bonds in these molecules show surprising variation. Amide-substituted derivatives and fused piperazinediones (six-membered fusion) exhibit very substantial barriers of 14-15 kcal/mol. Fused benzodiazepinediones (seven-membered fusion) have lower but still significant barriers (10 kcal/mol), while fused hydantoins (five-membered fusion) have barriers that are too low to measure by VT NMR (< or =10 kcal/mol). A rationale for the origin of the barriers is presented.
Tap-1 and Tap-2 Gene Therapy Selectively Restores Conformationally Dependent HLA Class I Expression in Type I Diabetic Cells (1995)

Genetic susceptibility to many autoimmune diseases, including insulin-dependent diabetes mellitus (IDDM) is statistically linked to the HLA class II region of chromosome 6. However, a distinguishing feature of patients with HLA class II-linked autoimmune disease is an abnormally low density of conformationally correct, self-peptide filled HLA class I molecules on the lymphocyte cell surface. The transporters associated with antigen processing (Tap-1 and Tap-2) are essential for normal class I expression and presentation of intracellular peptides, and these genes are located within the HLA class II region. The aims of this project were to determine if Tap genes could be implicated in the defective class I expression associated with IDDM by using a novel Epstein-Barr virus (EBV)-mediated gene transfer system to introduce a cloned, normal Tap-2 or Tap-1 gene into B cell lines from normal and IDDM patients and analyzing the effect on conformationally dependent class I expression. The results show that Tap-2 gene transfer in B cells from 40% of randomly selected IDDM patients increased expression of conformationally correct, cell-surface class I molecules to levels comparable with similarly treated B cells from normal control individuals. B cells from another 40% of IDDM patients responded to Tap-1 gene transfer. These effects were specific because B cells from normal individuals did not respond to Tap-1 or Tap-2 gene transfer with increased class I expression, and B cells from IDDM patients responding to Tap-2 gene transfer did not respond to Tap-1 gene transfer and vice versa. Thus, these complementation studies identify distinct, non-overlapping subsets of IDDM patients whose class I defect in B cells can be reversed by Tap-1 or Tap-2 gene transfer. The increase in class I expression induced by Tap gene transfer is associated with a reduction in the number of peptide-empty class I molecules as demonstrated by the response to exogenous peptide loading. Furthermore, the increase in self-peptide filled class I molecules induced by Tap gene transfer into B cells from IDDM patients is associated with restored antigen presentation to autologous T cells. These studies conclude that Tap gene dysfunctions may contribute to the defect in class I phenotype and antigen presentation demonstrated by IDDM patients. Defective presentation of self-peptides by antigen presenting cells can lead to the failed T cell education and tolerance to self antigens evident in IDDM. These studies functionally identify HLA class II region genes that contribute to an immunologic defect in IDDM.
Trimethoprim Derivatives for Labeling Dihydrofolate Reductase Fusion Proteins in Living Mammalian Cells (2008)

This chapter contains sections titled: Introduction Preparation of E. coli Expression Vectors Synthesis of Fluorescent Trimethoprim Derivatives Cell Growth and Transfection Protein Labeling and Microscopy Results and Discussion Conclusion References
Assessing the Impacts of Dedicated CAV Lanes in a Connected Environment: An Application of Intelligent Transport Systems in Corktown, Michigan (2021)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;The interaction of Connect and Automated vehicles (CAV) with regular vehicles in the traffic stream has been extensively researched. Most studies, however, focus on calibrating driver behavior models for CAVs based on various levels of automation and driver aggressiveness. Other related studies largely focus on the coordination of CAVs and infrastructure like traffic signals to optimize traffic. However, the effects of different strategic flow management of CAVs in the traffic stream in the comparative scenario-based analysis is understudied. Thus, this study develops a framework and simulations for integrating CAVs in a corridor section. We developed a calibrated model with CAVs for a corridor section in Corktown, Michigan, and simulate how dedicated CAV lane operations can be implemented without significant change in existing infrastructure. We create a simulation process that includes identifying hotspots using a macroscopic model for Southeast Michigan and focus on Corktown as an important section due to Ford’s redevelopment in the area. We further develop different strategies at the microscopic level where we include a suite of options such as converting a curbside lane to CAV lane only; using a center lane as a dedicated CAV lane; converting curbside parking into a dedicated CAV lane; and integrated novel signal optimization methods. Findings indicate that smart infrastructure re-configuration, such as changing signal timing and adding left-turn lanes, can solve some issues, but an omnipresent problem is regular vehicles turning across CAV lanes, which creates its congestion and reduces CAV lane performance. There is no turnkey CAV lane solution, but a Design of Experiment (DoE) based study can help find a solution which factors in the local conditions.&lt;/div&gt;&lt;/div&gt;