gebhart/patrepeval huggingface dataset:
Quaternary Sputtered Cu(In,Ga)Se2Absorbers for Photovoltaics: A Review (2016)

Quaternary sputtering is a promising alternative to more established deposition methods for the fabrication of Cu(In,Ga)Se <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> (CIGS) thin films for photovoltaics (PV). In this technique, a single sputtering target containing all four constituents is employed to deposit the CIGS film. Quaternary sputtering offers several advantages over other deposition methods, including excellent uniformity over large areas, high material usage, and less reliance on toxic Se precursors such as H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Se. Despite these advantages, several drawbacks remain. To date, devices fabricated by quaternary sputtering without additional selenization have been limited in efficiency to about 11%, and realizing bandgap grading in order to match the performance of the best evaporated devices presents a challenge. We discuss the prospects for quaternary sputtering as a fabrication technique for CIGS and highlight areas of research that may result in improved performance. Target fabrication and usage is reviewed. We also present results for films and devices including data for the optical constants of sputtered CIGS. Some recent previously unpublished results, including a study of impurities in CIGS sputtering targets and the first demonstration of a CIGS device on a flexible glass substrate, are discussed
Abstract 3624: Circulating sEGFR arises through a fibronectin/integrin-regulated proteolytic cleavage event: Analogy to HER2 shedding (2012)

Abstract A circulating isoform of EGFR has been identified as an emerging serum biomarker in cancer patients. Serum concentrations of EGFR have been evaluated as screening, diagnostic, prognostic, and theragnostic markers for diverse human malignancies, including breast, ovarian, endometrial, colorectal, and lung cancer. Yet full-length EGFR is rarely shed from normal or malignant cells. Here we demonstrate that an alternately spliced EGFR isoform, termed ‘sEGFR,’ gives rise to the circulating sEGFR protein through proteolytic cleavage of a cell surface precursor. This cleavage event is inhibited by fibronectin and stimulated by both an anti-Δ5/α1 integrin antibody and the metalloprotease activator 4-aminophenylmercuric acetate. Preliminary results identify ADAM17/TACE as at least one mediator of sEGFR shedding. Shed sEGFR binds to EGF with high affinity. Two FDA-approved therapeutic anti-EGFR antibodies, cetuximab (Erbitux) and panitumumab (Vectibix), inhibit shedding of sEGFR, implicating sEGFR as a potential alternative target for these antibodies, consistent with previous studies indicating that baseline serum sEGFR concentrations may predict responsiveness to anti-EGFR-targeted therapy. These observations bear striking similarity to aspects of trastuzumab regulation of HER2, shedding, and, by analogy, may have implications for the design of future clinical trials using EGFR-directed therapeutics, including cetuximab and panitumimab. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3624. doi:1538-7445.AM2012-3624
Subthreshold SPICE Model Optimization (2011)

The first step in integrated circuit design is the simulation of said design in software to verify proper functionally and design requirements. Properties of the process are provided by fabrication foundries in the form of SPICE models. These SPICE models contain the electrical data and physical properties of the basic circuit elements. A limitation of these models is that the data collected by the foundry only accurately model the saturation region. This is fine for most users, but when operating devices in the subthreshold region they are inadequate for accurate simulation results. This is why optimizing the current SPICE models to characterize the subthreshold region is so important. In order to accurately simulate this region of operation, MOSFETs of varying widths and lengths are fabricated and the electrical test data is collected. From the data collected the parameters of the model files are optimized through parameter extraction rather than curve fitting. With the completed optimized models the circuit designer is able to simulate circuit designs for the sub threshold region accurately.
Synovial Autoreactive T Cells in Rheumatoid Arthritis Resist IDO-Mediated Inhibition (2006)

A hallmark of T cell-mediated autoimmunity is the persistence of autoreactive T cells. However, it remains to elucidate the manner in which synovial T cells are sustained in patients with rheumatoid arthritis (RA). We found that dendritic cells (DC) and tissues from the synovial joints of RA patients expressed higher levels of IDO than DC from healthy donors. Interestingly, T cells derived from the joint synovial fluid (SF) of RA patients proliferated in response to either autologous or allogeneic IDO-positive DC, an outcome that was not affected by the addition of IDO inhibitor 1-methyl-D-tryptophan (1-MT). In contrast, addition of 1-MT to the culture stimulated with allogeneic or autologous IDO-positive DC significantly enhanced the proliferation of T cells derived from peripheral blood of healthy donors or from peripheral blood of RA patients. Furthermore, we found that functionally active tryptophanyl-tRNA-synthetase (TTS) was significantly elevated in T cells derived from the SF of RA patients, leading to enhanced storage of tryptophan in T cells and to subsequent resistance to IDO-mediated deprivation of tryptophan. The RA SF enhancement of TTS expression in T cells was blocked by mAb to IFN-gamma and TNF-alpha. These results suggest that the resistance of T cells to IDO-mediated deprivation of tryptophan represents a mechanism by which autoreactive T cells are sustained in vivo in RA patients. Specifically, blocking of the up-regulation of TTS expression in T cells presents an avenue for development of a novel therapeutic approach to treatment of RA.
Developing antisense oligonucleotides for a TECPR2 mutation-induced, ultra-rare neurological disorder using patient-derived cellular models (2022)

Mutations in the <i>TECPR2</i> gene are the cause of an ultra-rare neurological disorder characterized by intellectual disability, impaired speech, motor delay, and hypotonia evolving to spasticity, central sleep apnea, and premature death (SPG49 or HSAN9; OMIM: 615031). Little is known about the biological function of TECPR2, and there are currently no available disease-modifying therapies for this disease. Here we describe implementation of an antisense oligonucleotide (ASO) exon-skipping strategy targeting <i>TECPR2</i> c.1319delT (p.Leu440Argfs∗19), a pathogenic variant that results in a premature stop codon within <i>TECPR2</i> exon 8. We used patient-derived fibroblasts and induced pluripotent stem cell (iPSC)-derived neurons homozygous for the p.Leu440Argfs∗19 mutation to model the disease <i>in vitro</i>. Both patient-derived fibroblasts and neurons showed lack of TECPR2 protein expression. We designed and screened ASOs targeting sequences across the <i>TECPR2</i> exon 8 region to identify molecules that induce exon 8 skipping and thereby remove the premature stop signal. <i>TECPR2</i> exon 8 skipping restored in-frame expression of a TECPR2 protein variant (TECPR2ΔEx8) containing 1,300 of 1,411 amino acids. Optimization of ASO sequences generated a lead candidate (ASO-005-02) with ∼27 nM potency in patient-derived fibroblasts. To examine potential functional rescue induced by ASO-005-02, we used iPSC-derived neurons to analyze the neuronal localization of TECPR2ΔEx8 and showed that this form of TECPR2 retains the distinct, punctate neuronal expression pattern of full-length TECPR2. Finally, ASO-005-02 had an acceptable tolerability profile <i>in vivo</i> following a single 20-mg intrathecal dose in cynomolgus monkeys, showing some transient non-adverse behavioral effects with no correlating histopathology. Broad distribution of ASO-005-02 and induction of <i>TECPR2</i> exon 8 skipping was detected in multiple central nervous system (CNS) tissues, supporting the potential utility of this therapeutic strategy for a subset of patients suffering from this rare disease.
Progress in Large Integration Scale Circuits in SiON Technology (2007)

In this contribution the potentialities and the limitation of the silicon oxynitride (SiON) technology are reviewed and a number of integrated optical circuits and devices are presented. Mach-Zehnder, ring resonators, variable bandwidth filters, ring resonators based cross-bar matrices and a DQPSK receiver with interleaver and variable attenuators have been realized, characterized and tested in a 10 Gbit/s WDM system.
Evaluation of Cylinder State Estimator using Fuel Evaporation Assessment in a PFI Methanol HD SI Engine (2022)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Modern spark-ignited (SI) engines offer excellent emission reduction when operated with a stoichiometric mixture and a three-way catalytic converter. A challenge with stoichiometric compared to diluted operation is the knock propensity due to the high reactivity of the mixture. This limits the compression ratio, thus reducing engine efficiency and increasing exhaust temperature. The current work evaluated a model of conditions at inlet valve closing (IVC) and top dead center (TDC) for steady state operation. The IVC temperature model is achieved by a cycle-to-cycle resolved residual gas fraction estimator. Due to the potential charge cooling effect from methanol, a method was proposed to determine the fraction of fuel sourced from a wall film. Determining the level of charge cooling is important as it heavily impacts the IVC and TDC temperatures. This method is based on air flow measurement and comparing information from the compression event during a transient from fired to motored conditions, while keeping the intake density constant. Experiments were conducted on a high compression ratio (14:1) heavy duty (HD) single cylinder research engine (SCRE). The fuel was methanol, injected via port fuel injection (PFI). The results indicate that the latent heat of vaporization of the fuel is far from being fully utilized, due to inherent design limitations of the intake system. It was also found that charge cooling could be altered by utilizing features of the swirl optimized cylinder head, while the same features also hinted that some stratification was possible. Accurate estimation of the IVC state and the later thermodynamic evolution is important for any closed cycle analysis. The result from the IVC and TDC condition estimators indicate that it is possible to capture expected trends.&lt;/div&gt;&lt;/div&gt;
Simvastatin Inhibits the Activation of p21rasand Prevents the Loss of Dopaminergic Neurons in a Mouse Model of Parkinson's Disease (2009)

Parkinson's disease (PD) is second only to Alzheimer's disease as the most common devastating human neurodegenerative disorder. Despite intense investigation, no interdictive therapy is available for PD. We investigated whether simvastatin, a Food and Drug Administration-approved cholesterol-lowering drug, could protect against nigrostriatal degeneration after 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) intoxication to model PD in mice. First, MPP(+) induced the activation of p21(ras) and nuclear factor-kappaB (NF-kappaB) in mouse microglial cells. Inhibition of MPP(+)-induced activation of NF-kappaB by Deltap21(ras), a dominant-negative mutant of p21(ras), supported the involvement of p21(ras) in MPP(+)-induced microglial activation of NF-kappaB. Interestingly, simvastatin attenuated activation of both p21(ras) and NF-kappaB in MPP(+)-stimulated microglial cells. Consistently, we found a very rapid activation of p21(ras) in vivo in the substantia nigra pars compacta of MPTP-intoxicated mice. However, after oral administration, simvastatin entered into the nigra, reduced nigral activation of p21(ras), attenuated nigral activation of NF-kappaB, inhibited nigral expression of proinflammatory molecules, and suppressed nigral activation of glial cells. These findings paralleled dopaminergic neuronal protection, normalized striatal neurotransmitters, and improved motor functions in MPTP-intoxicated mice. Similarly, pravastatin, another cholesterol-lowering drug, suppressed microglial inflammatory responses and protected dopaminergic neurons in MPTP-intoxicated mice, but at levels less than simvastatin. Furthermore, both the statins administered 2 d after initiation of the disease were still capable of inhibiting the demise of dopaminergic neurons and concomitant loss of neurotransmitters, suggesting that statins are capable of slowing down the progression of neuronal loss in the MPTP mouse model. Therefore, we conclude that statins may be of therapeutic benefit for PD patients.
Strong exciton-photon coupling with colloidal quantum dots in a high-Q bilayer microcavity (2011)

We demonstrate evanescently coupled bilayer microcavities with Q-factors exceeding 250 fabricated by a simple spin-coating process. The cavity architecture consists of a slab waveguide lying upon a low refractive index spacer layer supported by a glass substrate. For a lossless guide layer, the cavity Q depends only on the thickness of the low index spacer and in principle can reach arbitrarily high values. We demonstrate the versatility of this approach by constructing cavities with a guide layer incorporating CdSe/ZnS core/shell quantum dots, where we observe strong coupling and hybridization between the 1S(e)-1S3/2(h) and 1S(e)-2S3/2(h) exciton states mediated by the cavity photon. This technique greatly simplifies the fabrication of high-Q planar microcavities for organic and inorganic quantum dot thin films and opens up new opportunities for the study of nonlinear optical phenomena in these materials.
Lignocellulose breakdown and utilization by fungi (1999)

Fungi are the main decomposers of dead plant material and many fungal species are known as plant pathogens. Saprophytic fungi are able to get energy and nutrients from a large variety of organic compounds and therefore they are found in practically all terrestrial habitats in which there is life. Fungi can colonize new locations efficiently by spreading through their spores. A saprophytic fungus is always competing for nutrients against bacteria and other fungal species in its habitat. In many cases fungi benefit from their ability to degrade complex plant polymers more completely than bacteria and they also compete by antagonism against other saprophytic microbes. Yeasts are not generally able to decompose plant cell walls with polymeric components and thus saprophytic fungi are mainly filamentous. Saprophytic fungal species can be found in all fungal classes.
The Role of Reverberation and Magnitude Spectra of Direct Parts in Contralateral and Ipsilateral Ear Signals on Perceived Externalization (2019)

Several studies show that the reverberation and spectral details in direct sounds are two essential cues for perceived externalization of virtual sound sources in reverberant environments. The present study investigated the role of these two cues in contralateral and ipsilateral ear signals on perceived externalization of headphone-reproduced binaural sound images at different azimuth angles. For this purpose, seven pairs of non-individual binaural room impulse responses (BRIRs) were measured at azimuth angles of −90°, −60°, −30°, 0°, 30°, 60°, and 90° in a listening room. The magnitude spectra of direct parts were smoothed, and the reverberation was removed, either in left or right ear BRIRs. Such modified BRIRs were convolved with a speech signal, and the resulting binaural sounds were presented over headphones. Subjects were asked to assess the degree of perceived externalization for the presented stimuli. The result of the subjective listening experiment revealed that the magnitude spectra of direct parts in ipsilateral ear signals and the reverberation in contralateral ear signals are important for perceived externalization of virtual lateral sound sources.
Euchromatin and Pericentromeric Heterochromatin: Comparative Composition in the Tomato Genome (2006)

Eleven sequenced BACs were annotated and localized via FISH to tomato pachytene chromosomes providing the first global insights into the compositional differences of euchromatin and pericentromeric heterochromatin in this model dicot species. The results indicate that tomato euchromatin has a gene density (6.7 kb/gene) similar to that of Arabidopsis and rice. Thus, while the euchromatin comprises only 25% of the tomato nuclear DNA, it is sufficient to account for approximately 90% of the estimated 38,000 nontransposon genes that compose the tomato genome. Moreover, euchromatic BACs were largely devoid of transposons or other repetitive elements. In contrast, BACs assigned to the pericentromeric heterochromatin had a gene density 10-100 times lower than that of the euchromatin and are heavily populated by retrotransposons preferential to the heterochromatin-the most abundant transposons belonging to the Jinling Ty3/gypsy-like retrotransposon family. Jinling elements are highly methylated and rarely transcribed. Nonetheless, they have spread throughout the pericentromeric heterochromatin in tomato and wild tomato species fairly recently-well after tomato diverged from potato and other related solanaceous species. The implications of these findings on evolution and on sequencing the genomes of tomato and other solanaceous species are discussed.
Distributed beamforming with software-defined radios: Frequency synchronization and digital feedback (2012)

We present an implementation of distributed transmit beamforming using software-defined radios. The transmit nodes synchronize in carrier frequency using a pilot signal sent by a master node, and employ feedback from the receiver to adjust their carrier phases so as to add up coherently at the receiver. Our implementation advances the state of the art for all-wireless distributed beamforming in two important ways. The first is the implementation of extended Kalman filters for frequency synchronization at the slave nodes, which is shown to be effective despite the high local oscillator (LO) offsets typical of software-defined radios, and the low duty cycle of the pilot transmitted by the master node. The second advance is the implementation of the well-known one bit feedback scheme for phase adjustment using digital feedback from the receiver. We present experimental results that show the efficacy of our implementation for frequency synchronization and beamforming.
Thiomethyltetrazines are Reversible Covalent Cysteine Warheads whose Dynamic Behavior can be "Switched off” via Bioorthogonal Chemistry Inside Live Cells (2023)

Electrophilic small molecules that can reversibly modify proteins are of growing interest in drug discovery. However, the ability to study reversible covalent probes in live cells can be limited by their reversible reactivity after cell lysis and in proteomic workflows, leading to scrambling and signal loss. We describe how thiomethyltetrazines function as reversible covalent warheads for cysteine modification and this dynamic labeling behavior can be "switched off” via bioorthogonal chemistry inside live cells. Simultaneously, the tetrazine serves as bioorthogonal reporter enabling the introduction of tags for fluorescent imaging or affinity purification. Thiomethyltetrazines can label isolated proteins, proteins in cellular lysates, and proteins in live cells with second-order rate constants spanning two orders of magnitude (k2 1–100 M-1s-1). Reversible modification by thiomethyltetrazines can be switched off upon the addition of trans-cyclooctene in live cells, converting the dynamic thiomethyltetrazine tag into a Diels-Alder adduct which is stable to lysis and proteomic workflows. Time-course quenching experiments were used to demonstrate temporal control over electrophilic modification. Moreover, it is shown that “locking in” the tag through Diels-Alder chemistry enables the identification of protein targets that are otherwise lost during sample processing. Three probes were further evaluated to identify unique pathways in a live-cell proteomic study. We anticipate that discovery efforts will be enabled by the trifold function of thiomethyltetrazines as electrophilic warheads, bioorthogonal reporters, and switches for “locking in” stability.
Boosting with AIDSVAX B/E Enhances Env Constant Region 1 and 2 Antibody-Dependent Cellular Cytotoxicity Breadth and Potency (2019)

Induction of protective antibodies is a critical goal of HIV-1 vaccine development. One strategy is to induce nonneutralizing antibodies (NNAbs) that kill virus-infected cells, as these antibody specificities have been implicated in slowing HIV-1 disease progression and in protection. HIV-1 Env constant region 1 and 2 (C1C2) monoclonal antibodies (MAbs) frequently mediate potent antibody-dependent cellular cytotoxicity (ADCC), making them an important vaccine target. Here, we explore the effect of delayed and repetitive boosting of RV144 vaccine recipients with AIDSVAX B/E on the C1C2-specific MAb repertoire. It was found that boosting increased clonal lineage-specific ADCC breadth and potency. A ligand crystal structure of a vaccine-induced broad and potent ADCC-mediating C1C2-specific MAb showed that it bound a highly conserved Env gp120 epitope. Thus, boosting to affinity mature these types of IgG C1C2-specific antibody responses may be one method by which to make an improved HIV vaccine with higher efficacy than that seen in the RV144 trial.<b>IMPORTANCE</b> Over one million people become infected with HIV-1 each year, making the development of an efficacious HIV-1 vaccine an important unmet medical need. The RV144 human HIV-1 vaccine regimen is the only HIV-1 clinical trial to date to demonstrate vaccine efficacy. An area of focus has been on identifying ways by which to improve upon RV144 vaccine efficacy. The RV305 HIV-1 vaccine regimen was a follow-up boost of RV144 vaccine recipients that occurred 6 to 8 years after the conclusion of RV144. Our study focused on the effect of delayed boosting in humans on the vaccine-induced Env constant region 1 and 2 (C1C2)-specific antibody repertoire. It was found that boosting with an HIV-1 Env vaccine increased C1C2-specific antibody-dependent cellular cytotoxicity potency and breadth.
SAR Studies on Carboxylic Acid Series M<sub>1</sub> Selective Positive Allosteric Modulators (PAMs) (2014)

There is mounting evidence from preclinical and early proof-of-concept studies suggesting that selective modulation of the M1 muscarinic receptor is efficacious in cognitive models of Alzheimer's disease (AD). A number of nonselective M1 muscarinic agonists have previously shown positive effects on cognitive function in AD patients, but were limited due to cholinergic adverse events thought to be mediated by pan activation of the M2 to M5 sub-types. Thus, there is a need to identify selective activators of the M1 receptor to evaluate their potential in cognitive disorders. One strategy to confer selectivity for M1 is the identification of allosteric agonists or positive allosteric modulators, which would target an allosteric site on the M1 receptor rather than the highly conserved orthosteric acetylcholine binding site. BQCA has been identified as a highly selective carboxylic acid M1 PAM and this review focuses on an extensive lead optimization campaign undertaken on this compound.