gebhart/patrepeval huggingface dataset:
Expression of a stress- and starvation-induced dps/pexB-homologous gene is controlled by the alternative sigma factor sigmaB in Bacillus subtilis (1997)

SigmaB-dependent general stress proteins (Gsps) of Bacillus subtilis are essential for the development of glucose-starvation-induced cross-resistance to oxidative challenge. However, the proteins directly involved in this nonspecific resistance to oxidative stress have to be identified. We found that one prominent Gsp displayed strong sequence similarity to the previously characterized oxidative-stress-inducible MrgA protein of B. subtilis and to the starvation-induced Dps/PexB protein of Escherichia coli. We therefore designated this prominent Gsp Dps. While MrgA belongs to the peroxide-stress-inducible proteins needed for the H2O2-inducible adaptive response to oxidative stress, Dps belongs to the proteins induced by heat, salt, or ethanol stress and after starvation for glucose but not by a sublethal oxidative challenge. Primer extension experiments identified two overlapping promoters upstream of the coding region of dps, one being sigmaB dependent (PB) and the other being sigmaB independent (P1). Both promoters contribute to the basal level of dps during growth. After stress or during entry into the stationary phase, transcription from PB strongly increased whereas transcription from P1 decreased. Mutant strains lacking Dps completely failed to develop glucose-starvation-induced resistance to oxidative stress. These results confirm our suggestion that sigmaB-dependent general stress proteins of B. subtilis are absolutely required for the development of nonspecific resistance to oxidative stress.
Integrated Optical Devices Based On Silica Waveguide Technologies (1988)

A wide variety of integrated optical devices was developed based on silica glass waveguide technologies. High performance waveguide with low loss and well-controlled configuration is formed on silicon substrate by a combination of flame hydrolysis deposition, photolithographic and reactive ion etching processes. This waveguide technology also has the great advantage of guiding groove structure for hybridizing optical fibers and chips onto the waveguide. Based on this silica glass waveguide technology, several types of integrated optical devices such as branching, WDM, polarization control, resonance and switching devices have been constructed and tested.
Cost and Life-Cycle Greenhouse Gas Implications of Integrating Biogas Upgrading and Carbon Capture Technologies in Cellulosic Biorefineries (2020)

Gaseous streams in biorefineries have been undervalued and underutilized. In cellulosic biorefineries, coproduced biogas is assumed to be combusted alongside lignin to generate process heat and electricity. Biogas can instead be upgraded to compressed biomethane and used as a transportation fuel. Capturing CO<sub>2</sub>-rich streams generated in biorefineries can also contribute to greenhouse gas (GHG) mitigation goals. We explore the economic and life-cycle GHG impacts of biogas upgrading and CO<sub>2</sub> capture and storage (CCS) at ionic liquid-based cellulosic ethanol biorefineries using biomass sorghum. Without policy incentives, biorefineries with biogas upgrading systems can achieve a comparable minimum ethanol selling price (MESP) and reduced GHG footprint ($1.38/liter gasoline equivalent (LGE) and 12.9 gCO<sub>2e</sub>/MJ) relative to facilities that combust biogas onsite ($1.34/LGE and 24.3 gCO<sub>2e</sub>/MJ). Incorporating renewable identification number (RIN) values advantages facilities that upgrade biogas relative to other options (MESP of $0.72/LGE). Incorporating CCS increases the MESP but dramatically decreases the GHG footprint (-21.3 gCO<sub>2e</sub>/MJ for partial, -110.7 gCO<sub>2e</sub>/MJ for full CCS). The addition of CCS also decreases the cost of carbon mitigation to as low as $52-$78/t CO<sub>2</sub>, depending on the assumed fuel selling price, and is the lowest-cost option if both RIN and California's Low Carbon Fuel Standard credits are incorporated.
Clinical-scale Lentiviral Vector Transduction of PBL for TCR Gene Therapy and Potential for Expression in Less-differentiated Cells (2008)

In human gene therapy applications, lentiviral vectors may have advantages over gamma-retroviral vectors because of their ability to transduce nondividing cells, their resistance to gene silencing, and a lack of integration site preference. In this study, we used VSV-G pseudotype third generation lentiviral vectors harboring specific antitumor T-cell receptor (TCR) to establish clinical-scale lentiviral transduction of peripheral blood lymphocyte (PBL). Spinoculation (1000g, 32 degrees C for 2 h) in the presence of protamine sulfate represents the most efficient and economical approach to transduce a large number of PBLs compared with RetroNectin-based methods. Up to 20 million cells per well of a 6-well plate were efficiently transduced and underwent an average 50-fold expansion in 2 weeks. TCR transduced PBL-mediated specific antitumor activities including interferon-gamma release and cell lysis. Compared with gamma-retroviral vectors, the TCR transgene could be preferentially expressed on a less-differentiated cell population.
Photosynthesis-deficient Mutants of Chlamydomonas reinhardii with Associated Light-sensitive Phenotypes (1981)

A series of non-photoautotrophic mutants of Chlamydomonas reinhardii was isolated by replica-plating mutagenized cells which had been grown in the dark. Many of these acetate-requiring mutants are photosensitive, showing poor growth on acetate medium in the light, but normal growth in the dark. Biochemical characterization showed that the photosensitive mutants all had specific lesions in photosynthesis or photosynthetic pigment accumulation. The acetate-requiring mutants which were not photosensitive were all able to fix CO(2). Among the light-sensitive mutants are 15 which show uniparental inheritance. These include six with specific lesions in photosystem II and one with an altered large subunit of ribulose-1,5-bisphosphate carboxylase. Since these two classes of uniparental mutants have been rare or not previously reported, it seems likely that photosensitivity is an important factor which limited their detection in previous mutant isolation experiments.
Highly attenuated poxvirus vectors: NYVAC, ALVAC and TROVAC. (1995)

Three highly attenuated and efficacious poxvirus-based vectors, NYVAC, ALVAC and TROVAC, are available for targeted applications as recombinant vaccines in both human and veterinary medicine. The attenuated phenotype of the three vectors is consistent with safe use for vaccination purposes, for the vaccinee, for unvaccinated contacts, and for introduction into the environment. The precise deletion of virulence and host range genes in the NYVAC vector precludes reversion to the virulent phenotype by back mutation. Dissemination of recombinant vaccines based on the NYVAC, ALVAC and TROVAC vectors is highly diminished, because of the genetic engineering in NYVAC and the natural attenuated phenotype of ALVAC and TROVAC. Studies have demonstrated that these recombinant vectors are genetically and phenotypically stable after serial passage in vitro as well as in vivo. NYVAC, ALVAC and TROVAC vectors are the only three poxvirus-based vectors that are classified as BSL1 agents.
Programming by sketching for bit-streaming programs (2005)

This paper introduces the concept of programming with sketches , an approach for the rapid development of high-performance applications. This approach allows a programmer to write clean and portable reference code, and then obtain a high-quality implementation by simply sketching the outlines of the desired implementation. Subsequently, a compiler automatically fills in the missing details while also ensuring that a completed sketch is faithful to the input reference code. In this paper, we develop StreamBit as a sketching methodology for the important class of bit-streaming programs (e.g., coding and cryptography).A sketch is a partial specification of the implementation, and as such, it affords several benefits to programmer in terms of productivity and code robustness. First, a sketch is easier to write compared to a complete implementation. Second, sketching allows the programmer to focus on exploiting algorithmic properties rather than on orchestrating low-level details. Third, a sketch-aware compiler rejects "buggy" sketches, thus improving reliability while allowing the programmer to quickly evaluate sophisticated implementation ideas.We evaluated the productivity and performance benefits of our programming methodology in a user-study, where a group of novice StreamBit programmers competed with a group of experienced C programmers on implementing a cipher. We learned that, given the same time budget, the ciphers developed in StreamBit ran 2.5x faster than ciphers coded in C. We also produced implementations of DES and Serpent that were competitive with hand optimized implementations available in the public domain.
Quantitative diffuse optical tomography for small animals using an ultrafast gated image intensifier (2008)

The quantitative accuracy of fluorescence and bioluminescence imaging of small animals can be improved by knowledge of the in situ optical properties of each animal. Obtaining in situ optical property maps is challenging, however, due to short propagation distances, requirements for high dynamic range, and the need for dense spatial, temporal, and spectral sampling. Using an ultrafast gated image intensifier and a pulsed laser source, we have developed a small animal diffuse optical tomography system with multiple synthetic modulation frequencies up to >1 GHz. We show that amplitude and phase measurements with useful contrast-to-noise ratios can be obtained for modulation frequencies over the range of approximately 250 to 1250 MHz. Experiments with tissue simulating phantoms demonstrate the feasibility of reconstructing the absorption and scattering optical properties in a small animal imaging system.
Fiber optic photoacoustic device: high efficiency and wide bandwidth ultrasonic source (2002)

General purpose fiber optic photacoustic source is proposed. The working principle is based on thermal conversion of laser pulses into a metallic film evaporated directly onto the tip of an fiber optic. It will be demonstrated both theoretically and experimentally, that metallization improves the spectral characteristics of the produced ultrasound with respect to direct irradiation of a liquid or biological tissue. In effect the proposed source exhibits a flat band, nearly ideal, at high frequencies. In addition, it will be shown that the metallization considerably improves photoacoustic conversion efficiency.
STAMP1 Is Both a Proliferative and an Antiapoptotic Factor in Prostate Cancer (2010)

STAMP1 is predicted to encode a six-transmembrane protein whose expression is highly prostate enriched and is deregulated in prostate cancer. However, the biological role of STAMP1 in prostate cancer cells, or its expression profile at the protein level, is unknown. Here, we find that ectopic expression of STAMP1 significantly increased proliferation of DU145 prostate cancer cells as well as COS-7 cells in vitro; conversely, small interfering RNA-mediated knockdown of STAMP1 expression in LNCaP cells inhibited cell growth and, at least partially, induced cell cycle arrest. In parallel, there were alterations in cell cycle-regulatory gene expression. Knockdown of STAMP1 expression in LNCaP cells also induced significant apoptosis under basal conditions as well as in response to tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) alone, or TRAIL + AKT inhibitor LY294002, previously established apoptotic agents in LNCaP cells. Consistently, LNCaP cells with short hairpin RNA-mediated knockdown of STAMP1 were dramatically retarded in their ability to grow as xenografts in nude mice. Interestingly, activation of extracellular signal-regulated kinase, which has previously been implicated in prostate cancer progression, was significantly increased on ectopic expression of STAMP1 in DU145 cells and, conversely, was strongly downregulated on STAMP1 knockdown in LNCaP cells. In the normal prostate, STAMP1 protein is localized to the cytosol and the cell membrane of the prostate epithelial cells; furthermore, its expression is increased in prostate cancer compared with normal prostate. Taken together, these data suggest that STAMP1 is required for prostate cancer growth, which may be a useful target in prostate cancer treatment.
Undersampled projection-reconstruction imaging for time-resolved contrast-enhanced imaging (2000)

In time-resolved contrast-enhanced 3D MR angiography, spatial resolution is traded for high temporal resolution. A hybrid method is presented that attempts to reduce this tradeoff in two of the spatial dimensions. It combines an undersampled projection acquisition in two dimensions with variable rate k-space sampling in the third. Spatial resolution in the projection plane is determined by readout resolution and is limited primarily by signal-to-noise ratio. Oversampling the center of k-space combined with temporal k-space interpolation provides time frames with minimal venous contamination. Results demonstrating improved resolution in phantoms and volunteers are presented using angular undersampling factors up to eight with acceptable projection reconstruction artifacts.
Executive and Attention Functioning Among Children in the PANDAS Subgroup (2008)

Evidence from past studies indicates that adults and children with Obsessive-Compulsive Disorder (OCD) and Tourette syndrome (TS) experience subtle neuropsychological deficits. Less is known about neuropsychological functioning of children and adolescents with a symptom course consistent with the PANDAS (Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal infection) subgroup of OCD and tics. To provide such information, we administered three tests of attention control and two of executive function to 67 children and adolescents (ages 5-16) diagnosed with OCD and/or tics and a symptom course consistent with the PANDAS subgroup and 98 healthy volunteers (HV) matched by age, sex, and IQ. In a paired comparison of the two groups, the PANDAS subjects were less accurate than HV in a test of response suppression. Further, in a two-step linear regression analysis of the PANDAS group in which clinical variables were added stepwise into the model and in the second step matching variables (age, sex, and IQ) were added, IQ emerged as a predictor of performance on this task. In the same analysis, ADHD diagnosis and age emerged as predictors of response time in a continuous performance task. Subdividing the PANDAS group by primary psychiatric diagnosis revealed that subjects with TS or OCD with tics exhibited a longer response time compared to controls than subjects with OCD only, replicating previous findings within TS and OCD. This study demonstrates that children with PANDAS exhibit neuropsychological profiles similar to those of their primary psychiatric diagnosis.
NEDD4: A Promising Target for Cancer Therapy (2014)

The Neuronally expressed developmentally downregulated 4 (NEDD4), functioning largely as an E3 ubiquitin ligase, has been demonstrated to play a critical role in the development and progression of human cancers. In this review, to understand the regulatory mechanism(s) of NEDD4 as well as the signaling pathways controlled by NEDD4, we briefly describe the NEDD4 upstream regulators and its downstream ubiquitin substrates. Moreover, we further discuss its oncogenic roles in human malignancies. Therefore, targeting NEDD4 could be a potential therapeutic strategy for treatment of human cancers.
Design of synthetic gene libraries encoding random sequence proteins with desired ensemble characteristics (1993)

Libraries of random sequence polypeptides are useful as sources of unevolved proteins, novel ligands, and potential lead compounds for the development of vaccines and therapeutics. The expression of small random peptides has been achieved previously using DNA synthesized with equimolar mixtures of nucleotides. For many potential uses of random polypeptide libraries, concerns such as avoiding termination codons and matching target amino acid compositions make more complex designs necessary. In this study, three mixtures of nucleotides, corresponding to the three positions in the codon, were designed such that semirandom DNA synthesized by repeated cycles of the three mixtures created an open reading frame encoding random sequence polypeptides with desired ensemble characteristics. Two methods were used to design the nucleotide mixtures: the manual use of a spreadsheet and a refining grid search algorithm. Using design targets of less than or equal to 1% stop codons and an amino acid composition based on the average ratios observed in natural, globular proteins, the search methods yielded similar nucleotide ratios, Semirandom DNA, synthesized with a designed, three-residue repeat pattern, can encode libraries of very high diversity and represents an important tool for the construction of random polypeptide libraries.
Structure and function of the sino-atrial node: A review (1986)

Journal Article Structure and function of the sino-atrial node: A review Get access L. N. BOUMAN, L. N. BOUMAN Department of Physiology, University of Amsterdam, Academic Medical CenterMeibergdreef 15, 1105 AZ Amsterdam, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar H. J. JONGSMA H. J. JONGSMA Department of Physiology, University of Amsterdam, Academic Medical CenterMeibergdreef 15, 1105 AZ Amsterdam, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar European Heart Journal, Volume 7, Issue 2, February 1986, Pages 94–104, https://doi.org/10.1093/oxfordjournals.eurheartj.a062047 Published: 01 February 1986 Article history Received: 08 August 1985 Published: 01 February 1986
Complexities of TGF-β Targeted Cancer Therapy (2012)

Many advanced tumors produce excessive amounts of Transforming Growth Factor-β (TGF-β) which, in normal epithelial cells, is a potent growth inhibitor. However, in oncogenically activated cells, the homeostatic action of TGF-β is often diverted along alternative pathways. Hence, TGF-β signaling elicits protective or tumor suppressive effects during the early growth-sensitive stages of tumorigenesis. However, later in tumor development when carcinoma cells become refractory to TGF-β-mediated growth inhibition, the tumor cell responds by stimulating pathways with tumor progressing effects. At late stages of malignancy, tumor progression is driven by TGF-β overload. The tumor microenvironment is a target of TGF-β action that stimulates tumor progression via pro-tumorigenic effects on vascular, immune, and fibroblastic cells. Bone is one of the richest sources of TGF-β in the body and a common site for dissemination of breast cancer metastases. Osteoclastic degradation of bone matrix, which accompanies establishment and growth of metastases, triggers further release of bone-derived TGF-β. This leads to a vicious positive feedback of tumor progression, driven by ever increasing levels of TGF-β released from both the tumor and bone matrix. It is for this reason, that pharmaceutical companies have developed therapeutic agents that block TGF-β signaling. Nonetheless, the choice of drug design and dosing strategy can affect the efficacy of TGF-β therapeutics. This review will describe pre-clinical and clinical data of four major classes of TGF-β inhibitor, namely i) ligand traps, ii) antisense oligonucleotides, iii) receptor kinase inhibitors and iv) peptide aptamers. Long term dosing strategies with TGF-β inhibitors may be ill-advised, since this class of drug has potentially highly pleiotropic activity, and development of drug resistance might potentiate tumor progression. Current paradigms for the use of TGF-β inhibitors in oncology have therefore moved towards the use of combinatorial therapies and short term dosing, with considerable promise for the clinic.
Molecular interactions in intermediate and transition states in the self-stimulated inhibition of enzymes. (1988)

Di-isopropyl fluorophosphate (DFP) and other organophosphorus inhibitors recruit the catalytic power of their target enzymes: the enzyme catalyzes its own irreversible phosphorylation. The magnitude of the catalytic acceleration can approach the factor by which the enzyme catalyzes its own acylation by natural substrates. The reaction of DFP with five serine proteases [chymotrypsin, elastase, dipeptidyl peptidase IV (DP IV), subtilisin and thermitase] exhibits in all cases the same pH dependence as does enzyme acylation by natural substrates. Chymotrypsin and elastase form a "fast" class of enzymes which react about ten-fold faster than the other three "slow" enzymes. All enzymes show k(HOH)/k(DOD) of about 2 but the proton inventory indicates one-proton character for "slow" enzymes and multiproton character for "fast" enzymes. Enthalpies of activation are about 33 kJ/mol (subtilisin, "slow") and 10 kJ/mol (elastase, "fast"). Entropies of activation are about -120 J.T-1.mol-1 (subtilisin, "slow") and -175J.T-1.s-1 (elastase, "fast"; T = temperature in K).
Dependence of Optical Transition Energies on Structure for Single-Walled Carbon Nanotubes in Aqueous Suspension:  An Empirical Kataura Plot (2003)

Spectrofluorimetric data for identified single-walled carbon nanotubes in aqueous SDS suspension have been accurately fit to empirical expressions. These are used to obtain the first model-independent prediction of first and second van Hove optical transitions as a function of structure for a wide range of semiconducting nanotubes. To allow for convenient use in support of spectral studies, the results are presented in equation, graphical, and tabular forms. These empirical findings differ significantly from Kataura plots computed using a simple tight-binding model. It is suggested that the empirically based results should be used in preference to conventional model-based predictions in spectroscopic nanotube research.
Mechanisms of Muscle Wasting — The Role of the Ubiquitin–Proteasome Pathway (1996)

All proteins in mammalian cells are continually being degraded and replaced. In the cytosol, nucleus, and organelles, individual proteins are degraded at widely differing rates; some cytosolic enzymes have half-lives as short as 10 minutes, whereas others last for days. The average rate of protein turnover also varies among tissues; the majority of proteins in rat hepatocytes are replaced every few days, whereas those in muscle or brain cells are replaced every one to two weeks. The amount of intracellular protein turned over each day is quite large. In a normal 70-kg adult, about 280 g of protein is synthesized . . .
New use for an old drug: oral ketamine for treatment-resistant depression (2016)

Treatment-resistant depression (TRD) is a disabling disorder that can interfere with a patient's capacity to understand and participate in medical care and thus negatively impact individual morbidity and mortality. Hospitalised patients with TRD may require rapid alleviation of severe symptomatology, particularly when suicidal or if unable to participate in care decisions. Ketamine is well known for its anaesthetic effects and its use as a 'street' drug; however, its action as an N-methyl-D-aspartate receptor antagonist makes ketamine a potential therapy for TRD. The majority of studies investigating ketamine for TRD have used intravenous drug delivery, demonstrating benefit for rapid alleviation and sustained response of depression symptoms. Oral ketamine for urgent alleviation of TRD symptoms is less reported. We describe rapid alleviation of severe TRD with oral ketamine in a severely ill postoperative hospitalised patient, and review the current literature on 'off-label' use of ketamine for treatment of refractory depression.