gebhart/patrepeval huggingface dataset:
Detection of interleukin 1 alpha and 1 beta in rabbit tissues during endotoxemia using sensitive radioimmunoassays (1991)

Interleukin 1 (IL-1) is a primary mediator of a wide variety of immunologic and inflammatory responses, including reactions to microbial infections. To study this cytokine in an animal model, we have developed specific and sensitive radioimmunoassays for the quantitation of rabbit IL-1 alpha and IL-1 beta. The sensitivity (limit of detection at 95% confidence level) of our assay for IL-1 alpha and 1 beta was 20-40 and 40-80 pg/ml, respectively. Recovery of IL-1 from tissues ranged from 75 to 107%, with a mean of 95% for IL-1 alpha and 89% (range 19-98) for IL-1 beta. We employed these assays in in vivo and in vitro studies. In an in vivo model, we measured the amount of rabbit IL-1 alpha and 1 beta protein present in brain, kidney, liver, lung, muscle, and spleen at various times after the injection of endotoxin. IL-1 was found in all tissues studied but largely in the spleen; IL-1 levels were transient, reaching peak levels by 4 h after injection of endotoxin and rapidly decreasing to low levels by 24 h. In similar in vitro studies, IL-1 alpha levels reached peak elevation 6 h after addition of endotoxin, whereas IL-1 beta was maximal at 24 h. IL-1 alpha was detected in all tissues; IL-1 beta was observed primarily in lung, kidney, and spleen. These studies establish the presence of IL-1 in various tissues during endotoxemia.
Separation and Detection of Carboxylic Acids by Ion Chromatography (1986)

Abstract Common carboxylic acids such as most Krebs cycle acids and other organic acids can be separated by either anion exchange or ion exclusion chromatography and detected by conductivity with chemical suppression. This is accomplished using a new generation of high dynamic capacity suppressors which allow separations on moderate and high capacity resins with concentrated eluants. For both anion exchange and ion exclusion chromatography, cation exchange membrane based suppressors are used to reduce the conductivity of the eluant while enhancing the conductivity of the organic acid analytes. The ability to choose between anion exchange and ion exclusion chromatography expands the versatility of ion chromatography by increasing the analyst's ability to solve co-elution problems.
Draft Genome Sequence of Saccharomyces cerevisiae LW2591Y, a Laboratory Strain for In Vivo Multigene Assemblies (2021)

<i>Saccharomyces cerevisiae</i> is an industrially preferred cell factory for the heterologous production of proteins and chemicals. Here, we present the draft genome sequence of the laboratory strain <i>Saccharomyces cerevisiae</i> LW2591Y, which has been designed for robust and efficient assembly of multigene pathways.
ChemInform Abstract: Asymmetric Synthesis of Highly Functionalized Tetracyclic Indole Bases Embodying the Basic Skeleton of Yohimbine‐ and Reserpine Type Alkaloids. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: SYNTHESIS AND BIOLOGICAL ACTIVITIES OF 5‐(HYDROXYMETHYL, AZIDOMETHYL, OR AMINOMETHYL)‐2′‐DEOXYURIDINE AND RELATED 5′‐SUBSTITUTED ANALOGS (1980)

Abstract Aus dem Bromid (Ia) erhält man das Azid (Ib), das ammoniakalisch zum Azidomethyldesoxyuridin (II) desacetyliert wird.
Abstract 5378: Actions of nanoparticulate tetraiodothyroacetic acid (Nanotetrac) on human prostate carcinoma xenograft growth, vascularity and integrin response to radiation (2014)

Abstract Tetraiodothyroacetic acid (tetrac) covalently bound to a nanoparticle (poly[lactic-co-glycolic acid]) (= Nanotetrac) has anti-cancer and anti-angiogenic properties that are initiated exclusively at a cell surface receptor on integrin αvβ3 of cancer cells and dividing blood vessel cells. The anti-cancer activities are pro-apoptotic by multiple mechanisms, disorder gene expression in multiple cancer cell survival pathways and are radiosensitizing. The anti-angiogenic effects involve disruption of actions of VEGF, bFGF, PDGF and EGF. In the present studies, susceptibility of human prostate cancer cell xenografts to activity of Nanotetrac was determined in grafts in the nude mouse or to the chick chorioallentoic membrane (CAM) model and radiosensitivity was estimated in the CAM system. Androgen-sensitive LNCaP cell xenografts in the CAM exposed to Nanotetrac (1 μg/CAM) showed 40% decreases in tumor weight and vascular branch points and 50% reduction in hemoglobin content at 7 d (P &amp;lt; 0.01). LNCaP xenograft volumes in the male mouse were reduced by 50% at 5 days (P &amp;lt; 0.01), approximating the volume of the tumor cell implant. In vivo imaging system (IVIS) scans of orthotopic androgen-independent PC3 cell xenografts in the nude mouse showed substantial reduction in tumor size vs. control (PBS) at 7 d (50% reduction) and at 17 d (75% reduction) post-implantation. Radiation studies in PC3 cell tumors established in the CAM system demonstrated that within 1 h of exposure to 1-2 Gy radiation, there was apparently defensive activation (assumption of ‘open conformation’) of αvβ3. Receptor activation response to radiation was blocked by Nanotetrac. We have shown in other cancer cell lines that Nanotetrac inhibits repair of radiation-induced double-stranded DNA breaks and propose that, based on the current observations, this DNA repair effect is due to inhibition of radiation-caused activation of αvβ3. In summary, examined in two models and acting at the cell surface, Nanotetrac substantially reduces volume/weight and vascularity of human prostate cancer xenografts. The agent also inhibited activation of integrin αvβ3 that is induced by radiation exposure and is seen to be a component of the radioresistance response. Citation Format: Shaker A. Mousa, Sudha Thangirala, Murat Yalcin, John T. Leith, Aleck Hercbergs, Hung-Yun Lin, Heng-Yuan Tang, Mary K. Luidens, Paul J. Davis. Actions of nanoparticulate tetraiodothyroacetic acid (Nanotetrac) on human prostate carcinoma xenograft growth, vascularity and integrin response to radiation. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5378. doi:10.1158/1538-7445.AM2014-5378
Defining the General Motors 2-Mode Hybrid Transmission (2007)

&lt;div class="htmlview paragraph"&gt;The new General Motors 2-Mode Hybrid transmission for full-size, full-utility SUVs integrates two electro-mechanical power-split operating modes with four fixed gear ratios and provides fuel savings from electric assist, regenerative braking and low-speed electric vehicle operation. A combination of two power-split modes reduces the amount of mechanical power that must be converted to electricity for continuously variable transmission operation. Four fixed gear ratios further improve power transmission capacity and efficiency for especially demanding maneuvers such as full acceleration, hill climbing, and towing. This paper explains the basics of electro-mechanical power-split transmissions, input-split and compound-split modes, and the addition of fixed gear ratios to these modes to create the 2-Mode Hybrid transmission for SUVs.&lt;/div&gt;
Practical benzylation of N,N‐substituted ethanolamines related to chemical warfare agents for analysis and detection by electron ionization gas chromatography–mass spectrometry (2023)

The benzylation of three low molecular weight N,N-disubstituted ethanolamines related to chemical warfare agents (CWAs) to furnish derivatives with improved gas chromatography-mass spectrometry (GC-MS) profiles is described. Due to their low molecular weight and polar nature, N,N-disubstituted ethanolamines are notoriously difficult to detect by routine GC-MS analyses during Organisation for the Prohibition of Chemical Weapons (OPCW) proficiency tests (PTs), particularly in scenarios when they are present at low levels (~1-10 ppm) amidst more abundant interferences. Our studies revealed that the optimal derivatization conditions involved the treatment of the ethanolamine with benzyl bromide in the presence of an inorganic base (e.g., Na<sub>2</sub> CO<sub>3</sub> ) in dichloromethane at 55°C for 2 h. This optimized set of conditions was then successfully applied to the derivatization of N,N-dimethylethanolamine, N,N-diethylethanolamine and N,N-diisopropylethanolamine present separately at 1 and 10 μg/mL concentrations in a glycerol-rich matrix sample featured in the 48th OPCW PT. The benzylated derivatives of the three ethanolamines possessed retention times long enough to clear the massive glycerol-containing matrix interferences. The protocol herein is introduced as an alternative method for derivatization of these CWA and pharmaceutically important species and should find broad applicability in laboratories where routine forensic analysis is carried out.
Functional Nucleic Acids in High Throughput Screening and Drug Discovery (2007)

In vitro selection can be used to generate functional nucleic acids such as aptamers and ribozymes that can recognize a variety of molecules with high affinity and specificity. Most often these recognition events are associated with structural alterations that can be converted into detectable signals. Several signaling aptamers and ribozymes constructed by both design and selection have been successfully utilized as sensitive detection reagents. Here we summarize the development of different types of signaling nucleic acids, and approaches that have been implemented in the screening format.
Dynamic Characterization of Viscoelastic Materials (2004)

&lt;div class="htmlview paragraph"&gt;In this study is analyzed the behavior of the viscoelastic materials used in DDS (double damping system) that transfer the torque from crankshaft to auxiliaries parts of the engine and the mathematic model it was done to validate the behavior of this materials.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The comparative data, from the synthetic and natural rubber, it was done to analyze the behavior of these different materials, since as, their stiffness and damping characteristics.&lt;/div&gt;
Robust Learning-Augmented Caching: An Experimental Study (2021)

Effective caching is crucial for the performance of modern-day computing systems. A key optimization problem arising in caching -- which item to evict to make room for a new item -- cannot be optimally solved without knowing the future. There are many classical approximation algorithms for this problem, but more recently researchers started to successfully apply machine learning to decide what to evict by discovering implicit input patterns and predicting the future. While machine learning typically does not provide any worst-case guarantees, the new field of learning-augmented algorithms proposes solutions that leverage classical online caching algorithms to make the machine-learned predictors robust. We are the first to comprehensively evaluate these learning-augmented algorithms on real-world caching datasets and state-of-the-art machine-learned predictors. We show that a straightforward method -- blindly following either a predictor or a classical robust algorithm, and switching whenever one becomes worse than the other -- has only a low overhead over a well-performing predictor, while competing with classical methods when the coupled predictor fails, thus providing a cheap worst-case insurance.
Analysis of the Functions of Recombination-Related Genes in the Generation of Large Chromosomal Deletions by Loop-Out Recombination in Aspergillus oryzae (2012)

Loop-out-type recombination is a type of intrachromosomal recombination followed by the excision of a chromosomal region. The detailed mechanism underlying this recombination and the genes involved in loop-out recombination remain unknown. In the present study, we investigated the functions of ku70, ligD, rad52, rad54, and rdh54 in the construction of large chromosomal deletions via loop-out recombination and the effect of the position of the targeted chromosomal region on the efficiency of loop-out recombination in Aspergillus oryzae. The efficiency of generation of large chromosomal deletions in the near-telomeric region of chromosome 3, including the aflatoxin gene cluster, was compared with that in the near-centromeric region of chromosome 8, including the tannase gene. In the Δku70 and Δku70-rdh54 strains, only precise loop-out recombination occurred in the near-telomeric region. In contrast, in the ΔligD, Δku70-rad52, and Δku70-rad54 strains, unintended chromosomal deletions by illegitimate loop-out recombination occurred in the near-telomeric region. In addition, large chromosomal deletions via loop-out recombination were efficiently achieved in the near-telomeric region, but barely achieved in the near-centromeric region, in the Δku70 strain. Induction of DNA double-strand breaks by I-SceI endonuclease facilitated large chromosomal deletions in the near-centromeric region. These results indicate that ligD, rad52, and rad54 play a role in the generation of large chromosomal deletions via precise loop-out-type recombination in the near-telomeric region and that loop-out recombination between distant sites is restricted in the near-centromeric region by chromosomal structure.
Figure S1 from Computational Staining of Pathology Images to Study the Tumor Microenvironment in Lung Cancer (2023)

&lt;p&gt;Supplemental Figure S1 Illustration of 100 patches extraction from the Region of Interest (ROI) circled by pathologists.&lt;/p&gt;
The immunosuppressant FK506 increases functional recovery and nerve regeneration following peripheral nerve injury (1994)

Regeneration of peripheral nerve fibers over long distances often requires extended periods of convalescence. Loss to society can be measured in terms of increased health care costs, decreased productivity and, in the case of job-related injuries, larger workers' compensation claims. The availability of drugs to increase axonal regeneration would be beneficial not only to patients but also to society in general by decreasing these costs. In the present paper, we present our initial studies on the regenerative effects of the new immunosuppressive agent FK506. Rats given a sciatic nerve crush (axotomy) received daily subcutaneous injections of FK506 (1.0 mg/kg); axotomized control animals received saline. Clinical signs of recovery in the hind feet were manifested two days earlier in FK506-treated than in saline-treated animals; movement in the toes, and walking on the hind feet and toes were observed at 16 and 17 days, respectively, in saline-treated rats and at 14 and 15 days, respectively, in FK506-treated rats. Measurement of interdigit distances in the hind feet at 18 days following axotomy showed a return toward normal position of the toes (increased interdigit distances) during walking in FK506-treated rats. Light and electron microscopy performed at 18 days following axotomy confirmed the clinical appearance of increased functional recovery in FK506-treated rats. Distal to the crush site, the sciatic nerve and its terminal branches from FK506-treated animals contained more myelinated fibers compared to saline-treated animals; in the soleus nerve, the numbers of myelinated axons was increased 2.75-fold. Taken together, the present results suggest that FK506 enhances recovery of function in the rat by increasing the rate of axonal regeneration following a sciatic nerve crush.
Coumarins from the Fruits of Seseli devenyense (2005)

Eight new coumarins were isolated from the fruits of Seseli devenyense Simonkai. Their structures were established from NMR and mass data and their absolute configurations from chemical degradation correlation reactions. The new structures are the decanoic and dodecanoic esters of (+)-lomatin (3, 4), the decanoates of (+)-cis-khellactone at positions 4' (5) and 3' (6) as well as the 2'S epimer of 8-(2,3-dihydroxy-3-methylbutyl)-7-hydroxychromen-2-one (7) named devenyol, its two O-monoglucosides at positions 3' and 7 named devenyosides A (8) and B (9), and the corresponding 3'- and 7-O-diglucoside named devenyoside C (10). This plant is an interesting example of stereochemical diversity based on biodiversity given that other members of the Apiaceae family produce exclusively the 2'R epimers of compounds 7-9.
Quantitative Proteomics Reveals the Induction of Mitophagy in Tumor Necrosis Factor-α-activated (TNFα) Macrophages (2013)

Macrophages play an important role in innate and adaptive immunity as professional phagocytes capable of internalizing and degrading pathogens to derive antigens for presentation to T cells. They also produce pro-inflammatory cytokines such as tumor necrosis factor alpha (TNF-α) that mediate local and systemic responses and direct the development of adaptive immunity. The present work describes the use of label-free quantitative proteomics to profile the dynamic changes of proteins from resting and TNF-α-activated mouse macrophages. These analyses revealed that TNF-α activation of macrophages led to the down-regulation of mitochondrial proteins and the differential regulation of several proteins involved in vesicle trafficking and immune response. Importantly, we found that the down-regulation of mitochondria proteins occurred through mitophagy and was specific to TNF-α, as other cytokines such as IL-1β and IFN-γ had no effect on mitochondria degradation. Furthermore, using a novel antigen presentation system, we observed that the induction of mitophagy by TNF-α enabled the processing and presentation of mitochondrial antigens at the cell surface by MHC class I molecules. These findings highlight an unsuspected role of TNF-α in mitophagy and expanded our understanding of the mechanisms responsible for MHC presentation of self-antigens.
Biochemical characterization of recombinant influenza A polymerase heterotrimer complex: Polymerase activity and mechanisms of action of nucleotide analogs (2017)

Influenza polymerase is a heterotrimer protein with both endonuclease and RNA-dependent RNA polymerase (RdRp) activity. It plays a critical role in viral RNA replication and transcription and has been targeted for antiviral drug development. In this study, we characterized the activity of recombinant RdRp purified at 1:1:1 ratio in both ApG-primed RNA replication and mRNA-initiated RNA transcription. The heterotrimer complex showed comparable activity profiles to that of viral particle derived crude replication complex, and in contrast to the crude replication complex, was suitable for detailed mechanistic studies of nucleotide incorporation. The recombinant RdRp was further used to examine distinct modes of inhibition observed with five different nucleotide analog inhibitors, and the apparent steady-state binding affinity Kapp was measured for selected analogs to correlate antiviral activity and enzymatic inhibition with substrate efficiency.
Content-adaptive speech enhancement by a sparsely-activated dictionary plus low rank decomposition (2014)

One powerful approach to speech enhancement employs strong models for both speech and noise, decomposing a mixture into the most likely combination. But if the noise encountered differs significantly from the system's assumptions, performance will suffer. In previous work, we proposed a speech enhancement model that decomposes the spectrogram into sparse activation of a dictionary of target speech templates, and a low-rank background model. This makes few assumptions about the noise, and gave appealing results on small excerpts of noisy speech. However, when processing whole conversations, the foreground speech may vary in its complexity and may be unevenly distributed throughout the recording, resulting in inaccurate decompositions for some segments. In this paper, we explore an adaptive formulation of our previous model that incorporates separate side information to guide the decomposition, making it able to better process entire conversations that may exhibit large variations in the speech content.
Media With pH Indicators for the Isolation of Dermatophytes (1970)

A comparison was made of four agar media, Sabouraud's glucose agar, mycosel (M), ink blue agar (IB), and dermatophyte test medium (DTM) for the isolation and identification of fungi from 100 dermatological clinical specimens. Except for yeasts, Sabouraud's glucose medium was the least desirable as an isolation medium since it supported the growth of significantly fewer dermatophytes and more contaminants (both fungal and bacterial) than the other three media (M, IB, or DTM). These three media were approximately the same in supporting fewer yeasts (pathogenic and nonpathogenic) and mycelial fungal contaminants than the Sabouraud's. The dermatophyte test medium was superior to the three others in suppressing bacteria. All dermatophytes isolated on the IB and DTM media turned the pH indicators alkaline, and so did certain fungal contaminants. The latter, however, could be distinguished from dermatophytes by their colony characteristics.
Recent developments in high-temperature photonic crystals for energy conversion (2012)

After decades of intense studies focused on cryogenic and room temperature nanophotonics, scientific interest is also growing in high-temperature nanophotonics aimed at solid-state energy conversion. These latest extensive research efforts are spurred by a renewed interest in high temperature thermal-to-electrical energy conversion schemes including thermophotovoltaics (TPV), solar–thermophotovoltaics, solar–thermal, and solar–thermochemical energy conversion systems. This field is profiting tremendously from the outstanding degree of control over the thermal emission properties that can be achieved with nanoscale photonic materials. The key to obtaining high efficiency in this class of high temperature energy conversion is the spectral and angular matching of the radiation properties of an emitter to those of an absorber. Together with the achievements in the field of high-performance narrow bandgap photovoltaic cells, the ability to tailor the radiation properties of thermal emitters and absorbers using nanophotonics facilitates a route to achieving the impressive efficiencies predicted by theoretical studies. In this review, we will discuss the possibilities of emission tailoring by nanophotonics in the light of high temperature thermal-to-electrical energy conversion applications, and give a brief introduction to the field of TPV. We will show how a class of large area 2D metallic photonic crystals can be designed and employed to efficiently control and tailor the spectral and angular emission properties, paving the way towards new and highly efficient thermophotovoltaic systems and enabling other energy conversion schemes based on high-performance high-temperature nanoscale photonic materials.
Epitaxial Growth Controlled in Three Dimensions. SENTAXY Selective Nucleation based Epitaxy. (1995)

非晶質基板上に堆積されたままの薄層の構造は,下地の長距離秩序の欠如のため短距離秩序のみ保持された非晶質か,良くて微細な結晶粒が無秩序な粒界を隔てて集合した多結晶となる。本研究は,新規な結晶成長法,SENTAXY(選択的単一核形成法)に基づき,非晶質基板上で核形成サイトの位置を人工的に制御することを提案する。すなわち,基板上の任意の位置で結晶核を発生させ,任意の大きさに結晶粒を成長させ,さらには粒界位置をも指定することが可能となる。本稿では,その基本的な考え方を説明し,シリコンにおける単一核を選択する手法を紹介し,その機構と解析について議論する。
Use of BMC for Ductile Structural Members (1997)

Peer Reviewed
Future Technological Advances in Cardiac CT (2019)

In this short overview of future technological advances in cardiac computed tomography (CT), we focus on technical challenges in cardiac CT – temporal resolution, spatial resolution, and low radiation dose. We show how they have been addressed so far and where technical progress may lead us in the future. Then, we introduce new CT system concepts that may be promising for cardiac CT. Finally we briefly touch new aspects of cardiac CT imaging, aimed at deriving more than just anatomical information from a CT scan of the heart.