gebhart/patrepeval huggingface dataset:
Cell-free prototyping enables implementation of optimized reverse β-oxidation pathways in heterotrophic and autotrophic bacteria (2022)

Carbon-negative synthesis of biochemical products has the potential to mitigate global CO<sub>2</sub> emissions. An attractive route to do this is the reverse β-oxidation (r-BOX) pathway coupled to the Wood-Ljungdahl pathway. Here, we optimize and implement r-BOX for the synthesis of C4-C6 acids and alcohols. With a high-throughput in vitro prototyping workflow, we screen 762 unique pathway combinations using cell-free extracts tailored for r-BOX to identify enzyme sets for enhanced product selectivity. Implementation of these pathways into Escherichia coli generates designer strains for the selective production of butanoic acid (4.9 ± 0.1 gL<sup>-1</sup>), as well as hexanoic acid (3.06 ± 0.03 gL<sup>-1</sup>) and 1-hexanol (1.0 ± 0.1 gL<sup>-1</sup>) at the best performance reported to date in this bacterium. We also generate Clostridium autoethanogenum strains able to produce 1-hexanol from syngas, achieving a titer of 0.26 gL<sup>-1</sup> in a 1.5 L continuous fermentation. Our strategy enables optimization of r-BOX derived products for biomanufacturing and industrial biotechnology.
The Cytoprotective Effects of the Glycoprotein 130 Receptor-coupled Cytokine, Cardiotrophin-1, Require Activation of NF-κB (2001)

Many cell types mount elaborate, compensatory responses to stress that enhance survival; however, the intracellular signals that govern these responses are poorly understood. Cardiotrophin-1 (CT-1), a stress-induced cytokine, belongs to the interleukin-6/glycoprotein 130 receptor-coupled cytokine family. CT-1 is released from the heart in response to hypoxic stress, and it protects cardiac myocytes from hypoxia-induced apoptosis, thus establishing a central role for this cytokine in the cardiac stress response. In the present study, CT-1 activated p38 and ERK MAPKs as well as Akt in cultured cardiac myocytes; these three pathways were activated in a parallel manner. CT-1 also induced the degradation of the NF-kappa B cytosolic anchor, I kappa B, as well as the translocation of the p65 subunit of NF-kappa B to the nucleus and increased expression of an NF-kappa B-dependent reporter gene. Inhibitors of the p38, ERK, or Akt pathways each partially reduced CT-1-mediated NF-kappa B activation, as well as the cytoprotective effects of CT-1 against hypoxic stress. Together, the inhibitors completely blocked CT-1-dependent NF-kappa B activation and cytoprotection. A cell-permeable peptide that selectively disrupted NF-kappa B activation also completely inhibited the cytoprotective effects of CT-1. These results indicate that CT-1 signals through p38, ERK, and Akt in a parallel manner to activate NF-kappa B and that NF-kappa B is required for CT-1 to mediate its full cytoprotective effects in cardiac myocytes.
Doppler evaluation of results of percutaneous aortic balloon valvuloplasty in calcific aortic stenosis. (1988)

To evaluate the short-term results of percutaneous aortic balloon valvuloplasty, 55 consecutive elderly patients with symptomatic, severe aortic stenosis who were at high risk for surgical intervention underwent the procedure, with follow-up by clinical evaluation and Doppler echocardiography. Over a mean follow-up of 6.2 months, there were three early deaths (less than 30 days) and eight late deaths. Nine patients underwent subsequent aortic valve surgery, and four had repeat balloon valvuloplasty. Doppler echocardiography revealed a reduction in aortic valve mean gradient from 48 +/- 18 to 33 +/- 12 mm Hg after the procedure (p less than 0.0001) but a return to 46 +/- 16 mm Hg at follow-up (p less than 0.05). The aortic valve area increased from 0.54 +/- 0.15 to 0.85 +/- 0.23 cm2 after the procedure (p less than 0.0001), but there was a significant decrease to 0.67 +/- 0.19 cm2 at follow-up (p less than 0.05). Of patients free of aortic valve operation or death after 30 days after the procedure, 76% were severely symptomatic before the procedure as compared with 38% at follow-up. In patients undergoing percutaneous aortic balloon valvuloplasty, there is a continued high short-term mortality and a significant incidence of restenosis over short-term follow-up. Nonetheless, a subset of patients do experience sustained clinical improvement from this procedure.
Cellulomonas fimi β-1,4-Glucanases (1991)

The basic structural and functional organization of four β-1, 4-glucanases from the cellulolytic bacterium Cellulomonas fimi has been established. Endoglucanase A (CenA) and an exoglucanase (Cex) each contain two independent structural and functional domains: a catalytic domain and an amino- or carboxyl-terminal cellulose-binding domain (CBD). The CBDs show significant sequence identity and similar structures are evident in glycanases from other bacteria. Endoglucanases B and C (CenB and CenC, respectively) are large (>100 kDa) enzymes composed of multiple domains. A CBD is found at the carboxyl-terminus of CenB. Both enzymes contain units of unknown function comprised of repeated blocks of amino acids. Conspicuous linker sequences occur at the junctions of the domains in all four enzymes and resemble sequences seen in other bacterial glycanases. The CBDs of CenA and Cex have been fused to heterologous proteins by genetic manipulation. Examples are presented to illustrate the potential of such fusions for protein immobilization or purification.
A Novel Gelatin Hydrogel Carrier Sheet for Corneal Endothelial Transplantation (2011)

We examined the feasibility of using gelatin hydrogels as carrier sheets for the transplantation of cultivated corneal endothelial cells. The mechanical properties, transparency, and permeability of gelatin hydrogel sheets were compared with those of atelocollagen sheets. Immunohistochemistry (ZO-1, Na+/K+-ATPase, and N-cadherin), hematoxylin and eosin staining, and scanning electron microscopy were performed to assess the integrity of corneal endothelial cells that were cultured on gelatin hydrogel sheets. The gelatin hydrogel sheets displayed greater transparency, elastic modulus, and albumin permeability compared to those of atelocollagen sheets. The corneal endothelial cells on gelatin hydrogel sheets showed normal expression levels of ZO-1, Na+/K+-ATPase, and N-cadherin. Hematoxylin and eosin staining revealed the formation of a continuous monolayer of cells attached to the gelatin hydrogel sheet. Scanning electron microscopy observations showed that the corneal endothelial cells were arranged in a regular, mosaic, and polygonal pattern with normal cilia. These results indicate that the gelatin hydrogel sheet is a promising material to transport corneal endothelial cells during transplantation.
Dependence of Cyclin E-CDK2 Kinase Activity on Cell Anchorage (1996)

Most nonmalignant cells are anchorage-dependent; they require substrate attachment for growth and, in some instances, survival. This requirement is lost on oncogenic transformation. The cyclin E-CDK2 complex, which is required for the G1-S transition of the cell cycle, was activated in late G1 phase in attached human fibroblasts, but not in fibroblasts maintained in suspension. In transformed fibroblasts the complex was active regardless of attachment. The lack of cyclin E-CDK2 activity in suspended cells appeared to result from increased expression of CDK2 inhibitors and a concomitant decrease in phosphorylation of CDK2 on threonine-160. Suppression of cyclin E-CDK2 activity may thus underlie the anchorage dependence of cell growth.
Differential expression of Fas (CD95) and Fas ligand on normal human phagocytes: implications for the regulation of apoptosis in neutrophils. (1996)

Human neutrophils, monocytes, and eosinophils are known to undergo apoptotic cell death. The Fas/Fas ligand pathway has been implicated as an important cellular pathway mediating apoptosis in diverse cell types. We conducted studies to examine the importance of the Fas/FasL system in normal human phagocytes. Although Fas expression was detected on neutrophils, monocytes, and eosinophils, constitutive expression of FasL was restricted to neutrophils. The three types of phagocytes demonstrated differential sensitivity to Fas-induced apoptosis. Only neutrophils were highly susceptible to rapid apoptosis in vitro after stimulation with activating anti-Fas IgM (mAb CH-11). Fas-mediated neutrophil apoptosis was suppressed by incubation with G-CSF, GM-CSF, IFN-gamma, TNF-alpha, or dexamethasone, as well as the selective tyrosine kinase inhibitors, herbimycin A and genistein. Spontaneous neutrophil death in vitro was partially suppressed by Fas-Ig fusion protein or antagonistic anti-Fas IgG1 (mAb ZB4). In coculture experiments, neutrophils released a soluble factor inducing death in Fas-susceptible Jurkat cells via a mechanism sensitive to the presence of Fas-Ig or anti-Fas IgG1. Immunoblot analysis using specific anti-human FasL IgG1 (mAb No. 33) identified a 37-kD protein in lysates of freshly isolated neutrophils and a 30-kD protein in the culture supernatant of neutrophils maintained in vitro. Our results suggest that mature neutrophils may be irrevocably committed to autocrine death by virtue of their constitutive coexpression of cell-surface Fas and FasL via a mechanism that is sensitive to proinflammatory cytokines, glucocorticoids, and inhibitors of tyrosine kinase activity. Furthermore, neutrophils can serve as a source of soluble FasL, which may function in a paracrine pathway to mediate cell death.
Fractional Laser Ablation for the Cutaneous Delivery of Triamcinolone Acetonide from Cryomilled Polymeric Microparticles: Creating Intraepidermal Drug Depots (2016)

The efficacy of some dermatological therapies might be improved by the use of “high dose” intraepidermal drug reservoir systems that enable sustained and targeted local drug delivery, e.g., in the treatment of keloids and hypertrophic scars. Here, a fractionally ablative erbium:YAG laser was used to enable “needle-less” cutaneous deposition of polymeric microparticles containing triamcinolone acetonide (TA). The microparticles were prepared using a freeze–fracture technique employing cryomilling that resulted in drug loading efficiencies of ∼100%. They were characterized by several different techniques, including scanning electron microscopy, powder X-ray diffraction and differential scanning calorimetry. TA was quantified by validated HPLC–UV and UHPLC–MS/MS analytical methods. In vitro release studies demonstrated the effect of polymer properties on TA release kinetics. Confocal laser scanning microscopy enabled visualization of cryomilled microparticles containing fluorescein and Nile Red in the cutaneous micropores and the subsequent release of fluorescein into the micropores and its diffusion throughout the epidermis and upper dermis. The biodistribution of TA, i.e. the amount of drug as a function of depth in skin, following microparticle application was much more uniform than with a TA suspension and delivery was selective for deposition with less transdermal permeation. These findings suggest that this approach may provide an effective, targeted and minimally invasive alternative to painful intralesional injections for the treatment of keloid scars.
Wanna Make Your TCP Scheme Great for Cellular Networks? Let Machines Do It for You! (2020)

Can we instead of designing yet another new TCP algorithm, design a TCP plug-in that can enable machines to automatically boost the performance of the existing/future TCP designs in cellular networks? We answer this question by introducing DeepCC. DeepCC leverages advanced deep reinforcement learning (DRL) techniques to let machines automatically learn how to steer throughput-oriented TCP algorithms toward achieving applications' desired delays in a highly dynamic network such as the cellular network. We used DeepCC plug-in to boost the performance of various old and new TCP schemes including TCP Cubic, Google's BBR, TCP Westwood, and TCP Illinois in cellular networks. Through both extensive trace-based evaluations and real-world experiments, we show that not only DeepCC can significantly improve the performance of TCP schemes, but also after accompanied by DeepCC, these schemes can outperform state-of-the-art TCP protocols including new clean-slate machine learning-based designs and the ones designed solely for cellular networks.
High-Pressure Water Intrusion Investigation of Pure Silica ITQ-7 Zeolite (2013)

Experimental water intrusion–extrusion isotherms were recorded at room temperature on pure silica ISV-type zeolite (ITQ-7 zeosil) possessing a 3D channel system. The water intrusion is obtained by applying a high hydraulic pressure corresponding to the intrusion step. When the pressure is released, the water extrusion occurs but at a lower pressure to that of the intrusion one. The ITQ-7 zeosil–water system behaves like a shock-absorber, but the phenomenon is nonreproducible. Several characterizations have been realized before and after water intrusion–extrusion experiments in order to reveal the presence or the absence of defects after such experiments. Structural modifications at the long-range order can be observed by XRD analysis after intrusion. At the short-range order, solid-state NMR spectroscopy shows evidence of the presence of Q2 ((HO−)2Si(−OSi)2) and Q3 ((HO–Si(−OSi)3) or (Si(−OSi)3O–)) groups revealing the breaking of some siloxane bridges after the intrusion step. The amount of defects increases (<2% before and 15% after intrusion step). However, after a regeneration step (calcination of the intruded-extruded sample), the ITQ-7 zeosil–water system displays again a shock-absorber behavior with a similar intrusion pressure.
Possible role of the V3 domain of gp120 in resistance to an amphotericin B derivative (MS8209) blocking human immunodeficiency virus entry (1996)

MS8209, an amphotericin B derivative blocking human immunodeficiency virus type 1 (HIV-1) entry after CD4 binding, neutralized the HIV-2 strains EHO and ROD10 but not ROD(CEM). In the V3 domain of gp120, ROD(CEM) differed from ROD10 at two positions (a threonine instead of an isoleucine at position 312 and an arginine instead of a glutamine at position 329), and drug resistance was conferred to HIV-1 by substitution of the ROD(CEM) V3 but not the ROD10 V3. V3 mutations may prevent the interaction of gp120 with MS8209 or modify the mechanism of virus entry, rendering it less accessible to neutralization.
Arenesulfonyl iodides: The third universal class of functional initiators for the metal‐catalyzed living radical polymerization of methacrylates and styrenes (2005)

Abstract The metal‐catalyzed living radical polymerization of methyl methacrylate and styrene initiated with freshly prepared p ‐toluenesulfonyl iodide (TsI) and catalyzed with CuX/2,2′‐bipyridine (bpy), where X is Cl, Br, or I, and various self‐regulated copper‐based catalytic systems, such as copper/bpy, copper(I) oxide/bpy, copper(I) sulfide/bpy, copper(I) selenide/bpy, and copper(I) telluride/bpy, is reported. The exchange of CI into CBr and CCl takes place when the living radical polymerization of methyl methacrylate is catalyzed by copper(I) bromide/bpy and copper(I) chloride/bpy, respectively. Therefore, the use of the TsI initiator facilitates the synthesis, starting from a single initiator, of poly(methyl methacrylate) containing CI, CBr, and CCl chain ends. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 3920–3931, 2005
Batteries and fuel cells working group report (1991)

Electrochemical energy systems are dominated by interfacial phenomena. Catalysis, corrosion, electrical and ionic contact, and wetting behavior are critical to the performance of fuel cells and batteries. Accordingly, development of processing techniques to control these surface properties is important to successful commercialization of advanced batteries and fuel cells. Many of the surface processing issues are specific to a particular electrochemical system. Therefore, the working group focused on systems that are of specific interest to DOE/Conservation and Renewable Energy. These systems addressed were: Polymer Electrolyte Membrane (PEM) Fuel Cells, Direct Methanol Oxidation (DMO) Fuel Cells, and Lithium/Polymer Batteries. The approach used by the working group for each of these systems was to follow the current path through the system and to identify the principal interfaces. The function of each interface was specified together with its desired properties. The degree to which surface properties limit performance in present systems was rated. Finally, the surface processing needs associated with the performance limiting interfaces were identified. This report summarizes this information.
Lanthanum and Lanthanum Silicide Contacts on N-Type Silicon (2017)

In this letter, we investigate contacts of a low work function rare-earth metal, La, and its silicides on n-Si. LaSi <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> /n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-</sup> -Si contacts show low Schottky barrier height (φ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">b</sub> ) of around 0.25-0.4 eV and promisingly low contact resistivity (ρ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> ) on moderately doped n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -Si. However, on highly doped n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">++</sup> -Si, we find Pc of LaSi <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> near one order higher than the TiSi <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> control. This experiment indicates that low φ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">b</sub> does not guarantee low Pc on highly doped substrates. We further discuss reasons behind this phenomenon.
OS Driver Test Effort Reduction via Operational Profiling (2009)

Operating Systems (OS’s) constitute the operational core for computing devices, and consequently, the OS’s ability to sustain operations determines the dependability level of the provided system services. In order to facilitate their applicability
ChemInform Abstract: Reactions of an Electrophilic Glycine Cation Equivalent with Grignard Reagents. (1986)

Abstract Das aus dem geschützten Aminosäureester (I) erhaltene Glycin‐Kation reagiert mit den Grignard‐Verbindungen (II) zu den Substitutionsprodukten (III); in gleicher Weise erhält man das Peptid (IV).
Atomic electron binding energies of multiply charged krypton ions by internal-conversion-electron spectroscopy (1990)

We determined electron binding energies from multiply charged Kr ions from internal-conversion-electron spectra for the 9.4-keV transition in $^{83}\mathrm{Kr}^{\mathit{m}}$. Because our radioactive source is a low-density gas, we can observe the electrons from ionic states produced by the vacancy cascade of the preceding highly converted transition. We report binding-energy shifts for the 2s, 3s, and 4s orbitals in the configuration of the atomic ground state. For charge state ${7}^{+}$, i.e., for Ni-like Kr and higher, we also observe the shifts from metastable states.
From Concept to Crystals via Prediction: Multi‐Component Organic Cage Pots by Social Self‐Sorting (2019)

We describe the a priori computational prediction and realization of multi-component cage pots, starting with molecular predictions based on candidate precursors through to crystal structure prediction and synthesis using robotic screening. The molecules were formed by the social self-sorting of a tri-topic aldehyde with both a tri-topic amine and di-topic amine, without using orthogonal reactivity or precursors of the same topicity. Crystal structure prediction suggested a rich polymorphic landscape, where there was an overall preference for chiral recognition to form heterochiral rather than homochiral packings, with heterochiral pairs being more likely to pack window-to-window to form two-component capsules. These crystal packing preferences were then observed in experimental crystal structures.
Comparative proteomic analysis of the brain and colon in three rat models of irritable bowel syndrome (2020)

Taken together, the data presented represent a comprehensive and quantitative proteomic analysis of the brain and colon in IBS models, providing new evidence of an abnormal brain-gut interaction in IBS. These data may be useful for further investigation of potential targets in the diagnosis and treatment of IBS.
Fizioterapija kod djece sa cističnom fibrozom (2019)

Cisticna fibroza je monogenska bolest i prenosi se autosomno – recesivno. Osnovni uzrok bolesti cini poremecaj rada CFTR (engl. cystic fibrosis transmembrane regulator) proteina koji se javlja kao posljedica mutacije gena. Do sada je otkriveno vise od 1000 mutacija CFTR-gena podijeljenih u sest klasa. Terapijski pristup u CF-u temelji se na lijecenju komplikacija i simptoma, a ne na lijecenju uzroka bolesti. Međutim, istražuje se vise oralno aktivnih supstancija – modifikatora CFTR-a – koje modificiraju funkciju CFTR-proteina. Time se pokusava korigirati podliježuci genski defekt koji uzrokuje CF. Bolest je moguce dijagnosticirati u trudnoci i tokom života. Prenatalno testiranje omogucuje otkrivanje bolesti u ranoj trudnoci, no otkrivanje bolesti do adolescencije promakne u otprilike 10% bolesnika. Cisticna fibroza kao multisistemska bolest rijetko pogađa samo jedan organski sustav. Najcesce su zahvaceni disni, reproduktivni i probavni sustav. Rijec je o kronicnoj bolesti koju je potrebno sto ranije prepoznati kako bismo kroz kompleksno trandisciplinarno lijecenje postigli sto bolju kvalitetu života oboljelih. Ucestalost pojavljivanja CF-a u bijele rase iznosi 1:2500 – 3500, a u crne 1:15000 – 17000. Fizioterapijska procjena se temelji na SOAP metodi koja se sastoji od subjektivnog pregleda, objektivnog pregleda te analize i plana terapije. Glavni ciljevi fizioterapijske intervencije je izbacivanje sekreta iz disnih puteva, povecanje pokretljivosti grudnog kosa cime se poboljsava ventilacija pluca, postizanje pravilnog disanja. Kod osoba koje boluju od cisticne fibroze zahtijeva se doživotna terapija i iznimno je važna edukacija roditelja i obitelji o fizioterapijskim metodama bolesti.
Raman lasing and soliton mode-locking in lithium niobate microresonators (2020)

The recent advancement in lithium-niobite-on-insulator (LNOI) technology is opening up new opportunities in optoelectronics, as devices with better performance, lower power consumption and a smaller footprint can be realised due to the high optical confinement in the structures. The LNOI platform offers both large <i>χ</i> <sup>(2)</sup> and <i>χ</i> <sup>(3)</sup> nonlinearities along with the power of dispersion engineering, enabling brand new nonlinear photonic devices and applications for the next generation of integrated photonic circuits. However, Raman scattering and its interaction with other nonlinear processes have not been extensively studied in dispersion-engineered LNOI nanodevices. In this work, we characterise the Raman radiation spectra in a monolithic lithium niobate (LN) microresonator via selective excitation of Raman-active phonon modes. The dominant mode for the Raman oscillation is observed in the backward direction for a continuous-wave pump threshold power of 20 mW with a high differential quantum efficiency of 46%. We explore the effects of Raman scattering on Kerr optical frequency comb generation. We achieve mode-locked states in an X-cut LNOI chip through sufficient suppression of the Raman effect via cavity geometry control. Our analysis of the Raman effect provides guidance for the development of future chip-based photonic devices on the LNOI platform.