gebhart/patrepeval huggingface dataset:
Engineering nonphotosynthetic carbon fixation for production of bioplastics by methanogenic archaea (2022)

The conversion of CO2 to value-added products allows both capture and recycling of greenhouse gas emissions. While plants and other photosynthetic organisms play a key role in closing the global carbon cycle, their dependence on light to drive carbon fixation can be limiting for industrial chemical synthesis. Methanogenic archaea provide an alternative platform as an autotrophic microbial species capable of non-photosynthetic CO2 fixation, providing a potential route to engineered microbial fermentation to synthesize chemicals from CO2 without the need for light irradiation. One major challenge in this goal is to connect upstream carbon-fixation pathways with downstream biosynthetic pathways, given the distinct differences in metabolism between archaea and typical heterotrophs. We engineered the model methanogen, Methanococcus maripaludis, to divert acetyl-coenzyme A toward biosynthesis of value-added chemicals, including the bioplastic polyhydroxybutyrate (PHB). A number of studies implicated limitations in the redox pool, with NAD(P)(H) pools in M. maripaludis measured to be <15% of that of Escherichia coli, likely since methanogenic archaea utilize F420 and ferredoxins instead. Multiple engineering strategies were used to precisely target and increase the cofactor pool, including heterologous expression of a synthetic nicotinamide salvage pathway as well as an NAD+-dependent formate dehydrogenase from Candida boidinii. Engineered strains of M. maripaludis with improved NADH pools produced up to 171 ± 4 mg/L PHB and 24.0 ± 1.9% of dry cell weight. The metabolic engineering strategies presented in this study broaden the utility of M. maripaludis for sustainable chemical synthesis using CO2 and may be transferable to related archaeal species.
Multi-omics tumor profiling technologies to develop precision medicine in multiple myeloma (2021)

Multiple myeloma (MM), the second most common hematologic cancer, is caused by accumulation of aberrant plasma cells in the bone marrow. Its molecular causes are not fully understood and its great heterogeneity among patients complicates therapeutic decision-making. In the past decades, development of new therapies and drugs have significantly improved survival of MM patients. However, resistance to drugs and relapse remain the most common causes of mortality and are the major challenges to overcome. The advent of high throughput omics technologies capable of analyzing big amount of clinical and biological data has changed the way to diagnose and treat MM. Integration of omics data (gene mutations, gene expression, epigenetic information, and protein and metabolite levels) with clinical histories of thousands of patients allows to build scores to stratify the risk at diagnosis and predict the response to treatment, helping clinicians to make better educated decisions for each particular case. There is no doubt that the future of MM treatment relies on personalized therapies based on predictive models built from omics studies. This review summarizes the current treatments and the use of omics technologies in MM, and their importance in the implementation of personalized medicine.
Recent Dearomatization Strategies of Benzofurans and Benzothiophenes (2021)

Abstract This review article discusses about the recent developments in the area of the strategies for the dearomatization of benzofurans and benzothiophenes (2010–2020). The readers can understand the current state of art of this intriguingly important area in organic synthesis for the generation of diversely functionalized molecules, polycyclic systems from highly abundant benzofurans and benzothiophenes. We hope that the current review article would help the synthetic community for the design and development of new strategies as well as further growth of this novel and rapidly growing area of research.
3D or Not 3D: Shaping the Genome during Development (2021)

One of the most fundamental questions in developmental biology is how one fertilized cell can give rise to a fully mature organism and how gene regulation governs this process. Precise spatiotemporal gene expression is required for development and is believed to be achieved through a complex interplay of sequence-specific information, epigenetic modifications, <i>trans</i>-acting factors, and chromatin folding. Here we review the role of chromatin folding during development, the mechanisms governing 3D genome organization, and how it is established in the embryo. Furthermore, we discuss recent advances and debated questions regarding the contribution of the 3D genome to gene regulation during organogenesis. Finally, we describe the mechanisms that can reshape the 3D genome, including disease-causing structural variations and the emerging view that transposable elements contribute to chromatin organization.
Transient-Enhanced Diffusion In Ion-Implanted Silicon (1987)

We discuss the transient-enhanced diffusion of Sb, As, P, In, Ga, and B in ion-implanted Si, where the near-surface region has been amorphized by the dopant or by a self-implantation process. With Sb, a large transient diffusion enhancement is observed proportional to dopant concentration. For Sb, As, P, and In, the enhancement follows the relative interstitialcy diffusion coefficient. We believe this behavior is caused by stable implantation-induced point defects present in the amorphous surface layer, which decay during thermal processing to release high concentrations of self interstitials. This process occurs in competition with the solid phase epitaxial (SPE) growth process, and for high dopant concentrations can occur in the amorphous phase ahead of the crystallization front. We believe this may be the origin of the dopant redistribution which can occur during SPE growth, which sets the upper limit to the dopant concentration which can be incorporated in the lattice by SPE growth. These effects are reduced for Ga and are absent for B, although transient enhanced diffusion of these species can still occur from defects emitted from the damaged crystal underlying the original amorphous/crystalline interface.
Manual and semi-automatic registration vs retrospective ECG gating for correction of cardiac motion (2003)

A manual and a semi-automatic image registration method were compared with retrospective ECG (rECG) gating to correct for cardiac motion in myocardial perfusion (MBF) measurement. 5 beagles were used in 11 experiments. For each experiment a 30 s cine CT scan of the heart was acquired after contrast injection. For the manual method, a reference end-diastole (ED) image was selected from the first cardiac cycle. ED images in subsequent cardiac cycles were manually selected to match the shape of the reference ED image. For each cardiac cycle in the semi-automatic method, the image with the maximum area and the most similar shape to the selected image of the previous cardiac cycle was chosen as ED image. MBFs were calculated from the images registered by the three methods and compared. The averages of the difference of MBF<sub>manual</sub> and MBF<sub>semi-auto</sub> and MBF<sub>rECG</sub> in the lateral free wall of LV were 3.6 and 3.4 ml/min/100g respectively. The corresponding standard deviations from the mean were 9.1 and 28.3 ml/min/100g respectively. We concluded from these preliminary results that image registration methods were better than rECG gating for correcting heart, which should facilitate more precise measurement of MBF.
Hand phantoms for browsing stance in mobile phones (2009)

In this paper several antennas and configurations were investigated, focusing on phantom hands for browsing stance. It has been found that ldquooverlappedrdquo and ldquointerlacedrdquo grip styles have a similar impact on both absorption and mismatch loss, as only the fingers in close proximity to the antenna give a significant contribution in determining the total loss. Moreover, allowing different hands' overlap configurations, it was found little difference in the loss amount. This suggests that a proper hand phantoms' configuration may mimic the influence of many grip styles that despite being topologically different, influence the antenna efficiency in a similar way.
TRIIODOTHYRONINE METABOLISM IN DIABETIC RATS (1978)

ABSTRACT Triiodothyronine (T 3 ) metabolism was assessed in untreated and in insulin-treated diabetic rats and the results compared with a corresponding control group. Male rats of the Wistar strain were made diabetic by the intraperitoneal injection of alloxan in a dose of 17.5 mg/100 g body weight and thereafter maintained normoglycaemic for a week and until 24 h before initiation of the study. The average glycaemia in control and in insulin-treated animals was 135 mg/100 ml, whereas in the untreated diabetic rats it was 455 mg/100 ml. Each animal was injected a tracer dose of [ 125 I]T 3 containing 2 μCi of 125 I and 15 ng of T 3 . Heparinized blood samples were obtained by cardiac puncture at 5, 18 and 24 h following the injection of the tracer. The excretion of inorganic 125 I in the 24-h collections of urine was also determined. The kinetics of [ 125 I]T 3 were studied by the extrapolation method using the straight line of plasma disappearance between 5 and 24 h. It was found that the untreated diabetic rats had a significant slowing of plasma disappearance of labelled T 3 . The decrease in fractional hormone turnover was balanced by a slight expansion of the distribution space, which presumably led to a larger hormone pool and a normal degradation rate of T 3 . These events seemed substantiated by the normal excretion of 125 I in the urine observed in untreated animals. A parallel study of plasma hormone binding using a red cell uptake method showed a significant reduction of binding avidity for T 3 by plasma proteins in the untreated diabetic animals. The administration of insulin restored plasma T 3 kinetics and binding avidity to normal, as observed in control rats. It was concluded that untreated diabetes mellitus induced changes in T 3 kinetics and in T 3 serum binding without altering hormone deiodination, parameter which reflects tissue utilization of T 3 .
Zika Virus Replication in Dorsal Root Ganglia Explants from Interferon Receptor1 Knockout Mice Causes Myelin Degeneration (2018)

Zika virus (ZIKV) is a neurotropic agent that targets the developing fetal brain in women infected during pregnancy. In addition to the developing central nervous system, ZIKV has been recently shown to infect cells of the peripheral nervous system (PNS), highlighting its potential to cause acute peripheral neuropathies in adults, such as Guillain-Barré Syndrome (GBS). Here we show that myelinating dorsal root ganglia (DRG) explants obtained from interferon-alpha/beta receptor knock-out mice are productively infected by ZIKV. Virus replication is cytopathic in both peripheral neurons and myelinating Schwann cells leading to myelin disruption. These results confirm and extend previous observations suggesting that the PNS is indeed a potential site of ZIKV infection, replication and cytopathicity.
Hydrogen-Bond Acidic Polymers for Chemical Vapor Sensing (2008)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydrogen-Bond Acidic Polymers for Chemical Vapor SensingJay W. GrateView Author Information Pacific Northwest National Laboratory, P.O. Box 999, Richland Washington 99352 Cite this: Chem. Rev. 2008, 108, 2, 726–745Publication Date (Web):January 26, 2008Publication History Received31 May 2007Published online26 January 2008Published inissue 1 February 2008https://pubs.acs.org/doi/10.1021/cr068109yhttps://doi.org/10.1021/cr068109yresearch-articleACS PublicationsCopyright © 2008 American Chemical SocietyRequest reuse permissionsArticle Views3971Altmetric-Citations187LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Aromatic compounds,Polymers,Sensors,Sorbents,Sorption Get e-Alerts
Interplay between magnetocrystalline anisotropy and exchange bias in epitaxial CoO/Co films (2016)

The interplay between magnetocrystalline anisotropy and exchange bias is investigated in CoO/Co bilayer films, which are grown epitaxially on MgO (0 0 1), by magnetization reversal measurements based on the anisotropic magnetoresistance (AMR) effect. While an asymmetric magnetization reversal survives after training for cooling field (CF) along the hard axis, the magnetization reversal becomes symmetric and is dominated in both branches of the hysteresis loop by domain wall motion before and after training for CF along the easy axis. When performing an in-plane hysteresis loop perpendicular to the CF, the hysteresis loop along the easy axis becomes asymmetric: magnetization rotation dominates in the ascending branch, while there is a larger contribution of domain wall motion in the descending branch. Furthermore, the azimuthal angular dependence of the AMR shows two minima after performing a perpendicular hysteresis loop, instead of only one minimum after training. Relying on the extended Fulcomer and Charap model, these effects can be related to an increased deviation of the average uncompensated antiferromagnetic magnetization from the CF direction. This model provides a consistent interpretation of training and asymmetry of the magnetization reversal for epitaxial films with pronounced magnetocrystalline anisotropy as well as for the previously investigated polycrystalline films.
Cytokine Response Modifier A Inhibition of Initiator Caspases Results in Covalent Complex Formation and Dissociation of the Caspase Tetramer (2006)

Active caspases are generally composed of two catalytic domains, each containing a large (p20) and a small (p10) subunit so that a fully active caspase has the organization (p20-p10)(2). The cowpox serpin crmA suppresses host apoptosis and inflammation by inhibiting endogenous caspases. We report on the mechanism crmA uses to inhibit caspases 1, 6, and 8. Native PAGE showed formation of tight crmA-caspase complexes. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry provided evidence for a covalent crmA-p20 thioester linkage. SDS-PAGE of isolated complexes showed near complete loss of the p10 subunit from initiator caspases 1 and 8 but not from the executioner caspase-6. This was confirmed for caspase-1 by sequencing and Western blotting. Size exclusion chromatography indicated a size of approximately 60 kDa for complexes with caspases 1 and 8, consistent with a crmA.p20 species, suggesting that the p20-p10 interface and possibly the p10-p10 interface had been disrupted. In contrast, crmA.caspase-6 complex behaved as an equilibrium mixture of crmA(2).(p20-p10)(2) and crmA.(p20-p10). Complex deacylation rates were all slow, suggesting effective kinetic trapping of the covalent thioacyl intermediate. These results suggest a novel serpin inhibition mechanism through which crmA down-regulates apoptosis and inflammation. This involves (i) rapid formation of covalent complex with initiator caspases 8 or 1, (ii) very slow deacylation, and (iii) loss of the caspase p10 subunit for initiator but not for executioner caspases, so that any free p20 formed by deacylation of initiator caspases cannot reassociate to active heterotetramer, thus resulting in irreversible inhibition of apoptosis and inflammation.
Multi-flow channel bioreactor enables real-time monitoring of cellular dynamics in 3D engineered tissue (2019)

The key to understanding, harnessing, and manipulating natural biological processes for the benefit of tissue engineering lies in providing a controllable dynamic environment for tissue development in vitro while being able to track cell activity in real time. This work presents a multi-channel bioreactor specifically designed to enable on-line imaging of fluorescently labeled cells embedded in replicated 3D engineered constructs subjected to different flow conditions. The images are acquired in 3D using a standard upright confocal microscope and further analyzed and quantified by computer vision. The platform is used to characterize and quantify the pace and directionality of angiogenic processes induced by flow. The presented apparatus bears considerable potential to advance scientific research, from basic research pursuing the effect of flow versus static conditions on 3D scaffolds and cell types, to clinically oriented modeling in drug screening and cytotoxicity assays.
Stereological analysis of single lung lobes in newborn mice exposed to hyperoxia (2017)

During lung development many internal and external factors can influence normal lung maturation. Mechanical ventilation and oxygen supplementation of preterm infants triggers bronchopulmonary dysplasia, a chronic lung disease characterised by enlarged septa thickness and less alveoli. Recently, several new methods for lung morphological analysis have been established, such as the stereological analysis of lungs embedded in plastic. A comparative, quantitative analysis of the structure of individual lung lobes has never been undertaken. In the present study, single lung lobes isolated from C57Bl/6 mice exposed to normoxia (21% O<sub>2</sub>) or hyperoxia (85% O<sub>2</sub>) from the day of birth for 14 days, were embedded in plastic, and analysed by stereology. For the whole-lung, the mean septal wall thickness was significantly increased from 10.2 μm in 21% O<sub>2</sub> to 15.3 μm in 85% O<sub>2</sub>. In the single lobe study, the septa thickness was increased only in the caudal and left lobe from 11.4 μm in 21% O<sub>2</sub> to 15.2 μm in 85% O<sub>2</sub> and 11.6 μm in 21% O<sub>2</sub> to 14.2 μm in 85% O<sub>2</sub>, respectively. The alveolar density in the whole-lung was decreased from 1.6 × 10<sup>7</sup> cm<sup>−3</sup> in 21% O<sub>2</sub> to 0.7 × 10<sup>7</sup> cm<sup>−3</sup> in 85% O<sub>2</sub>. In contrast, the single lobe analysis revealed a higher alveolar density in the cranial lobe 2.2 × 10<sup>7</sup> cm<sup>−3</sup> and in the middle lobe 2.0 × 10<sup>7</sup> cm<sup>−3</sup> in 21% O<sub>2</sub>, which was also noted in the in 85% O<sub>2</sub>, at 1.3 × 10<sup>7</sup> cm<sup>−3</sup> and 1.4 × 10<sup>7</sup> cm<sup>−3</sup>, respectively. The stereological study of each single lung lobe individually was more accurate and precise compared with the whole-lung analysis. Moreover, individual lung lobes in mice might follow a different development patterns, and this should be further investigated.
Development of the nano-HEB array for low-background far-IR applications (2010)

We present an overview of the recent progress made in the development of a far-IR array of ultrasensitive hot-electron nanobolometers (nano-HEB) made from thin titanium (Ti) films. We studied electrical noise, signal and noise bandwidth, single-photon detection, optical noise equivalent power (NEP), and a microwave SQUID (MSQUID) based frequency domain multiplexing (FDM) scheme. The obtained results demonstrate the very low electrical NEP down to 1.5&times;10<sup>-20</sup> W/Hz<sup>1/2</sup> at 50 mK determined by the dominating phonon noise. The NEP increases with temperature as ~ T<sup>3</sup> reaching ~ 10<sup>-17</sup> W/Hz<sup>1/2</sup> at the device critical temperature T<sub>C</sub> = 330-360 mK. Optical NEP = 8.6&times;10<sup>-18</sup> W/Hz<sup>1/2</sup> at 357 mK and 1.4&times;10<sup>-18</sup> W/Hz<sup>1/2</sup> at 100 mK respectively, agree with thermal and electrical data. The optical coupling efficiency provided by a planar antenna was greater than 50%. Single 8-&#956;m photons have been detected for the first time using a nano-HEB operating at 50-200 mK thus demonstrating a potential of these detectors for future photon-counting applications in mid-IR and far-IR. In order to accommodate the relatively high detector speed (~ &mu;s at 300 mK, ~ 100 &mu;s at 100 mK), an MSQUID based FDM multiplexed readout with GHz carrier frequencies has been built. Both the readout noise ~ 2 pA/Hz<sup>1/2</sup> and the bandwidth &gt; 150 kHz are suitable for nano-HEB detectors.
A Thermal Absolute-pressure Sensor With On-chip Digital Front-end Processor (1991)

Thermal conductivity absolute-pressure sensors are widely used in vacuum systems.1 Their operation is based on the pressure dependence of the heat transfer from a suspended hot filament through a gas. The filament temperature and IV curve are dependent on the heat transfer and hence on the gas pressure. This mechanism has been studied thoroughly by V. Ubisch and others.2 Recently, microbridge resistor structures consisting of a resistive doubly-supported beam suspended above the substrate have been used to detect absolute gas pressure.3 The pressure-dependent heat transfer in these structures occurs across the gap between the beam and the substrate.
Catalytically Doped Semiconductors for Chemical Gas Sensing: Aerogel‐Like Aluminum‐Containing Zinc Oxide Materials Prepared in the Gas Phase (2016)

Atmospheric contamination with organic compounds is undesired in industry and in society because of odor nuisance or potential toxicity. Resistive gas sensors made of semiconducting metal oxides are effective in the detection of gases even at low concentration. Major drawbacks are low selectivity and missing sensitivity toward a targeted compound. Acetaldehyde is selected due to its high relevance in chemical industry and its toxic character. Considering the similarity between gas‐sensing and heterogeneous catalysis (surface reactions, activity, selectivity), it is tempting to transfer concepts. A question of importance is how doping and the resulting change in electronic properties of a metal‐oxide support with semiconducting properties alters reactivity of the surfaces and the functionality in gas‐sensing and in heterogeneous catalysis. A gas‐phase synthesis method is employed for aerogel‐like zinc oxide materials with a defined content of aluminum (n‐doping), which were then used for the assembly of gas sensors. It is shown that only Al‐doped ZnO represents an effective sensor material that is sensitive down to very low concentrations (&lt;350 ppb). The advance in properties relates to a catalytic effect for the doped semiconductor nanomaterial.