gebhart/patrepeval huggingface dataset:
Smaug1 membrane-less organelles respond to AMPK and mTOR and affect mitochondrial function (2021)

Smaug is a conserved translational regulator that binds numerous mRNAs, including nuclear transcripts that encode mitochondrial enzymes. Smaug orthologs form cytosolic membrane-less organelles (MLOs) in several organisms and cell types. We have performed single-molecule fluorescence in situ hybridization (FISH) assays that revealed that SDHB and UQCRC1 mRNAs associate with Smaug1 bodies in U2OS cells. Loss of function of Smaug1 and Smaug2 (also known as SAMD4A and SAMD4B, respectively) affected both mitochondrial respiration and morphology of the mitochondrial network. Phenotype rescue by Smaug1 transfection depends on the presence of its RNA-binding domain. Moreover, we identified specific Smaug1 domains involved in MLO formation, and found that impaired Smaug1 MLO condensation correlates with mitochondrial defects. Mitochondrial complex I inhibition upon exposure to rotenone, but not strong mitochondrial uncoupling upon exposure to CCCP, rapidly induced the dissolution of Smaug1 MLOs. Metformin and rapamycin elicited similar effects, which were blocked by pharmacological inhibition of AMP-activated protein kinase (AMPK). Finally, we found that Smaug1 MLO dissolution weakens the interaction with target mRNAs, thus enabling their release. We propose that mitochondrial respiration and the AMPK-mTOR balance controls the condensation and dissolution of Smaug1 MLOs, thus regulating nuclear mRNAs that encode key mitochondrial proteins. This article has an associated First Person interview with the first authors of the paper.
p27Kip1 is required for PTEN-induced G1 growth arrest. (2001)

The tumor suppressor PTEN is one of the most commonly inactivated genes in human cancer. Glioblastoma multiforme cells harboring mutant PTEN have abnormally high levels of 3' phosphoinositides and elevated protein kinase B activity. Expression of wild-type PTEN in glioma cells, containing endogenous mutant PTEN, reduces 3' phosphoinositides levels, inhibits PKB activity, and induces G1 cell cycle arrest. We investigated the mechanism of the PTEN-induced growth arrest in glioma cell lines. Expression of PTEN is associated with increased expression of p27Kip1, decreased expression of cyclins A and D3, inhibition of cdk2 activity, and dephosphorylation of pRb. Inactivation of p53, by the human papilloma virus E6 oncoprotein, does not prevent PTEN-induced G1 arrest, implying that p53 is not required for G1 arrest. In contrast, p27Kip1 antisense oligonucleotides abrogated the growth arrest induced by PTEN. Furthermore, blocking p27Kip1 expression prevented the PTEN-induced reduction of cyclin-dependent kinase 2 activity, indicating that p27Kip1 functions upstream of cyclin-dependent kinase 2 in the PTEN regulatory cascade. These results implicate p27Kip1 as a critical mediator of PTEN-induced G1 arrest.
Making crafting visible while rendering labor invisible on the Etsy platform (2022)

Historically, crafts have been associated with women’s small-scale creative production in the home, equated with hobbies or amateur production, and devalued in comparison to both art and industrial production. During its early years, Etsy was seen as a champion of “handmade”, bringing visibility to crafts and providing economic value. This paper presents results of a qualitative study with 18 small online sellers of Etsy platform. Our study shows that Etsy’s sociotechnical design results in a high burden of invisible labor for sellers, including categories of labor not replicated by other online platforms. These new categories include negotiation and articulation work around defining and defending “handmade” products, understanding one’s intellectual property and how (and whether) to defend that IP elsewhere on the platform, understanding working of platform algorithms and adapting to changing platform regulations. Our findings provide new ways to frame the challenges faced by producers/sellers on emerging marketplace platforms.
Association of Hyperhomocysteinemia and Coronary Heart Disease in South Indian Population (2006)

Mccully first reported association of elevated levels of homocysteine with vascular disease. It was later confirmed by Wilken and Wilken in a case-control study. Development of aggressive, premature vascular disease with homocystinuria led to the hypothesis that mild to moderate elevations in plasma homocysteine might contribute to the development and progression of atherosclerosis in adults. Reduction of cardiovascular risk in homocystinuric patients with dietary methionine restriction and B vitamin supplementation suggested a causal role of higher levels of homocysteine in vascular pathology of homocystinuria.
Bond electronic polarization induced by spin (2006)

We study theoretically the electric polarization induced by noncollinear spin configurations in the limit of strong Hund coupling. We employ a model of two magnetic ions sandwiching an oxygen ion. It is shown that there appears a longitudinal polarization ${P}_{x}$ along the bond, which is roughly proportional to ${({m}_{r}^{x})}^{2}\ensuremath{-}{({m}_{l}^{x})}^{2}$ where ${m}_{r(l)}^{x}$ is the $x$ component of the spin orientation vector at right (left) magnetic ion. A numerical study of the model Hamiltonian yields both longitudinal and transverse electric dipole moments. The transverse polarization is shown to have a nonuniform as well as a uniform component, with the latter being consistent with the previous theory. The longitudinal polarization is nonuniform and oscillating with the period half that of the spin order, but the local magnitude is typically much larger than the uniform transverse polarization and may be detected by x-ray/neutron scattering experiments.
4MBA-labeled Ag-nanorod aggregates coated with SiO<sub>2</sub>: synthesis, SERS activity, and biosensing applications (2015)

A new nanostructure, silica-coated Ag nanorods (NRs) aggregate with 4-mercaptobenzoic acid molecules (4MBA-Ag NRs@SiO<sub>2</sub>), was prepared by a seed-mediated growth method and a modified Stöber method.
Backaction Evasion in Optical Lever Detection (2023)

We experimentally and theoretically investigate how measurement backaction from optical force noise can be evaded in an optical lever detection system probing a high Q membrane mechanical resonator.
Therapeutic Response to Dihydroartemisinin–Piperaquine for P. falciparum and P. vivax Nine Years after Its Introduction in Southern Papua, Indonesia (2018)

Dihydroartemisinin-piperaquine (DHP) has been the first-line treatment of uncomplicated malaria due to both <i>Plasmodium falciparum</i> and <i>Plasmodium vivax</i> infections in Papua, Indonesia, since March 2006. The efficacy of DHP was reassessed to determine whether there had been any decline following almost a decade of its extensive use. An open-label drug efficacy study of DHP for uncomplicated <i>P. falciparum</i> and <i>P. vivax</i> malaria was carried out between March 2015 and April 2016 in Timika, Papua, Indonesia. Patients with uncomplicated malaria were administered supervised DHP tablets once daily for 3 days. Clinical and laboratory data were collected daily until parasite clearance and then weekly for 6 weeks. Molecular analysis was undertaken for all patients with recurrent parasitemia. A total of 129 study patients were enrolled in the study. At day 42, the polymerase chain reaction-adjusted efficacy was 97.7% (95% confidence intervals [CI]: 87.4-99.9) in the 61 patients with <i>P. falciparum</i> malaria, and 98.2% [95% CI: 90.3-100] in the 56 patients with <i>P. vivax</i> malaria. By day 2, 98% (56/57) of patients with <i>P. falciparum</i> and 96.9% (63/65) of those with <i>P. vivax</i> had cleared their peripheral parasitemia; none of the patients were still parasitaemic on day 3. Molecular analysis of <i>P. falciparum</i> parasites showed that none (0/61) had K13 mutations associated previously with artemisinin resistance or increased copy number of <i>plasmepsin</i> 2-3 (0/61). In the absence of artemisinin resistance, DHP has retained high efficacy for the treatment of uncomplicated malaria despite extensive drug pressure over a 9-year period.
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>N</mml:mi></mml:math>-Body Interactions between Trapped Ion Qubits via Spin-Dependent Squeezing (2022)

We describe a simple protocol for the single-step generation of N-body entangling interactions between trapped atomic ion qubits. We show that qubit state-dependent squeezing operations and displacement forces on the collective atomic motion can generate full N-body interactions. Similar to the Mølmer-Sørensen two-body Ising interaction at the core of most trapped ion quantum computers and simulators, the proposed operation is relatively insensitive to the state of motion. We show how this N-body gate operation allows for the single-step implementation of a family of N-bit gate operations such as the powerful N-Toffoli gate, which flips a single qubit if and only if all other N-1 qubits are in a particular state.
THE MOVING LOCUS OF UREA SOLUTION ATOMIZING PARTICLES IN FURNACE OF BOILER (2010)

The atomizing particle size of a Y-jet partial-inner-mixed pneumatic atomizing selective non-catalytic reduction(SNCR) lance is decreasing along with the increase of gas loss rate,and with the increase of atomizing medium in case of the gas loss rate being the same.The moving locus of atomizing pariticles injected into a 100 MW four-corner tangential firing pulverized coal boiler has been studied by using CFD software platform and adopting numerical simulation method.It is obtained that the best injected atomizing particle size is between 0.3~0.5 mm in the case of injection rate being equal to 25 m/s.A denitrification test with injection of urea solution into boiler has been carried out,the denitrification efficiency is inceasing at first,and then decreasing along with the increase of atomizing particle size.In the event of the chemical equivalence of ammoniacal nitrogen being equal to 1.5,the maximum denitrification efficiency can reach 58%.
House Dust Endotoxin and Peripheral Leukocyte Counts: Results from Two Large Epidemiologic Studies (2017)

This is, to our knowledge, the first report of an association between house dust endotoxin and leukocyte count in a national survey. The finding was replicated in a farming population. Peripheral leukocyte count may be influenced by residential endotoxin exposure in diverse settings. https://doi.org/10.1289/EHP661.
Polymerization of methyl methacrylate with the neutral zirconocene enolate Cp2ZrMe[OC(Me)=CMe2] (2001)

The polymerization of methyl methacrylate (MMA) with the neutral enolate Cp2ZrMe[OC(OMe)=CMe2] in the absence and in the presence of zirconocene cations Cp2ZrMe+ to bypass the rate- limited initiation of the system was investigated. Only by itself the enolate is not active in polymerization, but as soon as the reaction system contains the cation MMA is quantitatively converted into syndiotactic-rich PMMA with high molecular weight (Mn > 100 000 g mol−1) and very narrow molecular weight distribution (Mw/Mn < 1.05). The rate of polymerization was found to be first order reffering to the neutral enolate and also reffering to the cation. Rate coefficents of all elementary reactions were determined and compared to those received by the kinetic investigation of the polymerization using the initiator system Cp2ZrMe2/Ph3CB(C6F5)4. The agreement of both sets of calculated coefficients is satisfying. These results confirm that the mechanism of Collins et al. is suitable to describe the properties of the polymerization process.
Nanopore Investigation of the Stereoselective Interactions between Cu<sup>2+</sup> and <scp>d</scp>,<scp>l</scp>-Histidine Amino Acids Engineered into an Amyloidic Fragment Analogue (2014)

Stereochemistry is an essential theme for a number of industries and applications, constructed around discriminating various chiral enantiomers, including amino acids, chiral metal complexes, and drugs. In this work, we designed a set of peptide mutants of the human amyloidic Aβ1-16 sequence, known to display an effective Cu(2+) coordinating pocket provided mainly by the intramolecular His-6, His-13, and His-14 residues, that were engineered to contain L- and D-His enantiomers in positions 6 and 13 and provide a local coordination environment with distinct Cu(2+) binding geometries and affinities. We examined the mechanism of selective chiral recognition of Cu(2+) by such mutant peptides, by quantifying their stochastic sensing in real time with a single α-hemolysin (α-HL) protein immobilized in a planar lipid membrane, while incubated in various concentrations of Cu(2+). Our data reveal that the Cu(2+)-binding affinity lies within the micromolar range, and decreases by orders of magnitude as L-His is replaced with its Denantiomer, with the effect being prevalent when such changes were inflicted on the His-6 residue. The presented results demonstrate the feasibility of tuning the metal selectivity in a relatively simple peptide substrate by enantiomeric replacement of key metal binding residues and illustrates the potential of the protein nanopores as a promising approach to quantify the chiral recognition of l/d amino acids by metals.
Pulsed power requirements for a high power KrF laser inertial confinement fusion test facility (2002)

A conceptual design for the pulsed power supply of a 68 kJ krypton fluoride (KrF) laser amplifier is discussed. The amplifier features double-sided electron beam pumping with eight diodes on either side of the laser cell. This amplifier is based on the technology developed for the recently completed Nike laser system. The authors envision a system in which thirty-two of these amplifiers are combined to produce a 2 MJ KrF laser direct drive inertial confinement test facility.
Presence and Stability of SARS-CoV-2 on Environmental Currency and Money Cards (2021)

The highly contagious nature of SARS-CoV-2 has led to several studies on the transmission of the virus. A little studied potential fomite of great concern in the community is currency, which has been shown to harbor microbial pathogens in several studies. Since the onset of the COVID-19 pandemic, many businesses in the United States have limited the use of banknotes in favor of credit cards. However, SARS-CoV-2 has shown greater stability on plastic in several studies. Herein, the stability of SARS-CoV-2 at room temperature on banknotes, money cards and coins was investigated. In vitro studies with live virus suggested SARS-CoV-2 was highly unstable on banknotes, showing an initial rapid reduction in viable virus and no viral detection by 24 hours. In contrast, SARS-CoV-2 was far more stable on money cards with live virus detected after 48 hours. Environmental swabbing of currency and money cards on and near the campus of Brigham Young University supported these results, with no detection of SARS-CoV-2 RNA on banknotes, and a low level on money cards. No viable virus was detected on either. These preliminary results suggest that the use of money cards over banknotes in order to slow the spread of this virus may be ill-advised. These findings should be investigated further through larger environmental studies involving more locations.
Add-on transmission attachments for the scanning electron microscope (2003)

This article presents simulation and experimental results for add-on transmission attachments that have been developed for the scanning electron microscope (SEM). A primary beam energy of around 30 keV is used to irradiate thin test specimens (&amp;lt;100 nm). A transmission lens attachment enables a conventional field emission SEM to improve its image resolution by an order of magnitude, providing an image magnification of several million and a spatial resolution down to 0.3 nm. In addition, a compact energy electron loss spectrometer attachment has been developed that uses the SEM’s built-in secondary electron detector.
Rapid, convenient, and highly sensitive detection of human hemoglobin in serum using a high-affinity bivalent antibody–enzyme complex (2021)

Human hemoglobin (Hb) is a biomarker of several diseases, and monitoring of Hb levels is required during emergent surgery. However, rapid and sensitive Hb detection methods are yet to be developed. The present study established a rapid, convenient, and highly sensitive detection method for Hb in human serum using a bivalent antibody-enzyme complex (AEC). AECs are promising sensing elements because of their ability to bind specific targets and their catalytic activity that produce signals. We recently reported a convenient and universal method to fabricate bivalent AECs with two antibody fragments, using the SpyCatcher/SpyTag system. The present study applied a bivalent AEC for highly sensitive and quantitative detection of human Hb. The bivalent anti-Hb AEC was successfully prepared by incubating both N- and C-terminus SpyCatcher-fused glucose dehydrogenase and SpyTag-fused anti-Hb single-chain variable fragments at 4 °C. As expected, the bivalent AEC for Hb with a multimeric structure showed higher affinity than the monovalent AEC, by means of avidity effects, unlike that for soluble epidermal growth factor receptor with a monomeric structure; this contributed to a great improvement in sensitivity. Finally, we established a rapid and wash-free homogeneous electrochemical detection system for Hb by integrating magnetic beads. The linear range of the system completely covered the clinically required Hb levels, even in human serum. This technology provides an ideal point-of-care test for Hb and other multimeric biomarkers.
Non-invasive monitoring of microbial triterpenoid production using nonlinear microscopy techniques (2023)

<b>Introduction:</b> Bioproduction of plant-derived triterpenoids in recombinant microbes is receiving great attention to make these biologically active compounds industrially accessible as nutraceuticals, pharmaceutics, and cosmetic ingredients. So far, there is no direct method for detecting triterpenoids under physiological conditions on a cellular level, information yet highly relevant to rationalizing microbial engineering. <b>Methods:</b> Here, we show in a proof-of-concept study, that triterpenoids can be detected and monitored in living yeast cells by combining coherent anti-Stokes Raman scattering (CARS) and second-harmonic-generation (SHG) microscopy techniques. We applied CARS and SHG microscopy measurements, and for comparison classical Nile Red staining, on immobilized and growing triterpenoid-producing, and non-producing reference <i>Saccharomyces cerevisiae</i> strains. <b>Results and Discussion:</b> We found that the SHG signal in triterpenoid-producing strains is significantly higher than in a non-producing reference strain, correlating with lipophile content as determined by Nile red staining. In growing cultures, both CARS and SHG signals showed changes over time, enabling new insights into the dynamics of triterpenoid production and storage inside cells.
Two Human Monoclonal HLA-Reactive Antibodies Cross-React with Mamu-B*008, a Rhesus Macaque MHC Allotype Associated with Control of Simian Immunodeficiency Virus Replication (2021)

MHC class I molecules play an important role in adaptive immune responses against intracellular pathogens. These molecules are highly polymorphic, and many allotypes have been characterized. In a transplantation setting, a mismatch between MHC allotypes may initiate an alloimmune response. Rhesus macaques (<i>Macaca mulatta</i>, <i>Mamu</i>) are valuable as a preclinical model species in transplantation research as well as to evaluate the safety and efficacy of vaccine candidates. In both lines of research, the availability of nonhuman primate MHC-reactive mAbs may enable in vitro monitoring and detection of presence of particular Mamu molecules. In this study, we screened a collection of thoroughly characterized HLA class I-specific human mAbs for cross-reactivity with rhesus macaque MHC class I allotypes. Two mAbs, OK4F9 and OK4F10, recognize an epitope that is defined by isoleucine (I) at amino acid position 142 that is present on the Indian rhesus macaque Mamu-B*008:01 allotype, which is an allotype known to be associated with elite control of SIV replication. The reactive pattern of a third mAb, MUS4H4, is more complex and includes an epitope shared on Mamu-A2*05:01 and -B*001:01-encoded Ags. This is the first description, to our knowledge, of human HLA-reactive mAbs that can recognize Mamu allotypes, and these can be useful tools for in vitro monitoring the presence of the relevant allelic products. Moreover, OK4F9 and OK4F10 can be powerful mAbs for application in SIV-related research.
Mechanism and rate constant of the reaction of atomic hydrogen with propyne (2000)

The potential energy surface for the reaction of atomic hydrogen with propyne has been studied at the G3//UB3LYP/6-31G(d) level of theory. Three reaction entrances were revealed, namely, terminal addition, nonterminal addition, and direct H-abstraction, leading to CH3CCH2, CH3CHCH, and H2+C3H3, respectively. The respective activation barriers are 1.7, 3.9, and 8.4 kcal/mol. The CH3-extrusion from CH3CHCH forms C2H2 via a barrier of about 32 kcal/mol. Several H-shift paths along the CCC skeleton were also examined for three C3H5 isomers. Multichannel RRKM and TST calculations have been carried out for the total and individual rate constants over a wide range of temperatures and pressures. The total rate constants possess both positive temperature dependence and typical “S” shaped fall-off behavior. At atmospheric pressure, the collisional stabilization of the initial adducts dominates the H+CH3CCH reaction at temperatures lower than 500 K, and at T&amp;gt;1000 K, CH3 and C2H2 are the major products. Moreover, the direct H-abstraction channel also contributes significantly to the overall reaction. The theoretical results are compared with those of previous studies.
ChemInform Abstract: Application of a Rhodium‐Catalyzed Addition/Cyclization Sequence Toward the Synthesis of Polycyclic Heteroaromatics. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Radical O→C Transposition: A Metal-Free Process for Conversion of Phenols into Benzoates and Benzamides (2011)

We report a metal-free procedure for transformation of phenols into esters and amides of benzoic acids via a new radical cascade. Diaryl thiocarbonates and thiocarbamates, available in a single high-yielding step from phenols, selectively add silyl radicals at the sulfur atom of the C═S moiety. This addition step, analogous to the first step of the Barton-McCombie reaction, produces a carbon radical which undergoes 1,2 O→C transposition through an O-neophyl rearrangement. The usually unfavorable equilibrium in the reversible rearrangement step is shifted forward via a highly exothermic C-S bond scission in the O-centered radical, which furnishes the final benzoic ester or benzamide product. The metal-free preparation of benzoic acid derivatives from phenols provides a potentially useful alternative to metal-catalyzed carbonylation of aryl triflates.