gebhart/patrepeval huggingface dataset:
Atomistic Insights into Structure and Dynamics of Neodymium(III) Complexation with a Bis-lactam Phenanthroline Ligand in the Organic Phase (2022)

Rare-earth elements (REEs) such as neodymium are critical materials needed in many important technologies, and rigid neutral bis-lactam-1,10-phenanthroline (BLPhen) ligands show one of the highest extraction performance for complexing Nd(III) in REE uptake and separation processes. However, the local structure of the complexes formed between BLPhen and Nd(III) in a typical organic solvent such as dichloroethane (DCE) is unclear. Here, we perform first-principles molecular dynamics (FPMD) simulations to unveil the structure of complexes formed by BLPhen with Nd(NO<sub>3</sub>)<sub>3</sub> in the DCE solvent. BLPhen can bind to Nd(III) in either 1:1 or 2:1 fashion. In the 1:1 complex, three nitrates bind to Nd(III) via the bidentate mode in the first solvation shell, leading to the formation of a neutral complex, [Nd(BLPhen)(NO<sub>3</sub>)<sub>3</sub>]<sup>0</sup>, in the organic phase. In contrast, there are two nitrates in the first solvation shell in the 2:1 complex, creating a charged complex, [Nd(BLPhen)<sub>2</sub>(NO<sub>3</sub>)<sub>2</sub>]<sup>+</sup>. The third nitrate was found to be far away from the metal center, migrating to the outer solvation shell. Our simulations show that the binding pocket formed by the two rigid BLPhen ligands allows ample space for two nitrates to bind to the Nd(III) center from opposite sides. Our findings of two nitrates in the first solvation shell of the 2:1 complex and the corresponding bond distances agree well with the available crystal structure. This study represents the first accurate FPMD modeling of the BLPhen-Nd(III) complexes in an explicit organic solvent and opens the door to more atomistic understanding of REE separations from first principles.
Predicting and optimizing asymmetric catalyst performance using the principles of experimental design and steric parameters (2011)

Using a modular amino acid based chiral ligand motif, a library of ligands was synthesized systematically varying the substituents at two positions. The effects of these changes on ligand structure were probed in the enantioselective allylation of benzaldehyde, acetophenone, and methylethyl ketone under Nozaki-Hiyama-Kishi conditions. The resulting three-dimensional datasets allowed for the construction of mathematical surface models which describe the interplay of substituent effects on enantioselectivity for a given reaction. The surface models were both extrapolated and manipulated to predict the enantioselective outcomes of several previously untested ligands. Analyses were also used to predict optimal ligand structure of a minimal dataset. Within the dataset, a linear free energy relationship was also discovered and a direct comparison of both the linear prediction as well as the three-dimensional prediction illustrates the potential predictive power of using a three-dimensional model approach to asymmetric catalyst development.
Passivated, Highly Reflecting, Laser Contacted Ge Rear Side for III-V Multi-Junction Solar Cells (2021)

This article describes the successful integration of a passivated, highly reflecting Ge rear side into a III-V multijunction solar cell. The use of lowly doped Ge and the new rear side leads to the aimed increase in Ge cell current up to 1.6 mA.cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> , demonstrated by external quantum efficiency and I-V measurements. For the contact formation, two different types of laser processes were conducted and evaluated-the laser fired contact route and the PassDop route. In both cases, the formation of a local back surface field preserves the passivation of the contact points. A laser pitch and laser power variation leads to a good performing back contact. The passivation effect is proven experimentally and is qualitatively accessed with cell simulations.
Sensitivity and Specificity of Lung Cancer Screening with Sputum Cytology and Chest X-Ray Film in a High Risk Group. (1994)

高危険群における胸部X線写真と喀痰細胞診を組み合わせた検査の, 肺癌発見に関する感度および特異度を算出し, あわせて喉頭癌も含めた値も算出した. 12町村で1986, 87年に胸部X線写真と喀痰細胞診の両者を受診したB. I. 600以上の40歳以上の男女, のべ4718名を対象として, 1988年末現在での肺癌, 喉頭癌の罹患の有無をがん登録と照合し調査した.肺癌の診断の12ヵ月前以内に陰性とされた集検を偽陰性と定義すると, 感度は75.0%, 特異度は97.0%であった. 喉頭癌も含めた感度, 特異度は, それぞれ76.9%, 97.1%であった. 他の2種の定義に基づいた感度, 特異度に関しても, あわせて算出した.
Ultraviolet Laser Ignition of Premixed Gases by Efficient and Resonant Multiphoton Photochemical Formation of Microplasmas (1987)

Abstract Ignition properties of premixed H2/O2 and H2/N2O flows at atmospheric pressure have been studied using an ultraviolet laser as the ignition source. Tuning the laser in the 225.6 nm wavelength region has yielded three minima in the amount of incident laser energy (ILE) that is required to ignite either mixture. The minima correspond exactly to the two-photon resonant excitation wavelengths for the three spin-orbit split ground electronic states of oxygen atoms. A determination of the ILE necessary to ignite both premixed flows as a function of equivalence ratio shows a minimum far into the fuel-lean region. Also, the minimum ILE value for the ignition of H2/O2 was found to be around 0.3 mJ, while ignition of the same mixture with the green beam from a frequency doubled Nd: YAG laser (532 nm) required an ILE value near 13 mJ. Additional time-resolved spectral studies were carried out on O2 and N2O flows alone. These indicated a resonant formation of a microplasma with a lifetime on the order of 100 nsec. All of these results lead to the conclusion that multiphoton photochemical ignition is a phenomenon consisting of three major components: (1) the multiphoton photochemical formation of oxygen atoms; (2) multiphoton ionization of these atoms to efficiently form free electrons in the laser focal volume; (3) the formation of a laser microplasma using the electrons formed in the previous process as seed electrons. As such, this new laser ignition source appears to be more efficient and more controllable than the well-known laser-produced spark (gas breakdown) process and it thus should be useful for further ignition studies.
Bismuth(iii) triflate as a novel and efficient activator for glycosyl halides (2021)

Presented herein is the discovery that bismuth(iii) trifluoromethanesulfonate (Bi(OTf)<sub>3</sub>) is an effective catalyst for the activation of glycosyl bromides and glycosyl chlorides. The key objective for the development of this methodology is to employ only one promoter in the lowest possible amount and to avoid using any additive/co-catalyst/acid scavenger except molecular sieves. Bi(OTf)<sub>3</sub> works well in promoting the glycosidation of differentially protected glucosyl, galactosyl, and mannosyl halides with many classes of glycosyl acceptors. Most reactions complete within 1 h in the presence of only 35% of green and light-stable Bi(OTf)<sub>3</sub> catalyst.
Security in wireless sensor networks (2004)

They are susceptible to a variety of attacks, including node capture, physical tampering, and denial of service, while prompting a range of fundamental research challenges.
WE‐DE‐201‐11: Sensitivity and Specificity of Verification Methods Based On Total Reference Air Kerma (TRAK) Or On User Provided Dose Points for Graphically Planned Skin HDR Brachytherapy (2016)

Purpose: To investigate the sensitivity and specificity of a novel verification methodology for image‐guided skin HDR brachytherapy plans using a TRAK‐based reasonableness test, compared to a typical manual verification methodology. Methods: Two methodologies were used to flag treatment plans necessitating additional review due to a potential discrepancy of 3 mm between planned dose and clinical target in the skin. Manual verification was used to calculate the discrepancy between the average dose to points positioned at time of planning representative of the prescribed depth and the expected prescription dose. Automatic verification was used to calculate the discrepancy between TRAK of the clinical plan and its expected value, which was calculated using standard plans with varying curvatures, ranging from flat to cylindrically circumferential. A plan was flagged if a discrepancy &gt;10% was observed. Sensitivity and specificity were calculated using as a criteria for true positive that &gt;10% of plan dwells had a distance to prescription dose &gt;1 mm different than prescription depth (3 mm + size of applicator). All HDR image‐based skin brachytherapy plans treated at our institution in 2013 were analyzed. Results: 108 surface applicator plans to treat skin of the face, scalp, limbs, feet, hands or abdomen were analyzed. Median number of catheters was 19 (range, 4 to 71) and median number of dwells was 257 (range, 20 to 1100). Sensitivity/specificity were 57%/78% for manual and 70%/89% for automatic verification. Conclusion: A check based on expected TRAK value is feasible for irregularly shaped, image‐guided skin HDR brachytherapy. This test yielded higher sensitivity and specificity than a test based on the identification of representative points, and can be implemented with a dedicated calculation code or with pre‐calculated lookup tables of ideally shaped, uniform surface applicators.
Forgotten people, forgotten diseases: the neglected tropical diseases and their impact on global health and development (2008)

The neglected tropical diseases (NTDs) are the most common infections of the world's poor, but few people know about these diseases and why they are so important. This second edition of Forgotten People, Forgotten Diseases provides an overview of the NTDs and how they devastate the poor, essentially trapping them in a vicious cycle of extreme poverty by preventing them from working or attaining their full intellectual and cognitive development. Author Dr Peter J. Hotez highlights a new opportunity to control and perhaps eliminate these ancient scourges, though alliances between nongovernmental development organisations and private-public partnerships to create a successful environment for mass drug administration and product development activities. Forgotten People, Forgotten Diseases is an essential resource for anyone seeking a roadmap to coordinate global advocacy and mobilization of resources to combat NTDs. This title is published by the American Society of Microbiology Press and distributed by Taylor and Francis in rest of world territories.
Importance of Spectroscopic Effects in Laser-based Flux Measurements (2020)

&amp;lt;p&amp;gt;A significant portion of the production and consumption of trace gases (e.g. CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, CH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;, N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O, NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;, etc.) occurs in areas without sufficient infrastructure or easily available grid power to run traditional closed-path flux stations. Open-path analyzer design allows such measurements with power consumption 10-150 times below present closed-path technologies, helping to considerably expand the global coverage and improve the estimates of gas emissions and budgets, informing the remote sensing and modeling communities and policy decisions, all the way to IPCC reports. Broad-band NDIR devices have been used for open-path CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O measurements since the late 1970s, but since recently, a growing number of new narrow-band laser-based instruments are being rapidly developed.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;The new design comes with its own challenges, specifically: (i) mirror contamination, and (ii) uncontrolled air temperature, pressure and humidity, affecting both the gas density and the laser spectroscopy of the measurements. While the contamination can be addressed via automated cleaning, and density effects can be addressed via the Webb-Pearman-Leuning approach, the spectroscopic effects of the in-situ temperature, pressure and humidity fluctuations on laser-measured densities remain a standing methodological question.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;Here we propose a concept accounting for such effects in the same manner as Webb et al. (1980) proposed to account for respective density effects. Derivations are provided for a general case of flux of any gas, examined using a specific example of CH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt; fluxes from a commercially available analyzer, and then tested using &amp;quot;zero-flux&amp;quot; experiment.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;The proposed approach helps reduce errors in open-path, enclosed, and temperature- or pressure-uncontrolled closed-path laser-based flux measurements due to the spectroscopic effects from few percent to multiple folds, leading to methodological advancement and geographical expansion of the use of such systems providing reliable and consistent results for process-level studies, remote sensing and Earth modeling applications, and GHG policy decisions.&amp;lt;/p&amp;gt;
De Novo Design and Evolution of Artificial Disulfide Isomerase Enzymes Analogous to the Bacterial DsbC (2008)

The Escherichia coli disulfide isomerase, DsbC is a V-shaped homodimer with each monomer comprising a dimerization region that forms part of a putative peptide-binding pocket and a thioredoxin catalytic domain. Disulfide isomerases from prokaryotes and eukaryotes exhibit little sequence homology but display very similar structural organization with two thioredoxin domains facing each other on top of the dimerization/peptide-binding region. To aid the understanding of the mechanistic significance of thioredoxin domain dimerization and of the peptide-binding cleft of DsbC, we constructed a series of protein chimeras comprising unrelated protein dimerization domains fused to thioredoxin superfamily enzymes. Chimeras consisting of the dimerization domain and the alpha-helical linker of the bacterial proline cis/trans isomerase FkpA and the periplasmic oxidase DsbA gave rise to enzymes that catalyzed the folding of multidisulfide substrate proteins in vivo with comparable efficiency to E. coli DsbC. In addition, expression of FkpA-DsbAs conferred modest resistance to CuCl2, a phenotype that depends on disulfide bond isomerization. Selection for resistance to elevated CuCl2 concentrations led to the isolation of FkpA-DsbA mutants containing a single amino acid substitution that changed the active site of the DsbA domain from CPHC into CPYC, increasing the similarity to the DsbC active site (CGYC). Unlike DsbC, which is resistant to oxidation by DsbB-DsbA and does not normally catalyze disulfide bond formation under physiological conditions, the FkpA-DsbA chimeras functioned both as oxidases and isomerases. The engineering of these efficient artificial isomerases delineates the key features of catalysis of disulfide bond isomerization and enhances our understanding of its evolution.
Investigating Prefix Propagation through Active BGP Probing (2006)

For an Internet Service Provider (ISP), the knowledge of which interdomain paths could be traversed by its BGP announcements - and thus traffic flows - is essential to predict the impact of network faults, to develop effective traffic engineering and peering strategies, and to assess the quality of upstream providers. However, current methodologies do not provide this information. We present methodologies to discover how the BGP announcements for an ISP’s prefix are propagated through the Internet using withdrawals and specially crafted AS-sets. The techniques allow an ISP to determine which paths could be traversed in the presence of network faults or different routing policies on the ISP’s part and to deduce the routing policies of other ISPs with respect to its network. We validate our techniques through experimentation in the IPv6 and IPv4 Internet, showing that they can be safely and effectively applied in real-world situations.
Intratesticular and plasma steroid profiles in fertile and infertile men (1982)

In 24 apparently healthy men who requested sterilization by vasectomy, we have measured the intratesticular and peripheral plasma levels of 9 unconjugated and 5 sulphoconjugated steroids. These steroid levels were then compared with those found in a group of 18 men, admitted to the hospital with complaints of infertility. With the exception of higher dihydrotestosterone levels in the infertile group, no differences were found between the two groups with regard to the peripheral plasma levels of the unconjugated or sulphoconjugated steroids studied. On the other hand, the intratesticular levels of cortisol, pregnenolone, androstenedione, dihydrotestosterone, pregnenolone sulphate and testosterone sulphate (but not those of testosterone) were significantly diminished in the infertile group. With the exception of dehydroepiandrosterone levels in the fertile group, and dehydroepiandrosterone sulphate and dihydrotestosterone sulphate in the infertile group, the intratesticular steroid levels were uncorrelated with the plasma levels. The data are interpreted as suggesting that a) male infertility may be associated with intratesticular alterations of steroid metabolism which are not reflected by the peripheral steroid levels; b) the plasma and intratesticular levels of testosterone are not sensitive enough indices for the endocrine evaluation of male infertility; c) the role of the sulphoconjugated forms of steroids in the maintenance of male fertility deserves further investigation.
Six-Membered Cyclic Carbonate Having Styrene Moiety as a Chemically Recyclable Monomer. Construction of Novel Cross-Linking−De-Cross-Linking System of Network Polymers (2005)

This article deals with (1) synthesis and anionic polymerization of a six-membered cyclic carbonate having styrene moiety, (2) anionic depolymerization of the obtained polymer, (3) radical cross-linking of the obtained polymer, and (4) anionic de-cross-linking of the cross-linked polymer. The monomer 5-ethyl-5-[(p-vinylphenyl) methoxymethyl]-1,3-dioxan-2-one (St6CC) underwent anionic polymerization with potassium tert-butoxide (t-BuOK) as an initiator in THF to afford the corresponding polycarbonate [poly(St6CC)]. It was confirmed that this polymerization was equilibrium polymerization by the relationships between the polymerization temperature and monomer conversion. Poly(St6CC) underwent anionic depolymerization with t-BuOK (5 mol % vs polymer repeating unit) as a catalyst in THF (0.1 M) at 20 °C for 24 h to recover St6CC in 60% yield. Treatment of poly(St6CC) with a radical initiator afforded the cross-linked polymer. Employment of styrene as the comonomer satisfactorily afforded the corresponding cross-linked polymer. It underwent anionic de-cross-linking with t-BuOK (10 mol % vs polymer repeating unit) in THF at 50 °C for 24 h to afford a THF-soluble polymer. The yield of the THF-soluble part increased as the styrene composition in the cross-linked polymer increased. It was suggested that the de-cross-linking efficiency depended on the cross-linking density.
Direct Synthesis of Imines from Alcohols and Amines with Liberation of H2 (2010)

A clean sweep: Aryl and aliphatic imines can be synthesized directly and efficiently from alcohols and amines under mild, neutral conditions with the liberation of only molecular hydrogen and water (see scheme; R=isopropyl, tert-butyl). This general, environmentally benign reaction is catalyzed by a de-aromatized ruthenium PNP pincer complex (0.2 mol %), and can proceed in toluene under an inert atmosphere or under air.
Blood Outgrowth and Proliferation of Endothelial Colony Forming Cells are Related to Markers of Disease Severity in Patients with Pulmonary Arterial Hypertension (2018)

In pulmonary arterial hypertension (PAH), lung-angioproliferation leads to increased pulmonary vascular resistance, while simultaneous myocardial microvessel loss contributes to right ventricular (RV) failure. Endothelial colony forming cells (ECFC) are highly proliferative, angiogenic cells that may contribute to either pulmonary vascular obstruction or to RV microvascular adaptation. We hypothesize ECFC phenotypes (outgrowth, proliferation, tube formation) are related to markers of disease severity in a prospective cohort-study of 33 PAH and 30 healthy subjects. ECFC were transplanted in pulmonary trunk banded rats with RV failure. The presence of ECFC outgrowth in PAH patients was associated with low RV ejection fraction, low central venous saturation and a shorter time to clinical worsening (5.4 months (0.6⁻29.2) vs. 36.5 months (7.4⁻63.4), <i>p</i> = 0.032). Functionally, PAH ECFC had higher proliferative rates compared to control in vitro, although inter-patient variability was high. ECFC proliferation was inversely related to RV end diastolic volume (<i>R</i>² = 0.39, <i>p</i> = 0.018), but not pulmonary vascular resistance. Tube formation-ability was similar among donors. Normal and highly proliferative PAH ECFC were transplanted in pulmonary trunk banded rats. While no effect on hemodynamic measurements was observed, RV vascular density was restored. In conclusion, we found that ECFC outgrowth associates with high clinical severity in PAH, suggesting recruitment. Transplantation of highly proliferative ECFC restored myocardial vascular density in pulmonary trunk banded rats, while RV functional improvements were not observed.
Problems and Promises of Introducing the Magnetic Resonance Imaging Linear Accelerator Into Routine Care: The Case of Prostate Cancer (2020)

The new radiotherapy high field, 1.5 Tesla MRI-guided linear accelerator (MR-Linac) is being clinically introduced. Sensing and evaluating opportunities and barriers at an early stage will facilitate its eventual scale-up. This study investigates the opportunities and barriers to the implementation of MR-Linac into prostate cancer care based on 43 semi-structured interviews with Dutch oncology care professionals, hospital and division directors, patients, payers and industry. The analysis was guided by the Non-adoption, Abandonment, Scale-up, Spread, and Sustainability framework of new medical technologies and services. Opportunities included: the acquirement of (1) advanced MRI-guided radiotherapy technology with (2) the potential for improved patient outcomes and (3) economic benefits, as well as (4) professional development and (5) a higher hospital quality profile. Barriers included: (1) technical complexities, (2) substantial staffing and structural investments, (3) the current lack of empirical evidence of clinical benefits, (4) professional silos, and (5) the presence of patient referral patterns. While our study confirms the expected technical and clinical prospects from the literature, it also reveals economic, organizational, and socio-political challenges.