gebhart/patrepeval huggingface dataset:
Correction: Author Correction: Integrated genomic analyses of de novo pathways underlying atypical meningiomas (2018)

Nature Communications 8: Article number: 14433 (2017) Published online 14 February 2017; Updated 20 April 2018 In this Article, a subset of the H3K27ac ChIP-seq data (15 benign meningiomas and 2 dura samples (Sample IDs: MN-297, MN-288, MN-292, MN-163, MN-1037, MN-105, MN-201, MN-249, MN-191, MN-1066, MN-169, MN-291, MN-24, MN-79, MN-1044, CONTROL1, CONTROL2) was reported previously in a publication by the corresponding author1.
Single-Cell, Time-Resolved Antimicrobial Effects of a Highly Cationic, Random Nylon-3 Copolymer on Live Escherichia coli (2015)

Synthetic random copolymers based on the nylon-3 (β-peptide) backbone show promise as inexpensive antimicrobial agents resistant to proteolysis. We present a time-resolved observational study of the attack of a particular copolymer MM63:CHx37 on single, live Escherichia coli cells. The composition and chain length of MM63:CHx37 (63% cationic subunits, 37% hydrophobic subunits, 35-subunit average length) were optimized to enhance antibacterial activity while minimizing lysis of human red blood cells. For E. coli cells that export GFP to the periplasm, we obtain alternating phase-contrast and green fluorescence images with a time resolution of 12 s over 60 min following initiation of copolymer flow. Within seconds, cells shrink and exhibit the same plasmolysis spaces that occur following abrupt external osmotic upshift. The osmoprotection machinery attempts to replenish cytoplasmic water, but recovery is interrupted by permeabilization of the cytoplasmic membrane (CM) to GFP. Evidently, the highly cationic copolymer and its counterions rapidly translocate across the outer membrane without permeabilizing it to GFP. The CM permeabilization event is spatially localized. Cells whose CM has been permeabilized never recover growth. The minimum inhibitory concentration (MIC) for cells lacking the osmolyte importer ProP is 4-fold smaller than for normal cells, suggesting that osmoprotection is an important survival strategy. In addition, at the time of CM permeabilization, we observe evidence of oxidative stress. The MIC under anaerobic conditions is at least 8-fold larger than under aerobic conditions, further implicating oxidative damage as an important bacteriostatic effect. Once the copolymer reaches the periplasm, multiple growth-halting mechanisms proceed in parallel.
The transformation of levopimaric acid into warburganal (1988)

The chiral resin acid levopimaric acid (1), isolated from pine oleoresin, is used as a starting material for the synthesis of (−)-warburganal (2). The synthesis proceeds via the endoperoxide of methyl levopimarate, which after ozonolysis, protection of the resulting aldehyde function, reduction, and treatment with sodium methoxide provides the tetranorditerpenoid 12a. The hemiacetal 12a is then transformed to a mixture of hemithioacetals. At this point the carbomethoxyl group at C-4 is reduced to a methyl group, and then a C-11, C-12 double bond is introduced. Ozonolysis followed by elimination of formic acid provides a mixture of olefins (27) that is hydroxylated at C-9. Removal of the protecting group then gives (−)-warburganal (2). The sequence requires 15 steps and the overall yield from levopimaric acid to warburganal is 2.7%.
Zusammenfassung (1980)

Die Zielsetzung der vorliegenden Untersuchungen bestand darin, den Bereich der Wahrnehmung und Konstruktion perspektivischer Darstellungen räumlicher Objekt(e)(-konfigurationen) in seiner Ausprägung in verschiedenen Medien bei 6 – 8jährigen Schülern zu analysieren.
The Use of Complementary and Alternative Therapies Among Middle-Aged and Older Cardiac Patients (2002)

This study investigated the prevalence, pattern, perceived benefits, and predictors of the use of complementary and alternative therapies (CAM) among middle-aged and older patients prior to cardiac surgery. Comprehensive information of 246 patients who came for preoperative medical assessment was obtained through face-to-face interviews. CAM utility of 225 was obtained by telephone the day before surgery. A computerized STS Adult Cardiac Database of Cardiac Surgery provided patients' medical information. One hundred eighty-two patients (80.9%) confirmed CAM use, including relaxation techniques, lifestyle-diet modification, spiritual healing, megavitamin therapy, massage, herbs or folk remedies, and imagery. Education, functional status, the number of non-cardiac chronic conditions, status as former cigarette smoker, public religiosity, and congestive heart failure predicted greater CAM utility, whereas cerebrovascular diseases and arrhythmia tended to predict less use. Findings suggest that there is considerable CAM use in this cardiac sample. Physicians and other health providers should investigate patients' CAM utility and promote collaborative medical care.
Why didn't my (great!) protocol get adopted? (2015)

What determines the eventual success of a protocol? Are certain features or properties more important? Do those vary according to a protocol's type? We explore these questions by applying data mining techniques to a rich repository of protocol specifications; IETF RFCs. While the investigation is still preliminary, some interesting findings have emerged. It confirms a number of intuitive results such as backward compatibility being key for protocol extensions and new versions, but not for new protocols. Similarly, the ability to improve performance is the single most important factor in the success of data plane protocols. Less intuitive findings, however, also emerge. Adding value to other protocols was the most significant factor in the success of new protocols, while extensions targeting security were the most likely to fail among new application and transport layer protocols. The paper offers a brief overview of our methodology and of the initial results it has afforded.
Total Chemical Synthesis and Catalytic Properties of the Enzyme Enantiomers L- and D-4-Oxalocrotonate Tautomerase (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal Chemical Synthesis and Catalytic Properties of the Enzyme Enantiomers L- and D-4-Oxalocrotonate TautomeraseMichael C. Fitzgerald, Igor Chernushevich, Kenneth G. Standing, Stephen B. H. Kent, and Christian P. WhitmanCite this: J. Am. Chem. Soc. 1995, 117, 45, 11075–11080Publication Date (Print):November 1, 1995Publication History Published online1 May 2002Published inissue 1 November 1995https://pubs.acs.org/doi/10.1021/ja00150a006https://doi.org/10.1021/ja00150a006research-articleACS PublicationsRequest reuse permissionsArticle Views452Altmetric-Citations62LEARN 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 Get e-Alerts
Transcending shift-invariance in the paraxial regime via end-to-end inverse design of freeform nanophotonics (2023)

Traditional optical elements and conventional metasurfaces obey shift-invariance in the paraxial regime. For imaging systems obeying paraxial shift-invariance, a small shift in input angle causes a corresponding shift in the sensor image. Shift-invariance has deep implications for the design and functionality of optical devices, such as the necessity of free space between components (as in compound objectives made of several curved surfaces). We present a method for nanophotonic inverse design of compact imaging systems whose resolution is not constrained by paraxial shift-invariance. Our method is end-to-end, in that it integrates density-based full-Maxwell topology optimization with a fully iterative elastic-net reconstruction algorithm. By the design of nanophotonic structures that scatter light in a non-shift-invariant manner, our optimized nanophotonic imaging system overcomes the limitations of paraxial shift-invariance, achieving accurate, noise-robust image reconstruction beyond shift-invariant resolution.
Oligonucleotide Sequence Mapping of Large Therapeutic mRNAs via Parallel Ribonuclease Digestions and LC-MS/MS (2019)

Characterization of mRNA sequences is a critical aspect of mRNA drug development and regulatory filing. Herein, we developed a novel bottom-up oligonucleotide sequence mapping workflow combining multiple endonucleases that cleave mRNA at different frequencies. RNase T1, colicin E5, and mazF were applied in parallel to provide complementary sequence coverage for large mRNAs. Combined use of multiple endonucleases resulted in significantly improved sequence coverage: greater than 70% sequence coverage was achieved on mRNAs near 3000 nucleotides long. Oligonucleotide mapping simulations with large human RNA databases demonstrate that the proposed workflow can positively identify a single correct sequence from hundreds of similarly sized sequences. In addition, the workflow is sensitive and specific enough to detect minor sequence impurities such as single nucleotide polymorphisms (SNPs) with a sensitivity of less than 1%. LC-MS/MS-based oligonucleotide sequence mapping can serve as an orthogonal sequence characterization method to techniques such as Sanger sequencing or next-generation sequencing (NGS), providing high-throughput sequence identification and sensitive impurity detection.
Computing exact aspect graphs of curved objects: solids of revolution (2003)

An approach to computing the exact orthographic aspect graph of curved objects is introduced. Curved corresponding to various visual events partition the Gaussian sphere into regions where the image structure is stable. A catalog of these events for piecewise-smooth objects is available from singularity theory. For a solid of revolution whose generator is an algebraic curve, each visual event is characterized by a system of polynomials whose roots can be computed by continuation methods. Within each region, the stable image structure is characterized by a variation of cylindrical algebraic decomposition and ray tracing. This approach has been implemented, and several examples are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Evidence for a major role of inhibin in the feedback control of FSH in the male rat (1989)

Adult rats (16-18/group) received a single intratesticular injection of 25, 100 or 400 microliters glycerol solution (7:3 in distilled water, v/v). Half of the rats in each group were given implants of testosterone, a testosterone-filled Silastic capsule (1.5 cm length) to provide serum values of testosterone within the normal range. After 1 week all animals were killed by decapitation. Serum concentrations of gonadotrophins, testosterone and immunoactive inhibin as well as testicular concentrations of testosterone and bioactive inhibin were determined. Testicular histology was studied in Paraplast-embedded tissue stained with PAS and haematoxylin-eosin. Glycerol treatment caused a dose-dependent ablation of spermatogenesis in a distinct area around the site of injection. Serum concentrations of FSH increased proportionally with increasing spermatogenic damage while serum LH and testosterone remained unaltered except with the highest glycerol dose. The rise in serum FSH was significantly correlated with serum (r = -0.70, P less than 0.001) and testicular (r = -0.66, P less than 0.001) concentrations of inhibin. A less pronounced correlation was found between LH and serum inhibin (r = 0.48). No correlation was found between the concentrations of LH and testicular inhibin or between serum concentrations of FSH and serum testosterone in the 25 and 100 microliters groups. Maintenance of low to normal serum testosterone concentrations by means of Silastic implants blocked the elevation of FSH in glycerol-treated animals but failed to affect significantly serum FSH in untreated rats. In all testosterone treated rats testicular inhibin concentrations were markedly reduced in the presence of lowered concentrations (7-14%) of testicular testosterone and unaltered serum FSH concentrations.
Polyphenic Risk Score Shows Robust Predictive Ability For Long-Term Future Suicidality (2022)

Abstract Suicides are preventable tragedies, if risk factors are tracked and mitigated. We had previously developed a new quantitative suicidality risk assessment instrument (Convergent Functional Information for Suicidality, CFI-S), which is in essence a simple polyphenic risk score, and deployed it in a busy urban Emergency Department, in a naturalistic cohort of consecutive patients. We report a four years follow-up of that population (n = 482). Overall, the single administration of the CFI-S was significantly predictive of suicidality over the ensuing 4 years (occurrence- ROC AUC 80%, severity- Pearson correlation 0.44, imminence-Cox regression Hazard Ratio 1.33). The best predictive single phenes (phenotypic items) were feeling useless (not needed), a past history of suicidality, and social isolation. We next used machine learning approaches to enhance the predictive ability of CFI-S. We divided the population into a discovery cohort (n=255) and testing cohort (n=227), and developed a deep neural network algorithm that showed increased accuracy for predicting risk of future suicidality (increasing the ROC AUC from 80% to 90%), as well as a similarity network classifier for visualizing patient’s risk. We propose that the widespread use of CFI-S for screening purposes, with or without machine learning enhancements, can boost suicidality prevention efforts. This study also identified as top risk factors for suicidality addressable social determinants.
CFD Technology for Rotorcraft Gearbox Windage Aerodynamics Simulation (2009)

A computational fluid dynamics (CFD) method is adapted, validated and applied to spinning gear systems with emphasis on predicting windage losses. Several spur gears and a disc are studied. The CFD simulations return good agreement with measured windage power loss. Turbulence modeling choices, the relative importance of viscous and pressure torques with gear speed and the physics of the complex 3-D unsteady flow field in the vicinity of the gear teeth are studied.
Reactivity of Monolayer Protected Silver Clusters toward Excess Ligand: A Calorimetric Study (2017)

Reactivity of monolayer protected atomically precise clusters of noble metals is of significant research interest. To date very few experimental data are available on the reaction thermodynamics of such clusters. Here we report a calorimetric study of the reaction of glutathione (GSH) protected silver clusters in the presence of excess ligand, GSH, using isothermal titration calorimetry (ITC). We have studied Ag11(SG)7 and Ag32(SG)19 clusters and compared their reactivity with GSH protected silver nanoparticles (AgNPs) and silver ions. Clusters show intermediate reactivity toward excess ligand compared to nanoparticles and silver ions. Several control experiments were performed to understand the degradation mechanism of these silver clusters and nanoparticles. The effect of dissolved oxygen in the degradation process was studied in detail, and it was found that it did not have a significant role, although alternate pathways of degradation with the involvement of oxygen cannot be ruled out. Direct confirmation of the fact that functionalized metal clusters fall in-between NPs and atomic systems in their stability is obtained experimentally for the first time. Several other thermophysical parameters of these clusters were also determined, including density, speed of sound, isentropic compressibility, and coefficient of thermal expansion.
Navigated transcranial magnetic stimulation following awake craniotomy for resection of glioma: Description of two cases (2020)

TBS may be safe in the immediate postoperative period for patients following brain tumor resection. Additional studies are needed to quantify the efficacy of TMS in improving neurologic deficits following tumor resection.
Improved integer programming approaches for chance-constrained stochastic programming (2013)

The Chance-Constrained Stochastic Programming (CCSP) is one of the models for decision making under uncertainty. In this paper, we consider the special case of the CCSP in which only the right-hand side vector is random with a discrete distribution having a finite support. The unit commitment problem is one of the applications of the special case of the CCSP. Existing methods for exactly solving the CCSP problems require an enumeration of scenarios when they model a CCSP problem using a Mixed Integer Programming (MIP). We show how to reduce the number of scenarios enumerated in the MIP model. In addition, we give another compact MIP formulation to approximately solve the CCSP problems.
Two-Dimensional Titanium Carbide MXene As a Cathode Material for Hybrid Magnesium/Lithium-Ion Batteries (2016)

As an alternative to pure lithium-ion, Li<sup>+</sup>, systems, a hybrid magnesium, Mg<sup>2+</sup>, and Li<sup>+</sup> battery can potentially combine the high capacity, high voltage, and fast Li<sup>+</sup> intercalation of Li-ion battery cathodes and the high capacity, low cost, and dendrite-free Mg metal anodes. Herein, we report on the use of two-dimensional titanium carbide, Ti<sub>3</sub>C<sub>2</sub>T<sub>x</sub> (MXene), as a cathode in hybrid Mg<sup>2+</sup>/Li<sup>+</sup> batteries, coupled with a Mg metal anode. Free-standing and flexible Ti<sub>3</sub>C<sub>2</sub>T<sub>x</sub>/carbon nanotube composite "paper" delivered ∼100 mAh g<sup>-1</sup> at 0.1 C and ∼50 mAh g<sup>-1</sup> at 10 C. At 1 C the capacity was maintained for >500 cycles at 80 mAh g<sup>-1</sup>. The Mo<sub>2</sub>CT<sub>x</sub> MXene also demonstrated good performance as a cathode material in this hybrid battery. Considering the variety of available MXenes, this work opens the door for exploring a new large family of 2D materials with high electrical conductivity and large intercalation capacity as cathodes for hybrid Mg<sup>2+</sup>/Li<sup>+</sup> batteries.
ChemInform Abstract: RING ANNULATION BY INTRAMOLECULAR NITRILE OXIDE CYCLOADDITION (1981)

Abstract Nitro‐cycloalkene (I) werden mit Phenylisocyanat in Gegenwart von Triethylamin über die Zwischenstufe der Nitriloxide durch intramolekulare Addition in tricyclische Isoxazoline (II) übergefuhrt.
Force control of a permanent magnet for minimally-invasive procedures (2008)

Magnetic actuation can be used for minimally invasive control of medical devices such as robotic catheters. However, current systems that use large permanent magnets are limited in their ability to modulate the magnetic force. In this paper we present a proof-of-concept system for closed-loop force control of a permanent magnet using shielding materials. Our system consists of a device that actuates pieces of high-permeability metal to redirect magnetic lines of flux. This is used to regulate the attractive force exerted by a large controlling magnet on a smaller moving magnet. We compare the performance of our system to FEA simulations and present experimental results for constant-force control at forces and distances that are medically relevant.
Retention Characteristics of Zero-capacitor RAM (Z-RAM) cell based on FinFET and Tri-Gate devices (2006)

In this paper we experimentally study for the first time the retention characteristics of Z-RAM cells based on CMOS FinFET and tri-gate devices. A retention time of few milliseconds is measured at room temperature on 100 nm devices. This FinFET based Z-RAM memory will allow manufacturing of very low cost DRAMs and eDRAMs for 45 and sub 45-nm generations.
Supplementary Methods, Figure Legends 1-3, Tables 1A-B from Engineered Thio-Trastuzumab-DM1 Conjugate with an Improved Therapeutic Index to Target Human Epidermal Growth Factor Receptor 2–Positive Breast Cancer (2023)

Supplementary Methods, Figure Legends 1-3, Tables 1A-B from Engineered Thio-Trastuzumab-DM1 Conjugate with an Improved Therapeutic Index to Target Human Epidermal Growth Factor Receptor 2–Positive Breast Cancer
Second-order-based blind signal separation in reverberant environments (2014)

The aim of this paper was to provide a derivation to explain the performance of the second-order-based blind signal separation (BSS) in reverberant environments. In particular, the second-order-based BSS algorithm, which exploits non-stationarity of the input signals, is investigated. The derivation provides a quantitative link between the reverberation parameter of the environment with the cost function of the BSS. Importantly, the theoretical finding complements existing literature on the interpretation of BSS and provides incremental insight to its performance.
Enhanced diameter bounding via structural transformation (2004)

Bounded model checking (BMC) has gained widespread industrial use due to its relative scalability. Its exhaustiveness over all valid input vectors allows it to expose arbitrarily complex design flaws. However, BMC is limited to analyzing only a specific time window, hence will only expose those flaws which manifest within that window and thus connect readily prove correctness. The diameter of a design has thus become an important concept - a bounded check of depth equal to the diameter constitutes a complete proof. While the diameter of a design may be exponential in the number of its state elements, in practice it often ranges from tens to a few hundred regardless of design size. Therefore, a powerful diameter overapproximation technique may enable automatic proofs that otherwise would be infeasible. Unfortunately, exact diameter calculation requires exponential resources, and overapproximation techniques may yield exponentially loose bounds. In this paper, we provide a general approach for enabling the use of structural transformations, such as redundancy removal, retiming, and target enlargement, to tighten the bounds obtained by arbitrary diameter approximation techniques. Numerous experiments demonstrate that this approach may significantly increase the set of designs for which practically useful diameter bounds may be obtained.
Total tau and Phosphorylated tau 181 Levels in the Cerebrospinal Fluid of Patients With Frontotemporal Dementia Due to P301L and G272V tau Mutations (2003)

The tauopathy in P301L and G272V does not appear to be associated with an evident increase in CSF levels of Ptau-181 in FTD patients with these tau mutations, in contrast with findings in patients with AD.