gebhart/patrepeval huggingface dataset:
Combining Different Privacy-Preserving Record Linkage Methods for Hospital Admission Data (2017)

Record linkage (RL) is the process of identifying pairs of records that correspond to the same entity, for example the same patient. The basic approach assigns to each pair of records a similarity weight, and then determines a certain threshold, above which the two records are considered to be a match. Three different RL methods were applied under privacy-preserving conditions on hospital admission data: deterministic RL (DRL), probabilistic RL (PRL), and Bloom filters. The patient characteristics like names were one-way encrypted (DRL, PRL) or transformed to a cryptographic longterm key (Bloom filters). Based on one year of hospital admissions, the data set was split randomly in 30 thousand new and 1,5 million known patients. With the combination of the three RL-methods, a positive predictive value of 83 % (95 %-confidence interval 65 %-94 %) was attained. Thus, the application of the presented combination of RL-methods seem to be suited for other applications of population-based research.
Computer-Aided Molecular Design:  Applications in Agrochemicals, Materials and Pharmaceuticals Edited by C. H. Reynolds (Rohm and Haas Company), M. K. Holloway (Merck Research Laboratories), H. K. Cox (Zeneca Ag Products). American Chemical Society, Washington, DC. 1995. x + 428 pp. 15 × 22.5 cm. $109.95. ISBN 0-8412-3160-5. (1997)

ADVERTISEMENT RETURN TO ISSUEPREVBook ReviewNEXTComputer-Aided Molecular Design: Applications in Agrochemicals, Materials and Pharmaceuticals Edited by C. H. Reynolds (Rohm and Haas Company), M. K. Holloway (Merck Research Laboratories), H. K. Cox (Zeneca Ag Products). American Chemical Society, Washington, DC. 1995. x + 428 pp. 15 × 22.5 cm. $109.95. ISBN 0-8412-3160-5.David R. LangleyView Author Information Bristol-Myers Squibb Pharmaceutical Research Institute 5 Research Parkway Wallingford, Connecticut 06492Cite this: J. Nat. Prod. 1997, 60, 8, 863Publication Date (Web):August 22, 1997Publication History Published online22 August 1997Published inissue 1 August 1997https://pubs.acs.org/doi/10.1021/np960637phttps://doi.org/10.1021/np960637pbook-reviewACS PublicationsCopyright © 1997 American Chemical Society and American Society of PharmacognosyRequest reuse permissionsArticle Views79Altmetric-Citations1LEARN 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:Agrochemicals,De novo modeling,Drug discovery,Materials,Pharmaceuticals Get e-Alerts
Immunoreactivity to Putative B-Cell Epitopes of Hepatitis G Virus Polyprotein in Viremic and Nonviremic Subjects (1999)

The hepatitis G virus (HGV) polyprotein was scanned by computer-aided prediction of antigenicity to search for B-cell epitopes. Four polypeptide sequences, V37D (amino acids [aa] 1685 to 1721), V36S (aa 2102 to 2137), P37R (aa 2156 to 2192), and C40P (aa 2280 to 2319), were identified and synthesized for use in immunoassays. Antibodies to these peptides were searched for in a panel of 239 serum samples, which were also tested for anti-E2 antibodies and HGV RNA. Furthermore, the course of HGV markers was studied prospectively in four patients who had been transfused with HGV RNA-positive blood. There was a negative association between immunoreactivity to V37D and P37R and presence of HGV RNA (2 of 53 and 1 of 53, respectively; P < 0.05); none of the subjects with dual antibody positivity was HGV RNA positive. Anti-V37D and anti-P37R antibodies compared favorably with anti-E2 antibodies as markers of recovery from HGV infection. These results might be useful for the development of new, more sensitive diagnostic assays.
PULSATING FLOW AND HEAT TRANSFER IN AN ANNULUS PARTIALLY FILLED WITH POROUS MEDIA (1997)

Abstract A numerical study is made of heat transfer characteristics from pulsating flow in a concentric annutus partially filled with porous media. The unsteady Navier-Stokes equations with the Brinkman-Forchheimer-extended Darcy model in the porous region art solved by using finite volume techniques. Changes in connective heat transfer and in effective anal heat conduction due to pulsation are investigated over broad ranges of the relevant parameters, i.e., the thickness of the porous layer and the frequency and amplitude of pulsation. The results obtained indicate that the effective axial thermal conductivity is substantially increased by pulsation, and this augmentation is more pronounced by partial fillings of porous material
Investing in shares in a multiannual time horizon – is trend following effective? (2015)

W artykule oceniono czteroletni kurs spółek, które w przeszłości w całej historii notowań zostały zidentyfikowane jako silnie wzrostowe. W odniesieniu do badanej populacji stwierdzono, że w długiej, wieloletniej perspektywie stawianie na trend w przypadku przedsiębiorstw silnie wzrostowych, ale o krótkiej historii notowań skutkuje niższymi stopami zwrotu z akcji niż w przypadku spółek dotychczas silnie wzrostowych, ale o długiej historii notowań. W badaniach uwzględniono spółki notowane na Giełdzie Papierów Wartościowych w Warszawie.
Distribution of Fiducial Registration Error in Rigid-Body Point-Based Registration (2009)

Rigid-body point-based registration is frequently used in computer assisted surgery to align corresponding points, or fiducials, in preoperative and intraoperative data. This alignment is mostly achieved by assuming the same homogeneous error distribution for all the points; however, due to the properties of the medical instruments used in measuring the point coordinates, the error distribution might be inhomogeneous and different for each point. In this paper, in an effort to understand the effect of error distribution in the localized points on the performed registration, we derive a closed-form solution relating the error distribution of each point with the performed registration accuracy. The solution uses maximum likelihood estimation to calculate the probability density function of registration error at each fiducial point. Extensive numerical simulations are performed to validated the proposed solution.
Understanding Local Defects in Li-Ion Battery Electrodes through Combined DFT/NMR Studies: Application to LiVPO<sub>4</sub>F (2017)

In a recent study, we showed by solid-state NMR that LiVPO4F, which is a promising material as positive electrode for Li-ion batteries, often exhibits some defects that may affect its electrochemical behavior. In this paper, we use DFT calculations based on the projector augmented-wave (PAW) method in order to model possible defects in this (paramagnetic) material and to compute the Fermi contact shifts expected for Li nuclei located in their proximity. The advantage of the PAW approach versus FP-LAPW we have been previously using is that it allows considering large supercells suitable to model a diluted defect. In the first part of this paper, we aim to validate the Fermi contact shifts calculation using the PAW approach within the VASP code. Then we apply this strategy for modeling possible defects in LiVPO4F. By analogy with the already existing homeotypic LiVOPO4 phase, we first replace one fluoride ion, along the VO2F4 chains, by an oxygen one and consider, in a second step, an association with a lithium vacancy. As a result, the agreement between the calculated NMR spectra and the experimental one is satisfying. In both cases, the local electronic structure and the spin transfer mechanisms from V3+ or V4+ ions to the Li nuclei are analyzed.
P257 The clinical decision support tool has low performance in predicting outcome to ustekinumab in Crohn’s disease (2022)

Abstract Background Several biologicals and small molecules have been added to the therapeutic arsenal of inflammatory bowel disease, which generated a wide interest in precision medicine. In this context, both clinical features and laboratory tests have shown some correlation with therapy outcome. Recently, an online clinical decision support tool1 (CDST) was built, using clinical and biochemical variables (e.g. disease location, prior anti-TNF exposure), to help physicians predict the outcome of various biological treatments in Crohn’s disease (CD). We sought to evaluate the predictive performance of this tool in patients with CD initiating ustekinumab (UST). Methods Baseline data were collected from consecutive CD patients who started UST IV induction followed by eight weekly UST 90 mg SC maintenance from December 2015 through March 2021 at our referral center. The probability of achieving clinical remission (low, intermediate, or high) was determined using the online CDST using patients’ data. Also, differences in rates of primary non-response and ustekinumab persistence were compared between CDST classifications. Primary non-response was defined as failing to attain endoscopic response (≥50% decrease in SES-CD) nor clinical response (a drop in the physician global assessment score or patients reported outcome), both assessed at month 6 after UST initiation. Finally, we studied the relation between the individual components used to construct the CDST and the three classifications in a univariate analysis. Results A total of 291 CD patients started UST, of whom 237 had objectively-assessed (CRP, fCal, symptoms or endoscopy) baseline disease activity. Using the CDST, the proportion of patients with “low”, “intermediate” or “high” probability to attain clinical remission were 11.8 % (n=28), 55.7 % (n=132) and 32.5 % (n=77), respectively. The CDST could not discriminate patients with primary non-response (p value = 0.18; Figure 1), nor identify trends in drug persistence (p value = 0.44; Figure 2). In the univariate analysis, 3 out of 9 components (active fistulizing disease, disease location and concomitant immunomodulatory use) were not significantly contributing to the CDST classification (Table 1). Conclusion The recently developed clinical decision support tool showed low performance in predicting short-term (primary clinical and endoscopic response) and long-term (drug persistence) real-life outcomes in CD patients starting UST. These findings underscore the necessity of incorporating molecular variables, in addition to clinical ones, to construct reliable and reproducible tools to predict therapeutic outcomes. 1. https://via.juxlyapps.com/pathway/archemedx/ibd-cdst/index.html#/disease-selection
Highly dispersed and disordered nickel–iron layered hydroxides and sulphides: robust and high-activity water oxidation catalysts (2018)

A rapid low-temperature microwave-assisted synthesis of nickel(iron) layered hydroxides and sulphides that exhibit robust catalytic activity for electrooxidation of alkaline water is introduced.
Localization of Receptors for Bombesin‐like Peptides in the Rat Brain<sup>1</sup> (1988)

BN-like peptides and receptors are present in discrete areas of the mammalian brain. By radioimmunoassay, endogenous BN/GRP, neuromedin B, and ranatensin-like peptides are present in the rat brain. High-to-moderate concentrations of BN/GRP are present in the rat hypothalamus and thalamus, whereas moderate-to-high densities of neuromedin B and ranatensin-like peptides are present in the olfactory bulb and hippocampus, as well as in the hypothalamus and thalamus. While the distribution of neuromedin B and ranatensin-like peptides appears similar, it is distinct from that of BN/GRP. When released from CNS neurons, these peptides may interact with receptors for BN-like peptides. BN, GRP, ranatensin, and neuromedin B inhibit specific [125I-Tyr4]BN binding with high affinity. By use of in vitro autoradiographic techniques to detect binding of [125I-Tyr4]BN to receptors for BN-like peptides, high grain densities were found in the olfactory bulb and tubercle, the nucleus accumbens, the suprachiasmatic and paraventricular nucleus of the hypothalamus, the central medial and paraventricular thalamic nuclei, the hippocampus, the dentate gyrus, and the amygdala of the rat brain. Some of these receptors may be biologically active and mediate the biological effects of BN-like peptides. For example, when BN is directly injected into the nucleus accumbens, pronounced grooming results and the effects caused by BN are reversed by spantide and [D-Phe12]BN. Thus, the putative BN receptor antagonists may serve as useful agents to investigate the biological significance of BN-like peptides in the CNS.
Simulating module anti-reflection coatings with SunSolve (2021)

Anti-reflection coatings are used on 92% of today’s module glass to reduce the front-surface reflection and increase the power output of the module. Currently, most anti-reflection coatings are designed to maximize transmittance at normal incidence to improve the power output at standard test conditions. However, in the field, where the meteorological conditions vary widely in time and space, it is not clear whether a maximum power gain at standard test conditions leads to maximum energy yield. Here, we use SunSolve Yield, a ray-tracing software, to investigate the optimum anti-reflection coating design by simulating the energy yield from a PV system under real-world conditions. We found that manufacturers could immediately provide a 0.3% increase in energy yield relative to their products today by simply increasing the ARC thickness by 20–40 nm thicker.
Large-scale machine learning using kernel methods (2006)

Kernel methods, such as Support Vector Machines (SVMs), are a core machine learning technology. They enjoy strong theoretical foundations and excellent empirical successes in many pattern-recognition applications. However, when kernel methods are applied to many emerging large-scale applications, such as video surveillance, multimedia information retrieval, and web mining, they suffer from the challenges of ineffective and inefficient training. In this dissertation, we explore these challenges and propose strategies to solve them. 
We first investigate the imbalanced-training challenge which causes the training of kernel methods to be ineffective. The imbalance-training problem occurs when the training instances of the target class are significantly outnumbered by the other training instances. In such situations, we show the class boundary trained from SVMs can be severely skewed toward the target class. We propose using conformal transformation on the kernel function in Reproducing Kernel Hilbert Space for tackling the challenge. 
The training performance of kernel methods greatly depends on the chosen kernel function or matrix. A kernel function or matrix defines a pairwise-similarity measurement between two data instances. We thus develop an algorithm to formulate a context-dependent distance function for measuring such similarity. We demonstrate that the learned distance function leads to improved performance for kernel-based clustering and classification tasks. Moreover, we also research the situations where the similarity measurement to formulate the kernel function might not induce a positive semi-definite (psd) kernel matrix, and hence cannot be used for training with kernel methods. We propose an analytical framework on evaluating several representative spectrum-transformation methods. 
Finally, we address the efficiency of kernel methods to achieve fast training on massive data. Especially, we focus on Support Vector Machines. The traditional solutions of SVMs suffer from the widely-known scalability problem. We propose an incremental algorithm, which performs approximate matrix-factorization operations, to speed up SVMs. Two approximate factorization schemes, Kronecker and incomplete Cholesky, are utilized in the primal-dual interior-point method (IPM) to directly solve the quadratic optimization problem in SVMs. 
Through theoretical analysis and extensive empirical studies, we show that our proposed approaches are able to perform more effectively, and efficiently, than traditional methods.
Structural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations (2017)

The human genome encodes two active Vaccinia-related protein kinases (VRK), VRK1 and VRK2. These proteins have been implicated in a number of cellular processes and linked to a variety of tumors. However, understanding the cellular role of VRKs and establishing their potential use as targets for therapeutic intervention has been limited by the lack of tool compounds that can specifically modulate the activity of these kinases in cells. Here we identified BI-D1870, a dihydropteridine inhibitor of RSK kinases, as a promising starting point for the development of chemical probes targeting the active VRKs. We solved co-crystal structures of both VRK1 and VRK2 bound to BI-D1870 and of VRK1 bound to two broad-spectrum inhibitors. These structures revealed that both VRKs can adopt a P-loop folded conformation, which is stabilized by different mechanisms on each protein. Based on these structures, we suggest modifications to the dihydropteridine scaffold that can be explored to produce potent and specific inhibitors towards VRK1 and VRK2.
Catalyst and process development for synthesis gas conversion to isobutylene. Quarterly report, January 1, 1993--March 31, 1993 (1993)

The objectives of this project are to develop a new catalyst, the kinetics for this catalyst, reactor models for trickle bed, slurry and fixed bed reactors, and simulate the performance of fixed bed trickle flow reactors, slurry flow reactors, and fixed bed gas phase reactors for conversion of a hydrogen lean synthesis gas to isobutylene. The six main accomplishments for the quarter are the following: (1) activity testing with the 7% (wt) Ce-ZrO{sub 2}, (2) activity testing the same catalyst with CO from an aluminum cylinder, (3) preparation of ZrO{sub 2} by heating zirconyl nitrate, (4) preparation of an active zirconia prepared by a modified sol gel procedure and evaluation of the catalytic activity of a commercial zirconia and the catalysts prepared by the sol gel procedure, (5) determining the effect of separator temperatures and oil flow rate on the performance of a trickle bed reactor, and (6) calculation of the equilibrium composition of the C{sub 2} to C{sub 5} olefins, and initiation of the development of a macrokinetic model. The details of each of these accomplishments are discussed.
New approaches for contactless power transmission systems integrated in PM motor drives transferring electrical energy to rotating loads (2011)

Two concepts for drive-integrated contactless energy transfer from the stator to the rotor of an electric motor are presented in this paper. Both drive systems offer the possibility of not only producing torque on the motor shaft, but also to power a rotating load. The power transfer is realized using the magnetic air gap fields. Problems inherent to contact-based methods (slip-rings and trailing cables), such as wear and limited mechanical angles, are resolved. The theoretical approach is explained for both methods. A comparison of the methods regarding the level of independence between torque generation and power transfer, efficiency and costs is made.
Validação do teste imunocromatográfico rápido IT-LEISH® para o diagnóstico da leishmaniose visceral humana (2008)

O teste imunocromatogrfico rpido IT-LEISH (DiaMed IT-LEISH) foi validado para o diagnstico da leishmaniose visceral (LV) em quatro reas endmicas do Brasil. O desempenho do IT-LEISH foi comparado ao da reao de imunofluorescncia indireta; e ao da reao imunoenzimtica, usando-se antgeno solvel de Leishmania chagasi e recombinante K39 (rK39). O estudo incluiu 332 pacientes com quadro clnico sugestivo de LV: 213 casos de LV confirmados parasitologicamente; e 119 no-casos, com confirmao de outra etiologia. O teste IT-LEISH apresentou sensibilidade de 93% e especificidade de 97%. As tcnicas RIFI (imunofluorescncia indireta), ELISA L. chagasi e ELISA rK39 apresentaram sensibilidade de 88%, 92% e 97% e especificidades de 81%, 77% e 84%, respectivamente. Os resultados confirmam a validade do teste IT-LEISH para o diagnstico da LV no Brasil.
Integrating Muscle Health in Predicting the Risk of Asymptomatic Vertebral Fracture in Older Adults (2021)

Although TLM was associated with bone quantity and quality in both sexes, sarcopenia and a low TBS were significant predictors of asymptomatic VF only in male participants.
Advances in organ-, body-, and disease-on-a-chip systems (2018)

Thought leader Michael Shuler provides an update on the <italic>Lab on a Chip</italic> organ-, body- and disease- on-a-chip thematic collection.
Protocatechuic acid production from lignin-associated phenolics (2021)

Biobased chemicals are gaining popularity and market in attempts to mitigate the deteriorating environmental and sustainability issues. Components of renewable agricultural and forest biomass residues are projected to serve as abundant precursors to synthesis of expanding range of products. Agroindustrial wastes comprises of several phenolic compounds associated with lignin via ether linkages such as ferulic acid, p-coumaric, syringic acid and vanillin. These aromatic chemicals have myriad industrial applications. In this study, p-coumaric acid and ferulic acid were found to be two major components in corn bran derived lignin hydrolysate. Engineered <i>Pseudomonas putida</i> KT2440 was constructed and found to convert p-coumaric acid and vanillic acid to protocatechuic acid in >90% and >50% yields, respectively. Engineering the strain included deletion of the gene encoding protocatechuate 3,4-dioxygenase, and overexpression of vanillate-O-demethylase gene from <i>Acinetobacter sp</i>. ADP1.
Modeling of nanosecond laser ablation with vapor plasma formation (2006)

A thermal model for nanosecond pulsed laser ablation is developed, where the heat conduction equation in the target and the gas dynamic equations in the vapor and ambient gas phase are coupled through the Knudsen layer (KL) relations for evaporation/recondensation at the target-vapor interface. The plasma formation and laser-plasma interactions are simulated in the model, which are found to have a significant effect on the laser-induced evaporation process. The shielding effect of the plasma reduces the laser energy reaching the target surface and therefore decreases the surface temperature, and the laser energy deposition in the plasma contributes to the increase of the vapor pressure above the KL. All of these will make the transition earlier from sonic evaporation stage to the subsonic evaporation and then to the recondensation stage, and therefore decrease the laser-induced evaporation depth. The simulation results are compared with experimental data for the plasma transmissivity, plasma front locations and velocities, laser ablation depth, and average plasma temperatures, and reasonably good agreements are obtained. This model is valid when the phase explosion does not occur, that is, when the target surface temperature does not reach or exceed the target material critical temperature.