gebhart/patrepeval huggingface dataset:
Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences (2020)

The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics.
Analysis of Phosphorus Flame Retardant Induced Leakage Currents in IC Packages Using SQUID Microscopy (2006)

A superconducting quantum interference device (SQUID) was used to assess leakage currents between adjacent leads of an encapsulated semiconductor device. An electrically conductive path was observed in the package interior. Red phosphorus, used as flame retardant in the mold compound, was identified as the cause of the leakage current path. This paper discusses the principle of SQUID, how it was used to verify and locate the sites of the failure, and the root cause of this new leakage current failure mechanism
Integrated Molecular Characterization of Uterine Carcinosarcoma (2020)

SummaryWe performed genomic, epigenomic, transcriptomic, and proteomic characterizations of uterine carcinosarcomas (UCSs). Cohort samples had extensive copy-number alterations and highly recurrent somatic mutations. Frequent mutations were found in TP53, PTEN, PIK3CA, PPP2R1A, FBXW7, and KRAS, similar to endometrioid and serous uterine carcinomas. Transcriptome sequencing identified a strong epithelial-to-mesenchymal transition (EMT) gene signature in a subset of cases that was attributable to epigenetic alterations at microRNA promoters. The range of EMT scores in UCS was the largest among all tumor types studied via The Cancer Genome Atlas. UCSs shared proteomic features with gynecologic carcinomas and sarcomas with intermediate EMT features. Multiple somatic mutations and copy-number alterations in genes that are therapeutic targets were identified.
Reduced mortality among COVID-19 ICU patients after treatment with HemoClear convalescent plasma in Suriname (2022)

Abstract Convalescent plasma is a promising therapy for coronavirus disease 2019 (COVID-19), but its efficacy in intensive care unit (ICU) patients in a low and middle income country setting such as Suriname is unknown. Bedside plasma separation using the HemoClear device made convalescent plasma therapy accessible as treatment option in Suriname. Two hundred patients with severe SARS-CoV-2 infection requiring intensive care were recruited. Fifty eight patients (29%) received COVID-19 convalescent plasma (CCP) treatment in addition to standard of care (SOC). The CCP treatment and SOC groups were matched by age, sex, and disease severity scores. Mortality in the CCP treatment group was significantly lower than in the SOC group (21% versus 39%; Fisher’s exact P = 0.0133). Multivariate analysis using ICU days showed that CCP treatment reduced mortality (hazard ratio [HR], 0.35; 95% CI, 0.18–0.66; P = 0.001), while complication of acute renal failure (creatinine levels &gt;110 mol/L; HR, 4.45; 95%CI, 2.54-7.80; P &lt; 0.0001) was independently associated with death. Decrease in chest X-ray score in the CCP treatment group (median -3 points, IQR -4 to -1) was significantly greater than in the SOC group (median -1 point, IQR -3 to 1, Mann Whitney P = 0.0004). Improvement in PaO2/FiOs ratio was also significantly greater in the CCP treatment group (median 83, IQR 8 to 140) than in the SOC group (median 35, IQR -3 to 92, Mann Whitney P = 0.0234). Further research is needed for HemoClear-produced CCP as therapy in SARS-CoV-2 infections together with adequately powered, randomized controlled trials. Importance This study compares mortality and other endpoints between intensive care unit (ICU) COVID-19 patients treated with convalescent plasma plus standard of care (CCP), and a control group of patients hospitalized in the same medical ICU facility treated with standard of care alone (SOC) in a low and middle income country (LMIC) setting using bedside donor whole blood separation by gravity (HemoClear) to produce the CCP. It demonstrates a significant 65% survival improvement in HemoClear-produced CCP recipients (HR 0.35; 95% CI, 0.19–0.66; P = 0.001). Although this is an exploratory study, it clearly shows the benefit of using the HemoClear-produced CCP in ICU patients in the Suriname LMIC setting. Additional studies can further substantiate our findings and their applicability to both LMICs and high income countries and the use of CCP as a prepared readiness method to combat new viral pandemics.
Methylphenidate improves prefrontal cortical cognitive function through α2 adrenoceptor and dopamine D1 receptor actions: Relevance to therapeutic effects in Attention Deficit Hyperactivity Disorder (2005)

BACKGROUND: Methylphenidate (MPH) is the classic treatment for Attention Deficit Hyperactivity Disorder (ADHD), yet the mechanisms underlying its therapeutic actions remain unclear. Recent studies have identified an oral, MPH dose regimen which when given to rats produces drug plasma levels similar to those measured in humans. The current study examined the effects of these low, orally-administered doses of MPH in rats performing a delayed alternation task dependent on prefrontal cortex (PFC), a brain region that is dysfunctional in ADHD, and is highly sensitive to levels of catecholamines. The receptor mechanisms underlying the enhancing effects of MPH were explored by challenging the MPH response with the noradrenergic alpha2 adrenoceptor antagonist, idazoxan, and the dopamine D1 antagonist, SCH23390. RESULTS: MPH produced an inverted U dose response whereby moderate doses (1.0-2.0 mg/kg, p.o.) significantly improved delayed alternation performance, while higher doses (2.0-3.0 mg/kg, p.o.) produced perseverative errors in many animals. The enhancing effects of MPH were blocked by co-administration of either the alpha2 adrenoceptor antagonist, idazoxan, or the dopamine D1 antagonist, SCH23390, in doses that had no effect on their own. CONCLUSION: The administration of low, oral doses of MPH to rats has effects on PFC cognitive function similar to those seen in humans and patients with ADHD. The rat can thus be used as a model for examination of neural mechanisms underlying the therapeutic effects of MPH on executive functions in humans. The efficacy of idazoxan and SCH23390 in reversing the beneficial effects of MPH indicate that both noradrenergic alpha2 adrenoceptor and dopamine D1 receptor stimulation contribute to cognitive-enhancing effects of MPH.
Polarization Offsets of Non Graded and Graded Ferroelectric Films (2005)

ABSTRACT Shifts of hysteresis loops along polarization axis are observed on non graded Pb(Zrx,Ti1-x)O3 ferroelectric films using a Sawyer-Tower circuit. The offsets become significant providing that the sense capacitor is large enough and the input resistance of the measurement set up is artificially increased. The offsets, consisting in DC voltages rather than DC polarizations, are thus not the exclusive feature of graded ferroelectric devices (GFD's). Our observations are consistent with the charging up of the sense capacitor by asymmetrical leakage currents in the film and strongly suggest that rectifying effects are probably involved in most of the vertical offsets observed on ferroelectric thin film capacitors. Assuming blocking contacts at the electrode—ferroelectric interfaces, we propose that the composition gradient in GFD's produces a variation of the band gap energy leading to potential barrier with different heights at the two interfaces. Such asymmetry of the energy band diagram is consistent with our hypothesis of asymmetrical leakage currents.
Supplementary Data from Garcinol Potentiates TRAIL-Induced Apoptosis through Modulation of Death Receptors and Antiapoptotic Proteins (2023)

Supplementary Data from Garcinol Potentiates TRAIL-Induced Apoptosis through Modulation of Death Receptors and Antiapoptotic Proteins
Catalytic Dehydrocoupling of Phenylsilane with "Cation-like" Zirconocene Derivatives: A New Approach to Longer Silicon Chains (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCatalytic Dehydrocoupling of Phenylsilane with "Cation-like" Zirconocene Derivatives: A New Approach to Longer Silicon ChainsVladimir K. Dioumaev and John F. HarrodCite this: Organometallics 1994, 13, 5, 1548–1550Publication Date (Print):May 1, 1994Publication History Published online1 May 2002Published inissue 1 May 1994https://pubs.acs.org/doi/10.1021/om00017a004https://doi.org/10.1021/om00017a004research-articleACS PublicationsRequest reuse permissionsArticle Views240Altmetric-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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Underrepresentation of Phenotypic Variability of 16p13.11 Microduplication Syndrome Assessed With an Online Self-Phenotyping Tool (Phenotypr): Cohort Study (2021)

Several phenotypes might be underrepresented in the previous 16p13.11 microduplication literature, and new possible phenotypes have been identified. Whenever possible, patients should continue to be referenced as a source of complete phenotyping data on their condition. Self-phenotyping may lead to a better understanding of the prevalence of phenotypes in genetic disorders and may identify previously unreported phenotypes.
Deep Learning for Multiwell Automatic Log Correction (2022)

Researchers have dedicated numerous applications of machine-learning (ML) techniques for ﬁ eld-scale automated interpretation of well-log data. A critical prerequisite for automatic log processing is to ensure that the log characteristics are reasonably consistent across multiple wells. Manually correcting logs for consistency is laborious, subjective, and error prone. For some wellbore logs, such as gamma ray and neutron porosity, borehole eﬀects and miscalibration can cause systematic inconsistencies or errors that might be present even after the application of wellbore and environmental corrections. Biased or consistently inaccurate data in the logs can confound ML approaches into learning erroneous relationships, leading to misinterpretations, such as wrong lithology prediction, reservoir estimation, and incorrect formation markers. To overcome such diﬃculties, we have developed a deep learning method to provide petrophysicists with a set of consistent logs through the multiwell automatic log correction (MALC) workﬂow. Presently, the corrections we target are systematic errors on the standard logs, especially gamma ray and neutron logs, random noises, and to a lesser extent, local formation property misreading due to washouts. We applied the proposed method in multiple ﬁ elds worldwide containing diﬀerent challenges, and in this paper, we include the results in two ﬁ eld examples. The ﬁrst one covers the correction of synthetic coherent noise added to ﬁ eld data, and the second example covers the correction applied to original measurements.
Inducible microsomal prostaglandin E synthase is overexpressed in colorectal adenomas and cancer. (2001)

Recently, an inducible microsomal human prostaglandin E synthase (mPGES) was identified. This enzyme converts the cyclooxygenase (COX) product prostaglandin (PG) H(2) to PGE(2), an eicosanoid that has been linked to carcinogenesis. Increased amounts of PGE(2) have been observed in many tumor types including colorectal adenomas and cancers. To further elucidate the mechanism responsible for increased levels of PGE(2) in colorectal tumors, we determined the amounts of mPGES and COX-2 in 18 paired samples (tumor and adjacent normal) of colorectal cancer. With immunoblot analysis, mPGES was overexpressed in 83% of colorectal cancers. COX-2 was also commonly up-regulated in these tumors; marked differences in the extent of up-regulation of mPGES and COX-2 were observed in individual tumors. Immunohistochemistry revealed increased mPGES immunoreactivity in neoplastic cells in both colorectal adenomas and cancers compared with adjacent normal colonic epithelium. Cell culture was used to investigate the regulation of mPGES and COX-2. Chenodeoxycholate markedly induced COX-2 but not mPGES in colorectal cancer cells. Tumor necrosis factor-alpha induced both mPGES and COX-2, but the time course and magnitude of induction differed. As reported previously for COX-2, overexpressing Ras caused a several-fold increase in mPGES promoter activity. Taken together, our results suggest that overexpression of mPGES in addition to COX-2 contributes to increased amounts of PGE(2) in colorectal adenomas and cancer. The mechanisms controlling the expression of these two enzymes are not identical.
Scanning laser-pulse mammography: matching fluid and off-axis measurements (2002)

The influence of a matching fluid on time-domain optical mammograms recorded in vivo in the compressed-breast geometry was investigated. Edge effects on transmitted intensity could be drastically reduced, but it is practically impossible to achieve perfect matching. Therefore, in contrast to measurements without matching fluid, quantification of the tissue’s optical properties close to the edges of the breast requires the use of inhomogeneous models for data analysis. Phantom measurements and simulations allow to quantitatively understand such edge effects. Off-axis measurements facilitate depth localization of inhomogeneities in the tissue.
Thymidylate synthase is a predictor of chemosensitivity to different 5-fluorouracil regimens in primary colorectal cancer. (2006)

B41 Purpose: To identify the good marker for the help of adjuvant 5-fluorouracil (5-FU) therapy to primary colorectal cancer by using different 5-FU regimens. Patients and methods: Primary colorectal cancer tissue from 24 patients were investigated to evaluate the relationship between the mRNA expression level of several 5-fluorouracil (5-FU)-related metabolic enzymes (thymidylate synthase (TS), dihydropyrimidine dehydrogenase (DPD), and thymidine phosphorylase(TP)) and chemosensitivity to 2 different 5-FU regimens (1. 5-FU concentration 1.0 μg/mL, 24 h exposure 2. 5-FU concentration 0.3 μg/mL, 144 h exposure). Chemosensitivity and mRNA expression levels were measured by using collagen gel droplet embedded culture drug sensitivity tests and real-time quantitative reverse transcription-polymerase chain reaction. Results: The TS mRNA expression level were significantly higher in 5-FU resistant group (T/C > 60%) compared with 5-FU sensitive one (T/C the average, 3.83) were more resistant to both 5-FU regimens than the one with lower TS mRNA (
Effects of vapor -liquid mass transfer in reaction -separation systems (2003)

The effect of mass transfer on feasible products is analyzed for two industrially relevant classes of vapor-liquid reactive separation problems: reactive distillation in monomer production and melt polycondensation for engineering thermoplastics and synthetic fibers. Two different approaches are used, a bifurcation analysis for reactive distillation and the attainable region technique for melt condensation polymerization. The Stefan-Maxwell model for mass transfer effects is combined with a flash cascade model for assessing feasible products of reactive distillation systems. The model fixed points are determined as a function of the Peclet number and other parameters, using a pseudo arc length continuation method. The approach is illustrated with two examples: a parameteric study of an idealized ternary system, and the esterification of acetic acid to produce isopropyl acetate. In the limit of little or no reaction, the fixed points are independent of the mass transfer resistance, and a model based on phase equilibrium can be used for feasibility. When the chemical reaction rates or extents of reaction are more significant, the fixed points do depend on the Peclet number, and mass transfer can influence the feasible products. However, best estimates of the mass transfer parameters and the processing conditions typical of reactive distillation indicate that these effects are small for the particular examples studied. In the second part of the dissertation we consider step-growth melt polymerization systems using a different approach to mass transfer which is more common for high viscosity polymeric systems. A concentration-based formulation is applied to develop hybrid reactor-separator models for the two phase CSTR and PFR with simultaneous vapor removal. The evaporation of the volatile byproducts, which is typically limited by liquid-phase mass transfer, is characterized with a single dimensionless parameter (Thiele modulus). A reaction-separation vector is defined which satisfies the same geometric properties as the reaction vector, thus the candidate attainable region can be constructed following the existing procedure for reaction/mixing systems. The technique is demonstrated on the polycondensation step in the production of Nylon 6,6. The effect of temperature, pressure, and Thiele modulus on the candidate attainable region for number average molecular weight is analyzed.
Critically Examining the Claimed Value of Convolutions over User-Item Embedding Maps for Recommender Systems (2020)

In recent years, algorithm research in the area of recommender systems has shifted from matrix factorization techniques and their latent factor models to neural approaches. However, given the proven power of latent factor models, some newer neural approaches incorporate them within more complex network architectures. One specific idea, recently put forward by several researchers, is to consider potential correlations between the latent factors, i.e., embeddings, by applying convolutions over the user-item interaction map. However, contrary to what is claimed in these articles, such interaction maps do not share the properties of images where Convolutional Neural Networks (CNNs) are particularly useful. In this work, we show through analytical considerations and empirical evaluations that the claimed gains reported in the literature cannot be attributed to the ability of CNNs to model embedding correlations, as argued in the original papers. Moreover, additional performance evaluations show that all of the examined recent CNN-based models are outperformed by existing non-neural machine learning techniques or traditional nearest-neighbor approaches. On a more general level, our work points to major methodological issues in recommender systems research.
Application of Vertical-Type High-Speed Twin-Roll Casting for Up-Grade Recycling and Clad Sheets Fabrication of Aluminum Alloys (2016)

A horizontal-type twin roll casting method has been popular for producing aluminum alloy strips, however, it is characterized by a relatively low productivity (1~6 m/min). In contrast, a vertical-type high-speed twin-roll casting method possesses an extremely high productivity (60~120 m/min (1~2 m/s)) and an excellent heat extraction ability. The rapid cooling effect provided significant microstructure refinement and mechanical properties improvement in various kinds of cast aluminum alloy products. Not only “product to product recycling” but also “up-grade recycling” can be achieved by making good use of these merits. Two examples of application showing the potential of vertical-type high-speed twin roll casting method are presented. (1) Several kinds of Al-Si base alloy were cast into the strips. Not only strength and toughness but also formability was increased in the twin roll cast products. In particular, great improvement in deformability shows the potential of the twin-roll cast aluminum alloy products as substitutes for some wrought aluminum alloy products. (2) The vertical-type tandem twin-roll caster was able to fabricate a clad strip by single step. The A4045/A3003/A4045 aluminum alloy clad sheets produced by the twin-roll casting showed better mechanical properties than the conventional hot-roll bonded clad sheets.
Patterns of electro-convection in planar-periodic nematic cells (2015)

Nematic liquid crystals are anisotropic fluids that can undergo electro-convective instabilities. These instabilities have been extensively studied for nematics in unidirectional planar alignment. We investigate the electro-convective instability patterns in planar-periodic cells, wherein, in the quiescent situation the nematic undergoes static twist deformations separated by defect lines. We find two regimes that depend on the sample thickness. For large thickness, electro-convective patterns are not affected by the twist, and the samples behave as they were in planar unidirectional alignment. For small thickness, either the convective motion vertically shifts the defect lines or the twist affects the electro-convective domains and resultant curved patterns are observed.
A Review of Domain Adaptation without Target Labels (2019)

Domain adaptation has become a prominent problem setting in machine learning and related fields. This review asks the question: How can a classifier learn from a source domain and generalize to a target domain? We present a categorization of approaches, divided into, what we refer to as, sample-based, feature-based, and inference-based methods. Sample-based methods focus on weighting individual observations during training based on their importance to the target domain. Feature-based methods revolve around on mapping, projecting, and representing features such that a source classifier performs well on the target domain and inference-based methods incorporate adaptation into the parameter estimation procedure, for instance through constraints on the optimization procedure. Additionally, we review a number of conditions that allow for formulating bounds on the cross-domain generalization error. Our categorization highlights recurring ideas and raises questions important to further research.