gebhart/patrepeval huggingface dataset:
A method for human teratogen detection by geometrically confined cell differentiation and migration (2015)

Unintended exposure to teratogenic compounds can lead to various birth defects; however current animal-based testing is limited by time, cost and high inter-species variability. Here, we developed a human-relevant in vitro model, which recapitulated two cellular events characteristic of embryogenesis, to identify potentially teratogenic compounds. We spatially directed mesoendoderm differentiation, epithelial-mesenchymal transition and the ensuing cell migration in micropatterned human pluripotent stem cell (hPSC) colonies to collectively form an annular mesoendoderm pattern. Teratogens could disrupt the two cellular processes to alter the morphology of the mesoendoderm pattern. Image processing and statistical algorithms were developed to quantify and classify the compounds' teratogenic potential. We not only could measure dose-dependent effects but also correctly classify species-specific drug (Thalidomide) and false negative drug (D-penicillamine) in the conventional mouse embryonic stem cell test. This model offers a scalable screening platform to mitigate the risks of teratogen exposures in human.
Animating Hair with Loosely Connected Particles (2003)

Abstract This paper presents a practical approach to the animation of hair at an interactive frame rate. In our approach,we model the hair as a set of particles that serve as sampling points for the volume of the hair, which covers thewhole region where hair is present. The dynamics of the hair, including hair‐hair interactions, is simulated usingthe interacting particles. The novelty of this approach is that, as opposed to the traditional way of modeling hair,we release the particles from tight structures that are usually used to represent hair strands or clusters. Therefore,by making the connections between the particles loose while maintaining their overall stiffness, the hair can bedynamically split and merged during lateral motion without losing its lengthwise coherence. Categories and Subject Descriptions (according to ACM CCS): I.3.7 [Computer Graphics]: Three‐DimensionalGraphics and Realism, I.3.3 [Computer Graphics]: Picture/Image Generation
Inheritance of seed coat color of Ethiopian mustard (Brassica carinata A. Braun) (2010)

The inheritance of seed coat color was investigated in Brassica carinata in F 1 , F 2 , F 3 and backcross progenies of crosses between brown- and yellow-seeded pure lines. Seed coat color in B. carinata was not influenced by xenia effect. Segregation pattern followed a mono-genic incomplete dominance inheritance model The occurrence of yellow/light yellow-brown seed trait in B. carinata may be due to an interaction between brown seed coat color gene and dominant repressor (Rp) genes. Key words: Brassica carinata, inheritance, seed coat color, dominant repressor
A new class of chiral materials hosting magnetic skyrmions beyond room temperature (2015)

Skyrmions, topologically protected vortex-like nanometric spin textures in magnets, have been attracting increasing attention for emergent electromagnetic responses and possible technological applications for spintronics. In particular, metallic magnets with chiral and cubic/tetragonal crystal structure may have high potential to host skyrmions that can be driven by low electrical current excitation. However, experimental observations of skyrmions have been limited to below room temperature for the metallic chiral magnets, specifically for the MnSi-type B20 compounds. Towards technological applications, transcending this limitation is crucial. Here we demonstrate the formation of skyrmions with unique spin helicity both at and above room temperature in a family of cubic chiral magnets: β-Mn-type Co-Zn-Mn alloys with a different chiral space group from that of B20 compounds. Lorentz transmission electron microscopy, magnetization and small-angle neutron scattering measurements unambiguously reveal formation of a skyrmion crystal under application of a magnetic field in both thin-plate and bulk forms.
An Epoch in Iowa Politics (1956)

In the year 1900, four years following the defeat of William J. Bryan and the Democratic party in 1896, Theodore Roosevelt was nominated on the Republican ticket for vice president with President McKinley, who was running for his second term. The choice was made upon the insistent demand of Senator Platt of New York, seeking thereby to effectually sidetrack Roosevelt, who that early had his eye on the presidency, and reluctantly accepted the nomination for the minor position on the Republican ticket, , Iowans with others proposed Congressman Jonathon P. Dolliver for the second place on the ticket and Major McKinley had indicated his approval, but Platt had his way. LaFayette Young of the Des Moines Capital was said to have had a speech all ready to place Dolliver in nomination, but changed it with the tide of affairs, to name Roosevelt instead, who had attained fame in the Spanish-American war as the popular hero of engagements in Cuba. Thus did Dolliver miss the presidency.
The Mevalonate Pathway ofStaphylococcus aureus (2008)

Isoprenoids are a class of ubiquitous organic molecules synthesized from the five-carbon starter unit isopentenyl pyrophosphate (IPP). Comprising more than 30,000 known natural products, isoprenoids serve various important biological functions in many organisms. In bacteria, undecaprenyl pyrophosphate is absolutely required for the formation of cell wall peptidoglycan and other cell surface structures, while ubiquinones and menaquinones, both containing an essential prenyl moiety, are key electron carriers in respiratory energy generation. There is scant knowledge on the nature and regulation of bacterial isoprenoid pathways. In order to explore the cellular responses to perturbations in the mevalonate pathway, responsible for producing the isoprenoid precursor IPP in many gram-positive bacteria and eukaryotes, we constructed three strains of Staphylococcus aureus in which each of the mevalonate pathway genes is regulated by an IPTG (isopropyl-beta-D-thiogalactopyranoside)-inducible promoter. We used DNA microarrays to profile the transcriptional effects of downregulating the components of the mevalonate pathway in S. aureus and demonstrate that decreased expression of the mevalonate pathway leads to widespread downregulation of primary metabolism genes, an upregulation in virulence factors and cell wall biosynthetic determinants, and surprisingly little compensatory expression in other isoprenoid biosynthetic genes. We subsequently correlate these transcriptional changes with downstream metabolic consequences.
Synthesis of 1,2,3‐Triazoles from Azide‐Derivatised Aminocyclitols by Catalytic Diazo Transfer and CuAAC Click Chemistry (2014)

Abstract Cu II ‐catalysed diazo transfer and Cu I ‐catalysed azide–alkyne 1,3‐dipolar cycloaddition (CuAAC) “click chemistry” were used to synthesis C 7 N aminocyclitol‐derivatised 1,2,3‐triazoles. In the course of this work, the ‐N=N‐ moiety was transferred onto C 7 N aminocyclitols such as validamine, valienamine and valiolamine by employing imidazole‐1‐sulfonyl azide as the diazo transfer reagent with catalysis by Cu II , Zn II and Ni II , in moderate to good yields. The obtained azidocyclitols were coupled with various terminal alkynes under modified Meldal's conditions with good to excellent yields. The stereo‐ and regiochemistry of the products were confirmed by 2D‐NMR (NOESY and HMBC). One‐pot syntheses of the corresponding 1,2,3‐triazoles, as safer and more efficient procedures, were also investigated and gave moderate to good yields.
5-Dehydroshikimate reductase in the tea plant (Camellia sinensis L.). Properties and distribution (1966)

1. A method for the extraction of 5-dehydroshikimate reductase (EC 1.1.1.25) from tea plant tissues in an active soluble state has been developed. It is dependent on the use, in the extraction medium, of an insoluble polyphenol adsorbent (Polyclar AT), which prevents the polyphenols present from precipitating all the proteins. 2. The enzyme has the following properties: pH optima at pH10.1 in glycine-sodium hydroxide buffer and at pH7.7 in tris-hydrochloric acid buffer; K(m) (NADP) 32mum and K(m) (shikimate) 0.43mm; and NADP-specificity. It was completely inhibited by 0.33mm-p-chloromercuribenzoate and this inhibition was completely reversed by 10mm-cysteine. Iodoacetate and arsenite inhibited the enzyme to a smaller extent. 3. The specific activity of the enzyme was higher in the parts of the actively growing shoot tips (third leaf>stem>second leaf>first leaf>bud) than in the mature leaves. However, the mature leaves had the greatest total activity. 4. The importance of these findings with respect to flavanol biosynthesis in tea plants is discussed.
Preparation and structure of a mixed niobium(I) isocyanide carbonyl complex with a bent C-N-C linkage [Erratum to document cited in CA115(6):63353f] (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation and structure of a mixed niobium(I) isocyanide carbonyl complex with a bent C-N-C linkage [Erratum to document cited in CA115(6):63353f]Ghazar Aharonian, Liliane G. Hubert-Pfalzgraf, Abdenasser Zaki, and Guy Le BorgneCite this: Inorg. Chem. 1991, 30, 26, 5052Publication Date (Print):December 1, 1991Publication History Published online1 May 2002Published inissue 1 December 1991https://pubs.acs.org/doi/10.1021/ic00026a040https://doi.org/10.1021/ic00026a040research-articleACS PublicationsRequest reuse permissionsArticle Views12Altmetric-Citations-LEARN 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
A Performance Comparison between Continuous-Wave and Time-Domain Diffuse Optical Tomography for Deep Inclusions by Using Small Source-Detector Separations (2017)

Continuous-wave (CW) is the most widely used and commercially available technique for performing biomedical diffuse optics tomography. Nevertheless, CW has been proved to suffer from non-uniqueness problems and large source-detector distances have to be used in order to detect inclusions that are deep from the surface. In order to overcome the former drawback frequency-domain approach has been developed although it also suffers from the latter deficiency. Recently, time domain (TD) diffuse optics has attracted huge interest from the scientific community due to its inherit capacity to associate photons arrival time with the maximum depth that they have reached ; the late arrival photons are the photons that have travelled most and presumably have gone deeper in the tissue. Moreover, not long ago it was proved that in TD there is no need of large source-detector distances for the reconstruction of deep layers of human tissue ; in fact small source-detector separations (s.d.s.) improve the contrast and the absolute number of detected photons. However, no comparison analysis has been done in terms of reconstruction quality when using small s.d.s. In this work finite element method is used to do a computational comparison between CW and TD approaches where special emphasis is put on the quality of reconstructions 1) with an inclusion at deep levels and 2) when using small s.d.s. TD reconstructions were done using Mellin-Laplace (TD-ML) transform which is fast to calculate and stable to noise. For the experiments, synthetic computationally generated data was used which was convolved with a single-photon avalanche diode detector instrumental response function.
Utilizing Electronic Health Records (EHR) and Tumor Panel Sequencing to Demystify Prognosis of Cancer of Unknown Primary (CUP) patients (2023)

Cancer of unknown primary (CUP) is a type of cancer that cannot be traced back to its original site and accounts for 3-5% of all cancers. It does not have established targeted therapies, leading to poor outcomes. We developed OncoNPC, a machine learning classifier trained on targeted next-generation sequencing data from 34,567 tumors from three institutions. OncoNPC achieved a weighted F1 score of 0.94 for high confidence predictions on known cancer types (65% of held-out samples). When applied to 971 CUP tumors from patients treated at the Dana-Farber Cancer Institute, OncoNPC identified actionable molecular alterations in 23% of the tumors. Furthermore, OncoNPC identified CUP subtypes with significantly higher polygenic germline risk for the predicted cancer type and significantly different survival outcomes, supporting its validity. Importantly, CUP patients who received first palliative intent treatments concordant with their OncoNPC-predicted cancer sites had significantly better outcomes (H.R. 0.348, 95% C.I. 0.210 - 0.570, p-value 2.32 × 10<sup>-5</sup>). OncoNPC thus provides evidence of distinct CUP subtypes and offers the potential for clinical decision support for managing patients with CUP.
Radiolabeled γ-AApeptides: A new class of PET tracers (2012)

1522 Objectives The goal of this study was to design, synthesize, and characterize 64Cu-labeled γ-AApeptides, a new class of peptidomimetics with superb stability, for positron emission tomography (PET) imaging applications. Methods A γ-AApeptide that mimics the tripeptide sequence RGD is termed γ-AA1, which was conjugated to DOTA via a linker and termed γ-AA2. Flow cytometry studies were performed in U87MG cancer cells (integrin αvβ3-positive) to evaluate the affinity of the γ-AApeptide-based conjugates for integrin αvβ3. γ-AA2 was labeled with 64Cu and the enzymatic stability of 64Cu-γ-AA2 was measured by radio HPLC. PET imaging, biodistribution, and blocking studies were performed on U87MG tumor-bearing mice to evaluate the in vivo tumor targeting efficacy of 64Cu-γ-AA2. Results γ-AA1 has similar binding affinity to integrin αvβ3 as the c(RGDyK) peptide. However, the enzymatic stability was much higher: 8% degradation of 64Cu-γ-AA2 and 100% degradation of 64Cu-labeled c(RGDyK) respectively after incubation with 0.1 mg/mL pronase at 37 °C for 2 h. Uptake of 64Cu-γ-AA2 in the U87MG tumor was clearly visible as early as 0.5 h p.i., which remained persistent over time (0.9±0.3, 1.0±0.2, 1.1±0.2, and 0.7±0.2 %ID/g at 0.5, 2, 4, and 24 h p.i., n = 3). 64Cu-γ-AA2 clears rapidly from the circulation and excellent tumor contrast was observed, with tumor/muscle ratio of 3.8±0.9, 4.8±1.8, 5.8±1.4, and 8.3±3.9 at 0.5 h, 2 h ,4 h, and 24 h p.i. respectively. Administering a blocking dose of c(RGDyK) significantly reduced the U87MG tumor uptake, thereby confirming in vivo target specificity of 64Cu-γ-AA2. Conclusions We report PET imaging of integrin αvβ3 with a 64Cu-labled γ-AApeptide-based RGD mimetic, which exhibited comparable integrin αvβ3 binding affinity as the c(RGDyK) peptide but significantly higher resistance to enzymatic degradation and better in vivo stability, despite its shorter sequence and linear nature. This study establishes γ-AApeptides as a novel class of enzymatically stable targeting ligands for molecular imaging applications
A novel mitochondrial point mutation in a maternal pedigree with sensorineural deafness (1994)

We have detected a novel mitochondrial mutation in a maternal pedigree, at least 13 of whose members have sensorineural hearing loss of varying severity, but who exhibit no other pathological features. The mutation, at np 7445, converts the 3' terminal T residue of tRNA-ser(UCN) to a C, and also brings about a silent alteration to the COI stop codon. The mutation destroys an XbaI site, within which a second mutation, at np 7444, has previously been reported in association with Leber's hereditary optic neuropathy. Predominantly mutant mtDNA was found in all 13 family members surveyed, whether or not they are overtly affected by deafness, and some individuals appeared homoplasmic, within the limits of detection. The novel mutation was not found in over 600 normal controls, nor in any of 27 other maternally unrelated individuals with deafness Other mutations found in mitochondrial disorders were also absent from this pedigree.
<title>Clouds and the Earth's Radiant Energy System (CERES) instrument level 1 science data validation plan for geolocated radiances</title> (1996)

From spacecraft platforms, the clouds and the Earth's radiant energy system (CERES) scanning thermistor bolometers are designed to measure broadband Earth-reflected solar shortwave (0.3 - 5.0 micrometer) and Earth-emitted long wave (5.0 - greater than 100 micrometer) radiances as well as emitted longwave radiances in the 8 - 12 micrometer water vapor window over geographical footprints as small as 10 kilometers at the nadir. In ground vacuum facilities, the thermistor bolometers and in-flight blackbody and tungsten lamp calibration systems are being calibrated using radiometric sources tied to the international temperature scale of 1990 (ITS'90). Using the in-flight calibration systems, the bolometers will be calibrated periodically before and after spacecraft launch to verify the stability of the bolometers responses and to determine response drifts/shifts if they occur. The in-flight systems calibration analyses along with validation analyses will be used to determine the flight data reduction coefficients (instrument gains and offsets) which will be used to convert the bolometer measurements into calibrated radiances at the top-of-the-atmosphere (approximately 30 km). If a bolometer response shifts or drifts more than 0.5% in the longwave region or more than 1.0% in the shortwave region, and if the validation studies verify the bolometer response change, the flight data reduction coefficients will be corrected. A coastline detection method, using strong contrasting longwave ocean-land scenes, will be used to assess error limits on the geographical locations of the radiances. The detection method was successfully used to assess upper limits (6 km) on the geolocation errors for the Earth radiation budget satellite (ERBS) bolometric measurements of longwave radiances. For CERES, the detection method may be extended to shortwave radiances. In this paper, elements of the CERES instrument level 1 validation plan radiometric strategies are presented as well as the geolocation validation approaches.
Comparison of skidding risks between dry and wet surface conditions (1995)

The increase in risk of a vehicle skidding on a wet surface at an expressway section is estimated in this paper using the traffic conflict technique. This is done by modelling the driver behaviour and the road surface conditions based on observations of traffic conflicts. When driving, drivers generally do not have knowledge of the skid resistance of the surface nor the ability to measure it. Hence, the risk of skidding is increased when the quality of the surface has deteriorated due to a rain, and when drivers have not changed their behaviour to compensate for the poor surface condition, especially at the onset or aftermath of a rain. This increase in risk can be determined using the derived models based on unchanged driver behaviour and reduced skid resistance. For the site investigated, the results showed that the risks have increased 3 to 6 times.
DDoS attack detection using packet size interval (2015)

Distributed Denial-of-Service (DDoS) attacks are a great threat to the Internet. Enabling accurately detection of Distribute Denial-of-Service attacks is important because it is the foundation of defense against the attacks. In this paper, we focus on the distribution difference of the packet size between normal traffic flows and attack traffic flows and propose an entropy-based detection measurement. The measurement can highlights the characteristics of attack traffic. The experimental results show that the proposed measurement can effectively and clearly distinguish attack flows from normal flows in both low and high packet rate.
Modulation of human malaria transmission by anti-gamete transmission blocking immunity (1988)

Natural Plasmodium vivax malaria infections in man evoke anti-gamete transmission blocking antibodies which influence the infectivity of malaria patients to the vector mosquito. In this study, entomological, immunological and parasitological data obtained through the monitoring of an epidemic of human vivax malaria in Sri Lanka were used in a mathematical simulation to assess the effect of naturally induced transmission blocking immunity on malaria transmission. A mathematical model to describe malaria transmission accounting for transmission blocking immunity was developed from the basic differential equations originally stated by R. Ross and the epidemic was simulated using the available data. An attempt was made to predict the monthly malaria incidence by means of the mathematical simulation, with and without accounting for transmission blocking immunity. A plausible mathematical solution of the epidemic could be obtained when transmission blocking immunity was accounted for, and it was not possible to obtain such a plausible solution in the absence of immunity. Thus, the postulated occurrence of transmission blocking immunity was essential to describe adequately this malaria epidemic, indicating that, at least in epidemic situations, naturally occurring transmission blocking immunity has a controlling influence on malaria incidence.
Impedance Identification of Integrated Power System Components using Recurrent Neural Networks (2007)

Impedance characteristics of shipboard power systems provide important information for studies on system stability and integration. Existing injection based impedance measurement techniques require multiple tests on the system to obtain characteristics over wide frequency ranges. In this paper, recurrent neural networks (RNNs) are used to model the small signal dynamics of power electronic systems based on a single test in which randomized signals are injected into the system. The trained RNN is then used to extract the small-signal impedances/admittances of the system. A number of tests have been carried out in simulation to verify the effectiveness of the proposed method.
Supplementary Figure 2 from MultiDimensional ClinOmics for Precision Therapy of Children and Adolescent Young Adults with Relapsed and Refractory Cancer: A Report from the Center for Cancer Research (2023)

&lt;p&gt;An adrenocortical carcinoma in Patient NCI0226 with a de-novo germline TP53 mutation. Germline DNA samples from brother and parents were not noted to have the mutation. The mutation was a novel two base substitution at codon c.358_359delCGinsAA, leading to an amino acid change, A159K. The mutation was heterozygous in the germline, and homozygous in tumor exome and transcriptome due to loss of heterozygosity of the wild-type allele.&lt;/p&gt;