gebhart/patrepeval huggingface dataset:
Rnf2 ( Ring1b ) deficiency causes gastrulation arrest and cell cycle inhibition (2003)

The highly homologous Rnf2 (Ring1b) and Ring1 (Ring1a) proteins were identified as in vivo interactors of the Polycomb Group (PcG) protein Bmi1. Functional ablation of Rnf2 results in gastrulation arrest, in contrast to relatively mild phenotypes in most other PcG gene null mutants belonging to the same functional group, among which is Ring1. Developmental defects occur in both embryonic and extraembryonic tissues during gastrulation. The early lethal phenotype is reminiscent of that of the PcG-gene knockouts Eed and Ezh2, which belong to a separate functional PcG group and PcG protein complex. This finding indicates that these biochemically distinct PcG complexes are both required during early mouse development. In contrast to the strong skeletal transformation in Ring1 hemizygous mice, hemizygocity for Rnf2 does not affect vertebral identity. However, it does aggravate the cerebellar phenotype in a Bmi1 null-mutant background. Together, these results suggest that Rnf2 or Ring1-containing PcG complexes have minimal functional redundancy in specific tissues, despite overlap in expression patterns. We show that the early developmental arrest in Rnf2-null embryos is partially bypassed by genetic inactivation of the Cdkn2a (Ink4aARF) locus. Importantly, this finding implicates Polycomb-mediated repression of the Cdkn2a locus in early murine development.
Unsupervised segmentation based on robust estimation and cooccurrence data (2002)

The accuracy of any image segmentation method depends on the correct estimation of the parameters of the different regions present in the image, as well as on the correct labelling of the pixels. Using robust estimators and relaxation labelling techniques, an unsupervised segmentation algorithm was developed. The mean gray value of each region is estimated from the histogram using robust clustering analysis. The gray level distribution of each individual region is approximated through the mean gray value cooccurrence data. The standard deviation of the gray levels of each region is estimated from this distribution using the least median of squares (LMedS) robust estimator. The labelling of the pixels is done through an iterative relaxation region growing process, taking into account both spectral and spatial information. The method is tested in various images and validated with synthetic data, where it is shown that the known true parameters are recovered accurately.
Oxidative Removal of the Benzyl Ether Protecting Group by Homogeneous Electron Transfer (1979)

Protection of the OH function by the benzyl group and mild removal of this protective group are of great preparative interest. In the case of the radical cations of the new polybrominated triarylamines (1), X, Y = H, Br, the oxidation potential suffices for cleavage of benzyl ethers under relatively mild conditions.
Identification of ATP‐NADH kinase isozymes and their contribution to supply of NADP(H) in Saccharomyces cerevisiae (2005)

ATP-NAD kinase phosphorylates NAD to produce NADP by using ATP, whereas ATP-NADH kinase phosphorylates both NAD and NADH. Three NAD kinase homologues, namely, ATP-NAD kinase (Utr1p), ATP-NADH kinase (Pos5p) and function-unknown Yel041wp (Yef1p), are found in the yeast Saccharomyces cerevisiae. In this study, Yef1p was identified as an ATP-NADH kinase. The ATP-NADH kinase activity of Utr1p was also confirmed. Thus, the three NAD kinase homologues were biochemically identified as ATP-NADH kinases. The phenotypic analysis of the single, double and triple mutants, which was unexpectedly found to be viable, for UTR1, YEF1 and POS5 demonstrated the critical contribution of Pos5p to mitochondrial function and survival at 37 degrees C and the critical contribution of Utr1p to growth in low iron medium. The contributions of the other two enzymes were also demonstrated; however, these were observed only in the absence of the critical contributor, which was supported by complementation for some pos5 phenotypes by the overexpression of UTR1 and YEF1. The viability of the triple mutant suggested that a 'novel' enzyme, whose primary structure is different from those of all known NAD and NADH kinases, probably catalyses the formation of cytosolic NADP in S. cerevisiae. Finally, we found that LEU2 of Candida glabrata, encoding beta-isopropylmalate dehydrogenase and being used to construct the triple mutant, complemented some pos5 phenotypes; however, overexpression of LEU2 of S. cerevisiae did not. The complementation was putatively attributed to an ability of Leu2p of C. glabrata to use NADP as a coenzyme and to supply NADPH.
Determination of Busulfan in Human Plasma Using an ELISA Format (2009)

High-dose busulfan is an important component of many bone marrow transplantation-preparative regimens. High busulfan plasma levels have been shown to increase the chance of venoocclusive disease and low levels are associated with recurrence of disease or graft rejection. Currently, busulfan levels are monitored by physical methods that are expensive and time consuming, resulting in relatively low overall use of busulfan testing for dose adjustment. Novel highly selective antibodies for busulfan have been generated and a microtiter plate immunoassay capable of quantifying busulfan levels in plasma has been developed. The assay was configured using a busulfan-horseradish peroxidase (HRP) conjugate as the reporter group and busulfan monoclonal antibodies. The assay requires 30 microL of plasma with no sample preparation. The immunoassay has a standard curve based on busulfan with a range of 75-2000 ng/mL. The time to first result is 30 minutes with up to 40 patient samples in duplicate; multiple plates can be run at once. The coefficient of variation (CV) on signal is <5% for an entire plate, and the 95% confidence interval for negative samples (n = 78) is below the lowest calibrator of 75 ng/mL. Cross-reactivity with the major inactive metabolites (tetrahydrothiophene, tetramethyl sulfone, and tetrahydrothiophene-3-ol-1,1-dioxide) was <0.1%. Results generated with clinical samples (n = 35 and n = 70) correlate well to gas chromatography-mass spectrometry (R = 0.976 and 0.985, respectively) with a slope of 1.05 +/- 0.05. This immunoassay method is suitable for determining levels of busulfan in human plasma. It offers the advantages of using a smaller sample size, does not require sample preparation, and is less labor intensive than other methods. The ability to make 240 determinations per hour enables effective and timely routine monitoring of busulfan levels in clinical practice.
Selectivity towards hydrodehalogenation and dehalo-coupling in the reduction of trichloromethyl derivatives with iron(II) chloride (1995)

The reductive electron transfer (ET) induced on a series of RCCl3 derivatives by iron(II) chloride has been studied. The main reaction products are the homocoupling dimer, RCCl2–CCl2R, and the H/Cl substitution derivative, RCHCl2, and the majority of the compounds examined exhibit a highly selective tendency to form just one of these products. As a general rule, the RCHCl2 compound is the main product when the R group contains substituents which make further reduction of the radical to the carbanion easier and behave as ligands towards the iron(II) ion. In the other cases, the dimer RCCl2–CCl2R is the main product. A few exceptions are found, and these are discussed in view of the possible effects of the R moiety on the different possible routes for the reaction products. The presence of unsaturated derivatives, RCClCClR (E/Z mixture), was observed in the case of the reactions where the homocoupling product was also obtained and is ascribed, on the basis of experimental evidence, to a dehalogenation mechanism of the dimer RCCl2–CCl2R assisted by the iron(II) ion.
Genomewide Association Study of Platelet Reactivity and Cardiovascular Response in Patients Treated With Clopidogrel: A Study by the International Clopidogrel Pharmacogenomics Consortium (2020)

Antiplatelet response to clopidogrel shows wide variation, and poor response is correlated with adverse clinical outcomes. CYP2C19 loss-of-function alleles play an important role in this response, but account for only a small proportion of variability in response to clopidogrel. An aim of the International Clopidogrel Pharmacogenomics Consortium (ICPC) is to identify other genetic determinants of clopidogrel pharmacodynamics and clinical response. A genomewide association study (GWAS) was performed using DNA from 2,750 European ancestry individuals, using adenosine diphosphate-induced platelet reactivity and major cardiovascular and cerebrovascular events as outcome parameters. GWAS for platelet reactivity revealed a strong signal for CYP2C19*2 (P value = 1.67e-33). After correction for CYP2C19*2 no other single-nucleotide polymorphism reached genomewide significance. GWAS for a combined clinical end point of cardiovascular death, myocardial infarction, or stroke (5.0% event rate), or a combined end point of cardiovascular death or myocardial infarction (4.7% event rate) showed no significant results, although in coronary artery disease, percutaneous coronary intervention, and acute coronary syndrome subgroups, mutations in SCOS5P1, CDC42BPA, and CTRAC1 showed genomewide significance (lowest P values: 1.07e-09, 4.53e-08, and 2.60e-10, respectively). CYP2C19*2 is the strongest genetic determinant of on-clopidogrel platelet reactivity. We identified three novel associations in clinical outcome subgroups, suggestive for each of these outcomes.
Characteristics of a spray plasma (1985)

An explanation is given about the meaning of empirical regression and on the domain of application of this biomathematical-statistical procedure. It may be helpful in data handling after the measurements and in a first stage of data processing especially if there is a large amount of datas. An empirical regression can provide the basis for a functional relationship analysis by giving hints for the choice of empirical mathematical functions. This will be useful and necessary in such cases where the measured values have a greater dispersion and one wants to get an analytical expression for the course of measured points. In the appendix a program listing of the ALGOL-program for empirical regression is presented. Detailed remarks are made in the text concerning the program structure, the data input and output resp. the program control parameters to enable the biological or medical user to adapt the program to their special problems without the help by a mathematician, and neither with deeper knowledge of mathematics nor with detailed insight to computer technical aspects of data processing.
The P. falciparum CSP repeat region contains three distinct epitopes required for protection by antibodies in vivo (2021)

Rare and potent monoclonal antibodies (mAbs) against the Plasmodium falciparum (Pf) circumsporozoite protein (CSP) on infective sporozoites (SPZ) preferentially bind the PfCSP junctional tetrapeptide NPDP or NVDP minor repeats while cross-reacting with NANP central repeats in vitro. The extent to which each of these epitopes is required for protection in vivo is unknown. Here, we assessed whether junction-, minor repeat- and central repeat-preferring human mAbs (CIS43, L9 and 317 respectively) bound and protected against in vivo challenge with transgenic P. berghei (Pb) SPZ expressing either PfCSP with the junction and minor repeats knocked out (KO), or PbCSP with the junction and minor repeats knocked in (KI). In vivo protection studies showed that the junction and minor repeats are necessary and sufficient for CIS43 and L9 to neutralize KO and KI SPZ, respectively. In contrast, 317 required major repeats for in vivo protection. These data establish that human mAbs can prevent malaria infection by targeting three different protective epitopes (NPDP, NVDP, NANP) in the PfCSP repeat region. This report will inform vaccine development and the use of mAbs to passively prevent malaria.
Züchtung von erucasäurefreiem Raps in Ungarn (1978)

Abstract Die neuesten Ergebnisse der Rapszüchtung in Ungarn werden behandelt, wobei zum Vergleich die Kenndaten des derzeitig in Ungern angebauten Winterrapses (Brassica napus) dienen. Zur Züchtung neuer Rapssorten wurden außer ungarischen Sorten auch erucasäurefreie Rapssorten kanadischer Herkunft und polnische Sorten benutzt. Durch Kreuzung der genannten Sorten wurden eine erucasäurefreie Linie (IR‐0) und eine erucasäurearme Linie (IR‐1) erhalten. Die Kenndaten dieser neuen Linien werden mitgeteilt. Die neuen Linien werden z. Z. in staatlichen Versuchsanstalten geprüft. Auf Grund der bisher vorliegenden Ergebnisse kann festgestellt werden, daß die neuen Sorten zahlreiche vorteilhafte Eigenschaften besitzen.
Radiomics and Machine Learning for Radiotherapy in Head and Neck Cancers (2019)

<b>Introduction:</b> An increasing number of parameters can be considered when making decisions in oncology. Tumor characteristics can also be extracted from imaging through the use of radiomics and add to this wealth of clinical data. Machine learning can encompass these parameters and thus enhance clinical decision as well as radiotherapy workflow. <b>Methods:</b> We performed a description of machine learning applications at each step of treatment by radiotherapy in head and neck cancers. We then performed a systematic review on radiomics and machine learning outcome prediction models in head and neck cancers. <b>Results:</b> Machine Learning has several promising applications in treatment planning with automatic organ at risk delineation improvements and adaptative radiotherapy workflow automation. It may also provide new approaches for Normal Tissue Complication Probability models. Radiomics may provide additional data on tumors for improved machine learning powered predictive models, not only on survival, but also on risk of distant metastasis, in field recurrence, HPV status and extra nodal spread. However, most studies provide preliminary data requiring further validation. <b>Conclusion:</b> Promising perspectives arise from machine learning applications and radiomics based models, yet further data are necessary for their implementation in daily care.
Quasi-linear Network Coding (2014)

We present a heuristic for designing vector non-linear network codes for non-multicast networks, which we call quasi-linear network codes. The method presented has two phases: finding an approximate linear network code over the reals, and then quantizing it to a vector non-linear network code using a fixed-point representation. Apart from describing the method, we draw some links between some network parameters and the rate of the resulting code.
Optimization-based decoding of Imaging Spatial Transcriptomics data (2023)

Software implementation of JSIT, together with example files, is available at https://github.com/jpbryan13/JSIT.
Efficient level-set based mask optimization with a vector imaging model (2018)

With the extension of lithography simulations from low-NA to hyper-NA for immersion lithography and from scalar optics to vector optics including the polarization effect at source, mask, lens and resist film stack, inverse lithography technology (ILT) schemes based on the scalar imaging models which provide sufficient accuracy for NA less than 0.4, cannot track the whole process of polarized light propagation through the optical components of the lithography system rendering their impotence in hyper-NA immersion systems. In this paper, we address the mask synthesis problem by developing a optimization framework based on the vector imaging model fully describing the vector nature of electromagnetic fields in the aerial imaging formation and the stratified media model for the resist image, which is further reduced to a variational level-set based time-dependent model combining an internal energy term forcing the level set function close to a signed distance function and an extra energy term that drives the zero level set toward desired mask features minimizing the pattern difference between the printed wafer and the desired pattern, thereby optimizing the mask layout without the costly re- initialization procedure and ensuring the stability of the evolution of level surfaces. Represented by a partial differential equation, the time-dependent model is readily solved by finite difference schemes. Acceleration of over 30 times of the optimization procedure is achieved by computing convolution operations in the frequency domain with fast fourier transfrom (FFT) and the repeated usage of data, together with a 50% convergency performance improvement by means of applying Polak-Ribi`ere-Polyak (PRP) conjugate gradient (CG) to updating the normal velocity of the level-set function, which are merited by the experimental results.
Transient Splenial Lesions in the Splenium of Corpus Callosum in Seven Patients: MR Findings and Clinical Correlations (2013)

Transient reversible lesions (TSL) in the splenium of corpus callosum are often found on MR imaging, with the patients recovering without any neurologic defects after mild clinical courses (1). MR imaging have shown restricted diffusion in the central portion of splenium of corpus callosum (2). Many studies have presented the causing factors of TSL, defining hypothetic pathogenesis. These lesions are well documented to be associated with antiepileptic drugs (3-8). The pathophysiology of TSL has been hypothesized in many studies (1, 6, 9-11). According to these studies, the main possible pathophysiology is the rapid resolution of intramyelinic edema or the influx of INTRODUCTION www.ksmrm.org JKSMRM 17(1) : 1-7, 2013
ChemInform Abstract: Synthesis and Characterization of Diallyl Telluride and Allyl Methyl Telluride. (1989)

Abstract The title compounds (III) and (VII) are prepared as shown and characterized by 1 H, 13 C, and 125 Te NMR, IR, and UV spectroscopy.
Dual mode operation of a hydromagnetic plasma thruster to achieve tunable thrust and specific impulse (2021)

We report here on initial studies of a pulsed hydromagnetic plasma gun that can operate in either a pre-filled or a gas-puff mode on demand. These modes enable agile and responsive performance through tunable thrust and specific impulse. Operation with a molecular nitrogen propellant is demonstrated to show that the hydromagnetic thruster is a candidate technology for air-harvesting and drag compensation in the very low Earth orbit. A dual mode operation is achieved by leveraging propellant gasdynamics to change the fill fraction and flow collisionality within the thruster. This results in the formation of distinct modes that are characterized by the current-driven hydromagnetic waves that they allow, namely, magneto-deflagration and magneto-detonation, respectively. These modes form the basis of using gasdynamics to enable responsive thruster performance. Using time-of-flight emission diagnostics to characterize near-field flow velocities, we find that a relatively dramatic transition occurs between modes as gas is allowed to expand in the thruster, with exhaust velocities ranging from 10 to 55 km/s in the deflagration and detonation regimes, respectively. Simulations of the processed mass bit offer the first glimpse into possible thruster performance and trade-offs between specific impulse and thrust. An impulse bit tunability of ∼22% is predicted, with differing propellant fill fractions when operating in a burst mode.
Preclinical Evaluation of the Supercritical Extract of Azadirachta Indica (Neem) Leaves In Vitro and In Vivo on Inhibition of Prostate Cancer Tumor Growth (2014)

Azadirachta indica, commonly known as neem, has gained worldwide prominence because of its medical properties, namely antitumor, antiviral, anti-inflammatory, antihyperglycemic, antifungal, and antibacterial activities. Despite these promising results, gaps remain in our understanding of the molecular mechanism of action of neem compounds and their potential for use in clinical trials. We investigated supercritical extract of neem leaves (SENL) for the following: molecular targets in vitro, in vivo efficacy to inhibit tumor growth, and bioactive compounds that exert antitumor activity. Treatment of LNCaP-luc2 prostate cancer cells with SENL suppressed dihydrotestosterone-induced androgen receptor and prostate-specific antigen levels. SENL inhibited integrin β1, calreticulin, and focal adhesion kinase activation in LNCaP-luc2 and PC3 prostate cancer cells. Oral administration of SENL significantly reduced LNCaP-luc2 xenograft tumor growth in mice with the formation of hyalinized fibrous tumor tissue, reduction in the prostate-specific antigen, and increase in AKR1C2 levels. To identify the active anticancer compounds, we fractionated SENL by high-pressure liquid chromatography and evaluated 16 peaks for cytotoxic activity. Four of the 16 peaks exhibited significant cytotoxic activity against prostate cancer cells. Mass spectrometry of the isolated peaks suggested the compounds with cytotoxic activity were nimbandiol, nimbolide, 2',3'-dihydronimbolide, and 28-deoxonimbolide. Analysis of tumor tissue and plasma samples from mice treated with SENL indicated 28-deoxonimbolide and nimbolide as the bioactive compounds. Overall, our data revealed the bioactive compounds in SENL and suggested that the anticancer activity could be mediated through alteration in androgen receptor and calreticulin levels in prostate cancer.
Activating Transcription Factor 4 Overexpression Inhibits Proliferation and Differentiation of Mammary Epithelium Resulting in Impaired Lactation and Accelerated Involution (2003)

The basic leucine zipper containing activating transcription factors (ATFs) modulates the expression of growth-regulating genes. In this study, we sought to determine specifically the consequences of ATF4 expression on mammary gland development in transgenic mice. Overexpression of ATF4 severely impaired normal development of the mammary gland, which was associated with reduced proliferation and differentiation of mammary alveolar epithelium and up-regulation of p21(WAF1) and p27(Kip1). In addition, there was also impaired lactation accompanied by decreased expression of alpha-lactoalbumin, whey acidic protein, and beta-casein, possibly because of the down-regulation of STAT5a tyrosine phosphorylation. Mammary gland involution in ATF4-transgenic mice was accelerated, compared with wild type littermates by whole mount analysis. In addition, day 18 of lactation in transgenic mice was phenotypically equivalent to day 3 of involution in wild type mice, as determined by the TUNEL assay and expression of Bax. The concentration of the proapoptotic molecule caspase-3 was increased during lactation in ATF4-transgenic animal. Mammary glands from ATF4-transgenic mice also showed significant nuclear translocation of activated STAT3 and up-regulation of one of its target genes, insulin-like growth factor-binding protein-5, which is thought to facilitate apoptosis by sequestering insulin-like growth factor. Together, these findings suggest that ATF4 may play a role during mammary gland development and that down-regulation of ATF4 may be important for the onset of involution in the mammary gland.