gebhart/patrepeval huggingface dataset:
Basic Numerical Tasks (2020)

As a warmup before developing more sophisticated numerical methods, we will first develop in this chapter some of the basic routines that are commonly used in scientific computation and numerical modeling. These include numerical differentiation, integration, interpolation, and curve fitting. Since numerical differentiation and integration are building blocks for algorithms like the finite difference method and the method of moments, we will return to these two key topics in later chapters with more rigorous treatments. Since the algorithm examples given throughout this book are based on the MATLAB® programing language, we will also introduce the MATLAB programing environment and some of the basic commands that will be used throughout the book. The simple algorithms introduced in this chapter are intended as an easy way to learn MATLAB programing. Many textbooks, monographs, and online references on numerical analysis are available that provide greater depth on these topics (e.g., [1,2]).
Development and Validation of a Next-Generation Sequencing Assay for BRCA1 and BRCA2 Variants for the Clinical Laboratory (2015)

The objective of this study was to design and validate a next-generation sequencing assay (NGS) to detect BRCA1 and BRCA2 mutations. We developed an assay using random shearing of genomic DNA followed by RNA bait tile hybridization and NGS sequencing on both the Illumina MiSeq and Ion Personal Gene Machine (PGM). We determined that the MiSeq Reporter software supplied with the instrument could not detect deletions greater than 9 base pairs. Therefore, we developed an alternative alignment and variant calling software, Quest Sequencing Analysis Pipeline (QSAP), that was capable of detecting large deletions and insertions. In validation studies, we used DNA from 27 stem cell lines, all with known deleterious BRCA1 or BRCA2 mutations, and DNA from 67 consented control individuals who had a total of 352 benign variants. Both the MiSeq/QSAP combination and PGM/Torrent Suite combination had 100% sensitivity for the 379 known variants in the validation series. However, the PGM/Torrent Suite combination had a lower intra- and inter-assay precision of 96.2% and 96.7%, respectively when compared to the MiSeq/QSAP combination of 100% and 99.4%, respectively. All PGM/Torrent Suite inconsistencies were false-positive variant assignments. We began commercial testing using both platforms and in the first 521 clinical samples MiSeq/QSAP had 100% sensitivity for BRCA1/2 variants, including a 64-bp deletion and a 10-bp insertion not identified by PGM/Torrent Suite, which also suffered from a high false-positive rate. Neither the MiSeq nor PGM platform with their supplied alignment and variant calling software are appropriate for a clinical laboratory BRCA sequencing test. We have developed an NGS BRCA1/2 sequencing assay, MiSeq/QSAP, with 100% analytic sensitivity and specificity in the validation set consisting of 379 variants. The MiSeq/QSAP combination has sufficient performance for use in a clinical laboratory.
Racial/Ethnic Disparities and Barriers to Diabetic Retinopathy Screening in Youths (2021)

In this cohort study, non-White youths were less likely to undergo diabetic eye examinations yet more likely to have diabetic retinopathy compared with White youths. Addressing barriers to diabetic retinopathy screening may improve access to diabetic eye examination and facilitate early detection.
Proteomic screening identifies calreticulin as a miR-27a direct target repressing MHC class I cell surface exposure in colorectal cancer (2016)

Impairment of the immune response and aberrant expression of microRNAs are emerging hallmarks of tumour initiation/progression, in addition to driver gene mutations and epigenetic modifications. We performed a preliminary survey of independent adenoma and colorectal cancer (CRC) miRnoma data sets and, among the most dysregulated miRNAs, we selected miR-27a and disclosed that it is already upregulated in adenoma and further increases during the evolution to adenocarcinoma. To identify novel genes and pathways regulated by this miRNA, we employed a differential 2DE-DIGE proteome analysis. We showed that miR-27a modulates a group of proteins involved in MHC class I cell surface exposure and, mechanistically, demonstrated that calreticulin is a miR-27a direct target responsible for most downstream effects in epistasis experiments. In vitro miR-27a affected cell proliferation and angiogenesis; mouse xenografts of human CRC cell lines expressing different miR-27a levels confirmed the protein variations and recapitulated the cell growth and apoptosis effects. In vivo miR-27a inversely correlated with MHC class I molecules and calreticulin expression, CD8(+) T cells infiltration and cytotoxic activity (LAMP-1 exposure and perforin release). Tumours with high miR-27a, low calreticulin and CD8(+) T cells' infiltration were associated with distant metastasis and poor prognosis. Our data demonstrate that miR-27a acts as an oncomiRNA, represses MHC class I expression through calreticulin downregulation and affects tumour progression. These results may pave the way for better diagnosis, patient stratification and novel therapeutic approaches.
Photoexcited Triplet State Properties of Brominated and Nonbrominated Ga(III)-Corroles as Studied by Time-Resolved Electron Paramagnetic Resonance (2010)

The effect of the corrole macrocycle bromination on its photoexcited triplet state parameters was examined in a comparison study of brominated and nonbrominated Ga(III) 5,10,15-tris(pentafluorophenyl)corroles, employing X-band (9.5 GHz) time-resolved electron paramagnetic resonance (TREPR) spectroscopy. It is demonstrated that the spectrum of the brominated Ga-corrole is characterized by an opposite polarization pattern and a larger zero-field splitting (ZFS) parameter |D|, compared to nonbrominated Ga-corrole. With the assignment of a negative sign for the ZFS parameter D, the dominant intersystem crossing (ISC) pathways are evaluated. Spectral line shape analysis reveals that in the brominated Ga-corrole,the out-of-plane triplet sublevel is overpopulated (A(Z) > A(X), A(Y)), while in nonbrominated Ga-corrole, the in-plane triplet sublevels are preferentially populated (A(X), A(Y) ≫ A(Z)). The differences in the photophysical properties of the corroles are attributed to the heavy atom effect upon corrole skeleton bromination, which enhances the spin-orbit coupling strength in the brominated complex, thus affecting its ISC and ZFS parameters.
Evaluation of Performability for Degradable Computer Systems (1987)

The performability of degradable heterogeneous computer systems containing k > 1 types of components is considered. Previous analyses of such systems have been numerical in nature and yielded algorithms with either exponential complexity in the number of system states n, or polynomial in n with approximate truncations of infinite series. In this paper, a closed form expression for the performability of degradable heterogeneous systems is derived. Furthermore, an algorithm with polynomial complexity, O(kn3), is presented and applied to study the performability of a multiprocessor computer system.
Interaction between neuropeptide Y (NPY) and brain‐derived neurotrophic factor in NPY‐mediated neuroprotection against excitotoxicity: a role for microglia (2008)

The neuroprotective effect of neuropeptide Y (NPY) receptor activation was investigated in organotypic mouse hippocampal slice cultures exposed to the glutamate receptor agonist alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA). Exposure of 2-week-old slice cultures, derived from 7-day-old C57BL/6 mice, to 8 microm AMPA, for 24 h, induced degeneration of CA1 and CA3 pyramidal cells, as measured by cellular uptake of propidium iodide (PI). A significant neuroprotection, with a reduction of PI uptake in CA1 and CA3 pyramidal cell layers, was observed after incubation with a Y(2) receptor agonist [NPY(13-36), 300 nm]. This effect was sensitive to the presence of the selective Y(2) receptor antagonist (BIIE0246, 1 microm), but was not affected by addition of TrkB-Fc or by a neutralizing antibody against brain-derived neurotrophic factor (BDNF). Moreover, addition of a Y(1) receptor antagonist (BIBP3226, 1 microm) or a NPY-neutralizing antibody helped to disclose a neuroprotective role of endogenous NPY in CA1 region. Cultures exposed to 8 microm AMPA for 24 h, displayed, as measured by an enzyme-linked immunosorbent assay, a significant increase in BDNF. In such cultures there was an up-regulation of neuronal TrkB immunoreactivity, as well as the presence of BDNF-immunoreactive microglial cells at sites of injury. Thus, an increase of AMPA-receptor mediated neurodegeneration, in the mouse hippocampus, was prevented by neuroprotective pathways activated by NPY receptors (Y(1) and Y(2)), which can be affected by BDNF released by microglia and neurons.
Theory of Optical Trapping by an Optical Vortex Beam (2010)

We propose a theory to explain optical trapping by optical vortices (OVs), which are emerging as important tools to trap mesoscopic particles. The common perception is that the trapping is solely due to the gradient force and that it may be characterized by three real force constants. However, we show that the OV trap can exhibit complex force constants, implying that the trapping must be stabilized by ambient damping. At different damping levels, particles exhibit remarkably different dynamics, such as stable trapping and periodic and aperiodic orbital motions.
<title>Imaging parameters of a kinestatic charge detector containing Kr, NH3, and CO2 at 80 atm</title> (1994)

In this paper, modulation transfer function and image noise measurements are presented for Kinestatic Charge Detectors employing high-pressure Kr gas doped with NH<SUB>3</SUB> and CO<SUB>2</SUB>. Kr improves spatial resolution over Xe because, at equal x-ray mean free path, it has both reduced fluorescence reabsorption and reduced electron range. NH<SUB>3</SUB> eliminates mobility dispersion (disparate ionic mobilities from multiple charge carriers) caused by gas impurities. CO<SUB>2</SUB> reduces electron attachment and thus ion-ion recombination because it lowers the electron temperature, thereby increasing electron drift velocity via the Ramsauer effect.
Evaluation of PCR electrospray-ionization mass spectrometry for rapid molecular diagnosis of bovine mastitis (2013)

Bovine mastitis, an inflammatory disease of the mammary gland, is one of the most costly diseases affecting the dairy industry. The treatment and prevention of this disease is linked heavily to the use of antibiotics in agriculture and early detection of the primary pathogen is essential to control the disease. Milk samples (n=67) from cows suffering from mastitis were analyzed for the presence of pathogens using PCR electrospray-ionization mass spectrometry (PCR/ESI-MS) and were compared with standard culture diagnostic methods. Concurrent identification of the primary mastitis pathogens was obtained for 64% of the tested milk samples, whereas divergent results were obtained for 27% of the samples. The PCR/ESI-MS failed to identify some of the primary pathogens in 18% of the samples, but identified other pathogens as well as microorganisms in samples that were negative by culture. The PCR/ESI-MS identified bacteria to the species level as well as yeasts and molds in samples that contained a mixed bacterial culture (9%). The sensitivity of the PCR/ESI-MS for the most common pathogens ranged from 57.1 to 100% and the specificity ranged from 69.8 to 100% using culture as gold standard. The PCR/ESI-MS also revealed the presence of the methicillin-resistant gene mecA in 16.2% of the milk samples, which correlated with the simultaneous detection of staphylococci including Staphylococcus aureus. We demonstrated that PCR/ESI-MS, a more rapid diagnostic platform compared with bacterial culture, has the significant potential to serve as an important screening method in the diagnosis of bovine clinical mastitis and has the capacity to be used in infection control programs for both subclinical and clinical disease.
Effect of PRRS vaccination on average daily gain: A comparison of intranasal and intranasal-intramuscular administration (1998)

SAS: Iowa Select Farms, Iowa Falls, Iowa 50126, e-mail: ssornsen@cnsinternet.com; JJZ: Iowa State University; DDP, MBR: NOBL Laboratories orcine reproductive and respiratory syndrome (PRRS) causes production and financial losses in swine herds worldwide.1–3 Several researchers have reported that PRRS virus (PRRSV) infection may have an adverse effect on nursery performance.4,5 Kerkaert, et al.,6 reported that chronic PRRSV infections in nurseries can reduce total profits up to 70%, with the losses due principally to decreased performance rather than increased mortality. Polson, et al.,5 observed that the financial losses that resulted from PRRSV infection varied according to mortality rates and duration of the disease episode. Nursery losses in the model ranged from $0.73–$18.21 per head. Mortality and the number of disadvantaged pigs can be increased twoor threefold, and average daily gain (ADG) may be decreased by as much as 25%–50% in the face of chronic PRRSV infections.1,5,7–9 Dee9 reported that ADG in PRRSV-infected nurseries was reduced by 0.22–0.33 lb (0.48–0.73 kg).8,10,11 Chronic PRRSV infections have been reported to reduce ADG of growing pigs by as much as 15%. These losses have prompted researchers and practitioners to search for methods to control the clinical effects of the disease.
Differential Expression of E‐ and P‐Selectin in the Microvasculature of Sickle Cell Transgenic Mice (2004)

Sickle cell disease promotes an increased P-selectin expression in several vascular beds. An accumulation of platelets may explain the increased P-selectin expression observed in some vascular beds.
단일서버에서의 누적적 공정서비스 모델 (2006)

Generalized Processor Sharing(GPS) 모델은 세션에게 서비스를 제공시 순시적 공정서비스를 통해 서버 용량을 분배한다. 이 공정서비스는 단지 현재 서버 내에 대기 중인 세션만을 고려하여 서버 용량을 분배하기 때문에, 서비스를 제공하는 순간 서비스를 받는 세션 간에는 공정한 서비스가 제공된다고 볼 수 있다. 그러나 긴 시간의 관점에서 보면 같은 가중치를 가지는 한 세션이 다른 세션에 비해 평균적으로 다른 용량으로 서비스 받는 문제가 발생한다. 본 연구에서는 긴 시간의 관점에서 모든 세션이 항상 공평한 서비스용량을 제공받을 수 있는 누적 공정서비스 모델(CFS)을 제안한다. 이 CFS 모델은 각 세션에게 누적적 공정 서비스 용량을 제공하기 때문에 세션관점 공정 서비스를 제공한다. 그리고 이 모델과 이 모델을 참조하여 각 세션의 패킷을 스케줄링 하는 패킷 누적공정 서비스(P_CFS)알고리즘의 특성과 성능을 분석하였다. 또한 성능평가를 통해 각 세션에게 긴 시간의 관점에서 세션의 가중치에 비례하는 서비스용량이 제공되는 것을 검증하였다.
Spleen cell-mediated suppression of IgG production to a non-parasite antigen during chronic Trypanosoma cruzi infection in mice. (1983)

Splenic plaque-forming cell (PFC) responses to TNP-BGG (thymus-dependent) and TNP-Ficoll (thymus-independent) were measured during acute and chronic T. cruzi infections produced in C57BL/10 mice. The number of anti-TNP PFC to both antigens was suppressed as has been shown. Approximately 40% of untreated mice survived acute disease to enter chronic T. cruzi infection characterized by a decrease in parasitemia, a reduction in spleen size, a return to normal of the IgM responses to TNP-BGG and TNP-Ficoll, persistant polyclonal activation, and continued suppression of the IgG responses to TNP-BGG. Mice that were drug-treated during the acute disease had high survival rates and similar immune response patterns, ie., suppressed IgG PFC responses to TNP-BGG and normal IgM PFC responses to TNP-BGG and TNP-Ficoll. The selective suppression of the IgG response was transferred to nonirradiated syngeneic recipients by Thy-1.2-positive cells present in the spleens of chronically infected mice. These observations may be interpreted to suggest the persistence of nonspecific suppressor T cells during chronic T. cruzi infections.
Amphiphilic Block Copolymer with a Molecular Recognition Site:  Induction of a Novel Binding Characteristic of Amylose by Self-Assembly of Poly(ethylene oxide)-block-amylose in Chloroform (2001)

Solution properties of amphiphilic methoxy poly(ethylene oxide)-block-amyloses (MPEO-amyloses) in chloroform were investigated by SLS and DLS. The results indicated that MPEO-amyloses dissolved in chloroform containing 2 wt % DMSO by their self-associations. The complexation of MPEO-amylose with methyl orange (MO) was significantly enhanced in the amylose domain of the associate in chloroform. The blue shift of the maximum absorption and strong induced circular dichroism with exciton coupling were observed in the MPEO-amylose MO complex in chloroform. The self-assembly of MPEO-amylose in chloroform shows a unique feature for binding with MO. MPEO-block-amylose is a novel amphiphilic polymer with amylose as a molecular recognition site.
Octahedral vs. trigonal-prismatic coordination. Structure of (Me4N)2[V(mnt)3] (1967)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOctahedral vs. trigonal-prismatic coordination. Structure of (Me4N)2[V(mnt)3]Edward I. Stiefel, Zvi. Dori, and Harry B. GrayCite this: J. Am. Chem. Soc. 1967, 89, 13, 3353–3354Publication Date (Print):June 1, 1967Publication History Published online1 May 2002Published inissue 1 June 1967https://pubs.acs.org/doi/10.1021/ja00989a048https://doi.org/10.1021/ja00989a048research-articleACS PublicationsRequest reuse permissionsArticle Views167Altmetric-Citations64LEARN 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
Logged virtual memory (1995)

l,oggged [Itrhra[ 71teruory ( LVM ) provides a log of writes to ol]e or more sImcified regions of the virtual address space. I,ogging is useflll for applications that, require rollback and/ur perslstjenre slich as parallel simulations and memory-mapped obje( t-oriented databases It can also }Je Ilsed for olltpllt,, de})nggmg and chstrihuted consistency maintenance. Tlus }japer describes logged virtual memory as an extensiou of the standard virtual memory system software and harxiwarr. our l,rotot,ype implementation and some perforrrance measurements from this prototype. Based on these measurements and the experience with our prototype, we arglle that logged virtual memory can be supported with moclest, extensions to standard virtual memory systems, provides significant benefit to applications and servers, and is faster than other log-generation technicples.
ARMC5 variants in PRKAR1A-mutated patients modify cortisol levels and Cushing’s syndrome (2020)

Mutations in the protein kinase A (PKA) regulatory subunit type 1A (PRKAR1A) and armadillo repeat-containing 5 (ARMC5) genes cause Cushing's syndrome (CS) due to primary pigmented nodular adrenocortical disease (PPNAD) and primary bilateral macronodular adrenocortical hyperplasia (PBMAH), respectively. Between the two genes, ARMC5 is highly polymorphic with several variants in the population, whereas PRKAR1A has very little, if any, non-pathogenic variation in its coding sequence. We tested the hypothesis that ARMC5 variants may affect the clinical presentation of PPNAD and CS among patients with PRKAR1A mutations. In this study, 91 patients with PPNAD due to PRKAR1A mutations were tested for abnormal cortisol secretion or CS and for ARMC5 sequence variants. Abnormal cortisol secretion was present in 71 of 74 patients with ARMC5 variants, whereas 11 of 17 patients negative for ARMC5 variants did not have hypercortisolemia. The presence of ARMC5 variants was a statistically strong predictor of CS among patients with PRKAR1A mutations (P < 0.001). Among patients with CS due to PPNAD, ARMC5 variants were associated with lower cortisol levels at baseline (P = 0.04) and after high dose dexamethasone administration (P = 0.02). The ARMC5 p.I170V variant increased ARMC5 protein accumulation in vitro and decreased viability of NCI-H295 cells (but not HEK 293T cells). PPNAD tissues with ARMC5 variants showed stronger ARMC5 protein expression than those that carried a normal ARMC5 sequence. Taken together, our results suggest that ARMC5 variants among patients with PPNAD due to PRKAR1A defects may play the role of a genetic modifier for the presence and severity of hypercortisolemia.
The transcriptional regulator BZR1 mediates trade-off between plant innate immunity and growth (2013)

The molecular mechanisms underlying the trade-off between plant innate immunity and steroid-mediated growth are controversial. Here, we report that activation of the transcription factor BZR1 is required and sufficient for suppression of immune signaling by brassinosteroids (BR). BZR1 induces the expression of several WRKY transcription factors that negatively control early immune responses. In addition, BZR1 associates with WRKY40 to mediate the antagonism between BR and immune signaling. We reveal that BZR1-mediated inhibition of immunity is particularly relevant when plant fast growth is required, such as during etiolation. Thus, BZR1 acts as an important regulator mediating the trade-off between growth and immunity upon integration of environmental cues. DOI: http://dx.doi.org/10.7554/eLife.00983.001.
Sca1+ murine pituitary adenoma cells show tumor-growth advantage (2014)

The role of tumor stem cells in benign tumors such as pituitary adenomas remains unclear. In this study, we investigated whether the cells within pituitary adenomas that spontaneously develop in Rb + /− mice are hierarchically distributed with a subset being responsible for tumor growth. Cells derived directly from such tumors grew as spheres in serum-free culture medium supplemented with epidermal growth factor and basic fibroblast growth factor. Some cells within growing pituitary tumor spheres (PTS) expressed common stem cell markers (Sca1, Sox2, Nestin, and CD133), but were devoid of hormone-positive differentiated cells. Under subsequent differentiating conditions (matrigel-coated growth surface), PTS expressed all six pituitary hormones. We next searched for specific markers of the stem cell population and isolated a Sca1 + cell population that showed increased sphere formation potential, lower mRNA hormone expression, higher expression of stem cell markers (Notch1, Sox2, and Nestin), and increased proliferation rates. When transplanted into non-obese diabetic-severe combined immunodeficiency gamma mice brains, Sca1 + pituitary tumor cells exhibited higher rates of tumor formation (brain tumors observed in 11/11 (100%) vs 7/12 (54%) of mice transplanted with Sca1 + and Sca1 − cells respectively). Magnetic resonance imaging and histological analysis of brain tumors showed that tumors derived from Sca1 + pituitary tumor cells were also larger and plurihormonal. Our findings show that Sca1 + cells derived from benign pituitary tumors exhibit an undifferentiated expression profile and tumor-proliferative advantages, and we propose that they could represent putative pituitary tumor stem/progenitor cells.