gebhart/patrepeval huggingface dataset:
Anomaly Detection in Large Sets of High-Dimensional Symbol Sequences (2006)

This paper addresses the problem of detecting and describing anomalies in large sets of high-dimensional symbol sequences. The approach taken uses unsupervised clustering of sequences using the normalized longest common subsequence (LCS) as a similarity measure, followed by detailed analysis of outliers to detect anomalies. As the LCS measure is expensive to compute, the first part of the paper discusses existing algorithms, such as the Hunt-Szymanski algorithm, that have low time-complexity. We then discuss why these algorithms often do not work well in practice and present a new hybrid algorithm for computing the LCS that, in our tests, outperforms the Hunt-Szymanski algorithm by a factor of five. The second part of the paper presents new algorithms for outlier analysis that provide comprehensible indicators as to why a particular sequence was deemed to be an outlier. The algorithms provide a coherent description to an analyst of the anomalies in the sequence, compared to more normal sequences. The algorithms we present are general and domain-independent, so we discuss applications in related areas such as anomaly detection.
Full Visible Range Covering InP/ZnS Nanocrystals with High Photometric Performance and Their Application to White Quantum Dot Light‐Emitting Diodes (2012)

High-quality InP/ZnS core–shell nanocrystals with luminescence tunable over the entire visible spectrum have been achieved by a facile one-pot solvothermal method. These nanocrystals exhibit high quantum yields (above 60%), wide emission spectrum tunability and excellent photostability. The FWHM can be as narrow as 38 nm, which is close to that of CdSe nanocrystals. Also, making use of these nanocrystals, we further demonstrated a cadmium-free white QD-LED with a high color rendering index of 91. The high-performance of the resulting InP/ZnS NCs coupled with their low intrinsic toxicity may further promote industrial applications of these NC emitters.
<title>Optimum Windows For Image Registration</title> (1979)

Two-dimensional cross-correlation techniques are applied to the problem of image registration under the assumption of small geometric distortion. Optimum window functions are derived for two performance measures of interest: peak-to-sidelobe ratio and mean-square error. The latter is examined in terms of the contribution due to distortion and the contribution due to noise. The case of Gaussian autocorrelation functions is examined in detail. Results for applying the theoretically derived window functions to real data are presented, showing significant improvement in correlator performance.
Abstract 1440: Novel imipridone ONC206 suppresses ovarian cancer progression through modulating immune cell response (2021)

Abstract Advanced ovarian cancer (stages III and IV) is the most lethal gynecologic malignancy in the United States. Survival of this cancer has not improved to a major extent over the past decade. High-grade serous ovarian cancer (HGSC), in particular, is notable for its initial sensitivity to chemotherapy using platinum and taxane combination following debulking surgery. However, the vast majority of these cancers (&amp;gt;75-80%) recur within 12-24 months after diagnosis, and patients die of progressively chemotherapy-resistant disease. The identification of prognostic or predictive markers, for ovarian cancer is crucial to the development of therapeutic targets and thus improvement of survival. ONC201 is the first clinical bitopic antagonist of dopamine receptor D2 (DRD2), that is well tolerated and currently being investigated in several clinical trials for oncology. ONC206 is a chemical derivative of ONC201 with the same impridone core structure, which is also a DRD2 antagonist that exhibits distinct receptor pharmacology and nanomolar potency in various preclinical cancer models. However, the effects of ONC206 on HGSC progression and the mechanism of action have not been thoroughly explored. Preliminary data demonstrated that overexpression of DRD2 is associated with poor overall survival rates in patients with advanced stage HGSC. ONC206-treated HGSC cells demonstrated significantly lower growth rates and higher percentage of apoptotic cells than ONC201-treated cells did in vitro. Besides, intraperitoneal injection of ONC206 (100 mg/kg) twice a week into HGSC-bearing immunocompetent mice demonstrated decreased tumor volume in vivo. In addition, by using suspension mass cytometry with a panel of 28 antibodies, fresh tumor tissues from ONC206-treated mice showed markedly increase in intratumoral NK cells and activated CD8+ T cells densities. These data suggest that ONC206 is more potent than ONC201 in suppressing HGSC growth directly. In addition, ONC206 may also suppresses HGSC growth through activating immune cell response in tumor tissues. Further studies that define the molecular mechanism by which DRD2 modulates the tumor suppressive effect of ONC206 on HGSC cells by suppressing HGSC directly or enhancing anti-tumor immune cell activity will be perform to establish ONC206 as a novel therapeutic agent in treatment of HGSC patients. Citation Format: Chi Lam Au Yeung, Wen Hu, Sammy Ferri-Borgogno, Rohinton S. Tarapore, Joshua E. Allen, Karen H. Lu, Samuel C. Mok. Novel imipridone ONC206 suppresses ovarian cancer progression through modulating immune cell response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1440.
Recommendations as a conversation with the user (2011)

Recommender systems provide users with products or content intended to satisfy their information needs. The primary evaluation measures for recommender systems emphasize either the perceived relevance of the recommendations or the actions driven by those recommendations (e.g., purchases on ecommerce sites or clicks on news and social networking sites). Unfortunately, this transactional emphasis neglects the inherently interactive nature of the user experience.
Sprouting adult CNS cholinergic axons express nile and associate with astrocytic surfaces expressing neural cell adhesion molecule (1996)

To assess the cellular and molecular substrates for cholinergic axon growth in the adult central nervous system (CNS), we implanted grafts of control and nerve growth factor (NGF)-producing genetically modified fibroblasts within the striatum of rats. Sprouting cholinergic axonal processes that grew into grafts of NGF-producing fibroblasts were fasciculated and followed the surface of astrocytic processes for long distances within the grafts. The close and long distance anatomical relationship between the sprouted axons and the astrocytes supported previous ultrastructural evidence that astrocytes may serve as a cellular substrate for sprouting cholinergic axons in vivo. The sprouted axon processes were associated with the expression of nerve growth factor-inducible large external (NILE) glycoprotein on their surfaces. NILE expression was not seen in control grafts where there was an absence of cholinergic ingrowth. NILE has been demonstrated to play a role in axon fasciculation in a number of other neural systems. The astrocytic processes in both control and NGF-producing fibroblast grafts expressed neural cell adhesion molecule (NCAM), suggesting that NCAM-mediated adhesion may be responsible for the close relationship between the axons and astrocytes within the grafts. NGF-induced heterotypic interactions between neuronal NILE and astroglial NCAM may also be required for adult cholinergic axonal sprouting.
Matrix Metalloproteinase 1 (MMP1) Is Associated with Early-Onset Lung Cancer (2008)

Matrix metalloproteinases (MMP) play a key role in the breakdown of extracellular matrix and in inflammatory processes. MMP1 is the most highly expressed interstitial collagenase degrading fibrillar collagens. Overexpression of MMP1 has been shown in tumor tissues and has been suggested to be associated with tumor invasion and metastasis. Nine haplotype tagging and additional two intronic single nucleotide polymorphisms (SNP) of MMP1 were genotyped in a case control sample, consisting of 635 lung cancer cases with onset of disease below 51 years of age and 1,300 age- and sex-matched cancer-free controls. Two regions of linkage disequilibrium (LD) of MMP1 could be observed: a region of low LD comprising the 5' region including the promoter and a region of high LD starting from exon 1 to the end of the gene and including the 3' flanking region. Several SNPs were identified to be individually significantly associated with risk of early-onset lung cancer. The most significant effect was seen for rs1938901 (P = 0.0089), rs193008 (P = 0.0108), and rs996999 (P = 0.0459). For rs996999, significance vanished after correction for multiple testing. For each of these SNPs, the major allele was associated with an increase in risk with an odds ratio between 1.2 and 1.3 (95% confidence interval, 1.0-1.5). The haplotype analysis supported these findings, especially for subgroups with high smoking intensity. In summary, we identified MMP1 to be associated with an increased risk for lung cancer, which was modified by smoking.
Parametrizing and fitting bounded algebraic curves and surfaces (2003)

An approach to fitting of implicit algebraic curves and surfaces to point data is introduced. Two families of polynomials with bounded zero sets are presented. Members of these families have the same number of degrees of freedom as general polynomials of the same degree. Methods for fitting members of these families of polynomials to measured data points are described. Experimental results for sets of points in R/sup 2/ and R/sup 3/ for curves and surfaces, respectively, are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
An update on the progress of galidesivir (BCX4430), a broad-spectrum antiviral (2021)

Galidesivir (BCX4430) is an adenosine nucleoside analog that is broadly active in cell culture against several RNA viruses of various families. This activity has also been shown in animal models of viral disease associated with Ebola, Marburg, yellow fever, Zika, and Rift Valley fever viruses. In many cases, the compound is more efficacious in animal models than cell culture activity would predict. Based on favorable data from in vivo animal studies, galidesivir has recently undergone evaluation in several phase I clinical trials, including against severe acute respiratory syndrome coronavirus 2, and as a medical countermeasure for the treatment of Marburg virus disease.
Steady-State Characteristics of the Push-Pull DC-to-DC Converter (1984)

Six modes of operation for the push-pull 4c-to-dc converter are presented by taking into account the magnetizing current of the transformer. If the inductance of the transformer is decreased, the region where the output voltage is abnormally high is expanded in the load characteristics.
Hyporesponsiveness to glucoprivation during postnatal period in the rat (1975)

2-Deoxy-D-glucose (2-DG), a glucose analogue, blocks glycolysis and induces intracellular glucoprivation. In the adult rat intraperitoneal administration of 2-DG or its injection into the lateral ventricle (IVT) of the brain induces hyperglycemia which is divorced from a rise in plasma insulin (IRI). In the present study, responsiveness to 2-DG-induced glucoprivation, after central or intraperitoneal injection of the drug, was studied in rats of 7, 14, 21, and 28 days of age and compared to that of the adult rat (50 days old). In 7-, 14-, 21-, and 28-day-old rats, the overall blood glucose (BG) response to IVT-injected 2-DG was equivalent to 4, 3.3, 17, and 33%, respectively, of the BG response present in the adult rat. Following intraperitoneal injection of 2-DG , the BG response evoked in the same age groups corresponded to 27, 31, 41, and 93%, respectively, of the adult response. Base-line plasma IRI levels were significantly lower in pups than in adults and increased progressively with age, but no difference was present in IRI levels between 2-DG-treated and control pups whether the 2-DG was given via the laterl ventricle or intraperitoneally. These results demonstrate the presence in the infant rat of clear-cut hyporesponsiveness to 2-DG-induced glucoprivation. The different response pattern between experiments involving central and peripheral 2-DG administration supports the existence of separate peripheral glucoreceptors for 2-DG and their earlier ontogenic activation. Since the infant mammal glucose is of minor relevance as an energy substrate, an interrelationship appears to be present between requirements for fuel(s) and homeostatic response to fuel deprivation.
25 EFFECT OF REPRODUCTIVE TRACT SIZE ON CONCEPTION RATES IN LACTATING DAIRY COWS UTILIZING A REPRODUCTIVE TRACT SCORING SYSTEM (2010)

Reproductive tract scoring (RTS) systems have been effective in evaluating fertility of heifers. A similar RTS system has not been reported in lactating dairy cows pertaining to conception rates following artificial insemination. Objectives of this study include development of a RTS system for lactating dairy cows and determining if RTS had an effect on artificial insemination (AI) success with various types of semen [conventional (CS), sexed (SS)]. During pre-breeding examinations (typically 30–60 DIM) by trained personnel, cows were assigned a RTS (1, 2, or 3) based on size and length of the cervix and uterine horns, but not including status of the ovaries. Tracts for RTS 1 were small, compact uterine horns resting within the pelvic cavity, RTS 2 were intermediate in size with uterine horns resting partially outside the pelvic cavity, and RTS 3 were large, deep tracts resting entirely outside the pelvis into the abdominal cavity. Additionally, cows were evaluated for RTS at a local abattoir before harvest, and tracts collected for volume and length measurements. Volume measurements were collected using Foley catheters and measuring water displaced in the uterine horns at a constant pressure. Length of the vagina, cervix, and uterine horns were measured using a flexible tape. Insemination data analysis was performed using mixed model analysis of variance in Glimmix SAS 9.2 (SAS Institute Inc., Cary, NC, USA). Insemination data included 613, 308, and 572 scores in first, second, and third+ lactation cows, respectively. First-lactation cows had 65.25% with RTS 1, 30.02% RTS 2, and 4.73% RTS 3. Second-lactation cows had 53.25% RTS 1, 39.29% RTS 2, and 7.47% RTS 3. Cows with 3+ lactations had 43.18% RTS 1, 43.88% RTS 2, and 12.94% RTS 3. Cows were artificially inseminated (n = 2401 inseminations) with either CS (n = 1981) or SS (n = 420). Conception rates for CS were 38.65%, 34.26%, and 24.41% for RTS 1, 2, and 3, respectively (P = 0.0154 for RTS 1 v. 3). Conception rates for CS (38.65%, RTS 1; 34.26%, RTS 2) were higher compared to SS (21.37%, RTS 1 (P = 0.0001); 20.72%, RTS 2 (P = 0.0186)). No differences were detected between CS (24.40%) and SS (22.35%) within RTS 3; however, observations were limited for SS inseminations with RTS 3. Preliminary data regarding total length (vagina, cervix, and uterine horns; RTS 1, 2, 3 = 103.1 cm, 114.9 cm, 134 cm, respectively) and volume (RTS 1, 2, 3 = 102 mL, 131 mL, 133.3 mL, respectively) suggest both increase as RTS increases but limited observations prevent conclusions at this time. Conception rates indicate smaller reproductive tracts have improved fertility in lactating dairy cows when using CS. Identification of larger reproductive tracts will allow for more economically efficient AI programs by utilising inexpensive, high fertility semen.
Observation of the forbidden doublet optical phonon in Raman spectra of strained Si for stress analysis (2010)

Using high numerical aperture lenses, we detected doublet optical phonon, forbidden by selection rules, in Raman spectra of Si strained in the (001) plane (bulk Si as well as strained Si device structure grown on SiGe). This allowed us to quantitatively determine stress and its distribution in strained Si with the ∼10% accuracy, assuming symmetric biaxial stress. At the same time, we demonstrate some deviations of the real stress from the assumed model. For better accuracy, one has to consider these deviations as well as a possibility of improvement of available Si phonon deformation potential values.
Simulations par dynamique moléculaire de la croissance de suies carbonées dans les plasmas (2016)

National audience
Immunogenicity and Effectiveness of Primary and Booster Vaccine Combination Strategies during Periods of SARS-CoV-2 Delta and Omicron Variants (2022)

In this study involving a cohort of employees of the National Airline company in Lebanon, we assessed humoral immunity levels and the effectiveness of two COVID-19 vaccines, Gam-COVID-Vac versus BNT162b2, after two doses and after a homologous and heterologous BNT162b2 booster, in addition to the impact of hybrid immunity. Vaccine effectiveness (VE) was retrospectively determined against laboratory-confirmed SARS-CoV-2 infection during the periods of Delta and Omicron variants' predominance, separately, and was calculated based on a case-control study design. The humoral immune response, measured by a SARS-CoV-2 anti-spike receptor-binding domain (RBD) IgG titer, was prospectively assessed after the aforementioned vaccination schemes at different time points. This study showed higher effectiveness of BNT162b2 after two doses (81%) compared to two doses of Gam-COVID-Vac (41.8%) against the Delta variant of SARS-CoV-2, which correlated with anti-spike antibody levels. Regarding the Omicron variant, protection against infection and antibody levels were severely compromised and the correlation between an anti-spike IgG titer and effectiveness was lost, unlike the situation during the Delta wave. Considering the booster vaccination schemes, a homologous BNT162b2 booster after a BNT162b2 primary vaccination induced a higher humoral immune response when compared to that induced by a heterologous BNT162b2 booster after a Gam-COVID-Vac primary vaccination. However, the VE of both booster regimens against the Omicron variant was almost equal (64% in the homologous regimen and 57% in heterologous regimen). Hybrid immunity evidenced a better humoral response and a greater and longer protection against Delta and Omicron infections compared to vaccination-induced immunity in COVID-19-naïve individuals. Finally, the findings show that VE waned with time during the same wave, highlighting the importance of reinforcing primary and booster COVID-19 vaccination mainly at the beginning of each wave during the surge of a new variant of concern.
Compressive coherence sensing (2009)

The 4D cross spectral density function is recovered using 2D rotational shear interferometer measurements and a matrix completion algorithm for low rank matrices. Imaging of point sources through turbulence is demonstrated.
Dissipative assembly of a membrane transport system (2014)

A membrane transport system functions only when activated by a chemical fuel.
New Concepts in AIDS Pathogenesis (1993)

The concept that HIV causes AIDS only by directly killing CD4 cells has been questioned by a number of investigators. There has been experimental support for a number of indirect mechanisms such as apoptosis, anergy, superantigen-induced cell proliferation and depletion, defective signaling, molecular mimicry, and autoimmunity. In this article we review the available evidence in support of these theories and suggest that in spite of their apparent differences, signaling by HIV through the T cell receptor could initiate the markedly different responses of activation, anergy, and apoptosis. However, the unifying mechanism as to how this is achieved remains unclear. It is likely that more than one of these mechanisms are involved in CD4 cell depletion during different phases of the disease. Understanding these mechanisms and their role in HIV pathogenesis would be important in new vaccine and therapeutic approaches.
Demonstrating elements of measurement-based quantum error correction (2014)

In measurement-based quantum computing an algorithm is performed by measurements on highly entangled resource states. To date, several implementations were demonstrated, most of them assuming perfect noise-free environments. Here we consider measurement-based information processing in the presence of noise and demonstrate quantum error detection. We implement the protocol using a four-qubit photonic cluster state where we first encode a general qubit nonlocally such that phase errors can be detected. We then read out the error syndrome and analyze the output states after decoding. Our demonstration shows a building block for measurement-based quantum computing which is crucial for realistic scenarios.
Abstract 66: Clonal Hematopoiesis of Indeterminate Potential and Incident Type 2 Diabetes Risk (2023)

Introduction: Clonal hematopoiesis of indeterminate potential (CHIP) is an aging-related accumulation of somatic mutations in hematopoietic stem cells, leading to clonal expansion. CHIP presence has been implicated in elevated risks for coronary heart disease (CHD) and death, but its association with incident type 2 diabetes (T2D) is unknown. Hypothesis: We hypothesized that CHIP is associated with elevated risk of incident T2D. Methods: CHIP was derived from whole genome sequencing of blood DNA in NHLBI Trans-omics for Precision Medicine (TOPMed) cohorts. We analyzed 17,637 participants without prior T2D, cardiovascular disease, or cancer at blood draw, with prospective follow-up for incident T2D. We evaluated baseline prevalence of CHIP vs. no CHIP with incident T2D risk using Cox regression. We also investigated CHIP variants previously related to CHD: DNMT3A , TET2 , ASXL1 , JAK2 , and TP53 . We estimated multivariable-adjusted hazard ratios and 95% confidence intervals (HR [CI]) adjusted for age, sex, body mass index, smoking, alcohol, and education. We combined cohort estimates via fixed effects meta-analysis. Results: On average, participants were age 63.4 years (SD=11.5) and 76% female. Prevalence of CHIP was 6.0% (1,055) at baseline. There were 2,467 incident T2D cases over mean=9.8 years follow-up. Compared to those without a mutation, having CHIP was associated with a 23% higher T2D risk, both overall (combined HR=1.23; 95% CI=1.04, 1.45), and among those with CHD-related CHIP mutations (87% of total CHIP): HR=1.23 (1.03, 1.46). Although those with CHIP mutations of TET2 (HR=1.48; 1.05, 2.08) and ASXL1 (HR=1.76; 1.03, 2.99) had larger elevations in T2D risk, and DNMT3A was suggestive of increased T2D risk (HR=1.15; 0.93, 1.43), statistical power was limited for JAK2 and TP53 mutation analyses. Conclusions: CHIP was associated with higher incidence of T2D. CHIP mutations located on loci previously implicated in aging and CHD were also related to T2D, suggesting shared pathology of atherosclerosis and T2D.