gebhart/patrepeval huggingface dataset:
Abstract LB-214: Imputation of single cell cancer genotypes (2019)

Abstract Recent advances in sequencing technologies and emerging single cell sequencing promise to profoundly impact cancer studies. One of the most important problems is reconstruction of history of cancer mutations. Existing methods model cells DNA as haplotypes and reconstruct perfect (or almost perfect) phylogeny of mutations from single cell DNA sequencing data. In this paper we propose to reconstruct genotypes (rather than haplotypes) which in absence of repeated and omitted mutations is equivalent to reconstruction of the mutation phylogeny. Single cell genotype reconstruction is proposed to perform in two steps - first the sequencing data are used for imputation of cell genotypes treated as individual human genomes and then the resulted genomes are fitted to perfect phylogeny by eliminating 4-gamete rule violations using integer linear programs. Our simulation results show advantage of single cell genotype imputation over existing methods. Note: This abstract was not presented at the meeting. Citation Format: Alex Zelikovsky, Igor Mandric, Pavel Skums, Ion Mandoiu, Bogdan Pasaniuc, Pramod Srivastava. Imputation of single cell cancer genotypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-214.
Multi-output-port spectral pulse-shaping for simulating complex interferometric structures (2012)

qWe demonstrate a novel spectral pulse shaper based reconfigurable interferometric filter with multiple output ports. Using this device we implement a DPSK and DQPSK demodulator and an all-optical discrete Fourier transform filter.
COMPLETE SEQUENCE OF THE GLYCOSYLATED AMINO TERMINAL SEGMENT OF PORCINE PRO‐OPIOMELANOCORTIN (1981)

The complete sequence of an anterior pituitary glycopeptide corresponding to the first 80 amino acid residues of the amino terminal of pro-opiomelanocortin (POMC) after excision of the signal peptide is reported. This peptide isolated from pig pituitaries shows considerable sequence conservation with its predicted homologues from bovine, murine and human species.
Hollow Mesoporous Zirconia Nanocapsules for Drug Delivery (2010)

Abstract Hollow mesoporous zirconia nanocapsules ( hm ‐ZrO 2 ) with a hollow core/porous shell structure are demonstrated as effective vehicles for anti‐cancer drug delivery. While the highly porous feature of the shell allows the drug, doxorubicin(DOX), to easily pass through between the inner void space and surrounding environment of the particles, the void space in the core endows the nanocapsules with high drug loading capacity. The larger the inner hollow diameter, the higher their DOX loading capacity. A loading of 102% related to the weight of hm ‐ZrO 2 is achieved by the nanocapsules with an inner diameter of 385 nm. Due to their pH‐dependent charge nature, hm ‐ZrO 2 loaded DOX exhibit pH‐dependent drug releasing kinetics. A lower pH offers a faster DOX release rate from hm ‐ZrO 2 . Such a property makes the loaded DOX easily release from the nanocapsules when up‐taken by living cells. Although the flow cytometry reveals more uptake of hm ‐ZrO 2 particles by normal cells, hm ‐ZrO 2 loaded DOX release more drugs in cancer cells than in normal cells, leading to more cytotoxicity toward tumor cells and less cytotoxicity to healthy cells than free DOX.
A <i>Pseudomonas aeruginosa</i> Quorum-Sensing autoinducer analog enhances the activity of antibiotics against resistant strains (2017)

In this study, we have investigated the effects of the newly synthesized analog of Pseudomonas aeruginosa quorum-sensing autoinducer named AIA-1 (autoinducer analog) against antibiotic-resistant bacteria. In vitro susceptibility and killing assays for P. aeruginosa PAO1ΔoprD mutant and clinical isolates were performed by using antibiotics and AIA-1. In an in vivo assay, a luminescent carbapenem-resistant strain derived from PAO1ΔoprD was injected into neutropenic ICR mice and bioluminescence images were acquired after the treatment with antibiotics and AIA-1. Additionally, we investigated the effects of the combination use against carbapenem-resistant Enterobacteriaceae (CRE). Using killing assays in P. aeruginosa, the survival rates in the presence of antibiotics and AIA-1 significantly decreased in comparison with those with antibiotics alone. Furthermore, dual treatment of biapenem and AIA-1 was more effective than biapenem alone in a mouse infection model. AIA-1 did not change the MICs in P. aeruginosa, suggesting that AIA-1 acts on the mechanism of antibiotic tolerance. Conversely, the MICs of antibiotics decreased in the presence of AIA-1 in some CRE strains, indicating that AIA-1 may require additional mechanism to act on CRE. In conclusion, AIA-1 may be a potent drug for clinical treatment of infections caused by antibiotic-resistant bacteria. J. Med. Invest. 64: 101-109, February, 2017.
Maculatic Acids—Sex Attractant Pheromone Components of Bald‐Faced Hornets (2018)

Abstract Yellowjackets in the genera Vespula and Dolichovespula are prevalent eusocial insects of great ecological and economic significance, but the chemical signals of their sexual communication systems have defied structural elucidation. Herein, we report the identification of sex attractant pheromone components of virgin bald‐faced hornet queens (Dolichovespula maculata). We analyzed body surface extracts of queens by coupled gas chromatographic–electroantennographic detection (GC‐EAD), isolated the compounds that elicited responses from male antennae by high‐performance liquid chromatography (HPLC), and identified these components by GC mass spectrometry (MS), HPLC‐MS, and NMR spectroscopy. In laboratory olfactometer experiments, synthetic (2 Z ,7 E )‐3,7‐dimethyldeca‐2,7‐diendioic acid (termed here maculatic acid A) and (2 Z ,7 E )‐10‐methoxy‐3,7‐dimethyldeca‐10‐oxo‐deca‐2,7‐dienoic acid (termed here maculatic acid C) in binary combination significantly attracted bald‐faced hornet males. These are the first sex attractant pheromone components identified in yellowjackets.
Predicting Individual Differences for Learner Modeling in Intelligent Tutors from Previous Learner Activities (2016)

This study examines how accurately individual student differences in learning can be predicted from prior student learning activities. Bayesian Knowledge Tracing (BKT) predicts learner performance well and has often been employed to implement cognitive mastery. Standard BKT individualizes parameter estimates for knowledge components, but not for learners. Studies have shown that individualizing parameters for learners improves the quality of BKT fits and can lead to very different (and potentially better) practice recommendations. These studies typically derive best-fitting individualized learner parameters from learner performance in existing data logs, making the methods difficult to deploy in actual tutor use. In this work, we examine how well BKT parameters in a tutor lesson can be individualized based on learners' prior performance in reading instructional text, taking a pretest, and completing an earlier tutor lesson. We find that best-fitting individual difference estimates do not directly transfer well from one tutor lesson to another, but that predictive models incorporating variables extracted from prior reading, pretest and tutor activities perform well, when compared to a standard BKT model and a model with best-fitting individualized parameter estimates.
Vertical transmission of SARS‐CoV2 during pregnancy: A high‐risk cohort (2021)

Vertical transmission is possible in pregnant women with COVID-19 and a shorter interval between maternal symptoms and delivery is an influencing factor.
Upstream bandwidth optimization of thin client protocols through latency‐aware adaptive user event buffering (2010)

Abstract Thin client computing trades local processing for network bandwidth by off‐loading application logic to remote servers. User input and display updates are exchanged between client and server through a thin client protocol. In a wireless device context, it is important to achieve bandwidth efficient thin client protocols because bandwidth availability is limited and the power consumption of the wireless network interface card is directly related to the amount of data that is sent and received. This paper presents and evaluates a novel client‐based mechanism which is transparent to the server to reduce upstream bandwidth consumption. Typically, thin client protocols encode user input as a series of small packets, resulting in a major packetization overhead. By buffering user events at the thin client protocol layer, this overhead can be reduced. However, buffering strategies might result in increased response delays for the user. Therefore, models of the upstream bandwidth and the user perceived responsiveness of pull thin client protocols are presented and validated. These models are used in an adaptive framework, which determines the appropriate buffering time to minimize the bandwidth as much as possible without degrading the responsiveness. For lower network roundtrip times and users actively generating input, it is shown how bandwidth savings up to 78% can be achieved while keeping the average user perceived responsiveness below 150 ms. Copyright © 2010 John Wiley &amp; Sons, Ltd.
ROTATIONAL ALIGNMENT OF THE TIBIAL COMPONENT IN TKA AFTER USING THE SELF ALIGNMENT TECHNIQUE: A CT-SCAN STUDY (2012)

Introduction Proper rotational alignment of the tibial component in total knee arthroplasty (TKA) could be achieved using several techniques. The self adjustment methodology allows the alignment of the tibial component under the femoral component after several flexion-extension movements. Our hypothesis was that this technique allowed a posterior tibial component alignment parallel to the femoral component posterior bicondylar axis. The aim of this study was to access this hypothesis using a post-operative CT-scan study. Materials and Methods This prospective CT-scan study involved 94 TKA. Theses TKA were divided in two groups: group1: 50 knees with a pre-operative genu varum deformity (mean HKA: 172.2°), operated using a medial parapatellar approach, and group 2: 44 knees with a preoperative valgus deformity (mean HKA: 188.7°), operated using a lateral parapatellar approach. Four measures were done on each post-operative CT-scan: angle between anatomical transepicondylar axis and femoral component posterior bicondylar axis (FCPCA), angle between FCPCA and tibial component marginal posterior axis, angle between tibial component marginal posterior axis and bony tibial plateau marginal posterior axis (BTPMPA), angle between transepicondylar axis and tibial component marginal posterior axis. Each measure was repeated, after one month by the same independent observer. Statistical evaluation used non-parametric Wilcoxon–Mann–Whitney test to compare each group of measures, and intraobserver reproducibility was assessed using ANOVA test, with an error rate of 5%. Results Intraobserver measurements were reproducible. Mean FCPCA was to 3,1° (SD:1,91) in group 1 and 4,7° (DS: 2,96) in group 2. Tibial component was positioned in external rotation in both groups, in relation to FCPCA: (group 1: mean angle: 0,7° (SD:4,45), group 2: mean angle: 0,9° (SD:4,53)) and in relation to BTPMPA: (group1: mean angle: 6,1° (SD: 5,85); group2: mean angle: 12,5° (SD: 8,6)). There was no statistical difference between these two groups. Tibial component was positioned in internal rotation in relation to anatomical transepicondylar axis: (Group1: mean angle: 1,9° (SD: 4,93); group 2: mean angle: 3° (SD: 4.38)) Discussion By using the self adjustment technique, tibial component is aligned parallel to the femoral component regardless of the initial frontal deformity and the surgical approach. However, there was a difference in tibial component axis and BTPMPA, between the two groups. This difference should be explained by the difference in morphology of the tibial plateau bone in knee with genu valgum deformity. The self adjustment technique is a reliable method to obtain a proper rotational alignment of the tibial component in TKA.
A predictive model for risk of early grade ≥ 3 infection in patients with multiple myeloma not eligible for transplant: analysis of the FIRST trial (2018)

Infections are a major cause of death in patients with multiple myeloma. A post hoc analysis of the phase 3 FIRST trial was conducted to characterize treatment-emergent (TE) infections and study risk factors for TE grade ≥ 3 infection. The number of TE infections/month was highest during the first 4 months of treatment (defined as early infection). Of 1613 treated patients, 340 (21.1%) experienced TE grade ≥ 3 infections in the first 18 months and 56.2% of these patients experienced their first grade ≥ 3 infection in the first 4 months. Risk of early infection was similar regardless of treatment. Based on the analyses of data in 1378 patients through multivariate logistic regression, a predictive model of first TE grade ≥ 3 infection in the first 4 months retained Eastern Cooperative Oncology Group performance status and serum β<sub>2</sub>-microglobulin, lactate dehydrogenase, and hemoglobin levels to define high- and low-risk groups showing significantly different rates of infection (24.0% vs. 7.0%, respectively; P < 0.0001). The predictive model was validated with data from three clinical trials. This predictive model of early TE grade ≥ 3 infection may be applied in the clinical setting to guide infection monitoring and strategies for infection prevention.
Assessment of a New Method to Distinguish Esophageal from Tracheal Intubation by Measuring the Endotracheal Cuff Pressure in a Porcine Model (2005)

The cuff pressure in the esophageal intubation was significantly higher than that in the endotracheal intubation under the same inflated volume from 1 to 10 mL. This may provide the basis for an adjunctive, simple, rapid, and reliable method to verify endotracheal intubation.
Identification and reconstruction of phylogeny among three species of Cleome using nrDNA-ITS sequence (2022)

Three species of genus Cleome, C. arabica, C. ramosissima and C. amblyocarpa were identified using nuclear ribosomal DNA internal transcribed spacer sequence (nrDNA-ITS). The phylogenetic tree was made using different methods viz., neighbor-joining (NJ), maximum parsimony (MP), and maximum likelihood for accuracy of the results, and congruence finding in phylogeny. Cleome ramosissima and C. amblyocarpa were found to be clustered in one group according to the sequence similarity. However, C. arabica clustered in a separate clade. The nrDNA-ITS marker clearly differentiated and showed phylogenetic relationships among the three species. Thus, nrDNA-ITS marker could be effectively used for other species of Cleome for their identification and phylogenetic studies.
Top-down control of visual attention in object detection (2004)

Current computational models of visual attention focus on bottom-up information and ignore scene context. However, studies in visual cognition show that humans use context to facilitate object detection in natural scenes by directing their attention or eyes to diagnostic regions. Here we propose a model of attention guidance based on global scene configuration. We show that the statistics of low-level features across the scene image determine where a specific object (e.g. a person) should be located. Human eye movements show that regions chosen by the top-down model agree with regions scrutinized by human observers performing a visual search task for people. The results validate the proposition that top-down information from visual context modulates the saliency of image regions during the task of object detection. Contextual information provides a shortcut for efficient object detection systems.
Simulation and measurement of spatial resolution in detection of annihilation radiation with BGO crystals (2005)

Spatial resolution performance measurements of PET scanners are sensitive to the long tails of the angular distribution of the annihilation radiation, to a degree not previously appreciated. The non-Gaussian nature of the positron range, angular distribution of annihilation radiation, and scatter-induced spatial distribution of scintillator energy deposition prevents simple (e.g. quadrature-based arguments) methods of performance estimation, and requires full numerical convolution of the 3D spatial profiles. The authors have developed a Monte Carlo simulation of 511 keV gamma ray interactions with scintillator crystals to model the spatial distributions obtained in projection measurements of annihilation radiation from point sources. The authors find good agreement between the simulations and experimental results obtained with BGO-based crystals, both for optically-isolated crystals embedded in a crystal matrix, and for a conventional, Anger-based BGO block detector. There is approximately a 0.3 mm difference in the coincidence response function FWHM between 4 mm isolated and Anger crystals which is reproduced by the Monte Carlo calculations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Interplay Between Solute Atoms and Vacancy Clusters in Magnesium Alloys (2021)

Atomic-scale calculations indicate that both stress effects and chemical binding contribute to the redistribution of solute in the presence of vacancy clusters in magnesium alloys. As the size of the vacancy cluster increases, chemical binding becomes more important relative to stress. By affecting the diffusivity of vacancies and vacancy clusters, solute atoms facilitate clustering and stabilize the resulting vacancy clusters, increasing their potential to promote solute segregation and to serve as heterogeneous nucleation sites during precipitation. Experimental observation of solute segregation in simultaneously deformed and aged Mg-Al alloys provides support for this mechanism.
The putative oncogene Spi-1: murine chromosomal localization and transcriptional activation in murine acute erythroleukemias. (1989)

We have shown previously that spleen focus forming virus integration near the Spi-1 putative oncogene is observed in 95% of erythroid Friend tumors (Moreau-Gachelin et al., 1988). Here we describe how the proviral insertion in the Spi-1 domain is associated with the enhanced transcription of a 1.4 kb mRNA normally expressed at a low level in normal cells. The gene is localized on murine chromosome 2, band E3. The structure of the Spi-1 gene was determined by sequencing genomic and cDNA clones. The gene has an open reading frame encoding a protein of 218 amino acids, extending over five exons. Proviruses always integrate outside, upstream and in the opposite orientation of the protein-encoding domain. This suggests that SFFV integration activates the expression of Spi-2 gene that may contribute to the erythroleukemic process.
Association between multidrug resistance protein 4 polymorphism and adverse events in childhood acute lymphoblastic leukemia (2011)

One of the major problems in treating childhood acute lymphoblastic leukemia (ALL) is 6-mercaptopurine (6-MP)-related toxicity, resulting from the accumulation of 6-thioguanine nucleotide (6-TGN) in cells. Multidrug resistance protein 4 ( MRP 4), a transport protein, plays an important role in the efflux of cytotoxic drugs, including toxic 6-TGN from cells. A single nucleotide polymorphism in human MRP 4 rs3765534 C>T dramatically reduces MRP 4 function and results in the intracellular accumulation o f 6-TGN . Th e ai m o f thi s stud y wa s t o investigat e th e associatio n betwee n MRP 4 rs376553 4 C> T geneti c polymorphis m an d advers e event s i n Tha i childhoo d AL L treate d wit h 6-MP . Th e subject s wer e childre n les s tha n 1 5 year s o f ag e wh o wer e diagnose d wit h AL L a t ou r institutio n betwee n 200 4 an d 2007 . The y receive d 6-M P durin g induction , consoli - dation, and maintenance phases of therapy. The common 6-MP related toxicities wer e recorded . Th e polymorphis m o f MRP 4 rs376553 4 C> T wa s identi f i e d usin g real-tim e poly - merase chain reaction. The association between genetic variation and side effects of 6-M P wa s analyzed . A tota l o f 18 6 childre n wit h AL L wer e include d i n thi s study . Th e genotyping showed 171 homozygous wild type (CC) and 15 heterozygous (CT) of this MRP 4 polymorphism. The allele frequency of C and T alleles were 96% and 4%, respectively . Childre n wit h C T genotyp e wer e a t ris k o f neutropeni a durin g 6-M P exposur e (OR = 3; 95% CI, 1.7-99.9; p = 0.03). Our study demonstrated that MRP 4 rs3765534 T allel e signi f icantl y increase d ris k o f 6-M P relate d neutropeni a i n childre n wit h ALL .
Genetic factors influence the development of mechanical hypersensitivity, motor deficits and morphological damage after transient spinal cord ischemia in the rat (1994)

Zsuzsanna, Wiesenfeld-Hallin∗,a; Jing-Xia, Haoa,b; Xiao-Jun, Xua; Håkan, Aldskogiusc; Åke, Seigerb Author Information
An atom-by-atom assembler of defect-free arbitrary two-dimensional atomic arrays (2016)

Large arrays of individually controlled atoms trapped in optical tweezers are a very promising platform for quantum engineering applications. However, deterministic loading of the traps is experimentally challenging. We demonstrate the preparation of fully loaded two-dimensional arrays of up to ~50 microtraps, each containing a single atom and arranged in arbitrary geometries. Starting from initially larger, half-filled matrices of randomly loaded traps, we obtain user-defined target arrays at unit filling. This is achieved with a real-time control system and a moving optical tweezers, which together enable a sequence of rapid atom moves depending on the initial distribution of the atoms in the arrays. These results open exciting prospects for quantum engineering with neutral atoms in tunable two-dimensional geometries.
Spatiotemporal GMM for Background Subtraction with Superpixel Hierarchy (2017)

We propose a background subtraction algorithm using hierarchical superpixel segmentation, spanning trees and optical flow. First, we generate superpixel segmentation trees using a number of Gaussian Mixture Models (GMMs) by treating each GMM as one vertex to construct spanning trees. Next, we use the -smoother to enhance the spatial consistency on the spanning trees and estimate optical flow to extend the -smoother to the temporal domain. Experimental results on synthetic and real-world benchmark datasets show that the proposed algorithm performs favorably for background subtraction in videos against the state-of-the-art methods in spite of frequent and sudden changes of pixel values.
Recommendations for euthanasia of experimental animals: Part 1 (1996)

Working Party: Mrs Bryony Close (Chair), Dr Keith Banister, Dr Vera Baumans, Dr Eva-Maria Bernoth, Dr Niall Bromage, Dr John Bunyan, Professor Dr Wolff Erhardt, Professor Paul Flecknell, Dr Neville Gregory, Professor Dr Hansjoachim Hackbarth, Professor David Morton & Mr Clifford Warwick Correspondence to: Mrs B Close, Battleborough Croft, Battleborough Lane, Brent Knoll, Highbridge. Somerset TA94DS, UK