gebhart/patrepeval huggingface dataset:
Optical coherence tomography scanning with a handheld vitreoretinal micromanipulator (2012)

An active handheld micromanipulator has been developed that is capable of automated intraocular acquisition of B-mode and C-mode optical coherence tomography scans that are up to 4 mm wide. The manipulator is a handheld Gough-Stewart platform actuated by ultrasonic linear motors. The manipulator has been equipped with a Fourier-domain common-path intraocular OCT probe that fits within a 25-gauge needle. The paper describes the systems and techniques involved, and presents preliminary results of B-mode and C-mode scans.
AVA: A Video Dataset of Spatio-temporally Localized Atomic Visual Actions (2017)

This paper introduces a video dataset of spatio-temporally localized Atomic Visual Actions (AVA). The AVA dataset densely annotates 80 atomic visual actions in 430 15-minute video clips, where actions are localized in space and time, resulting in 1.58M action labels with multiple labels per person occurring frequently. The key characteristics of our dataset are: (1) the definition of atomic visual actions, rather than composite actions; (2) precise spatio-temporal annotations with possibly multiple annotations for each person; (3) exhaustive annotation of these atomic actions over 15-minute video clips; (4) people temporally linked across consecutive segments; and (5) using movies to gather a varied set of action representations. This departs from existing datasets for spatio-temporal action recognition, which typically provide sparse annotations for composite actions in short video clips. We will release the dataset publicly. AVA, with its realistic scene and action complexity, exposes the intrinsic difficulty of action recognition. To benchmark this, we present a novel approach for action localization that builds upon the current state-of-the-art methods, and demonstrates better performance on JHMDB and UCF101-24 categories. While setting a new state of the art on existing datasets, the overall results on AVA are low at 15.6% mAP, underscoring the need for developing new approaches for video understanding.
外阴佩吉特病的相关恶性肿瘤 (2018)

外阴佩吉特病(VPD)是一种罕见的皮肤疾病,常见于绝经后的白人女性,它会引起外阴周围的皮肤瘙痒或灼烧。这种疾病有不同的类型,并且在过去,所有类型的 VPD 都与乳腺、肠道和泌尿系统的恶性肿瘤(如癌症)有关。这项来自荷兰的研究着眼于皮肤非侵入性 VPD, 其中在诊断时它只影响皮肤。研究人员想知道,与一般人群(没有 VPD 的人)相比,这种类型的 VPD 是否确实增加了患乳腺癌、肠道或泌尿系统恶性肿瘤的风险,并且评估是否所有 VPD 患者都应该进行常规的恶性肿瘤筛查。从荷兰的全国病理报告档案中获得了 2000 年至 2015 年期间任何类型 VPD 患者的肿瘤学(癌症)历史数据。从荷兰癌症登记处获得了随访数据和来自普通人群的对照组。在 VPD 患者中, 76.9% 诊断为皮肤非侵入性 VPD。研究人员发现,虽然其他类型的 VPD 可能与恶性肿瘤有关,但皮肤非侵入性 VPD 组患乳腺、肠道或泌尿道恶性肿瘤的风险并未增加。这表明,在诊断为皮肤非侵入性 VPD 的患者中,对这些恶性肿瘤的常规筛查可能没有必要。
Quantifying Sensory Eye Dominance in the Normal Visual System: A New Technique and Insights into Variation across Traditional Tests (2010)

This new quantitative dichoptic motion coherence threshold technique suggests that there are two separate sensory eye dominance strength distributions among observers with normal binocular vision: weak and strong eye dominance. This finding may provide a basis for clinical decision-making by indicating whether eye dominance is likely to be an important consideration in a particular patient.
Primary congenital and developmental glaucomas (2017)

Glaucoma is the leading cause of irreversible blindness worldwide. Although most glaucoma patients are elderly, congenital glaucoma and glaucomas of childhood are also important causes of visual disability. Primary congenital glaucoma (PCG) is isolated, non-syndromic glaucoma that occurs in the first three years of life and is a major cause of childhood blindness. Other early-onset glaucomas may arise secondary to developmental abnormalities, such as glaucomas that occur with aniridia or as part of Axenfeld-Rieger syndrome. Congenital and childhood glaucomas have strong genetic bases and disease-causing mutations have been discovered in several genes. Mutations in three genes (CYP1B1, LTBP2, TEK) have been reported in PCG patients. Axenfeld-Rieger syndrome is caused by mutations in PITX2 or FOXC1 and aniridia is caused by PAX6 mutations. This review discusses the roles of these genes in primary congenital glaucoma and glaucomas of childhood.
New Hole-Transporting Amorphous Molecular Materials with High Glass-Transition Temperatures for Organic Light-Emitting Diodes (2000)

Abstract New hole-transporting amorphous molecular materials with high glass-transition temperatures (Tgs), 4,4′,4″-tris[9,9-dimethyl-2-fluorenyl(phenyl)amino]triphenylamine (TFATA) and N,N,N′,N′-tetrakis(9,9-dimethyl-2-fluorenyl)-[1,1′-biphenyl]-4,4′-diamine (FFD), have been developed. TFATA and FFD exhibit hole drift mobilities of 1.7 × 10−5 and 4.1 × 10−3 cm2V−1s−1, respectively, at 293 K at an electric-field of 1.0 × 105 Vcm−1 in their amorphous glasses. These materials permit the fabrication of thermally stable, high-performance organic light emitting diodes.
MetaboKit: a comprehensive data extraction tool for untargeted metabolomics (2020)

We have developed MetaboKit, a comprehensive software package for compound identification and relative quantification in mass spectrometry-based untargeted metabolomics analysis. In data dependent acquisition (DDA) analysis, MetaboKit constructs a customized spectral library with compound identities from reference spectral libraries, adducts, dimers, in-source fragments (ISF), MS/MS fragmentation spectra, and more importantly the retention time information unique to the chromatography system used in the experiment. Using the customized library, the software performs targeted peak integration for precursor ions in DDA analysis and for precursor and product ions in data independent acquisition (DIA) analysis. With its stringent identification algorithm requiring matches by both MS and MS/MS data, MetaboKit provides identification results with significantly greater specificity than the competing software packages without loss in sensitivity. The proposed MS/MS-based screening of ISFs also reduces the chance of unverifiable identification of ISFs considerably. MetaboKit's quantification module produced peak area values highly correlated with known concentrations in a DIA analysis of the metabolite standards at both MS1 and MS2 levels. Moreover, the analysis of Cdk1Liv-/- mouse livers showed that MetaboKit can identify a wide range of lipid species and their ISFs, and quantitatively reconstitute the well-characterized fatty liver phenotype in these mice. In DIA data, the MS1-level and MS2-level peak area data produced similar fold change estimates in the differential abundance analysis, and the MS2-level peak area data allowed for quantitative comparisons in compounds whose precursor ion chromatogram was too noisy for peak integration.
Electromagnetic modelling for microwave heating applications (2002)

Microwave power applications are nowadays wide-spread throughout industry, science, and private households. The best known is thermal processing of foods, but one should also note drying of textiles, fibres, paper and board, preheating and curing of plastics and rubber, and controlling chemical reactions. In all these areas, a majority of design work on microwave heating systems and processes has been based on intuitive perceptions and engineering experience. Electromagnetic modelling, which is a potentially powerful alternative, is rarely considered and almost never used. The idea behind this paper is to enhance the use of electromagnetic modelling in microwave power industry and research. Modelling may provide a new level of knowledge on what simplifications can or cannot be made, and be an important tool for analysing causes of unacceptable variability in production.
RESTRICTED LIKELIHOOD RATIO TESTS IN NONPARAMETRIC LONGITUDINAL MODELS (2004)

We assume that repeated measurements are taken on each of several subjects that are randomly sampled from some population. The observations on a particular subject are expressed as the sum of an average curve for the population and a deviation of the subject's curve from the average plus independent errors. Both curves are modeled nonparametrically as splines. We use roughness penalties on the splines, which is equivalent to assuming a linear mixed model. Within this linear mixed model, we consider likelihood ratio tests of several scientifically relevant hypotheses about the two curves, for example, that the subject deviations are all zero or that they are each constant. The large-sample null distributions of the test statistics are shown to be non-standard, but we develop bootstrap techniques that can compute the exact null distributions much more rapidly than a direct application of the bootstrap.
Dechlorination of Excess Trichloroethene by Bimetallic and Sulfidated Nanoscale Zero-Valent Iron (2018)

Nanoscale zerovalent iron (nZVI) likely finds its application in source zone remediation. Two approaches to modify nZVI have been reported: bimetal (Fe-Me) and sulfidated nZVI (S-nZVI). However, previous research has primarily focused on enhancing particle reactivity with these two modifications under more plume-like conditions. In this study, we systematically compared the trichloroethene (TCE) dechlorination pathway, rate, and electron selectivity of Fe-Me (Me: Pd, Ni, Cu, and Ag), S-nZVI, and nZVI with excess TCE simulating source zone conditions. TCE dechlorination on Fe-Me was primarily via hydrogenolysis while that on S-nZVI and nZVI was mainly via β-elimination. The surface-area normalized TCE reduction rate ( k<sup>'</sup><sub>SA</sub>) of Fe-Pd, S-nZVI, Fe-Ni, Fe-Cu, and Fe-Ag were ∼6800-, 190-, 130-, 20-, and 8-fold greater than nZVI. All bimetallic modification enhanced the competing hydrogen evolution reaction (HER) while sulfidation inhibited HER. Fe-Cu and Fe-Ag negligibly enhanced electron utilization efficiency (ε<sub>e</sub>) while Fe-Pd, Fe-Ni, and S-nZVI dramatically increased ε<sub>e</sub> from 2% to ∼100%, 69%, and 72%, respectively. Adsorbed atomic hydrogen was identified to be responsible for the TCE dechlorination on Fe-Me but not on S-nZVI. The enhanced dechlorination rate along with the reduced HER of S-nZVI can be explained by that FeS conducting major electrons mediated TCE dechlorination while Fe oxides conducting minor electrons mediated HER.
CMU-CAM System (1985)

This paper describes a software system for Computer Aided Manufacturing (CAM) of VLSI circuits being developed at Carnegie-Mellon University. In developing the system, a major effort was devoted towards the computational efficiency of the algorithms implemented. The results obtained with this system indicate that it can be used for a variety of real-life tasks, such as optimal process design, process diagnosis and control, in commercial fabrication lines. We believe that such a system provides an attractive extension for the CAM systems that are currently being introduced to VLSI fabrication processes.
Immunological efficacy of a prime-boost pneumococcal vaccination in HIV-infected adults (2007)

Objective: To evaluate whether a strategy combining a prime with a 7-valent conjugate pneumococcal vaccine (PCV) followed by a boost with the 23-valent polysaccharide vaccine (PPV) would improve immunogenicity against Streptococcus pneumoniae polysaccharides in HIV-infected patients. Design: Randomized controlled phase II trial. Methods: Two-hundred and twelve patients with CD4 cell counts of 200–500 cells/μl and HIV RNA< 4 log10 copies/ml, regardless of antiretroviral treatment, were randomized to receive either PCV at week 0 and PPV at week 4 (n = 106) or PPV alone at week 4 (n = 106). The proportion of responders to 0, 1–2, 3–4, 5–7 serotypes shared by the two vaccines was evaluated at week 8 and compared using a proportional odds model allowing for adjustment for CD4 cell count, HIV RNA and antiretroviral treatment. Results: At week 8, the profile of response was better in the prime-boost group compared to the PPV group, as determined by the frequency of patients who reached both a twofold increase of serotype-specific IgG levels and IgG level ≥ 1 μg/ml [proportional odds ratio (OR), 2.09; 95% confidence interval (CI), 1.25–3.51; P = 0.005]. No differences in responders were found 4 weeks after PCV or PPV alone, suggesting that PCV primed for response to PPV. Early differences between groups remained significant at week 24 (proportional OR, 2.14; 95% CI, 1.30–3.54; P = 0.003). Conclusions: In a setting of practical care, a PCV prime-PPV boost strategy enhances the frequency, breadth and magnitude of antibody responses against SPP in HIV-infected adults.
La déficience en hormone de croissance chez l'adulte et son traitement (2001)

Les adultes deficients en hormone de croissance (GH) decedent prematurement, principalement a cause de la frequence elevee des affections cardiovasculaires. Depuis que la GH est produite par les techniques de biologie moleculaire, il est possible de proposer un traitement substitutif. Ce traitement ameliore le bilan lipidique, entraine une redistribution de la graisse d'androide en gynoide, une reduction de la masse graisseuse, une augmentation de la masse des tissus maigres et du volume de l'eau extracellulaire. Le poids des patients est legerement reduit par le traitement substitutif. La masse de muscle strie squelettique est augmentee, ainsi que le contenu osseux (BMC) et la densite osseuse (BMD). La fonction cardiaque et la qualite de vie sont ameliorees
Overlap of Genetic Loci for Central Serous Chorioretinopathy With Age-Related Macular Degeneration (2023)

In this 3-cohort genetic association study, 5 genetic risk loci for CSC were identified, highlighting a likely role for genes involved in choroidal vascular function and complement regulation. Results suggest that polygenic AMD risk was associated with reduced risk of CSC and that this genetic overlap was largely due to loci containing complement genes.
Resource Deflation (2019)

Data centers and clouds are increasingly offering low-cost computational resources in the form of transient virtual machines. Whenever demand for computational resources exceeds their availability, transient resources can reclaimed by preempting the transient VMs. Conventionally, these transient VMs are used by low-priority applications that can tolerate the disruption caused by preemptions.
MaMMUT: A Simple Architecture for Joint Learning for MultiModal Tasks (2023)

The development of language models have moved from encoder-decoder to decoder-only designs. In addition, we observe that the two most popular multimodal tasks, the generative and contrastive tasks, are nontrivial to accommodate in one architecture, and further need adaptations for downstream tasks. We propose a novel paradigm of training with a decoder-only model for multimodal tasks, which is surprisingly effective in jointly learning of these disparate vision-language tasks. This is done with a simple model, called MaMMUT. It consists of a single vision encoder and a text decoder, and is able to accommodate contrastive and generative learning by a novel two-pass approach on the text decoder. We demonstrate that joint learning of these diverse objectives is simple, effective, and maximizes the weight-sharing of the model across these tasks. Furthermore, the same architecture enables straightforward extensions to open-vocabulary object detection and video-language tasks. The model tackles a diverse range of tasks, while being modest in capacity. Our model achieves the state of the art on image-text and text-image retrieval, video question answering and open-vocabulary detection tasks, outperforming much larger and more extensively trained foundational models. It shows very competitive results on VQA and Video Captioning, especially considering its capacity. Ablations confirm the flexibility and advantages of our approach.
Novel Antimalarial Tetrazoles and Amides Active against the Hemoglobin Degradation Pathway in Plasmodium falciparum (2021)

Malaria control programs continue to be threatened by drug resistance. To identify new antimalarials, we conducted a phenotypic screen and identified a novel tetrazole-based series that shows fast-kill kinetics and a relatively low propensity to develop high-level resistance. Preliminary structure-activity relationships were established including identification of a subseries of related amides with antiplasmodial activity. Assaying parasites with resistance to antimalarials led us to test whether the series had a similar mechanism of action to chloroquine (CQ). Treatment of synchronized <i>Plasmodium falciparum</i> parasites with active analogues revealed a pattern of intracellular inhibition of hemozoin (Hz) formation reminiscent of CQ's action. Drug selections yielded only modest resistance that was associated with amplification of the multidrug resistance gene 1 (<i>pfmdr1</i>). Thus, we have identified a novel chemical series that targets the historically druggable heme polymerization pathway and that can form the basis of future optimization efforts to develop a new malaria treatment.
ChemInform Abstract: A NEW SYNTHESIS OF AMPICILLIN AND RELATED INVESTIGATIONS (1976)

Abstract Zur stereospezifischen Herstellung von (geschützten) Aminen werden sterisch definierte Halogenverbindungen mit Urotropin zu entsprechenden Salzen kondensiert, und die Stereochemie der Umwandlungsreaktionen wird erörtert.
High heritability of ascending aortic diameter and multi-ethnic prediction of thoracic aortic disease. (2020)

Enlargement of the aorta is an important risk factor for aortic aneurysm and dissection, a leading cause of morbidity in the developed world. While Mendelian genetics account for a portion of thoracic aortic disease, the contribution of common variation is not known. Using standard techniques in computer vision, we performed automated extraction of Ascending Aortic Diameter (AsAoD) from cardiac MRI of 36,021 individuals from the UK Biobank. A multi-ethnic genome wide association study and trans-ethnic meta-analysis identified 99 lead variants across 71 loci including genes related to cardiovascular development (HAND2, TBX20) and Mendelian forms of thoracic aortic disease (ELN, FBN1). A polygenic risk score predicted prevalent risk of thoracic aortic aneurysm within the UK Biobank (OR 1.50 per standard deviation (SD) polygenic risk score (PRS), p=6.30x10-03) which was validated across three additional biobanks including FinnGen, the Penn Medicine Biobank, and the Million Veterans Program (MVP) in individuals of European descent (OR 1.37 [1.31 - 1.43] per SD PRS), individuals of Hispanic descent (OR 1.40 [1.16 - 1.69] per SD PRS, p=5.6x10-04), and individuals of African American descent (OR 1.08 [1.00 - 1.18] per SD PRS, p=0.05). Within individuals of European descent who carried a diagnosis of thoracic aneurysm, the PRS was specifically predictive of the need for surgical intervention (OR 1.57 [1.15 - 2.15] per SD PRS, p=4.45x10-03). Using Mendelian Randomization our data highlight the primary causal role of blood pressure in reducing dilation of the thoracic aorta. Overall our findings link normal anatomic variation to extremes observed in Mendelian syndromes and provide a roadmap for the use of genetic determinants of human anatomy in both understanding cardiovascular development while simultaneously improving prediction and prevention of human disease.
An overview of cancer treatments (2009)

The first of four articles on cancer treatments. This article provides an overview of traditional anticancer therapies, their mechanisms of action and their limitations.
Predicting Electrophoretic Mobility of Tryptic Peptides for High-Throughput CZE-MS Analysis (2017)

A multiparametric sequence-specific model for predicting peptide electrophoretic mobility has been developed using large-scale bottom-up proteomic CE-MS data (5% (∼0.8M) acetic acid as background electrolyte). Peptide charge (Z) and size (molecular mass, M) are the two major factors determining electrophoretic mobility, in complete agreement with previous studies. The extended size of the data set (>4000 peptides) permits access to many sequence-specific factors that impact peptide mobility. The presence of acidic residues Asp and Glu near the peptide N-terminus is by far the most prominent among them. The induction effect of the side chain of N-terminal Asp reduces the basicity of the N-terminal amino group and, as hence, its charge, by ∼0.27 units, lowering mobility. The correlation of the model (R<sup>2</sup> ∼ 0.995) indicates that the peptide separation process in CZE is relatively simple and can be predicted to a much higher precision than current RP-HPLC models. Similar to RP-HPLC prediction studies, we anticipate future developments that introduce peptide migration standards, collect larger data sets for modeling through the alignment of multiple CZE-MS acquisitions, and study of the behavior of peptides carrying post-translational modifications. The increased size of data sets will also permit investigation of the fine-scale effects of peptide secondary structure on peptide mobility. We observed that peptides with higher helical propensity tend to have higher than predicted electrophoretic mobility; the incorporation of these features into CZE migration models will require significantly larger data sets.
Functional analysis of novel mutations in y+LAT-1 amino acid transporter gene causing lysinuric protein intolerance (LPI) (2000)

Lysinuric protein intolerance (LPI; MIM 222700) is an autosomal recessive disorder characterized by defective transport of the cationic amino acids lysine, arginine and ornithine at the basolateral membrane of the polar epithelial cells in the intestine and renal tubules, and by hyperammonemia after high-protein meals. LPI is caused by mutations in the SLC7A7 (solute carrier family 7, member 7) gene encoding y(+)LAT-1 (y(+)L amino acid transporter-1), which co-induces together with 4F2 heavy chain (4F2hc) system y(+)L in Xenopus oocytes. All Finnish LPI patients share the same founder mutation 1181-2A-->T (LPI(Fin)) not found in LPI patients elsewhere. Mutation screening of 20 non-Finnish LPI patients revealed 10 novel mutations: four deletions, two missense mutations, two nonsense mutations, a splice site mutation and a tandem duplication. Five LPI mutations (L334R, G54V, 1291delCTTT, 1548delC and LPI(Fin)) were studied functionally. All mutant proteins failed to co-induce amino acid transport activity when expressed with 4F2hc in Xenopus oocytes. Immunostaining experiments revealed that frameshift mutants 1291delCTTT, 1548delC and LPI(Fin)remained intracellular on expression with 4F2hc. In contrast, the missense mutants L334R and G54V reached the oocyte plasma membrane when co-expressed with 4F2hc, demonstrating that they are transport-inactivating mutations. This finding, together with the strong degree of conservation among all members of this family of amino acid transporters, indicates that residues L334 and G54 play a crucial role in the function of the y(+)LAT-1 transporter.
Command filtering and path planning for remote manipulation of a long reach flexible robot (2002)

We focus on the fusion of autonomous and teleoperated commands. This combination provides full use of the robot's workspace without requiring large motion amplification between a master and slave robot. Combining autonomous and teleoperated commands provides the potential for large variations in the commanded momentum of the flexible robot. These variations excite the lightly damped, low resonant frequencies associated with these manipulators. Two techniques are proposed to reduce the vibration during sudden stops in the commanded motion of a flexible manipulator. First a new command filtering approach that permits shorter delay times than standard input shaping methods is presented. Next, we propose dynamic alteration of the desired trajectory. Our investigation shows that filtering techniques exhibit an oscillatory response, more so than standard PD control algorithms, during hard stopping conditions. However the shorter time delay filtering algorithm has less vibration than standard input shaping techniques. Furthermore, any vibration may be eliminated by commanding the robot to decelerate instead of immediately stopping the motion.
Query log analysis in the context of information retrieval for children (2010)

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