gebhart/patrepeval huggingface dataset:
Adaptive wavelet packet image coding using an estimation-quantization framework (2002)

We extend the statistical model-based estimation-quantization (EQ) wavelet image coding algorithm introduced by LoPresto, Ramchandran and Orchard (see Proceedings of the Data Compression Conference, Snowbird, UT, 1997) to include an adaptive transform component. For this, we resort to the rich, space-frequency diverse, and easy-to-search library of transforms provided by the family of wavelet packet (WP) bases and their adaptive extensions. We use rate-distortion criteria to find the best basis jointly with the statistical model-based best adaptive quantization and entropy coding strategy of LoPresto et al. based on an efficient and fast tree pruning algorithm. A key underlying attribute of our paradigm is that the spatially-varying generalized Gaussian mixture model for wavelet coefficients introduced by LoPresto et al. is also applicable to the more arbitrary framework of (adaptive) wavelet packet transform coefficients as well. Our WP-EQ framework produces excellent results on standard test images. The most attractive property of our paradigm is its "universality" and robustness: based on an overall performance criterion that considers diverse classes of input test images that have varying space-frequency characteristics, it is more powerful than most of the existing image coding algorithms, using reasonable complexity, and a generic, integrated, non-training based framework.
Automated Talairach Atlas labels for functional brain mapping (2000)

An automated coordinate-based system to retrieve brain labels from the 1988 Talairach Atlas, called the Talairach Daemon (TD), was previously introduced [Lancaster et al., 1997]. In the present study, the TD system and its 3-D database of labels for the 1988 Talairach atlas were tested for labeling of functional activation foci. TD system labels were compared with author-designated labels of activation coordinates from over 250 published functional brain-mapping studies and with manual atlas-derived labels from an expert group using a subset of these activation coordinates. Automated labeling by the TD system compared well with authors' labels, with a 70% or greater label match averaged over all locations. Author-label matching improved to greater than 90% within a search range of +/-5 mm for most sites. An adaptive grey matter (GM) range-search utility was evaluated using individual activations from the M1 mouth region (30 subjects, 52 sites). It provided an 87% label match to Brodmann area labels (BA 4 & BA 6) within a search range of +/-5 mm. Using the adaptive GM range search, the TD system's overall match with authors' labels (90%) was better than that of the expert group (80%). When used in concert with authors' deeper knowledge of an experiment, the TD system provides consistent and comprehensive labels for brain activation foci. Additional suggested applications of the TD system include interactive labeling, anatomical grouping of activation foci, lesion-deficit analysis, and neuroanatomy education.
Observer Performance for Detection of Pulmonary Nodules at Chest CT over a Large Range of Radiation Dose Levels (2020)

Background There is a wide variation in radiation dose levels that can be used with chest CT in order to detect indeterminate pulmonary nodules. Purpose To compare the performance of lower-radiation-dose chest CT with that of routine dose in the detection of indeterminate pulmonary nodules 5 mm or greater. Materials and Methods In this retrospective study, CT projection data from 83 routine-dose chest CT examinations performed in 83 patients (120 kV, 70 quality reference mAs [QRM]) were collected between November 2013 and April 2014. Reference indeterminate pulmonary nodules were identified by two nonreader thoracic radiologists. By using validated noise insertion, five lower-dose data sets were reconstructed with filtered back projection (FBP) or iterative reconstruction (IR; 30 QRM with FBP, 10 QRM with IR, 5 QRM with FBP, 5 QRM with IR, and 2.5 QRM with IR). Three thoracic radiologists circled pulmonary nodules, rating confidence that the nodule was a 5-mm-or-greater indeterminate pulmonary nodule, and graded image quality. Analysis was performed on a per-nodule basis by using jackknife alternative free-response receiver operating characteristic figure of merit (FOM) and noninferiority limit of -0.10. Results There were 66 indeterminate pulmonary nodules (mean size, 8.6 mm ± 3.4 [standard deviation]; 21 part-solid nodules) in 42 patients (mean age, 51 years ± 17; 21 men and 21 women). Compared with the FOM for routine-dose CT (size-specific dose estimate, 6.5 mGy ± 1.8; FOM, 0.86 [95% confidence interval: 0.80, 0.91]), FOM was noninferior for all lower-dose configurations except for 2.5 QRM with IR. The sensitivity for subsolid nodules at 70 QRM was 60% (range, 48%-72%) and was significantly worse at a dose of 5 QRM and lower, whether or not IR was used (<i>P</i> < .05). Diagnostic image quality decreased with decreasing dose (<i>P</i> < .001) and was better with IR at 5 QRM (<i>P</i> < .05). Conclusion CT images reconstructed at dose levels down to 10 quality reference mAs (size-specific dose estimate, 0.9 mGy) had noninferior performance compared with routine dose in depicting pulmonary nodules. Iterative reconstruction improved subjective image quality but not performance at low dose levels. © RSNA, 2020 <i>Online supplemental material is available for this article</i>. See also the editorial by White and Kazerooni in this issue.
Single-cycle, pulse-shaped critical path monitor in the POWER7&#x002B; microprocessor (2013)

A 32nm SOI critical path monitor (CPM) that can provide timing measurements to a Digital PLL for dynamic frequency adjustments in the 8-core POWER7+™ microprocessor is described. The CPM calibrates to within 2% of cycle time from nominal to turbo voltages. Its voltage sensitivity is 10mV/bit. It tracks processor temperature sensitivity to within 1.5% of nominal frequency, and has a sample jitter less than 1.5% of nominal frequency. The ability to detect noise dynamically allows the system to operate the processor closer to its optimal frequency for any given voltage, resulting in lower voltage for power savings or higher frequency for performance improvements.
In Situ X-ray Investigation of the Formation of Metallic Silver Phases During the Thermal Decomposition of Silver Behenate and Thermal Development of Photothermographic Films (2007)

Metallic silver formation, resulting from the thermal decomposition of silver behenate, AgBe, and from the thermally induced reduction of AgBe incorporated into a photothermographic imaging construction, has been compared by in situ x-ray investigation. In the case of the thermal decomposition of individual AgBe crystals, the main factor that determines the growth of the silver particles is the change in the AgBe crystal structure, leading to the formation of intermediate mesomorphic phases that still retain characteristic layer structure. By contrast, development of AgBe-containing photothermographic films generates silver particles by the reduction of intermediate silver complexes, which are in a liquid state during the development process. The silver nanoparticles resulting from these processes exhibit different sizes and morphologies that are important for optimizing the optical properties of photothermographic films.
Less is More: Extreme Optics with Zero Refractive Index (2017)

By simultaneously controlling the electric and magnetic properties of a nanostructured composite material (metamaterial), we can create materials with a refractive index of zero. We present a novel on-chip platform to explore zero-index metamaterials.
Aerobic Membrane Bioreactor for Ammonium‐Rich Wastewater Treatment (2007)

The major research objective involving ammonia-rich synthetic wastewater (centrate) treatment using a membrane bioreactor (MBR) was to determine the suitable hydraulic retention time (HRT), solids retention time (SRT), and ammonium loading rate for complete nitrification of centrate. The experiments were performed using a laboratory-scale 2-L MBR, which was supplied with synthetic wastewater (1000 mg nitrogen/L and 350 mg chemical oxygen demand [COD]/L). The entire study period was divided into five different experimental runs based on various HRTs and SRTs. Batch nitrification rate tests and microbial studies using fluorescent in situ hybridization were also conducted. The MBR was able to achieve more than 95% ammonium removal efficiency and 90% carbonaceous soluble COD removal efficiency. The experimental results showed that complete nitrification of centrate during treatment can be achieved at a 1-day HRT and 50-day SRT. The suitable ammonium loading rate was found to be 0.3 mg nitrogen/mg volatile suspended solids/d.
Using physically Based Rendering to Benchmark Structured Light Scanners (2014)

Abstract Structured light scanning is ubiquituous in 3D acquisition. It is capable of capturing high geometric detail at a low cost under a variety of challenging scene conditions. Recent methods have demonstrated robustness in the presence of artifacts due to global illumination, such as inter‐reflections and sub‐surface scattering, as well as imperfections caused by projector defocus. For comparing approaches, however, the quantitative evaluation of structured lighting schemes is hindered by the challenges in obtaining ground truth data, resulting in a poor understanding for these methods across a wide range of shapes, materials, and lighting configurations. In this paper, we present a benchmark to study the performance of structured lighting algorithms in the presence of errors caused due to the above properties of the scene. In order to do this, we construct a synthetic structured lighting scanner that uses advanced physically based rendering techniques to simulate the point cloud acquisition process. We show that, under conditions similar to that of a real scanner, our synthetic scanner replicates the same artifacts found in the output of a real scanner. Using this synthetic scanner, we perform a quantitative evaluation of four different structured lighting techniques – gray‐code patterns, micro‐phase shifting, ensemble codes, and unstructured light scanning. The evaluation, performed on a variety of scenes, demonstrate that no one method is capable of adequately handling all sources of error – each method is appropriate for addressing distinct sources of error.
Influenza A virus polymerase acidic protein E23R substitution is a marker of reduced susceptibility to baloxavir (2022)

In our ongoing efforts to identify baloxavir resistance markers, we demonstrated that the influenza A polymerase acidic (PA) protein E23R substitution is genetically stable, increases baloxavir EC<sub>50</sub> values (13- to 19-fold vs. wild-type), synergizes with PA I38T, and only modestly decreases viral fitness. E23R is, therefore, a potential threat to baloxavir treatment efficacy.
Pipeline monitoring based on ultrasonic guided acoustic wave and fiber optic sensor fusion (2022)

In this paper, we demonstrated a fiber acoustic sensor based on a single-mode–multimode–single-mode (SMS) fiber structure. The SMS fiber structure consists of a multimode fiber (MMF) sandwiched between two single-mode fibers (SMFs). Whenever the MMF fiber experiences vibration disturbances, the fiber experiences tensile and compressive strains. By demodulating the vibration-induced intensity fluctuations, the vibrations signals can be quantified. Through employing several SMS sensors in parallel and connecting, and controlling by an optical switch, quasi-distributed sensing can be realized. The proposed sensor system is demonstrated in a laboratory environment and has the capability of detecting a wide range of vibration frequencies from 10 Hz to 400 kHz. In addition, the fiber sensor system is field-tested, where several SMS fiber sensors are mounted on 8.5” diameter steel pipe and excite acoustic emissions based on a magnetostrictive guided wave collar system. The proposed highly sensitive fiber sensor can be potentially used in practical applications of pipeline health condition monitoring.
Xdigitise: visualization of hybridization experiments (2002)

Xdigitise can be downloaded from http://www.molgen.mpg.de/~xdigitise.
Spectral Efficiency of OTFS Based Orthogonal Multiple Access with Rectangular Pulses (2021)

In this paper we consider Orthogonal Time Frequency Space (OTFS) modulation based multiple-access (MA). We specifically consider Orthogonal MA methods (OMA) where the user terminals (UTs) are allocated non-overlapping physical resource in the delay-Doppler (DD) and/or time-frequency (TF) domain. To the best of our knowledge, in prior literature, the performance of OMA methods have been reported only for ideal transmit and receive pulses. In [20] and [21], OMA methods were proposed which were shown to achieve multi-user interference (MUI) free communication with ideal pulses. Since ideal pulses are not realizable, in this paper we study the spectral efficiency (SE) performance of these OMA methods with practical rectangular pulses. For these OMA methods, we derive the expression for the received DD domain symbols at the base station (BS) receiver and the effective DD domain channel matrix when rectangular pulses are used. We then derive the expression for the achievable sum SE. These expressions are also derived for another well known OMA method where guard bands (GB) are used to reduce MUI (called as the GB based MA methods) [19]. Through simulations, we observe that with rectangular pulses the sum SE achieved by the method in [21] is almost invariant of the Doppler shift and is higher than that achieved by the methods in [19], [20] at practical values of the received signal-to-noise ratio.
Preliminary Evaluation of a Genitourinary Skills Training Curriculum for Medical Students (2009)

An intensive skills training curriculum significantly improved medical student comfort and knowledge with regard to basic genitourinary skills including testicular examination, rectal examination, and Foley catheter placement in the male and female patient. Further followup will be performed to determine the application of these skills during clinical clerkship rotations.
Corrigendum (1989)

E. Breuer, R. Karaman, A. Goldblum, D. Gibson, H. Leader, B. V. L. Potter, J. H. Cummins, S. A. Harkin, R. H. Jones, D. J. Tapolczay and E. J. Thomas, J. Chem. Soc., Perkin Trans. 1, 1989, 1367 DOI: 10.1039/P19890001367
Precise transcript targeting by CRISPR-Csm complexes (2023)

Robust and precise transcript targeting in mammalian cells remains a difficult challenge using existing approaches due to inefficiency, imprecision and subcellular compartmentalization. Here we show that the clustered regularly interspaced short palindromic repeats (CRISPR)-Csm complex, a multiprotein effector from type III CRISPR immune systems in prokaryotes, provides surgical RNA ablation of both nuclear and cytoplasmic transcripts. As part of the most widely occurring CRISPR adaptive immune pathway, CRISPR-Csm uses a programmable RNA-guided mechanism to find and degrade target RNA molecules without inducing indiscriminate trans-cleavage of cellular RNAs, giving it an important advantage over the CRISPR-Cas13 family of enzymes. Using single-vector delivery of the Streptococcus thermophilus Csm complex, we observe high-efficiency RNA knockdown (90-99%) and minimal off-target effects in human cells, outperforming existing technologies including short hairpin RNA- and Cas13-mediated knockdown. We also find that catalytically inactivated Csm achieves specific and durable RNA binding, a property we harness for live-cell RNA imaging. These results establish the feasibility and efficacy of multiprotein CRISPR-Cas effector complexes as RNA-targeting tools in eukaryotes.
An Efficient Closed-Form Method for Optimal Hybrid Force-Velocity Control (2021)

This paper derives a closed-form method for computing hybrid force-velocity control. The key idea is to maximize the kinematic conditioning of the mechanical system, which includes a robot, free objects, a rigid environment and contact constraints. The method is complete, in that it always produces an optimal/near optimal solution when a solution exists. It is efficient, since it is in closed form, avoiding the iterative search of our previous work. We test the method on 78,000 randomly generated test cases. The method outperforms our previous search-based technique by being from 7 to 40 times faster, while consistently producing better solutions in the sense of robustness to kinematic singularity. We also test the method in several representative manipulation experiments.
Supplementary Figure 2 from Aberrant Silencing of Cancer-Related Genes by CpG Hypermethylation Occurs Independently of Their Spatial Organization in the Nucleus (2023)

Supplementary Figure 2 from Aberrant Silencing of Cancer-Related Genes by CpG Hypermethylation Occurs Independently of Their Spatial Organization in the Nucleus
Combined use of ToF sensors and standard cameras for 3D video acquisition (2009)

3D video applications usually require the availability of\nhigh resolution depth and color information. Depth information\ncan be acquired at video rate by Time-of-Flight matrix\nsensors, but these devices usually have a limited resolution\nand image quality. A common solution to this issue is the\ncombined use of ToF sensors and color cameras. This paper\nfirstly presents a generalized multi-camera calibration technique\nthat aims at calibrating together the ToF sensor with\ntwo synchronized cameras exploiting the color information\nfrom both type of sensors but also the depth measures of the\nToF sensor. In the second part of the work we will present an\nad-hoc interpolation technique to obtain high resolution depth\ninformation exploiting side information from the color camera\ntogether with the ToF measures and a novel surface prediction\nscheme. Finally we will show how the high resolution\ndepth map obtained with the proposed approach can be used\nin order to warp the available video streams to arbitrary viewpoints\nin 3D video applications. Experimental results have\nshown how the proposed method allows to obtain a more accurate\ncalibration and to improve the quality of the depth data\nand warped views if compared with standard approaches.
Mouse Dux is myotoxic and shares partial functional homology with its human paralog DUX4 (2016)

D4Z4 repeats are present in at least 11 different mammalian species, including humans and mice. Each repeat contains an open reading frame encoding a double homeodomain (DUX) family transcription factor. Aberrant expression of the D4Z4 ORF called DUX4 is associated with the pathogenesis of Facioscapulohumeral muscular dystrophy (FSHD). DUX4 is toxic to numerous cell types of different species, and over-expression caused dysmorphism and developmental arrest in frogs and zebrafish, embryonic lethality in transgenic mice, and lesions in mouse muscle. Because DUX4 is a primate-specific gene, questions have been raised about the biological relevance of over-expressing it in non-primate models, as DUX4 toxicity could be related to non-specific cellular stress induced by over-expressing a DUX family transcription factor in organisms that did not co-evolve its regulated transcriptional networks. We assessed toxic phenotypes of DUX family genes, including DUX4, DUX1, DUX5, DUXA, DUX4-s, Dux-bl and mouse Dux. We found that DUX proteins were not universally toxic, and only the mouse Dux gene caused similar toxic phenotypes as human DUX4. Using RNA-seq, we found that 80% of genes upregulated by Dux were similarly increased in DUX4-expressing cells. Moreover, 43% of Dux-responsive genes contained ChIP-seq binding sites for both Dux and DUX4, and both proteins had similar consensus binding site sequences. These results suggested DUX4 and Dux may regulate some common pathways, and despite diverging from a common progenitor under different selective pressures for millions of years, the two genes maintain partial functional homology.
Treatment for patients with multiple myeloma complicated by renal failure by thalidomide-based regimens. (2010)

e13093 Background: Thalidomide has been shown to be highly effective and to rapidly induce tumor response in patients with multiple myeloma. Moreover, thalidomide is a convenient oral and relatively inexpensive agent that is only minimally excreted through the kidneys. However there is limited data regarding the reversibility of renal failure, the kinetics of serum creatinine, and the safety of thalidomide when administered to newly diagnosed multiple myeloma and renal failure. Methods: We evaluated 29 consecutive patients with newly diagnosed multiple myeloma and renal failure, defined as a serum creatinine ≥2 mg/dl. All patients received thalidomide with dexamethasone or in combination with cyclophosphamide. Results: Reversal of renal failure was documented in 55% of all patients and the median time to reversal was 24 days (range, 4-132). Moreover, 13 patients (45%) had 50% decrease in serum creatinine and the median time to decrease was 36 days (range, 4-120). Some decrease of creatinine was documented in 90% of patients. The objective response rate was 66%. Toxicities were similar to those seen in myeloma patients without renal failure. Conclusions: Thalidomide- based regimens result in high rates of renal function restoration in patients with newly diagnosed myeloma renal failure complications. Morever, the toxicity and efficacy of thalidomide based regimens in myeloma patients with renal failure similar to those observed in patients without renal failure. Further studies will more formally evaluate the impact of thalidomide based regimens in this patient population. No significant financial relationships to disclose.
Identification of a Selective, Non-Prostanoid EP2 Receptor Agonist for the Treatment of Glaucoma: Omidenepag and its Prodrug Omidenepag Isopropyl (2018)

EP2 receptor agonists are expected to be effective ocular hypotensive agents; however, it has been suggested that agonism to other EP receptor subtypes may lead to undesirable effects. Through medicinal chemistry efforts, we identified a scaffold bearing a (pyridin-2-ylamino)acetic acid moiety as a promising EP2-selective receptor agonist. (6-((4-(Pyrazol-1-yl)benzyl)(pyridin-3-ylsulfonyl)aminomethyl)pyridin-2-ylamino)acetic acid 13ax (omidenepag, OMD) exerted potent and selective activity toward the human EP2 receptor (h-EP2). Low doses of omidenepag isopropyl (OMDI), a prodrug of 13ax, lowered intraocular pressure (IOP) in ocular normotensive monkeys. OMDI was selected as a clinical candidate for the treatment of glaucoma.
Merits of symmetric scanning for detection of coherence function in incoherent imaging system (1976)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Shusou Wadaka and Takuso Sato, "Merits of symmetric scanning for detection of coherence function in incoherent imaging system," J. Opt. Soc. Am. 66, 145-147 (1976) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Cognitive Computing for Security. (2015)

Final report for Cognitive Computing for Security LDRD 165613. It reports on the development of hybrid of general purpose/ne uromorphic computer architecture, with an emphasis on potential implementation with memristors.
Thermal Behavior of Next Generation of Raman Pump Lasers in Telco Equipment (2003)

The present investigation concluded that the thermal behavior of the laser diode can be numerically modeled using the parabolic transient conduction equation. In addition, the current study compared the thermal performance of the continuous wave pump lasers versus the modulated wave pump lasers. This comparison revealed that the temperature of the modulated wave pump laser can approach the temperature of the continuous wave pump laser with the same average power dissipation when the frequency approaches infinity. Finally, the resulting thermal behavior was correlated and expressed in an empirical form, which physically described the thermal performance of the modulating pump laser.