gebhart/patrepeval huggingface dataset:
Optimal Rebinning of Time-of-Flight PET Data (2011)

Time-of-flight (TOF) positron emission tomography (PET) scanners offer the potential for significantly improved signal-to-noise ratio (SNR) and lesion detectability in clinical PET. However, fully 3D TOF PET image reconstruction is a challenging task due to the huge data size. One solution to this problem is to rebin TOF data into a lower dimensional format. We have recently developed Fourier rebinning methods for mapping TOF data into non-TOF formats that retain substantial SNR advantages relative to sinograms acquired without TOF information. However, mappings for rebinning into non-TOF formats are not unique and optimization of rebinning methods has not been widely investigated. In this paper we address the question of optimal rebinning in order to make full use of TOF information. We focus on FORET-3D, which approximately rebins 3D TOF data into 3D non-TOF sinogram formats without requiring a Fourier transform in the axial direction. We optimize the weighting for FORET-3D to minimize the variance, resulting in H(2)-weighted FORET-3D, which turns out to be the best linear unbiased estimator (BLUE) under reasonable approximations and furthermore the uniformly minimum variance unbiased (UMVU) estimator under Gaussian noise assumptions. This implies that any information loss due to optimal rebinning is as a result only of the approximations used in deriving the rebinning equation and developing the optimal weighting. We demonstrate using simulated and real phantom TOF data that the optimal rebinning method achieves variance reduction and contrast recovery improvement compared to nonoptimized rebinning weightings. In our preliminary study using a simplified simulation setup, the performance of the optimal rebinning method was comparable to that of fully 3D TOF MAP.
Biochemical and structural characterization of a novel halotolerant cellulase from soil metagenome (2016)

Cellulase catalyzes the hydrolysis of β-1,4-linkages of cellulose to produce industrially relevant monomeric subunits. Cellulases find their applications in pulp and paper, laundry, food and feed, textile, brewing industry and in biofuel production. These industries always have great demand for cellulases that can work efficiently even in harsh conditions such as high salt, heat, and acidic environments. While, cellulases with high thermal and acidic stability are already in use, existence of a high halotolerant cellulase is still elusive. Here, we report a novel cellulase Cel5R, obtained from soil metagenome that shows high halotolerance and thermal stability. The biochemical and functional characterization of Cel5R revealed its endoglucanase activity and high halostability. In addition, the crystal structure of Cel5R determined at 2.2 Å resolution reveals a large number of acidic residues on the surface of the protein that contribute to the halophilic nature of this enzyme. Moreover, we demonstrate that the four free and non-conserved cysteine residues (C65, C90, C231 and C273) contributes to the thermal stability of Cel5R by alanine scanning experiments. Thus, the newly identified endoglucanase Cel5R is a promising candidate for various industrial applications.
Multi‐contrast reconstruction with Bayesian compressed sensing (2011)

Clinical imaging with structural MRI routinely relies on multiple acquisitions of the same region of interest under several different contrast preparations. This work presents a reconstruction algorithm based on Bayesian compressed sensing to jointly reconstruct a set of images from undersampled k-space data with higher fidelity than when the images are reconstructed either individually or jointly by a previously proposed algorithm, M-FOCUSS. The joint inference problem is formulated in a hierarchical Bayesian setting, wherein solving each of the inverse problems corresponds to finding the parameters (here, image gradient coefficients) associated with each of the images. The variance of image gradients across contrasts for a single volumetric spatial position is a single hyperparameter. All of the images from the same anatomical region, but with different contrast properties, contribute to the estimation of the hyperparameters, and once they are found, the k-space data belonging to each image are used independently to infer the image gradients. Thus, commonality of image spatial structure across contrasts is exploited without the problematic assumption of correlation across contrasts. Examples demonstrate improved reconstruction quality (up to a factor of 4 in root-mean-square error) compared with previous compressed sensing algorithms and show the benefit of joint inversion under a hierarchical Bayesian model.
Multisite multivendor validation of a quantitative MRI and CT compatible fat phantom (2021)

The proposed fat phantom successfully mimicked quantitative liver signal for both MRI and CT. The proposed fat phantom in this study may facilitate broader application and harmonization of liver fat quantification techniques using MRI and CT across institutions, vendors and imaging platforms.
OR05-05 Lethal ERα-Dependent Hyperactivation of the Unfolded Protein Response Induces Complete Regression Without Recurrence of Primary and Metastatic Breast Cancer (2020)

Abstract Metastatic estrogen receptor α (ERα) positive breast cancer is presently incurable and most patients die within 7 years. From a medicinal chemistry program, we identified a novel small molecule that acts through ERα to kill breast cancer cells and often induces complete regression without recurrence of large, therapy-resistant primary breast tumors and of lung, bone, and liver metastases. To target metastatic ERα positive breast cancer, we exploited our finding that estrogen-ERα activates an extranuclear tumor-protective, signaling pathway, the anticipatory unfolded protein response (UPR). We repurposed this tumor protective pathway by targeting it with the small molecule, ErSO. ErSO kills cancer cells by acting non-competitively through ERα to induce lethal hyperactivation of the anticipatory UPR, triggering rapid necrotic cell death. Using luciferase to image primary tumors and metastases containing lethal ERαD538G and ERαY537S mutations seen in metastatic breast cancer, oral and injected ErSO exhibited unprecedented antitumor activity. In mouse xenografts bearing large breast tumors, oral and injected ErSO induced complete regression (&gt;115,000 fold mean regression) in about 45% of mice (18/39). Although durable response for 4-6 months without additional treatment was common, tumors that did recur remained fully sensitive to ErSO re-treatment. Consistent with the essential nature of the UPR pathway targeted by ErSO, in more than 100 tumor-bearing mice, we have never seen an ErSO-resistant tumor. In just 7 days, oral ErSO induced complete regression of most lung, bone, and liver metastases. ErSO is well-tolerated in mice and blood-brain-barrier penetrant. Injected ErSO induced profound regression of challenging brain tumors. On average, ErSO-treated tumors were &gt;180-fold smaller than vehicle-treated tumors. These xenograft studies used human cancer cells in mice that lack a functional immune system and therefore did not exploit the known ability of inducers of necrotic cell death to activate immune cells and induce immunogenic cell death. Notably, medium from breast cancer cells killed by ErSO contained high levels of immune cell activators, robustly activated mouse and human macrophages and increased macrophage migration. Moreover, use of ErSO is not limited to breast cancer. ErSO rapidly kills ERα positive ovarian and endometrial cancer cells that do not require estrogen for growth. ErSO’s potent activity against advanced primary and metastatic ERα-positive breast cancers represents a paradigm shift in leveraging ERα for anticancer efficacy.
Topics in statistical machine translation (2009)

In the past, we presented tutorials called "Introduction to Statistical Machine Translation", aimed at people who know little or nothing about the field and want to get acquainted with the basic concepts. This tutorial, by contrast, goes more deeply into selected topics of intense current interest. We aim at two types of participants:
Preventing Hot Gas Ingestion by Film-Cooling Jets via Flow-Aligned Blockers (2006)

Flow aligned blockers are proposed to minimize the entrainment of hot gases underneath film-cooling jets by the counter-rotating vortices within the jets. Computations, based on the ensemble-averaged Navier-Stokes equations closed by the realizable k-ε turbulence model, were used to assess the usefulness of rectangular prisms as blockers in increasing film-cooling adiabatic effectiveness without unduly increasing surface heat transfer and pressure loss. The Taguchi’s design of experiment method was used to investigate the effects of the height of the blocker (0.2D, 0.4D, 0.8D), the thickness of the blocker (D/20, D/10, D/5), and the spacing between the pair of blockers (0.8D, 1.0D, 1.2D), where D is the diameter of the film-cooling hole. The effects of blowing ratio (0.37, 0.5, 0.65) were also studied. Results obtained show that blockers can greatly increase film-cooling effectiveness. By using rectangular prisms as blockers, the laterally averaged adiabatic effectiveness at 15D downstream of the film-cooling hole is as high as that at 1D downstream. The surface heat transfer was found to increase slightly near the leading edge of the prisms, but reduced elsewhere from reduced temperature gradients that resulted from reduced hot gas entrainment. However, pressure loss was found to increase somewhat because of the flat rectangular leading edge, which can be made more streamlined.
A PCR-based specific assay reveals a population of bacteria within the Chloroflexi associated with the reductive dehalogenation of polychlorinated biphenyls (2005)

Polychlorinated biphenyls (PCBs) accumulate and persist in sediments posing a risk to human health and the environment. Highly chlorinated PCBs are reductively dechlorinated in anaerobic sediments and two bacteria, designated o-17 and DF-1, from a novel phylogenetic group that reductively dechlorinate PCBs have recently been identified. However, there is a paucity of knowledge about the distribution, diversity and ecology of PCB-dechlorinating bacteria due to difficulty in obtaining pure cultures and the lack of detection by universal PCR 16S rRNA gene primer sets in sediments. A specific PCR primer was developed and optimized for detection of o-17/DF-1 and other closely related bacteria in the environment. Using this primer set it was determined that bacteria of this group were enriched in sediment microcosms from Baltimore Harbour concurrent with active dechlorination of 2,2',3,4,4',5'-hexachlorobiphenyl. Additional 16S rRNA gene sequences that had high levels of similarity to described PCB dechlorinators were detected in sediments from the Elizabeth River tributary of Chesapeake Bay, which had confirmed PCB-dechlorinating activities. Phylogenetic comparison of these detected 16S rRNA gene sequences revealed a relatively diverse group of organisms within the dehalogenating Chloroflexi that are distinct from the Dehalococcoides spp. Results from this study indicate that reductive PCB dechlorination activity may be catalysed by a previously undescribed group of micro-organisms that appear to be prevalent in PCB-impacted sites.
Physical basis of magneto-optic recording (1992)

The material classes currently used or discussed as magneto-optic (MO) media, namely rare- earth transition-metal (RE-TM) alloys, Pt/Co multilayers (ML) and garnets are reviewed with emphasis on those properties which limit their use for MO recording. A comparison between RE-TM and Pt/Co with respect to thermal sensitivity and recording with shorter wavelengths is performed. We conclude that RE-TM based disks are the more sensitive medium and are also good candidates for `blue' recording due to their fine microstructure. We then discuss the energy balance for the stability of domains in exchange-coupled layers, media and stack designs to obtain stable domains, and the role of interface wall motion in the domain formation in such layers.
A Biomechanically Motivated Two-Phase Strategy for Biped Upright Balance Control (2006)

Balance maintenance and upright posture recovery under unexpected environmental forces are key requirements for safe and successful co-existence of humanoid robots in normal human environments. In this paper we present a two-phase control strategy for robust balance maintenance under a force disturbance. The first phase, called the reflex phase, is designed to withstand the immediate effect of the force. The second phase is the recovery phase where the system is steered back to a statically stable “home” posture. The reflex control law employs angular momentum and is characterized by its counter-intuitive quality of “yielding” to the disturbance. The recovery control employs a general scheme of seeking to maximize the potential energy and is robust to local ground surface feature. Biomechanics literature indicates a similar strategy in play during human balance maintenance.
Radiation therapy calculations using an on-demand virtual cluster via cloud computing (2010)

Computer hardware costs are the limiting factor in producing highly accurate radiation dose calculations on convenient time scales. Because of this, large-scale, full Monte Carlo simulations and other resource intensive algorithms are often considered infeasible for clinical settings. The emerging cloud computing paradigm promises to fundamentally alter the economics of such calculations by providing relatively cheap, on-demand, pay-as-you-go computing resources over the Internet. We believe that cloud computing will usher in a new era, in which very large scale calculations will be routinely performed by clinics and researchers using cloud-based resources. In this research, several proof-of-concept radiation therapy calculations were successfully performed on a cloud-based virtual Monte Carlo cluster. Performance evaluations were made of a distributed processing framework developed specifically for this project. The expected 1/n performance was observed with some caveats. The economics of cloud-based virtual computing clusters versus traditional in-house hardware is also discussed. For most situations, cloud computing can provide a substantial cost savings for distributed calculations.
Cloning and Nucleotide Sequence of the Isoamylase Gene from a Strain of Pseudomonas sp. (1989)

A strain of Pseudomonas sp., SMP1, isolated from a soil sample collected in the Monterotondo area (Rome), secreted isoamylase activity into the culture medium. The enzyme was purified and optimal reaction and stability conditions were determined by varying pH and temperature. The chemico-physical properties of the enzyme were similar to those of the isoamylase purified in Japan more than 20 years ago from 'Pseudomonas amyloderamosa' strain SB15. A genomic library of SMP1 was prepared in Escherichia coli using pUC12 as vector. Two isoamylase-producing colonies were identified out of 6300 screened. The hybrid plasmids isolated from the two clones showed common restriction patterns. The chromosomal portion of one of these plasmids (pSM257) was completely sequenced. Comparison between the deduced amino acid sequence of the isoamylase and the published sequences of other amylolytic enzymes showed the presence of conserved domains.
Strain-engineered self-assembled semiconductor quantum dot lattices (2001)

We demonstrate a self-assembling method for growing semiconductor quantum dots into ordered lattices. The quantum dot nucleation and positioning into lattices was achieved using a periodic subsurface stressor lattice. Three different two-dimensional (2D) square lattices are demonstrated. The unit cell dimensions, orientation, and the number of quantum dots in the basis are tunable. We find that the 2D lattice can be replicated at periodic intervals along the growth direction to form a three-dimensional (3D) lattice of quantum dots.
A Time-Adaptive Heuristic for Cognitive Cloud Offloading in Multi-RAT Enabled Wireless Devices (2016)

We introduce the concept of cognitive cloud offloading where all viable wireless interfaces of a multiple radio enabled device are used for computation offloading. We propose a time and wireless adaptive heuristic for offloading computationally intensive applications to a remote cloud with goals of reducing the energy consumption on the mobile device, execution time of the application, and efficient use of the multiple radio interfaces available at the device. The proposed algorithms simultaneously determine: 1) execution place of each application component (mobile/cloud); 2) amount of the associated data to be sent via each available interface of the multiple radio access technology device; and 3) scheduling order of the application components. We define a net utility function that trades off mobile device resources (battery, CPU, and memory) with realtime communication costs, such as latency and communication energy, subject to constraints that ensure queue stability of radio interfaces. Simulations using real data from an HTC smartphone running multi-component applications with Amazon EC2 as the cloud, and two radios, LTE and WiFi, show that cognitive cloud offloading provides higher net utility in comparison to the best-interface protocol. Scalability of the proposed heuristic is further analyzed using various levels for component dependency graphs and energy-delay trade-off factors.
Resonance ionization image detectors: basic characteristics and potential applications (1997)

A type of spectrally selective imaging optical detector that is based on resonance ionization in an atomic vapor is proposed. It has the potential for improved spatial, spectral, and temporal resolutions compared with those of available techniques. Figures of merit are calculated and compared with those of existing techniques. Several potential applications such as the imaging of moving objects, ultrasonic fields, high-energy particle detection, and optical communications are discussed.
Magnetic and magneto-optical properties of Tb-Fe-Co amorphous films (1987)

Characteristics of Tb-Fe-Co amorphous films have been systematically investigated in order to optimize compositions suitable for magneto-optical recording medium with high readout signal. In order to optimize alloy composition, Curie temperature TC and compensation temperature Tcomp are summarized as functions of both Tb and Co contents. Crystallization temperature Tx of Tb-Fe-Co amorphous films has been also measured to be about 400 °C and tends to increase with replacing Fe by either Co or Tb. To evaluate Tb-Fe-Co films as a magneto-optical recording medium, carrier C and modulation noise Nmod (defined by the difference in noise before and after writing) are measured as a function of external field Hex. It is found that written bits of large Nmod show an irregular shape, while those of small Nmod are of regular one. To reduce Nmod and obtain high readout C/N, films with lower saturation magnetization Ms (that is, low demagnetization field) at just below writing temperature are preferred.
Isolation and characterization of a cDNA clone encoding a novel peptide (OSF) that enhances osteoclast formation and bone resorption (1998)

Using an expression cloning approach, we identified and cloned a novel intracellular protein produced by osteoclasts that indirectly induces osteoclast formation and bone resorption, termed OSF. Conditioned media from 293 cells transiently transfected with the 0.9 kb OSF cDNA clone stimulated osteoclast-like cell formation in both human and murine marrow cultures in the presence or absence 10(-9) M 1,25-dihydroxyvitamin D3. In addition, conditioned media from 293 cells transfected with the OSF cDNA clone enhanced the stimulatory effects of 1,25-(OH)2D3 on bone resorption in the fetal rat long bone assay. In situ hybridization studies using antisense oligomers showed expression of OSF mRNA in highly purified osteoclast-like cells from human giant cell tumors of the bone. Northern blot analysis demonstrated ubiquitous expression of a 1.3 kb mRNA that encodes OSF in multiple human tissues. Sequence analysis showed the OSF cDNA encoded a 28 kD peptide that contains a c-Src homology 3 domain (SH3) and ankyrin repeats, suggesting that it was not a secreted protein, but that it was potentially involved in cell signaling. Consistent with these data, immunoblot analysis using rabbit antisera against recombinant OSF demonstrated OSF expression in cell lysates but not in the culture media. Furthermore, recombinant OSF had a high affinity for c-Src, an important regulator of osteoclast activity. Taken together, these data suggest that OSF is a novel intracellular protein that indirectly enhances osteoclast formation and osteoclastic bone resorption through the cellular signal transduction cascade, possibly through its interactions with c-Src or other Src-related proteins.
Design and evaluation of an integrated avionics alerting system (2002)

While today's aircraft have integrated alerting systems for conditions inside the aircraft (ECAM, EICAS), there is no comparable fully integrated alerting system for conditions outside of the aircraft. Current and near-future, separate alerting systems warn of conditions such as time-critical terrain, traffic, wind shear, clear air turbulence, wake vortices, each using different alerting and display philosophies to present information to the flight crew. Separate systems contribute to alert proliferation and the potential for multiple conflicting alerts during emergency situations. An integrated alerting system should deconflict alerts, and present information in an integrated fashion. In response to these issues, we have developed the Alerting and Notification of Conditions Outside the Aircraft (ANCOA) concept. Key aspects of the concept include: (1) deconflicting currently separate alerts such as TCAS and EGPWS; (2), categorization (weather, traffic, ground) and prioritization (time-critical, tactical and strategic) of alerts to reduce pilot information processing requirements; (3) directional, multidimensional aural cueing to allow quick "pre-processing" of the condition (this aids in time-critical responses and prioritizing the alerted condition relative to the ongoing task); and (4) integrated graphic presentation of conditions external to the aircraft to support better situation awareness. This paper discusses the theory and implementation of the ANCOA concept, and presents a usability study to evaluate the display configuration, ease-of-use, functionality, and navigation of information within an initial simulator prototype. Nine pilots participated in six scenarios under various conditions in the Honeywell Laboratories Medium-Fidelity Flight Simulator. Additionally, pilots conducted an information categorization task, filled out pre- and post-questionnaires, and were interviewed for qualitative assessments. The data were used to assess if the ANCOA integrated system could effectively prioritize and de-conflict information, support improved detection and identification of threats, increase overall situation awareness, and support better planning decisions. A revised prototype is presented, based on the results of the evaluation.