gebhart/patrepeval huggingface dataset:
Data from Visualizing Implanted Tumors in Mice with Magnetic Resonance Imaging Using Magnetotactic Bacteria (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; To determine if magnetotactic bacteria can target tumors in mice and provide positive contrast for visualization using magnetic resonance imaging.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; The ability of the magnetotactic bacterium, &lt;i&gt;Magnetospirillum magneticum&lt;/i&gt; AMB-1 (referred to from here as AMB-1), to confer positive magnetic resonance imaging contrast was determined &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt;. For the latter studies, AMB-1 were injected either i.t. or i.v. Bacterial growth conditions were manipulated to produce small (∼25-nm diameter) magnetite particles, which were observed using transmission electron microscopy. Tumor targeting was confirmed using &lt;sup&gt;64&lt;/sup&gt;Cu-labeled bacteria and positron emission tomography and by determination of viable cell counts recovered from different organs and the tumor.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We show that AMB-1 bacteria with small magnetite particles generate T1-weighted positive contrast, enhancing &lt;i&gt;in vivo&lt;/i&gt; visualization by magnetic resonance imaging. Following i.v. injection of &lt;sup&gt;64&lt;/sup&gt;Cu-labeled AMB-1, positron emission tomography imaging revealed increasing colonization of tumors and decreasing infection of organs after 4 hours. Viable cell counts showed that, by day 6, the bacteria had colonized tumors but were cleared completely from other organs. Magnetic resonance imaging showed a 1.22-fold (&lt;i&gt;P&lt;/i&gt; = 0.003) increased positive contrast in tumors on day 2 and a 1.39-fold increase (&lt;i&gt;P&lt;/i&gt; = 0.0007) on day 6.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; Magnetotactic bacteria can produce positive magnetic resonance imaging contrast and colonize mouse tumor xenografts, providing a potential tool for improved magnetic resonance imaging visualization in preclinical and translational studies to track cancer. (Clin Cancer Res 2009;15(16):5170–7)&lt;/p&gt;&lt;/div&gt;
Calcium phosphate‐coated porous titanium implants for enhanced skeletal fixation (1988)

Porous titanium fiber implants for cementless skeletal fixation by bone ingrowth were treated with a calcium phosphate coating applied by a plasma flame-spray technique. In a paired experiment, treated and control implants were inserted in the humeri and olecranons of 36 adult dogs for periods of 1, 2, 4, and 6 weeks. After the animals were sacrificed, a biomechanical evaluation of the strength of skeletal fixation of the implants and a histologic evaluation of bone ingrowth was done. The mean shear strength of skeletal fixation at four weeks for the calcium phosphate-coated implants was 24% greater (P less than .01) than for paired controls. No difference in strength of fixation between treated and control implants was present at other time periods. The osteoconductive properties of the ceramic coating were demonstrated by bone forming in direct contact with the calcium phosphate coating on the metal fibers of the treated implants. No significant increase for the volume of bone ingrowth was established for treated implants compared to paired controls at any time period.
Single-step preparation and catalytic activity of mesoporous MCM-41 and SBA-15 silicas functionalized with perfluoroalkylsulfonic acid groups analogous to Nafion® (2004)

Preparation of hybrid organic-inorganic MCM-41 and SBA-15 silicas functionalized with perfluoroalkylsulfonic acid groups has been achieved in a single step by reacting the mesoporous silicas with 1,2,2-trifluoro-2-hydroxy-1-trifluoromethylethane sulfonic acid beta-sultone; the catalysts showed higher activity than commercial Nafion-silica composite for the esterification of long chain fatty acids with ethanol.
Structural sparseness and spatial phase alignment in natural scenes (2007)

The Fourier phase spectrum plays a central role regarding where in an image contours occur, thereby defining the spatial relationship between those structures in the overall scene. Only a handful of studies have demonstrated psychophysically the relevance of the Fourier phase spectrum with respect to human visual processing, and none have demonstrated the relative amount of local cross-scale spatial phase alignment needed to perceptually extract meaningful structure from an image. We investigated the relative amount of spatial phase alignment needed for humans to perceptually match natural scene image structures at three different spatial frequencies [3, 6, and 12 cycles per degree (cpd)] as a function of the number of structures within the image (i.e., "structural sparseness"). The results showed that (1) the amount of spatial phase alignment needed to match structures depends on structural sparseness, with a bias for matching structures at 6 cpd and (2) the ability to match partially phase-randomized images at a given spatial frequency is independent of structural sparseness at other spatial frequencies. The findings of the current study are discussed in terms of a network of feature integrators in the human visual system.
Spherical Nucleic Acid Nanoparticle Conjugates as an RNAi-Based Therapy for Glioblastoma* (2020)

1626Glioblastoma multiforme (GBM) is a neurologically debilitating disease that culminates in death 14 to 16 months after diagnosis. An incomplete understanding of how cataloged genetic aberrations promote therapy resistance, combined with ineffective drug delivery tothe central nervous system, has rendered GBM incurable. Functional genomics efforts have implicated several oncogenes in GBM pathogenesis but have rarely led to the implementation of targeted therapies. This is partly because many “undruggable” oncogenes cannot be targeted by small molecules or antibodies. We preclinically evaluate an RNA interference (RNAi)–based nanomedicine platform, based on spherical nucleic acid (SNA) nanoparticle conjugates, to neutralize oncogene expression in GBM. SNAs consist of gold nanoparticles covalently functionalized with densely packed, highly oriented small interfering RNA duplexes. In the absence of auxiliary transfection strategies or chemical modifications, SNAs efficiently entered primary and transformed glial cells in vitro. In vivo, the SNAs penetrated the blood–brain barrier and blood–tumor barrier to disseminate throughout xenogeneic glioma explants. SNAs targeting the oncoprotein Bcl2Like12 (Bcl2L12)—an effector caspase and p53 inhibitor overexpressed in GBM relative to normal brain and low-grade astrocytomas—were effective in knocking down endogenous Bcl2L12 mRNA and protein levels, and sensitized glioma cells toward therapy-induced apoptosis by enhancing effector caspase and p53 activity. Further, systemically delivered SNAs reduced Bcl2L12 expression in intracerebral GBM, increased intratumoral apoptosis, and reduced tumor burden and progression in xenografted mice, without adverse side effects. Thus, silencing antiapoptotic signaling using SNAs represents a new approach for systemic RNAi therapy for GBM and possibly other lethal malignancies.
Noise predictive maximum likelihood detection combined with parity-based post-processing (2001)

The performance of magnetic recording systems that include conventional modulation codes combined with multiple parity bits is studied. Various performance measures, including bit error rate at the output of time inverse precoder, byte error probability at the input of the Reed-Solomon (RS) decoder and sector error rate, are used to evaluate the performance of various coding/detection schemes. Suboptimum detection/decoding schemes consisting of a 16-state noise-predictive maximum-likelihood (NPML) detector followed by parity-based noise-predictive post-processing, and maximum-likelihood sequence detection/decoding on the combined channel/parity trellis are considered. For conventional modulation codes, it is shown that although the dual-parity post-processor gains 0.5 dB over the single-parity post-processor in terms of bit- and byte-error-rate performance, the sector-error-rate performance of both schemes is almost the same. Furthermore, the sector-error-rate performance of optimum 64-state combined channel/parity detection for the dual-parity code is shown to be approximately 0.1 dB better than that of optimum 32-state combined channel/parity detection for the single-parity code. These performance gains can be even more substantial if appropriate coding techniques that eliminate certain error events and minimize error burst length or multiparity codes in conjunction with combined parity/channel detection are used.
Synthesis of 1,3-Dienes via Ligand-Enabled Sequential Dehydrogenation of Aliphatic Acids (2023)

1,3-Dienes are common scaffolds in biologically active natural products as well as building blocks for chemical synthesis. Developing efficient methods for the synthesis of diverse 1,3-dienes from simple starting materials is therefore highly desirable. Herein, we report a Pd(II)-catalyzed sequential dehydrogenation reaction of free aliphatic acids via β-methylene C-H activation, which enables one-step synthesis of diverse <i>E,E</i>-1,3-dienes. Free aliphatic acids of varying complexities, including the antiasthmatic drug seratrodast, were found to be compatible with the reported protocol. Considering the high lability of 1,3-dienes and lack of protecting strategies, dehydrogenation of aliphatic acids to reveal 1,3-dienes at the late stage of synthesis offers an appealing strategy for the synthesis of complex molecules containing such motifs.
Bone Induction by Demineralized Bone Powder and Partially Purified Osteogenin Using a Fibrin-Sealant Carrier (2020)

This chapter investigates the use of fibrin sealant as a carrier for known osteoinductive substances, such as demineralized bone and osteogenin. A major challenge in the field of bone induction is the development of a suitable biocompatible and biodegradable carrier for bone morphogenetic proteins (BMPs). The carrier plays an important role in bone induction. It should place the BMPs at the desired location for bone deposition, prevent the prolapse of soft tissue into the skeletal defect, enable bone ingrowth, and maintain bony contours if necessary. Commercial fibrin sealant from pooled, virally-inactivated human plasma has been used clinically as a hemostatic agent in Europe and Canada. At twenty-eight days postimplantation, most of the demineralized bone particles that were either implanted alone or in a fibrin sealant matrix showed trabecular bone formation. Fibrin sealant also imparts desirable handling characteristics to the osteoinductive implants.
One-dimensional ghost imaging with an electron microscope: a route towards ghost imaging with inelastically scattered electrons (2021)

In quantum mechanics, entanglement and correlations are not just a mere sporadic curiosity, but rather common phenomena at the basis of an interacting quantum system. In electron microscopy, such concepts have not been extensively explored yet in all their implications; in particular, inelastic scattering can be reanalyzed in terms of correlation between the electron beam and the sample. While classical inelastic scattering simply implies loss of coherence in the electron beam, performing a joint measurement on the electron beam and the sample excitation could restore the coherence and the lost information. Here, we propose to exploit joint measurement in electron microscopy for a surprising and counter-intuitive application of the concept of ghost imaging. Ghost imaging, first proposed in quantum photonics, can be applied partially in electron microscopy by performing joint measurement between the portion of the transmitted electron beam and a photon emitted from the sample reaching a bucket detector. This would permit us to form a one-dimensional virtual image of an object that even has not interacted with the electron beam directly. This technique is extremely promising for low-dose imaging that requires the minimization of radiation exposure for electron-sensitive materials, because the object interacts with other form of waves, e.g., photons/surface plasmon polaritons, and not the electron beam. We demonstrate this concept theoretically for any inelastic electron-sample interaction in which the electron excites a single quantum of a collective mode, such as a photon, plasmon, phonon, magnon, or any optical polariton.
Senseye: a multi-tier heterogeneous camera sensor network (2007)

Rapid technological developments in sensing devices, embedded platforms and wireless communication technologies, have enabled and led to a large research focus in sensor networks. Traditional sensor networks have been designed as networks of homogeneous sensor nodes. Single-tier networks consisting of homogeneous nodes achieve only a subset of application requirements and often sacrifice others. In this thesis, I propose the notion of multi-tier heterogeneous sensor networks, sensors organized hierarchically into multiple tiers. With intelligent use of resources across tiers, multi-tier heterogeneous sensor networks have the potential to simultaneously achieve the conflicting goals of network lifetime, sensing reliability and functionality. 
I consider a class of sensor networks---camera sensor networks---wireless networks with image sensors. I address the issues of automatic configuration and initialization and design of camera sensor networks. 
Like any sensor network, initialization of cameras is an important pre-requisite for camera sensor networks applications. Since, camera sensor networks have varying degrees of infrastructure support and resource constraints a single initialization procedure is not appropriate. I have proposed the notions of accurate and approximate initialization to initialize cameras with varying capabilities and resource constraints. I have developed and empirically evaluated Snapshot, an accurate calibration protocol tailored for sensor network deployments. I have also developed approximate initialization techniques that estimate the degree of overlap and region of overlap estimates at each camera. Further, I demonstrate usage of these estimates to instantiate camera sensor network applications. As compared to manual calibration, which can take a long time (order of hours) to calibrate several cameras, is inefficient and error prone, the automated calibration protocol is accurate and greatly reduces the time for accurate calibration---tens of seconds to calibrate a single camera and can easily scale to calibrate several cameras in order of minutes. The approximate techniques demonstrate feasibility of initializing low-power resource constrained cameras with no or limited infrastructure support. 
With regards to design of camera sensor networks, I present the design and implementation of SensEye, a multi-tier heterogeneous camera sensor network and address the issue of energy-reliability tradeoff. Multi-tier networks provide several levels of reliability and energy usage based on the type of sensor used for application tasks. Using SensEye I demonstrate how multi-tier networks can achieve simultaneous system goals of energy efficiency and reliability.
Amplified spontaneous emission at dense wavelength-division multiplexing regime: direct detection of photon statistics (2003)

Photon statistics of amplified spontaneous emission noise has been measured by direct detection, confirming the Bose-Einstein distribution in the few-modes regime, as characteristic of dense wavelength-division multiplexing optical systems, up to the single-mode condition.
Accuracy of Urinary Neutrophil Gelatinase-Associated Lipocalin in Quantifying Acute Kidney Injury after Partial Nephrectomy in Patients with Normal Contralateral Kidney (2015)

Background 
To evaluate the efficacy of urinary neutrophil gelatinase-associated lipocalin (uNGAL) for predicting the degree of acute kidney injury (AKI) in patients following partial nephrectomy (PN).
Methods 
This prospective study included 176 patients who underwent open or laparoscopic PN for solid renal tumors between June 2013 and May 2014. Urine samples were collected preoperatively and at 3, 24, and 48 h after renal pedicle clamp removal. Changes in uNGAL levels were analyzed for all patients and between subgroups that were dichotomized based on preoperative eGFR values of <60 and ≥60 mL/min/1.73m2, open and laparoscopic surgery, and according to the onset of AKI. Linear mixed models were used to investigate preoperative and perioperative features associated with postoperative uNGAL and eGFR changes at 6 months postoperatively.
Results 
Among 146 patients included in the final analysis, 10 (6.8%) patients had preoperative eGFR <60 mL/min/1.73m2. In the overall group, uNGAL levels increased following PN. However, all subgroups demonstrated comparable changes in uNGAL levels over time. Multivariate analyses failed to reveal any correctable clinical features associated with postoperative uNGAL changes, whereas preoperative serum creatinine levels and the onset of AKI correlated with eGFR at 6 months postoperatively.
Conclusions 
uNGAL levels may increase following PN. However, it does not appear to be a useful marker for quantifying the degree of AKI or predicting postoperative renal function in patients with normal contralateral kidney and relatively good preoperative renal function. Further analysis is necessary to assess the usefulness of uNGAL in patients with poor preoperative renal function.
Novel stacked capacitor technology for 1-Gbit DRAMs with (Ba,Sr)TiO3 thin films (1997)

Novel stacked cell capacitors with (Ba,Sr)TiO3 (BST) films were prepared as dielectrics for Gbit-scale DRAMs. The BST films were deposited by the liquid source chemical vapor deposition (CVD) method, and Ru was used as an electrode material for storage nodes and cell plates. For BST films on Ru electrodes, a two-step film deposition process by repetition of low-temperature deposition and subsequent-high temperature annealing was shown to result in smooth surface morphology and conformal step coverage; in addition, no residues were formed on the mask side walls during Ru etching in oxygen-containing plasmas. The surfaces of the Ru electrodes were not oxidized during the BST deposition and annealing process, and these results indicate that Ru is a most possible material for capacitor electrodes. The electrical properties obtained for the 25-nm-thick BST films on Ru electrodes are: leak current density 2 × 10−8 A/cm2, silicon dioxide equivalent thickness 0.5 nm. Using these techniques, minute stacked capacitors were fabricated with storage nodes 0.24 μm wide, 0.60 μm deep, and 0.2 μm high (spaced 0.14 mm apart), and their applicability for 1-Gbit DRAM memory cells was examined. © 1997 Scripta Technica, Inc., Electron Comm Jpn Pt 2, 80(5): 70–78, 1997
Efficient sample generation for scalable meta learning (2015)

Meta learning techniques such as cross-validation and ensemble learning are crucial for applying machine learning to real-world use cases. These techniques first generate samples from input data, and then train and evaluate machine learning models on these samples. For meta learning on large datasets, the efficient generation of samples becomes problematic, especially when the data is stored distributed in a block-partitioned representation, and processed on a shared-nothing cluster. We present a novel, parallel algorithm for efficient sample generation from large, block-partitioned datasets in a shared-nothing architecture. This algorithm executes in a single pass over the data, and minimizes inter-machine communication. The algorithm supports a wide variety of sample generation techniques through an embedded user-defined sampling function. We illustrate how to implement distributed sample generation for popular meta learning techniques such as hold-out tests, k-fold cross-validation, and bagging, using our algorithm and present an experimental evaluation on datasets with billions of datapoints.
A programmable accelerator for next generation wireless communications (2009)

We present a MIMO decoder accelerator architecture that offers versatility and re-programmability while maintaining a very high performance-cost metric. The accelerator is meant to address the MIMO decoding bottlenecks associated with the convergence of multiple high speed wireless standards onto a single device. It is scalable in the number of antennas, bandwidth, modulation format, and most importantly, present and emerging decoder algorithms. It features a Harvard-like architecture with complex vector operands and a deeply pipelined fixed-point complex arithmetic processing unit. Memory allows efficient access to operands in matrix form, while a custom state machine enhances performance in light of OFDM. The accelerator shows an advantage of up to 3 orders of magnitude in power-delay product for typical MIMO decoding operations relative to a general purpose DSP. 1.
HVM capabilities of CPE run-to-run overlay control (2015)

With the introduction of N2x and N1x process nodes, leading-edge factories are facing challenging demands of shrinking design margins. Previously un-corrected high-order signatures, and un-compensated temporal changes of high-order signatures, carry an important potential for improvement of on-product overlay (OPO). Until recently, static corrections per exposure (CPE), applied separately from the main APC correction, have been the industry’s standard for critical layers [1], [2]. This static correction is setup once per device and layer and then updated periodically or when a machine change point generates a new overlay signature. This is a non-ideal setup for two reasons. First, any drift or sudden shift in tool signature between two CPE update periods can cause worse OPO and a higher rework rate, or, even worse, lead to yield loss at end of line. Second, these corrections are made from full map measurements that can be in excess of 1,000 measurements per wafer [3]. Advanced overlay control algorithms utilizing Run-to-Run (R2R) CPE can be used to reduce the overlay signatures on product in High Volume Manufacturing (HVM) environments. In this paper, we demonstrate the results of a R2R CPE control scheme in HVM. The authors show an improvement up to 20% OPO Mean+3Sigma values on several critical immersion layers at the 28nm and 14 nm technology nodes, and a reduction of out-of-spec residual points per wafer (validated on full map). These results are attained by closely tracking process tool signature changes by means of APC, and with an affordable metrology load which is significantly smaller than full wafer measurements.
Mutual coupling reduction between two monopole antennas using fractal based DGS (2015)

This paper presents the implementation of a fractal based defected ground structure DGS to reduce the interaction between two closely spaced planer monopole patch antennas. The design achieves a -7 dB reduction in mutual coupling level with antennas' edge to edge separation of λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sub> /25 over a bandwidth of 51.8 % (2 - 3.4) GHz in which the reflection coefficient is less than -10 dB and a realized total gain of 4.8 dB. The proposed structure is a good candidate for IEEE 802.11 WLAN applications operating at 2.4 GHz. The design and simulation results have been obtained using the commercial software High Frequency Structure Simulator (HFSS), Ver. 15.