gebhart/patrepeval huggingface dataset:
Creating support circuits for the nervous system: Considerations for “brain-machine” interfacing (2009)

This paper discusses designing technology for brain-machine interfaces (BMI). Advances in BMI technology might potentially help improve devices treating neurological conditions. Designing a BMI system is a complex engineering problem drawing on such diverse fields as applied physics, circuit design, algorithms and biology. Fundamental to device design is the neurophysiology of the ‘brain circuits’ and how a circuit designer chooses to interface with these networks. To put these concepts in context, we describe recent work in prototyping bi-directional BMIs that seek to provide adaptive neuromodulation of a neural circuit based on detected electrical biomarkers in the brain. This application highlights how advancements in merging silicon and biological systems, reflected in BMI design, seeks to help advance the treatment of a variety of neurological disorders.
Hinges and Curved Lamina Emergent Torsional Joints in Cylindrical Developable Mechanisms (2020)

Abstract Cylindrical developable mechanisms are devices that conform to and emerge from a cylindrical surface. These mechanisms can be formed or cut from the cylinder wall itself. This paper presents a study on adapting traditional hinge options to achieve revolute motion in these mechanisms. A brief overview of options is given, including classical pin hinges, small-length flexural pivots, initially curved beams, and an adaptation of the membrane thickness-accommodation technique. Curved Lamina Emergent Torsional (LET) joints are then evaluated in detail, and a thin-walled modeling assumption is checked analytically and empirically. A small-scale cylindrical developable mechanism is then evaluated with Nitinol curved LET joints.
Characterization of non-active site TrkA selective kinase inhibitors and implications on obtaining kinase selectivity (2017)

Current therapies for chronic pain can have insufficient efficacy and lead to side effects, necessitating research on novel targets against pain. Although originally identified as an oncogene, TrkA is linked to pain and elevated levels of NGF, the ligand for TrkA, are associated with chronic pain. Antibodies that block TrkA interaction with its ligand, NGF, are in clinical trials for pain relief. Here, we describe the identification of TrkA-specific inhibitors and the structural basis for their selectivity over other Trk family kinases. The x-ray structures reveal a novel binding site outside the kinase active site that utilizes residues from the kinase domain and the juxtamembrane region. Three modes of binding with the juxtamembrane region are characterized through a series of ligand-bound complexes. The structures indicate a critical pharmacophore on the compounds that leads to the distinct binding modes. The mode of interaction can allow TrkA selectivity over TrkB and TrkC or promiscuous, pan-Trk inhibition. This highlights the difficulty in characterizing the structure-activity relationship of a chemical series in the absence of structural information due to substantial differences in the interacting residues. These structures illustrate the flexibility of binding to sequences outside of, but adjacent to, the kinase domain of TrkA. This knowledge allows development of compounds with specificity for TrkA or the family of Trk proteins and has implications on obtaining selectivity for kinase targets in drug discovery.
Pulse shaping in volume reflection holograms (1993)

Ultrashort pulses are shaped by reflection from dynamic volume holograms recorded in azo-dye-doped epoxies. The spectral resolution and controllability of the reflection geometry are optimal for this application.
Nitric oxide induces murine thymocyte apoptosis by oxidative injury and a p53-dependent mechanism (2001)

Previously, we showed that NO induces thymocyte apoptosis via a caspase-1-dependent mechanism [(1) ]. In the present study, we investigated the role of heme oxygenase, catalase, bax, and p53 in this process. The NO donor, S-nitroso-N-acetyl penicillamine (SNAP), induced DNA fragmentation in thymocytes in a time- and concentration-dependent way. SNAP (100 microM) induced 50--60% apoptosis; higher doses did not increase the rate of apoptosis significantly. SNAP decreased catalase and heme iron (Fe) levels without affecting superoxide dismutase, glutathione, or total Fe stores in thymocytes. SNAP significantly increased the expression of heme oxygenase 1 (HSP-32), p53, and bax but not bcl-2. Treatment with the heme oxygenase inhibitor, tin protoporphyrin IX inhibited SNAP-induced thymocyte apoptosis. Furthermore, thymocytes from p53 null mice were resistant to NO-induced apoptosis. Our data suggest that NO may induce its cytotoxic effects on thymocytes by modulating heme oxygenase and catalase activity as well as up-regulating pro-apoptotic proteins p53 and bax.
Properties of Biologic Scaffolds and Their Response to Mesenchymal Stem Cells (2014)

This study enables the clinician and scientist to choose scaffold materials according to their specific interaction with MSCs.
Figure S1 from Spatial Architecture and Arrangement of Tumor-Infiltrating Lymphocytes for Predicting Likelihood of Recurrence in Early-Stage Non–Small Cell Lung Cancer (2023)

&lt;p&gt;Figure S1. Patient selection workflow for the datasets included in this study.&lt;/p&gt;
Chapter 16. Photodynamic Therapy for Helicobacter pylori Infections (2011)

Helicobacter pylori infection in the stomach causes peptic ulcers and gastric cancer. Antibiotic therapy leads to 80%-eradication but has side effects and increasing antibiotic resistance is becoming problematic. Antimicrobial photodynamic therapy has been studied as an alternative approach to killing the bacteria in the stomach lining. In vitro photoinactivation with several photosensitizers has been reported, and an ex vivo study in ferret stomach samples, and a human clinical trial using ALA-PDT have been published. We discovered that H. pylori is susceptible to killing by visible light without added PS. Violet light is most effective (six logs10 of kill by 20-J/cm2 and both the bacterial pellets and culture supernatant accumulate significant amounts of the photoactive porphyrins, coproporphyrin and protoporphyrin. A Phase I clinical trial included patients with dyspepsia and HP infection. At endoscopy a 1-cm2 site in the pyloric antrum was exposed to 405-nm violet light (140-mW/cm2, 40-J), via a diode laser-coupled optical fiber. Biopsies were taken from the control and illuminated sites and average killing of &gt;90% of bacteria. A second clinical trial used whole-stomach illumination with 405-nm light at endoscopy. Quantitative culture from biopsies showed the largest reduction (2 logs) in bacterial load was in the antrum, followed by the body and fundus. There was a correlation between log reduction and initial bacterial load in the antrum.
Inactivity and hormonal deregulation increase human skeletal muscle protein loss (2006)

We sought to quantify changes in human skeletal muscle protein kinetics during prolonged inactivity with and without accompanying hypercortisolemia. Oral hydrocortisone sodium succinate (~22 μg/dL) was administered to an experimental group (EXP: male, n=6, 28± 2 y; 84±4 kg; 178± 3 cm;) throughout 28 days of bedrest. The control group (CON: male, n=6; 38±8 y; 86±10 kg; 179±3 cm) received no exogenous cortisol (~10 μg/dL). Femoral arterio‐venous blood samples and a vastus lateralis muscle biopsy were obtained during a primed constant infusion of L‐[ring‐ 2 H 5 ] phenylalanine before and after bed rest. Postabsorptive net balance became more negative in the EXP group following bedrest, a change largely facilitated by a ~40% reduction in protein synthesis in the EXP group. 3‐pool model data representing protein synthesis (F om ) and breakdown (F mo ) (nmol/min/100mL leg) before and after bedrest. A similar superscript represents a statistical difference (p&lt;0.05). image The EXP group experienced a decrease in plasma testosterone (Day 1: 503.5±56.3 vs. Day 28: 409.5±28.6 ng/dL) and sex hormone binding globulin (SHBG) (Day 1: 22.5±2.5 vs. 12.2±1.5 nmol/L), (p&lt;0.05). This was consistent with 3‐fold greater loss of lean leg mass (LLM) in the EXP group (EXP: −1.4±0.1 vs. CON: −0.4±0.1 kg), (p&lt;0.05). In conclusion, a combination of inactivity and hypercortisolemia leads to hormonal deregulation which in‐turn further exacerbates muscle protein catabolism. Supported by funding from NPFR00205.
SaberLDA: Sparsity-Aware Learning of Topic Models on GPUs (2020)

Latent Dirichlet Allocation (LDA) is a popular tool for analyzing discrete count data such as text and images, which are required to model datasets and a large number of topics, e.g., tens of thousands of topics for industry scale applications. Although distributed CPU systems have been used to address this problem, they are slow and resource inefficient. GPU-based systems have emerged as a promising alternative because of their high computational power and memory bandwidth. However, existing GPU-based LDA systems can only learn thousands of topics, because they use dense data structures, and have linear time complexity to the number of topics. In this article, we propose SaberLDA, a GPU-based LDA system that implements a sparsity-aware algorithm to achieve sublinear time complexity to learn a large number of topics. To address the challenges introduced by sparsity, we propose a novel data layout, a warp-based sampling kernel, an efficient sparse matrix counting method, and a fine-grained load balancing strategy. SaberLDA achieves linear speedup on 4 GPUs and is 6-10 times faster than existing GPU systems in thousands of topics. It can learn 40,000 topics from a dataset of billions of tokens in two hours, which was previously only achievable using clusters of tens of CPU servers.
Toward scalable keyword search over structured data (2011)

The success of search engines has spawned substantial interest in keyword search over structured data (KWS-S) in order to accommodate users who cannot issue a formal structured query or are unaware of the underlying structure of the data. KWS-S systems accept keywords as input, however unlike search engines, instead of documents they return relationships between the user's keywords. While KWS-S solutions have been around for over a decade, their widespread adoption has been hindered by several roadblocks.Trying to address some of these roadblocks is the motivation for this dissertation. 
We observed that current KWS-S solutions have unpredictable performance. In particular, for certain queries it takes too long to produce answers, and for others the system may even fail to return (e.g., after exhausting memory). We argue that as today's users have been spoiled by the performance of Internet search engines. KWS-S systems should return whatever answers they can produce quickly and then provide users with options for exploring any portion of the answer space not covered by these answers. Our basic idea is to produce answers that can be generated quickly as in today's KWS-S systems, then to show query forms that characterize the unexplored portion of the answer space. We address the challenges in generating, searching and using query forms to to allows us to bypass the performance problems inherent to KWS-S without compromising query coverage. 
Another problem that we tackle is that of non-answers. We note that, in general, when analyzing data sets, users not only gain information from queries that return answers—they also get information from queries that return no answers. With this in mind, we propose a KWS-S system that also exposes non-answer queries to the user. Additionally our system uses sub-queries of the non-answer queries to provide some insight into the reasons for the non-answer queries.
CRC-assisted error correction in a convolutionally coded system (2008)

In communication systems employing a serially concatenated cyclic redundancy check (CRC) code along with a convolutional code (CC), erroneous packets after CC decoding are usually discarded. The list Viterbi algorithm (LVA) and the iterative Viterbi algorithm (IVA) are two existing approaches capable of recovering erroneously decoded packets. We here employ a soft decoding algorithm for CC decoding, and introduce several schemes to identify error patterns using the posterior information from the CC soft decoding module. The resultant iterative decoding-detecting (IDD) algorithm improves error performance by iteratively updating the extrinsic information based on the CRC parity check matrix. Assuming errors only happen in unreliable bits characterized by small absolute values of the log-likelihood ratio (LLR), we also develop a partial IDD (P-IDD) alternative which exhibits comparable performance to IDD by updating only a subset of unreliable bits. We further derive a soft-decision syndrome decoding (SDSD) algorithm, which identifies error patterns from a set of binary linear equations derived from CRC syndrome equations. Being noniterative, SDSD is able to estimate error patterns directly from the decoder output. The packet error rate (PER) performance of SDSD is analyzed following the union bound approach on pairwise errors. Simulations indicate that both IDD and IVA are better tailored for single parity check (PC) codes than for CRC codes. SDSD outperforms both IDD and LVA with weak CC and strong CRC. Applicable to AWGN and flat fading channels, our algorithms can also be extended to turbo coded systems.
Miniaturization of Electrostatic Fluid Accelerators (2006)

Existing thermal management methods for electronics do not meet technology needs and remain a major bottleneck in the evolution of computing, sensing, and information technology. The decreasing size of microelectronics components and the resulting increasing thermal output density require novel cooling solutions. Electrohydrodynamic ionic wind pumps, also known as electrostatic fluid accelerators (EFA), have the potential of becoming a critical element of electronic thermal management solutions. In order to take full advantage of EFA-based thermal management, it is essential to miniaturize EFA technology. This paper demonstrates the successful operation of a meso-scale microfabricated silicon EFA. A cantilever structure fabricated in bulk silicon with a radius of tip curvature of 25 μm is used as the corona electrode. The device was fabricated using a Deep Reactive Ion Etching (DRIE) microfabrication process. Forced convection cooling is demonstrated using infrared imaging, showing a 25°C surface temperature reduction over an actively heated substrate. The fabrication and test results of a meso-scale microfabricated EFA are presented in this paper.
On Diversity and Multiplexing Gain of Multiple Antenna Systems with Transmitter Channel Information (2004)

We quantify the multiplexing-diversity tradeoff of a multiple-input multiple-output (MIMO) system, when the channel state information (CSI) is known perfectly at the receiver and partially at the transmitter.The partial knowledge of CSI at the transmitter consists of the quantized value of one of the eigenvalues and perfect knowledge of eigenvectors of the channel matrix.The key result is that while multiplexing gain cannot be increased beyond minimum number of transmit and receive antennas, diversity order for each multiplexing gain can be substantially increased by using only a few bits of feedback at the transmitter.For example, with 1 bit of feedback in a 2 3 system, for multiplexing gains of 0, 1, and 2, diversity gains of 42, 6, and 2 can be achieved, respectively.Thus, while the tradeoff between diversity advantage and multiplexing gain is still present, its behavior is significantly changed by channel knowledge at the transmitter.The major reason for this different tradeoff can be attributed to addition of long-term power control, which allows the transmitter to switch between modes for reducing outage and increasing throughput based on signal to noise ratio along different eigenvalues.
Expression ofreg/PSP, a Pancreatic Exocrine Gene: Relationship to Changes in Islet β-Cell Mass (1991)

A cDNA termed reg was recently isolated by differential screening of a library prepared from regenerating islets isolated from pancreatic remnants of rats subjected to 90% pancreatectomy and nicotinamide treatment. This led to speculation that this gene may be involved in expansion of beta-cell mass. In the current study we have measured reg expression after implantation and resection of a solid insulinoma tumor into rats, maneuvers known, respectively, to reduce and reexpand the volume of beta-cells in the islet. Animals with an implanted insulinoma tumor became profoundly hypoglycemic. Islet beta-cells declined from the normal 75% of total islet volume to less than 30%, in concert with a marked reduction in the reg mRNA level. Removal of the tumor resulted in a sharp increase in beta-cell replication, as measured by [3H]thymidine incorporation and a return to normal beta-cell volume within 4 days of tumor resection. This was associated with a transient induction in reg expression compared to that in tumor-bearing animals, effectively returning the amount of reg mRNA to the levels found in normal animals within 48 h; at later time points after tumor removal (3-7 days) reg expression declined, but then rose toward normal. In situ hybridization analysis localized the initial induction in reg mRNA expression to the exocrine pancreas. Continuous infusion of insulin into normal rats for 4 days, a maneuver that does not significantly reduce beta-cell mass, resulted in dramatically reduced insulin mRNA in islets, but no change in the levels of reg mRNA. We conclude that the diminution in pancreatic beta-cell mass caused by subcutaneous implantation of an insulinoma is associated with reduced reg gene expression and that the increase in beta-cell replication after resection of the tumor is preceded by return of reg gene expression toward normal.
MOS Transistors in beam-recrystallized polysilicon (1982)

The fabrication of transistors with their active channels in recrystallized polysilicon offers the long-desired possibility of readily achievable, total dielectric isolation. Devices with properties approaching those of single-crystal transistors can be obtained in large-grain polysilicon, and the properties can be further improved by using seeded recrystallization to remove the remaining grain boundaries. This paper addresses some of the remaining problem areas which must be controlled before the technique can become a practical process, as well as showing some novel structures, including a new dynamic RAM cell.
Managing imported fire ants in urban areas (2009)

1. This document is ENY226 (LH059), one of a series of the Entomology and Nematology Department, UF/IFAS Extension. Originally published as Imported Fire Ants on Lawns and Turf by David H. Oi and Philip G. Koehler, February 1991. Revised as eXtension resource November 2012. This EDIS publication is updated quarterly to reflect changes made to the eXtension resource. Last updated September 2015. For more recent updates, refer to the version posted on the Imported Fire Ants site, http://www.extension.org/pages/11004/managing-imported-fire-ants-in-urban-areas-printableversion. Visit the EDIS website at http://edis.ifas.ufl.edu.
Indium phosphide boudle heterojunction bipolar transistors with T-shaped emitter metal features having cutoff frequencies in excess of 200 GHz (2005)

We demonstrate Indium Phosphide Double Heterojunction Bipolar Transistors with simultaneous cutoff frequency Fmax of 288 GHz and current gain cutoff frequency Ft of 251 GHz.
An Improved Successive Filter-Based Dropping Algorithm for Massive MIMO With Max-Min Power Control (2021)

In line-of-sight massive MIMO, there are use cases where the channel vectors of some users become highly correlated. Highly correlated users lead to a large reduction in the sum-rate of linear and nonlinear precoders with max-min power control. To alleviate the loss in the sum-rate, some users can be dropped and rescheduled. The optimal dropping strategy can be found by an exhaustive search. In this letter, a successive filter-based dropping algorithm (SFDA) is proposed, which improves upon the existing dropping algorithms in the literature. At each step, the user with the highest filter norm is dropped. By comparing the sum-rate of all the steps, the best set of dropped users is found. In contrast to previous threshold-based algorithms in the literature, SFDA does not require a predefined threshold for the spatial correlation of users. Compared to an exhaustive search, the complexity of SFDA is reduced. Simulations results show when a 100 antennas base station serves 10 users, SFDA improves the 5th percentile sum-rate compared to previous algorithms in the literature up to 6 bits/channel use.
Capacitance based scanner for thickness mapping of thin dielectric films (2000)

We have recently developed a technique capable of mapping variations in the thickness of thin dielectric films. This technique is based on accurately recording the capacitance between a spherical probe and the conductive substrate of a dielectric film. Once the capacitance has been recorded, and assuming the dielectric constant is known, the thickness of the film can be readily extracted, with better than 0.2 μm accuracy. In the current experimental configuration, the probe can be raster scanned with respect to the surface of the dielectric film, enabling one to record three-dimensional images and observe any spatial variations in sample thickness. The spatial resolution (i.e., the imaging resolution) of the technique is primarily dictated by the size of the probe and currently rests at ∼200 μm. This technique is applicable to any dielectric film on a conductive substrate, assuming the dielectric constant is known.
Theoretical realization of holey fiber with flat chromatic dispersion and large mode area: an intriguing defected approach (2006)

We present a novel design approach for realizing holey fibers (HFs) with flat dispersion characteristics and large mode area based on the existence of an artificially defected air-hole ring in the cladding, and on the inclusion of additional defected air holes in the core of the fiber. This unique type of HF can be used for achieving remarkable flat dispersion characteristics as well as a large mode area, which are particularly useful for high-speed data transmission. The validation of the proposed design is done by adopting an efficient full-vectorial finite element method for optical characterization of HFs. The proposed fiber can be employed in reconfigurable optical transmission systems for performing wavelength division multiplexing operation. Typical characteristics of the proposed HF are a flattened dispersion of 6.3 +/- 0.5 ps/km/nm from 1.45 to 1.65 microm and an effective mode area as large as 100 microm2 in the same frequency range.