gebhart/patrepeval huggingface dataset:
PAX6 MiniPromoters drive restricted expression from rAAV in the adult mouse retina (2016)

Current gene therapies predominantly use small, strong, and readily available ubiquitous promoters. However, as the field matures, the availability of small, cell-specific promoters would be greatly beneficial. Here we design seven small promoters from the human paired box 6 (PAX6) gene and test them in the adult mouse retina using recombinant adeno-associated virus. We chose the retina due to previous successes in gene therapy for blindness, and the PAX6 gene since it is: well studied; known to be driven by discrete regulatory regions; expressed in therapeutically interesting retinal cell types; and mutated in the vision-loss disorder aniridia, which is in need of improved therapy. At the PAX6 locus, 31 regulatory regions were bioinformatically predicted, and nine regulatory regions were constructed into seven MiniPromoters. Driving Emerald GFP, these MiniPromoters were packaged into recombinant adeno-associated virus, and injected intravitreally into postnatal day 14 mice. Four MiniPromoters drove consistent retinal expression in the adult mouse, driving expression in combinations of cell-types that endogenously express Pax6: ganglion, amacrine, horizontal, and Müller glia. Two PAX6-MiniPromoters drive expression in three of the four cell types that express PAX6 in the adult mouse retina. Combined, they capture all four cell types, making them potential tools for research, and PAX6-gene therapy for aniridia.
Engineering of Cellobiose Dehydrogenases for Improved Glucose Sensitivity and Reduced Maltose Affinity (2016)

Abstract Cellobiose dehydrogenase (CDH) is a fungal extracellular flavocytochrome capable of direct electron transfer (DET). Unlike other CDHs, the pH optimum for CDHs from Corynascus thermophilus ( Ct CDH) and Humicola insolens ( Hi CDH) is close to the human physiological pH in blood (7.4). These are, therefore, interesting candidates for glucose measurements in human blood and the application in enzymatic fuel cells is, however, limited by their relatively low activity with this substrate. In this work, the substrate specificities of Ct CDH and Hi CDH have been altered by a single cysteine to tyrosine substitution in the active sites of Ct CDH (position 291) and Hi CDH (position 285), which resulted in improved kinetic constants with glucose while decreasing the activity with several disaccharides, including maltose. The DET properties of the generated CDH variants were tested in the absence and in the presence of substrates, on graphite electrodes and thiolic self‐assembled monolayer (SAM)‐modified Au electrodes. Seven different thiols with different spacer lengths were used, containing ‐COOH, ‐OH, and ‐NH 2 end groups. The length and head functionality of the thiol govern the efficiency of the DET reaction and indicate different DET properties of Ct CDH and Hi CDH
Planogram rebinning with the frequency-distance relationship (2008)

We present an efficient rebinning algorithm for positron emission tomography (PET) systems with panel detectors. The rebinning algorithm is derived in the planogram coordinate system which is the native data format for PET systems with panel detectors and is the 3-D extension of the 2-D linogram transform developed by Edholm. Theoretical error bounds and numerical results are included.
Dihydro‐Resveratrol Ameliorates Lung Injury in Rats with Cerulein‐Induced Acute Pancreatitis (2016)

Acute pancreatitis is an inflammatory process originated in the pancreas; however, it often leads to systemic complications that affect distant organs. Acute respiratory distress syndrome is indeed the predominant cause of death in patients with severe acute pancreatitis. In this study, we aimed to delineate the ameliorative effect of dihydro-resveratrol, a prominent analog of trans-resveratrol, against acute pancreatitis-associated lung injury and the underlying molecular actions. Acute pancreatitis was induced in rats with repetitive injections of cerulein (50 µg/kg/h) and a shot of lipopolysaccharide (7.5 mg/kg). By means of histological examination and biochemical assays, the severity of lung injury was assessed in the aspects of tissue damages, myeloperoxidase activity, and levels of pro-inflammatory cytokines. When treated with dihydro-resveratrol, pulmonary architectural distortion, hemorrhage, interstitial edema, and alveolar thickening were significantly reduced in rats with acute pancreatitis. In addition, the production of pro-inflammatory cytokines and the activity of myeloperoxidase in pulmonary tissues were notably repressed. Importantly, nuclear factor-kappaB (NF-κB) activation was attenuated. This study is the first to report the oral administration of dihydro-resveratrol ameliorated acute pancreatitis-associated lung injury via an inhibitory modulation of pro-inflammatory response, which was associated with a suppression of the NF-κB signaling pathway.
An efficient robust sound classification algorithm for hearing aids (2004)

An efficient robust sound classification algorithm based on hidden Markov models is presented. The system would enable a hearing aid to automatically change its behavior for differing listening environments according to the user's preferences. This work attempts to distinguish between three listening environment categories: speech in traffic noise, speech in babble, and clean speech, regardless of the signal-to-noise ratio. The classifier uses only the modulation characteristics of the signal. The classifier ignores the absolute sound pressure level and the absolute spectrum shape, resulting in an algorithm that is robust against irrelevant acoustic variations. The measured classification hit rate was 96.7%-99.5% when the classifier was tested with sounds representing one of the three environment categories included in the classifier. False-alarm rates were 0.2%-1.7% in these tests. The algorithm is robust and efficient and consumes a small amount of instructions and memory. It is fully possible to implement the classifier in a DSP-based hearing instrument.
Functional Expression of a Bacterial Heavy Metal Transporter in Arabidopsis Enhances Resistance to and Decreases Uptake of Heavy Metals   (2003)

Large parts of agricultural soil are contaminated with lead (Pb) and cadmium (Cd). Although most environments are not heavily contaminated, the low levels observed nonetheless pose a high risk of heavy metal accumulation in the food chain. Therefore, approaches to develop plants with reduced heavy metal uptake are important. Recently, many transgenic plants with increased heavy metal resistance and uptake of heavy metals were developed for the purpose of phytoremediation. However, to reduce heavy metal in the food chain, plants that transfer less heavy metals to the shoot are required. We tested whether an Escherichia coli gene, ZntA, which encodes a Pb(II)/Cd(II)/Zn(II) pump, could be useful for developing plants with reduced heavy metal content. Yeast cells transformed with this gene had improved resistance to Pb(II) and Cd(II). In Arabidopsis plants transformed with ZntA, ZntA was localized at the plasma membrane and improved the resistance of the plants to Pb(II) and Cd(II). The shoots of the transgenic plants had decreased Pb and Cd content. Moreover, the transgenic protoplasts showed lower accumulation of Cd and faster release of preloaded Cd than wild-type protoplasts. These results show that a bacterial transporter gene, ZntA, can be functionally expressed in plant cells, and that that it may be useful for the development of crop plants that are safe from heavy metal contamination.
A 3.8mW 8b 1GS/s 2b/cycle interleaving SAR ADC with compact DAC structure (2012)

An 8b 1GS/s ADC is presented that interleaves two 2b/cycle SARs. To enhance speed and save power, the prototype utilizes segmentation switching and custom-designed DAC array with high density in a low parasitic layout structure. It operates at 1GS/s from 1V supply without interleaving calibration and consumes 3.8mW of power, exhibiting a FoM of 24fJ/conversion step. The ADC occupies an active area of 0.013mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> in 65nm CMOS including on-chip offset calibration.
Magnetic head incorporating a glass composition of barium oxide and phosphorus pentoxide (1990)

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Novel Methodology for the Preparation of 5-Substituted Tetrahydro[2,3-D]pyrimidines (1998)

Abstract A convenient, concise route for the preparation of tetrahydropyrido[2,3-d]pyrimidines functionalized at the 5-position is presented starting from acyclic aldehydes. Key steps involve a high yielding Knoevenagel condensation, 1,4 conjugate addition with an allylcuprate and a pyrimidine annulation using guanidine hydrochloride. An improved synthesis of the starting aldehyde, ethyl 4-propalbenzoate is presented.
Chiral grating in optical fiber (2004)

A novel means of implementing periodicity into a glass fiber, which allows for polarization as well as wavelength selectivity is investigated. Three types of polarization sensitive chiral fiber gratings are studied: (1) chiral long-period gratings (CLPGs) which resonantly couple core modes to copropagating cladding optical modes, (2) nonresonant chiral intermediate-period gratings (CIPGs) which scatter light out of the core, and (3) resonant chiral short-period gratings (CSPGs) which reflect light within the fiber core. Each of these gratings interacts only with circularly polarized light with the same handedness as the grating and freely transmits light of the orthogonal polarization.
The magnetooptic bubble display (1977)

The various factors that affect the properties of magneto-optic (M/O) bubble displays which use bismuth substituted iron garnets are discussed. A composite bias magnet-ferrite drive coil assembly is described which allows optical access to the display chip. The drive coils required 300 mW to produce an in-plane field of 30 Oe when operated at 10 kHz, and the bias field was uniform to ± 1.5% over an area of radius equal to 1/10 that of the bias magnet. Also discussed is the brightness and heating of the display. A screen brightness of 160 candelas/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> is possible using a X20 projection lens, and the temperature rise of the display chip could be less than 1°C if adequate heat sinking were used. Finally a prototype hand-held display is described which contains a 1.3 k bit capacity display chip. Examples of characters written into that chip are given.
Document Filtering using Semantic Information from a Machine Readable Dictionary (1993)

Large scale information retrieval systems need to refine the flow of documents which will receive further fine-grain analysis to those documents with a high potential for relevance to their respective users. This paper reports on research we have conducted into the usefulness of semantic codes from a machine readable dictionary for filtering large sets of incoming documents for their broad subject appropriateness to a topic of interest. The Subject Field Coder produces a summary-level semantic representation of a text's contents by tagging each word in the document with the appropriate, disambiguated Subject Field Code (SFC). The within-document SFCs are normalized to produce a vector of the SFCs representing that document's contents. Queries are likewise represented as SFC vectors and then compared to SFC vectors of incoming documents, which are then ranked according to similarity to the query SFC vector. Only those documents whose SFC vectors exhibit a predetermined degree of similarity to the query SFC vector are passed to later system components for more refined representation and matching. The assignment of SFCs is fully automatic, efficient and has been empirically tested as a reasonable approach for ranking documents from a very large incoming flow of documents. We report details of the implementation, as well as results of an empirical testing of the Subject Field Coder on fifty queries.
(R-(Z))-4-amino-3-chloro-2-pentenedioic acid, a new antibiotic. Fermentation, isolation and characterization. (1984)

A new unsaturated glutamic acid analog, 4-amino-3-chloro-2-pentenedioic acid ( ACPA ) was isolated from a fermentation broth produced by a strain of Streptomyces. ACPA has a very narrow antibacterial spectrum, which is virtually limited to Micrococcus luteus.
Encrypted optical memory using double-random phase encoding (1997)

We describe an encrypted optical memory that uses double-random phase encoding at the input plane and the Fourier plane. This technique allows the images to be stored as independent white complex stationary processes. Experimental results and computer simulations are presented.
A novel optical touch switch structure (2004)

This paper proposes for the first time a novel optical touch switch structure based on the use of light total internal reflection (TIR) concept. Key features include ease of implementation, prevention of the light beam incident on the user's eyes, and ability to accept both strong and weak mechanical forces from users.
Laser Ignition of Natural Gas Engines Using Fiber Delivery (2005)

A practical impediment to implementation of laser ignition systems has been the open-path beam delivery used in past research. In this contribution, we present the development and implementation of a fiber-optically delivery laser spark ignition system. To our knowledge, the work represents the first demonstration of fiber coupled laser ignition (using a remote laser source) of a natural gas engine. A Nd:YAG laser is used as the energy source and a coated hollow fiber is used for beam energy delivery. The system was implemented on a single-cylinder of a Waukesha VGF 18 turbo charged natural gas engine and yielded consistent and reliable ignition. In addition to presenting the design and testing of the fiber delivered laser ignition system, we present initial design concepts for a multiplexer to ignite multiple cylinders using a single laser source, and integrated optical diagnostic approaches to monitor the spark ignition and combustion performance.
Localization and Trajectory Tracking of an Autonomous Spherical Rolling Robot Using IMU and Odometry (2015)

Pose estimation and trajectory tracking of a spherical rolling robot is a complex problem owing to kinematics and dynamics of the system and the constraint of not being able to add range sensors like ultrasonic or infrared distance sensors on the robot. The pose estimate for the robot under study, needs to be derived purely using inertial measurement unit (IMU) and odometry from analog wheel encoders, which in turn include high uncertainties. Adding to this, the system kinematic and dynamic model to accurately predict the behavior is quite complex. In this paper we present a simplified kinematic model, sensor filtering techniques and the control strategy adopted to locate and navigate the robot to a desired waypoint autonomously. A filter block provides clean heading output from the IMU and incremental pulses from an analog wheel encoder; the pose estimator uses heading and incremental pulses to calculate its position according to the system kinematic model. A pure-pursuit algorithm generates left & right wheel velocities to keep the robot on a commanded waypoint, using the robot kinematic model and localization data. The validity of our kinematic model and performance of our waypoint tracking are verified with the ground truth using a motion capture system and onboard sensors, where the application domain is bio-inspired, micro (small scale) robotics.
Coactivation and Corepression in Transcriptional Regulation by Steroid/Nuclear Hormone Receptors (1998)

Transcriptional regulation by steroid/nuclear receptors is the central theme of hormone action that controls key aspects of cell differentiation, development, and homeostasis. The molecular mechanisms of gene activation and repression by the receptors have been investigated extensively in recent years. Particularly, several new proteins involved in this signaling pathway have been identified, cloned, and demonstrated to modulate transcription in concert with nuclear receptors. In the absence of hormone, unliganded receptors interact with a family of transcriptional corepressors, including SMRT and N-CoR, which target histone deacetylases to establish a condensed and repressed chromatin structure. Upon hormone binding, the corepressor complex is replaced by a coactivator complex, containing SRC1/TIF2/RAC3 and CBP/p300, which target histone acetyltransferases to generate a transcriptionally accessible chromatin structure. These studies initiate a new era in the history of hormone research and provide novel entry points for understanding the mechanisms of transcriptional regulation by steroid/nuclear receptors.
Preparation of superconducting thin films of transition-metal interstitial compounds (1969)

Sputtering technique forms transition-metal interstitial compounds into superconducting thin films having transition temperatures similar to those of the bulk materials. Since the magnetic-field and current-carrying properties of the films exceed those of the bulk materials, they may have applications other than in tunneling devices.
Detecting DGA malware using NetFlow (2015)

Botnet detection systems struggle with performance and privacy issues when analyzing data from large-scale networks. Deep packet inspection, reverse engineering, clustering and other time consuming approaches are unfeasible for large-scale networks. Therefore, many researchers focus on fast and simple botnet detection methods that use as little information as possible to avoid privacy violations. We present a novel technique for detecting malware using Domain Generation Algorithms (DGA), that is able to evaluate data from large scale networks without reverse engineering a binary or performing Non-Existent Domain (NXDomain) inspection. We propose to use a statistical approach and model the ratio of DNS requests and visited IPs for every host in the local network and label the deviations from this model as DGA-performing malware. We expect the malware to try to resolve more domains during a small time interval without a corresponding amount of newly visited IPs. For this we need only the NetFlow/IPFIX statistics collected from the network of interest. These can be generated by almost any modern router. We show that by using this approach we are able to identify DGA-based malware with zero to very few false positives. Because of the simplicity of our approach we can inspect data from very large networks with minimal computational costs.
A multifunctional prosthesis control system based on time series identification of EMG signals using microprocessors. (1977)

This paper describes a real-time system for separation among several limb functions, in order to provide multifunctional control of an upper-limb prosthesis for above-elbow amputees. The system employs microprocessor hardware and is based on identification of voluntary myoelectric signals resulting from isometric contractions of the musculature of the residual limb, and on subsequent discrimination of these signals for control of the several degrees of motion of the prosthesis. The system requires only one to two electrode sites. (Contrary to the usual placement of electrode pairs directly over specific muscle bellies, to eliminate crosstalk, we prefer to place our electrode pair between muscles so as to acquire the different weakly-correlated signals associated with each of several different voluntary functions). The system satisfies the various practical constraints of weight, volume, and speed, as arise in practical prostheses. Preliminary amputee tests on the system have resulted in an 85 percent success rate using 8-bit double-precision micro-computer hardware.
Content-aware network data compression using joint memorization and clustering (2013)

Recent studies have shown the existence of considerable amount of packet-level redundancy in the network flows. Since application-layer solutions cannot capture the packet-level redundancy, development of new content-aware approaches capable of redundancy elimination at the packet and sub-packet levels is necessary. These requirements motivate the redundancy elimination of packets from an information-theoretic point of view. For efficient compression of packets, a new framework called memory-assisted universal compression has been proposed. This framework is based on learning the statistics of the source generating the packets at some intermediate nodes and then leveraging these statistics to effectively compress a new packet. This paper investigates both theoretically and experimentally the memory-assisted compression of network packets. Clearly, a simple source cannot model the data traffic. Hence, we consider traffic from a complex source that is consisted of a mixture of simple information sources for our analytic study. We develop a practical code for memory-assisted compression and combine it with a proposed hierarchical clustering to better utilize the memory. Finally, we validate our results via simulation on real traffic traces. Memory-assisted compression combined with hierarchical clustering method results in compression of packets close to the fundamental limit. As a result, we report a factor of two improvement over traditional end-to-end compression.
Novel Engineered Peptides of a Phage Lysin as Effective Antimicrobials against Multidrug-Resistant Acinetobacter baumannii (2016)

Acinetobacter baumannii is a Gram-negative bacterial pathogen responsible for a range of nosocomial infections. The recent rise and spread of multidrug-resistant A. baumannii clones has fueled a search for alternative therapies, including bacteriophage endolysins with potent antibacterial activities. A common feature of these lysins is the presence of a highly positively charged C-terminal domain with a likely role in promoting outer membrane penetration. In the present study, we show that the C-terminal amino acids 108 to 138 of phage lysin PlyF307, named P307, alone were sufficient to kill A. baumannii (>3 logs). Furthermore, P307 could be engineered for improved activity, the most active derivative being P307SQ-8C (>5-log kill). Both P307 and P307SQ-8C showed high in vitro activity against A. baumannii in biofilms. Moreover, P307SQ-8C exhibited MICs comparable to those of levofloxacin and ceftazidime and acted synergistically with polymyxin B. Although the peptides were shown to kill by disrupting the bacterial cytoplasmic membrane, they did not lyse human red blood cells or B cells; however, serum was found to be inhibitory to lytic activity. In a murine model of A. baumannii skin infection, P307SQ-8C reduced the bacterial burden by ∼2 logs in 2 h. This study demonstrates the prospect of using peptide derivatives from bacteriophage lysins to treat topical infections and remove biofilms caused by Gram-negative pathogens.