gebhart/patrepeval huggingface dataset:
Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels (2015)

Clostridium phytofermentans was isolated from forest soil and is distinguished by its capacity to directly ferment plant cell wall polysaccharides into ethanol as the primary product, suggesting that it possesses unusual catabolic pathways. The objective of the present study was to understand the molecular mechanisms of biomass conversion to ethanol in a single organism, Clostridium phytofermentans, by analyzing its complete genome and transcriptome during growth on plant carbohydrates. The saccharolytic versatility of C. phytofermentans is reflected in a diversity of genes encoding ATP-binding cassette sugar transporters and glycoside hydrolases, many of which may have been acquired through horizontal gene transfer. These genes are frequently organized as operons that may be controlled individually by the many transcriptional regulators identified in the genome. Preferential ethanol production may be due to high levels of expression of multiple ethanol dehydrogenases and additional pathways maximizing ethanol yield. The genome also encodes three different proteinaceous bacterial microcompartments with the capacity to compartmentalize pathways that divert fermentation intermediates to various products. These characteristics make C. phytofermentans an attractive resource for improving the efficiency and speed of biomass conversion to biofuels.
Rapid speaker adaptation in eigenvoice space (2000)

This paper describes a new model-based speaker adaptation algorithm called the eigenvoice approach. The approach constrains the adapted model to be a linear combination of a small number of basis vectors obtained offline from a set of reference speakers, and thus greatly reduces the number of free parameters to be estimated from adaptation data. These "eigenvoice" basis vectors are orthogonal to each other and guaranteed to represent the most important components of variation between the reference speakers. Experimental results for a small-vocabulary task (letter recognition) given in the paper show that the approach yields major improvements in performance for tiny amounts of adaptation data. For instance, we obtained 16% relative improvement in error rate with one letter of supervised adaptation data, and 26% relative improvement with four letters of supervised adaptation data. After a comparison of the eigenvoice approach with other speaker adaptation algorithms, the paper concludes with a discussion of future work.
A high performance phase change memory with fast switching speed and high temperature retention by engineering the Ge<inf>x</inf>Sb<inf>y</inf>Te<inf>z</inf> phase change material (2011)

Phase change memory has long suffered from conflicting material properties between switching speed and thermal stability. This study explores the engineering of GeSbTe ternary alloys along an isoelectronic tie line and the Ge/Sb <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> Te <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> tie line with the hope of finding a high performance material. Our efforts resulted in a new material that considerably outperforms the conventional GST-225. The switching speed is similar to undoped GST-225, with ∼ 30% lower reset current, and nearly 100°C higher T <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</inf> , thus much better thermal stability. The promising properties of this new material are demonstrated in a 128Mb chip and tested both at wafer level and as packaged dies. These devices showed 1E8 cycling endurance and withstood 190 °C testing.
Detection of atomic hydrogen and deuterium by resonant three-photon ionization (1978)

Resonantly enhanced three-photon ionization spectroscopy is employed for the detection of ground-state atomic hydrogen and deuterium. Concentrations as low as 4×109 atoms/cm3 in the presence of 1017 atoms/cm3 of buffer gas are detected with an implicit time resolution of less than 10 nsec. A useful dynamic range of at least 4×104 is demonstrated and saturation of the ionization in a 2×10−4-cm3 focal volume is observed. The presence of H can easily be distinguished from that of D and the three-dimensional spatial distribution of H or D can be determined.
Nanocrystalline hydroxyapatite enhances osteoblast function (2003)

Osteoblast (bone-forming cells) adhesion, proliferation and formation of calcium-containing mineral deposits is enhanced on ceramics (such as alumina and titania) of grain sizes less than 100 nm. Conventional hydroxyapatite (HA), the major inorganic constitutent of physiological bone, has been shown to enhance osteoblast function. The present in vitro study, the first of its kind, investigated osteoblast function (specifically, adhesion and proliferation) on nanocrystalline (that is, grain sizes less than 100 nm) HA. Osteoblast adhesion as well as proliferation were significantly (p<0.01) greater on nanocrystalline (50 nm grain size) than on conventional (250 nm grain size) HA at all time periods tested. Since enhanced osteoblast function undoubtedly contributes to greater biomaterial bonding to juxtaposed bone (an event that will aid in the clinical success of orthopaedic/dental implants), the improved cytocompatibility properties of nanocrystalline HA should be considered when designing biomaterials of the future.
Highly Efficient Method for Introducing Successive Multiple Scarless Gene Deletions and Markerless Gene Insertions into the <i>Yersinia pestis</i> Chromosome (2008)

An efficient two-step recombination method for markerless gene deletion and insertion that can be used for repetitive genetic modification in Yersinia pestis was developed. The method combines lambda Red recombination and counterselective screening (sacB gene) and can be used for genetic modification of Y. pestis to construct live attenuated vaccines.
Sensitivity improvement of a 1-um ladar system incorporating an opticalfiber preamplifier [also Erratum 33(12)4108(Dec1994)] (1993)

In an effort to increase the SNR of a continuous wave, 1-μm all solid state ladar system, a rare-earth-doped optical fiber amplifier is investigated as a preamplifier for ladar return signals. The experimental system is detailed and a theoretical analysis of the fiber amplifier's effect on both heterodyne and direct detection schemes is provided. Beginning with the optical powers incident on the detector, the signal and noises are analyzed, through the detector electronics, to predict the SNR. The SNR is then plotted as a function of the return signal power, and a SNR threshold is defined to determine a minimum detectable signal power. The return signals required to attain the SNR threshold are then compared for four cases: direct detection with and without the fiber amplifier and heterodyne detection with and without the fiber amplifier. For the direct detection scheme considered, our results predict a sensitivity increase of 20.6 dB with the addition of the fiber amplifier, yet for heterodyne detection the predicted sensitivity increase is only 3.1 dB.
Lyssaviruses and rabies: current conundrums, concerns, contradictions and controversies (2017)

Lyssaviruses are bullet-shaped, single-stranded, negative-sense RNA viruses and the causative agents of the ancient zoonosis rabies. Africa is the likely home to the ancestors of taxa residing within the Genus <i>Lyssavirus</i>, Family <i>Rhabdoviridae</i>. Diverse lyssaviruses are envisioned as co-evolving with bats, as the ultimate reservoirs, over seemingly millions of years. In terms of relative distribution, overt abundance, and resulting progeny, rabies virus is the most successful lyssavirus species today, but for unknown reasons. All mammals are believed to be susceptible to rabies virus infection. Besides reservoirs among the Chiroptera, meso-carnivores also serve as major historical hosts and are represented among the canids, raccoons, skunks, mongooses, and ferret badgers. Perpetuating as a disease of nature with the mammalian central nervous system as niche, host breadth alone precludes any candidacy for true eradication. Despite having the highest case fatality of any infectious disease and a burden in excess of or comparative to other major zoonoses, rabies remains neglected. Once illness appears, no treatment is proven to prevent death. Paradoxically, vaccines were developed more than a century ago, but the clear majority of human cases are unvaccinated. Tens of millions of people are exposed to suspect rabid animals and tens of thousands succumb annually, primarily children in developing countries, where canine rabies is enzootic. Rather than culling animal populations, one of the most cost-effective strategies to curbing human fatalities is the mass vaccination of dogs. Building on considerable progress to date, several complementary actions are needed in the near future, including a more harmonized approach to viral taxonomy, enhanced de-centralized laboratory-based surveillance, focal pathogen discovery and characterization, applied pathobiological research for therapeutics, improved estimates of canine populations at risk, actual production of required vaccines and related biologics, strategies to maximize prevention but minimize unnecessary human prophylaxis, and a long-term, realistic plan for sustained global program support to achieve success in disease control, prevention, and elimination.
Application of Single Molecule Detection to DNA Sequencing and Sizing (1993)

Abstract We are developing a laser‐based technique for the rapid sequencing of 40‐kb or larger fragments of DNA at a rate of 100 to 1000 bases per second. Our approach relies on fluorescent labeling of the bases in a single fragment of DNA, attachment of this labeled DNA fragment to a support, movement of the supported DNA into a flowing sample stream, and detection of the individual, fluorescently labeled bases by laser‐induced fluorescence as they are cleaved from the DNA fragment by an exonuclease. The ability to sequence large fragments of DNA will reduce significantly the amount of subcloning and the number of overlapping sequences required to assemble megabase segments of sequence information. We are also applying our sensitive fluorescence detection to sizing of DNA fragments. Large, fluorescently stained restriction fragments of lambda phage DNA are sized by passing individual fragments through a focused, continuous‐wave laser beam in an ultrasensitive flow cytometer at a rate of ∼60 fragments per second. The size of the fluorescence burst emitted by each stained fragment as it passes through the laser beam is measured in one millisecond. We have demonstrated flow cytometric sizing of DNA fragments in a ∼0.1‐pg sample of a restriction digest of lambda DNA in 164 seconds with sizing accuracy better than 98%.
Microfabricated thermal modulator for comprehensive two-dimensional micro gas chromatography: design, thermal modeling, and preliminary testing (2010)

In comprehensive two-dimensional gas chromatography (GC x GC), a modulator is placed at the juncture between two separation columns to focus and re-inject eluting mixture components, thereby enhancing the resolution and the selectivity of analytes. As part of an effort to develop a microGC x microGC prototype, in this report we present the design, fabrication, thermal operation, and initial testing of a two-stage microscale thermal modulator (microTM). The microTM contains two sequential serpentine Pyrex-on-Si microchannels (stages) that cryogenically trap analytes eluting from the first-dimension column and thermally inject them into the second-dimension column in a rapid, programmable manner. For each modulation cycle (typically 5 s for cooling with refrigeration work of 200 J and 100 ms for heating at 10 W), the microTM is kept approximately at -50 degrees C by a solid-state thermoelectric cooling unit placed within a few tens of micrometres of the device, and heated to 250 degrees C at 2800 degrees C s(-1) by integrated resistive microheaters and then cooled back to -50 degrees C at 250 degrees C s(-1). Thermal crosstalk between the two stages is less than 9%. A lumped heat transfer model is used to analyze the device design with respect to the rates of heating and cooling, power dissipation, and inter-stage thermal crosstalk as a function of Pyrex-membrane thickness, air-gap depth, and stage separation distance. Experimental results are in agreement with trends predicted by the model. Preliminary tests using a conventional capillary column interfaced to the microTM demonstrate the capability for enhanced sensitivity and resolution as well as the modulation of a mixture of alkanes.
<title>Dynamic rate-control method for real-time video streaming over the Internet</title> (2002)

This paper proposes a dynamic bit rate control method for real-time video streaming over the Internet. It is based on the feedback mechanism using RTCP(RTP control protocol) which provides network congestion parameters such as inter-arrival jitter, fraction lost, and round trip time by SR (Sender Report)/RR( Receiver Report). The proposed method firstly detects network congestion, then the network state is categorized into four congestion levels by analyzing the network congestion parameters such as jitter and packet loss derived from RR packets arriving periodically, then the coding bit rate is determined according to the current congestion level. The proposed dynamic bit rate control mechanism has also been implemented in the MPEG-4 video transmission system. The experimental results show that the proposed method can successfully suppress the packet loss and control the coding bit rate appropriately even for a congested network which does not guarantee QoS such as bandwidth resources and/or maximum delay.
Far-Infrared p-Ge Laser: Pulse Dynamics and Repetition-Rate Enhancement (1996)

A significant repetition-rate increase is found using copper heat sinks in a Voigt-configured permanent-magnet p-Ge laser with wavelengths near 200 μm. Studies of time resolved emission reveal unusual pulse dynamics which depend on the magnitude and duration of the applied electric field. Spectral content, free-space beam profiles, and polarization are essentially independent of these temporal effects. Lasing persists above 10 K, raising the possibility of a practical p-Ge laser without need for liquid helium as a coolant.
New technologies to detect and monitor Phytophthora ramorum in plant, soil, and water samples (2013)

The focus of our research efforts has been to develop methods to quickly identify plants, soil, and water samples infested with Phytophthora spp., and to rapidly confirm the findings using novel isothermal DNA technologies suitable for field use. These efforts have led to the development of a rapid Immunostrip® that reliably detects virtually all strains of Phytophthora spp. in plant, soil, and water samples within minutes. Two formats of a rapid molecular method were developed to accurately confirm the results. These methods are able to specifically identify P. ramorum in crude extracts prepared from distilled water, rain water, pond water, sandy soil and loamy soil at concentrations as low as 125pg/ul of sample. This detection paradigm allows for accurate monitoring of the location and spread of P. ramorum, giving field personnel the necessary tools required for mitigation actions with confidence.
Design of a small residual dispersion fiber and a corresponding dispersion compensating fiber for dense wavelength division multiplexing systems (2003)

We present the designs of a small residual dispersion fiber (SRDF) and a corresponding dispersion-compensating fiber (DCF), where the dispersion slopes of these fibers are so adjusted that a small length of the DCF will approximately compensate the accumulated dispersion in SRDF simultaneously at all wavelengths in the range of 1530 to 1565 nm [gain window (C-band) of erbium-doped fiber amplifiers]. The maximum values of the effective dispersion and the slope of the effective dispersion in the wavelength range of 1530 to 1565 nm are ∼0.08 ps/ km nm and ∼0.01 ps/km nm 2 , respectively.
Two Stereoinduction Events in One C−H Activation Step: A Route towards Terphenyl Ligands with Two Atropisomeric Axes (2018)

Herein we disclose the synthesis of original chiral scaffolds-ortho-orientated terphenyls presenting two atropisomeric Ar-Ar axes. These unusual structures were built up by using the C-H activation approach, and remarkably, both chiral axes were controlled with excellent stereoselectivity in a single transformation. During the reaction, not only does atroposelective functionalization of a biaryl precursor occur to establish one stereogenic axis, but an unprecedented atropo-stereoselective C-H arylation also takes place to generate the second stereogenic element. These enantiomerically pure ortho-terphenyls show an original tridimensional structure and thus constitute a unique foundation for building up a library of enantiomerically pure bidentate ligands, such as the new ligands S/N-Biax and diphosphine BiaxPhos.
The imaging performance of a LaBr<sub>3</sub>-based PET scanner (2009)

A prototype time-of-flight (TOF) PET scanner based on cerium-doped lanthanum bromide [LaBr(3) (5% Ce)] has been developed. LaBr(3) has a high light output, excellent energy resolution and fast timing properties that have been predicted to lead to good image quality. Intrinsic performance measurements of spatial resolution, sensitivity and scatter fraction demonstrate good conventional PET performance; the results agree with previous simulation studies. Phantom measurements show the excellent image quality achievable with the prototype system. Phantom measurements and corresponding simulations show a faster and more uniform convergence rate, as well as more uniform quantification, for TOF reconstruction of the data, which have 375 ps intrinsic timing resolution, compared to non-TOF images. Measurements and simulations of a hot and cold sphere phantom show that the 7% energy resolution helps to mitigate residual errors in the scatter estimate because a high energy threshold (>480 keV) can be used to restrict the amount of scatter accepted without a loss of true events. Preliminary results with incorporation of a model of detector blurring in the iterative reconstruction algorithm not only show improved contrast recovery but also point out the importance of an accurate resolution model of the tails of LaBr(3)'s point spread function. The LaBr(3) TOF-PET scanner demonstrated the impact of superior timing and energy resolutions on image quality.
Serum Calcitonin Precursors in Sepsis and Systemic Inflammation<sup>1</sup> (1998)

High serum levels of the calcitonin (CT) prohormone, procalcitonin (pro-CT), and its component peptides occur in systemic inflammation and sepsis. Using two different assays, we undertook a prospective study to determine the utility of serum precalcitonin peptides (pre-CT) as markers in this condition. Twenty-nine patients meeting criteria for the systemic inflammatory response syndrome were studied daily in two intensive care units. Sera were collected, and APACHE II scores were determined until recovery or death. All patients had markedly elevated serum pre-CT. Prognostically, peak values were the most important. The highest values portended mortality, and a lower level could be ascertained below which all patients survived. Peak pre-CT levels were significantly higher in patients with infection documented by blood cultures than in those patients with no documented infection from any source (P < 0.05). Mature CT remained normal or only moderately elevated. Compared with the serum pre-CT levels, receiver operating characteristic curve analysis revealed that the APACHE II scores, although more cumbersome, were better overall predictors of mortality. Thus, pre-CT is an important serum marker for systemic inflammatory response syndrome and is predictive of outcome. It also provides data concerning the presence of severe infection and may prove to be clinically useful for proactive patient care.
Optimal tradeoff between efficiency and Jain's fairness index in resource allocation (2012)

In this paper, we study tradeoff policies between efficiency and the Jain's fairness index of the benefits received by M users in general resource allocation scenarios. Analyzing the commonly-used α-fair tradeoff policy, it is shown that, except for the case of M =2 users, this policy does not necessarily achieve the optimal Efficiency-Jain tradeoff. In particular, it is shown that, when the number of users M >;2, the gap between the efficiency achieved by the α-fair and the optimal Efficiency-Jain tradeoff policy can be unbounded, for the same Jain's index. Finding the optimal Efficiency-Jain tradeoff for arbitrary set of admissible benefits is generally difficult. To alleviate this difficulty, we derive sufficient conditions, which, when satisfied by the set of admissible benefits, lead to efficiently computable optimal tradeoff and benefit vectors. Numerical results for a typical communication network scenario are provided to confirm analytical findings.
Antiplatelet α‐Methylidene‐γ‐butyrolactones: Synthesis and evaluation of quinoline, flavone, and xanthone derivatives (1996)

Abstract As a continuation of our previous studies on the synthesis and antiplatelet activity of coumarin derivatives of α‐methylidene‐γ‐butyrolactones, certain quinoline, flavone, and xanthone derivatives were synthesized and evaluated for antiplatelet activity against thrombin (Thr)‐, arachidonic acid (AA)‐, collagen (Col)‐, and platelet‐activating factor (PAF)‐induced aggregation in washed rabbit platelets. These compounds were synthesized from quinolin‐8‐ol, flavon‐7‐ol, and xanthon‐3‐ol, respectively, via alkylation and Reformatsky ‐type condensation ( Schemes 1–3 ). By the comparison with comparison with coumarin α‐methylidene‐γ‐butyrolactone 3a , flavone and xanthone derivatives, 3b and 3c , respectively, are more selective in which only AA‐ and collagen‐induced aggregation are strongly inhibited. Most of the quinoline derivatives ( 9a–e ) exhibited broad‐spectrum antiplatelet activities.
Risk-Aware Framework for Activating and Deactivating Policy-Based Response (2010)

With the growth of modern systems and infrastructures, automated and intelligent response systems become the holy grail of the security community. An interesting approach proposes to use dynamic access control policies to specify response policies for such systems. These policies should been forced when an ongoing attack, that threatens the monitored system, is detected. However, existing work do not present a clear methodology to specify the Response policies. In particular, the deactivation issue is not yet tackled. In this paper, we first present how to specify response policies. Second, a risk-aware framework is proposed to activate and deactivate response policies. Hence, the success likelihood of the threat, and the cumulative impact of both of the threat and the response, are all considered.
Discovery of a diaminoquinoxaline benzenesulfonamide antagonist of HIV-1 Nef function using a yeast-based phenotypic screen (2013)

Our findings demonstrate the utility of a yeast-based growth reversion assay for the identification of small molecule Nef antagonists. Inhibitors of Nef function discovered with this assay, such as DQBS, may complement the activity of current antiretroviral therapies by enabling immune recognition of HIV-infected cells through the rescue of cell surface MHC-I.