gebhart/patrepeval huggingface dataset:
The primary structure of branched‐chain α‐oxo acid dehydrogenase from <i>Bacillus subtilis</i> and its similarity to other α‐oxo acid dehydrogenases (1993)

The bfmB mutant of Bacillus subtilis requires branched short-chain carboxylic acids for growth because the organism is known to be defective in branched-chain alpha-oxo acid dehydrogenase. The DNA in the region of bfmB has now been cloned and sequenced, and the gene has been analyzed. The results show that there are three open reading frames in the area, each of which is preceded by a putative ribosome binding site, and the last of which is followed by a putative transcription termination site with inverted repeats. The amino acid sequences deduced by analysis of the reading frames are highly similar (with 32-49% identity) to the E1 alpha, El beta and E2 components of pyruvate, 2-oxoglutarate and branched-chain alpha-oxo acid dehydrogenases from different sources. The thiamin diphosphate binding, putative subunit interaction and phosphorylation sites of the E1 alpha of four reported branched-chain alpha-oxo acid dehydrogenases from different sources are very similar to those of the first open reading frame (E1 alpha) of bfmB. A similar result is also obtained with the lipoyl-binding site (lysine) and its domain of the E2 component of alpha-oxo acid dehydrogenases from different sources. The present data, along with the reported biochemical data, lead to the conclusion that bfmB encodes a branched-chain alpha-oxo acid dehydrogenase, which is composed of E1 alpha, E1 beta and E2 genes. This organization is identical to that of the 2-oxoglutarate dehydrogenase in B. subtilis.
The search for improved in-vitro systems should not be ignored: embryo co-culture may be one of them (1993)

Journal Article The search for improved in-vitro systems should not be ignored: embryo co-culture may be one of them Get access Ariff Bongso, Ariff Bongso 1 Department of Obstetrics & Gynaecology, National University of Singapore, National University HospitalLower Kent Ridge Road, Singapore 0511 1To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Chui-Yee Fong, Chui-Yee Fong Department of Obstetrics & Gynaecology, National University of Singapore, National University HospitalLower Kent Ridge Road, Singapore 0511 Search for other works by this author on: Oxford Academic PubMed Google Scholar Soon-Chye Ng, Soon-Chye Ng Department of Obstetrics & Gynaecology, National University of Singapore, National University HospitalLower Kent Ridge Road, Singapore 0511 Search for other works by this author on: Oxford Academic PubMed Google Scholar Shan Ratnam Shan Ratnam Department of Obstetrics & Gynaecology, National University of Singapore, National University HospitalLower Kent Ridge Road, Singapore 0511 Search for other works by this author on: Oxford Academic PubMed Google Scholar Human Reproduction, Volume 8, Issue 8, 1 August 1993, Pages 1155–1160, https://doi.org/10.1093/oxfordjournals.humrep.a138219 Published: 01 August 1993
Mixed signal integrated circuits based on GaAs HEMTs (1998)

During the past five years numerous mixed signal integrated circuits (ICs) have been designed, processed, and characterized based on our 0.2 /spl mu/m gate length AlGaAs/GaAs quantum well HEMT technology. Utilizing the inherent advantages of the AlGaAs/GaAs material system, optical, analog, microwave, and digital functions have been integrated monolithically. Examples are a chip set for 40 Gb/s optoelectronic data transmission systems, 15 and 34 GHz PLLs, a 35 GHz phase shifter for phased array antenna applications, a 2-kb ROM with subnanosecond access time for direct digital signal synthesis, and a 6-k gate array.
Control of surface-emitting laser diodes by modulating the distributed Bragg mirror reflectivity: Small-signal analysis (1993)

Cavity-loss control of surface emitting distributed Bragg reflector lasers by electro-optic modulation of the Bragg mirror reflectivity is shown to be more efficient at high frequencies than the conventional control by current modulation. Combining both means of control offers additional possibilities, such as the elimination of relaxation oscillations and the achievement of a pure frequency-modulation regime.
Adaptive heterogeneous coordinated beamforming algorithm in LTE-advanced systems (2013)

The impact of downlink co-channel interference (CCI) is increasingly highlighted in heterogeneous networks (Het-Nets) where the macrocell base stations (MBSs) and low-power nodes share the same spectrum resource. In this paper, we focus on mitigation of downlink CCI from MBS to picocells, which are severely affected, through the application of coordinated beam forming (CBF) technique. The closed-form expressions of average throughput for an arbitrary user with and without using CBF are derived, where a trade-off is observed between suppressing the CCI to picocells and increasing the throughput of the macrocell. Furthermore, to maximize the HetNet throughput, two adaptive algorithms are proposed to determine the CBF set of picocells based on the instantaneous throughput and the average throughput, respectively. The analysis of average throughput is validated by simulation results, and total throughput of the HetNet is improved by use of our proposed algorithms.
Physical characteristics of setting of acrylic bone cements (1974)

Abstract An investigation was conducted to determine the general physical characteristics of self‐curing acrylic resin systems in terms of their potential utilization in total hip arthroplasty. Exothermic temperature, working and setting times were monitored with thermocouples placed in acrylic masses insulated via a Teflon mold. Mechanical strengths were run in an Instron testing machine. The same trends were noted in all systems studied. As thickness or mass increased, the maximum temperature and the setting time increased. As the powder to liquid ratio increased (thereby relatively less liquid), the maximum temperature, set times and dough times decreased, while the working time was essentially unaffected. As the ambient temperature decreased, the maximum temperature decreased while the dough, working and setting times increased. The mechanical strengths of the systems cured at one atmosphere are low compared to high temperature and pressure curing. Flowability of the materials decreases quickly as final set time is approached. Although trends are similar in many self‐curing acylic systems minors shifts in complex proprietary compositions can produce a wide span or working and setting times. Because the surgical team controls such parameters as the mass employed, the amount of liquid introduced, and the ambient temperature it is important that they continuously re‐evaluate their handling procedures particularly if new acrylic cements would be introduced.
Modeling and Simulation of Annular Pressure Buildup (APB) Mitigation Using Rupture Disk (2016)

Abstract Manufactured to burst/collapse at a specific pressure difference and installed in the casing wall, a rupture disk is a common device used to mitigate annular pressure buildup (APB) and to protect casing strings. This paper focuses on the modeling and simulation of the effects of a rupture disk burst/collapse event on APB in casing/tubing annuli. After the rupture disk bursts (or collapses), fluid will move through the open disk from one annulus to another, resulting in changing pressures. In this work, three pressure balance models (piston model, miscible fluid model, and immiscible fluid model) were established to calculate the annulus fluid pressure and volume changes after the rupture disk opens. The piston model, assuming no fluid exchange between two annuli, provides the simplest solution. It is accurate if the two annuli contain nearly identical fluids. The miscible fluid model is intended for annuli with the same fluid type, but with different density values. The immiscible fluid model is intended for annuli with different immiscible fluid types, such as oil-based mud in the internal annulus and water-based mud in the outer annulus. The pressure balance models were implemented and integrated into a commercial casing and tubing design software platform. A numerical approach was used for trapped and connected annuli; an analytical approach was used for connected annuli with at least one ventilation or leakoff point. This combination provides optimized simulation performance and accuracy. When multiple annuli are connected with open rupture disks, global pressure equilibrium is reached through iterations of handling two connected APB regions at a time. In a case study in which the casing ballooning effect is negligible, numerical simulation results were found to be consistent with the results of analytical calculation; the difference is within 0.1%. The application of the rupture disk for APB management was also demonstrated in another case study using field data. The simulation results show that the rupture disk is a viable and cost-effective option for APB management.
Antimicrobial Lipopolypeptides Composed of Palmitoyl Di- and Tricationic Peptides: <i>In Vitro</i> and <i>in Vivo</i> Activities, Self-Assembly to Nanostructures, and a Plausible Mode of Action (2008)

Antimicrobial lipopeptides are produced nonribosomally in bacteria and fungi during cultivation. They are composed of a cationic or an anionic peptide covalently bound to a specifically modified aliphatic chain. Most of the peptidic moieties have complex cyclic structures. Here we report that conjugation of a palmitic acid to the N-terminus of very short cationic di- and tripeptides composed of all l- and d, l-amino acids endowed them with potent antimicrobial activities. Interestingly, cell specificity was determined by the sequence of the short peptidic chain. Palmitoyllysine served as a control and was inactive toward all microorganisms tested. Replacing an l-amino acid with its d-enantiomer did not affect the activity of the corresponding lipopeptides. Importantly, selected lipopeptides were also potent in vivo in a mouse model of Candida albicans infection. Bacterial leakage experiments and negative staining electron microscopy suggest that their mode of action involves permeation and disintegration of the microorganism's membrane, similar to many long antimicrobial peptides and lipopeptides. Interestingly, each lipopeptide assembled in solution into a nanostructure with a unique morphology which could partially explain differences in their biological activity. Besides adding important information on the parameters necessary for antimicrobial lipopeptides to kill microorganisms, the simple composition of these minilipopeptides and their diverse cell specificities make them attractive candidates for various applications.
Assisted GPS solution in cellular networks (2006)

The ‘Wireless Enhanced 911’ rules, which were issued in 1996, state that the position of a mobile device should be sent to Public Safety Answering Point (‘PSAP’) once a 9-1-1 call takes place from it. The rules imposed the cellular carriers to integrate a technology into their networks so that the mobile device location can be transferred once a 9-1-1 call is made. One of the chosen technologies was the Global Positioning System (GPS). The solution suggests integrating a GPS receiver into every cellular device. But the GPS receiver, as a stand alone solution, has some major performance limitations in regards to the Wireless Enhanced 911 requirements. The Assisted GPS (A-GPS) technology improves the GPS receiver performances. It reduces the time it takes the receiver to calculate its location. It also enhances the receiver’s reception sensitivity and improves the calculated position accuracy. With the A-GPS technology, the GPS receiver solution becomes compatible with the rules requirements. Two of the four large wireless carriers in the U.S. had chosen the A-GPS as their location solution in their networks. The A-GPS technology became an important part of the cellular industry. The intention of the thesis is to explore the A-GPS solution and to show its necessity in today’s GPS-based solutions. The following aspects are reviewed in the thesis – how the A-GPS solution works, how it improves the GPS receiver performances, the technology that is being used to implement it, and how it integrates to the cellular network. Another A-GPS related aspect that is reviewed in the thesis is the integration of location-based applications in cellular networks. The location-based applications service is a new and growing market in the cellular industry as a result of the deployed location solutions.
Extracting object silhouettes by perceptual edge grouping (2002)

This paper presents a qualitative approach to extract object silhouettes based on principles of perceptual organization. A physical edge of object, i.e., silhouette, is modeled as a set of sequentially connected generic segments partitioned at perceptually significant points of the edge. Each segment consists of a series of proximate edge pixels which satisfy a descriptive property of the grouping. An object silhouette is reconstructed by combining the edge segments together.
Device driver reuse via virtual machines (2009)

Device drivers constitute a significant portion of an operating system's source code. The effort to develop a new driver set is a sobering hurdle to the pursuit of novel operating system ventures. A practical solution is to reuse drivers, but this can contradict design goals in a new operating system. We offer a new approach to device-driver reuse, with a focus on promoting novel operating-system construction, which insulates the new operating system from the invariants of the reused drivers, while also addressing development effort. Our solution runs the drivers along with their original operating systems inside virtual machines, with some minor reuse infrastructure added to the driver's operating system to interface with the rest of the system. This approach turns the drivers into de-privileged applications of the new operating system, which separates their architectures and reduces cross-influences, and improves system dependability. Virtual machines help reuse drivers, but they also penalize performance. The known solution for improving virtual machine performance, para-virtualization, modifies the operating system to run on a hypervisor, which has an enormous cost: substantial development effort, and abandonment of many of virtualization's benefits such as modularity. These costs contradict our goals for driver reuse: to reduce development effort, and to easily reuse from a variety of operating systems. Thus we introduce a new approach to constructing virtual machines: pre-virtualization. Our solution combines the performance of para-virtualization with the modularity of traditional virtual machines. We still modify the operating system, but according to a set of principles called soft layering that preserves modularity, and via automation which reduces implementation costs. With pre-virtualization we can easily reuse device drivers. We describe our driver-reuse approach applied to a real system: we run virtual machines on the L4Ka::Pistachio microkernel, with reused Linux drivers. We include an evaluation and demonstrate that we achieve throughput comparable to the native Linux drivers, but with moderately higher CPU and memory utilization. Additionally, we describe how to apply pre-virtualization to multiple hypervisor environments. We include an evaluation of pre-virtualization, and demonstrate that it achieves comparable performance to para-virtualization for both the L4Ka::Pistachio and Xen hypervisors, with modularity.
Constructing a three-dimensional graphene structure via bonding layers by ion beam irradiation (2019)

In recent years, the use of the multilayer graphene sheets has been considered more than the single-layer due to the cost-effectiveness and the possibility of mass production. But this type of graphene has some kind of structural weakness due to the weak physical link between its layers. Then, in order to strengthen, many structural modifications are proposed by various techniques to manage the mechanisms at interlayer distances. In this study, the focused ion beam irradiation method has been examined to cross-link and strengthen multi-layer graphene sheets with the help of the molecular dynamics simulation technique. Then, uniaxial and transverse tensile tests were performed to check the mechanical properties of obtained cross-linked multilayer graphene sheets. The results of this research can be considered for the creation of a new class of graphene structures. Such structures could be implemented as a membrane in water desalination or as a storage foam in hydrogen or carbon dioxide storage.
A Concise Synthesis of Topsentin A and Nortopsentins B and D (2000)

[reaction: see text] A concise synthesis of topsentin A (R(1) = R(2) = H) and nortopsentins B (R(1) = Br, R(2) = H) and D (R(1) = R(2) = H) is described from oxotryptamine 5 via reduction of acyl cyanide 4. Regiospecific bromination of 3-cyanoindole afforded 6-bromo-3-cyanoindole (10) as the major product.
Prenatal Exposure to Nicotine Impairs Performance of the 5-Choice Serial Reaction Time Task in Adult Rats (2011)

Cigarette smoking is associated with a wide variety of adverse reproductive outcomes, including increased infant mortality and decreased birth weight. Prenatal exposure to tobacco smoke, of which nicotine is a major teratogenic component, has also been linked to the acceleration of the risk for different psychiatric disorders, including conduct disorder and attention deficit hyperactivity disorder (ADHD). Whether this increased risk is influenced by the direct effects of gestational nicotine exposure on the developing fetus remains uncertain. In this study we provide experimental evidence for the effects of prenatal nicotine exposure on measures of attention and impulsivity in adult male rats. Offspring of females exposed during pregnancy to 0.06 mg/ml nicotine solution as the only source of water (daily consumption: 69.6±1.4 ml/kg; nicotine blood level: 96.0±31.9 ng/ml) had lower birth weight and delayed sensorimotor development measured by negative geotaxis, righting reflex, and grip strength. In the 5-choice serial reaction time test, adult rats showed increased numbers of anticipatory responses and omissions errors, more variable response times, and lower accuracy with evidence of delayed learning of the task demands when the 1 s stimulus duration was introduced. In contrast, prenatal nicotine exposure had no effect on exploratory locomotion or delay-discounting test. Prenatal nicotine exposure increased expression of the D5 dopamine receptor gene in the striatum, but did not change expression of other dopamine-related genes (DRD4, DAT1, NR4A2, and TH) in either the striatum or the prefrontal cortex. These data suggest a direct effect of prenatal nicotine exposure on important aspects of attention, inhibitory control, or learning later in life.
Complete Protection against Severe Acute Respiratory Syndrome Coronavirus-Mediated Lethal Respiratory Disease in Aged Mice by Immunization with a Mouse-Adapted Virus Lacking E Protein (2013)

Zoonotic coronaviruses, including the one that caused severe acute respiratory syndrome (SARS), cause significant morbidity and mortality in humans. No specific therapy for any human coronavirus is available, making vaccine development critical for protection against these viruses. We previously showed that recombinant SARS coronavirus (SARS-CoV) (Urbani strain based) lacking envelope (E) protein expression (rU-ΔE) provided good but not perfect protection in young mice against challenge with virulent mouse-adapted SARS-CoV (MA15). To improve vaccine efficacy, we developed a second set of E-deleted vaccine candidates on an MA15 background (rMA15-ΔE). rMA15-ΔE is safe, causing no disease in 6-week-, 12-month-, or 18-month-old BALB/c mice. Immunization with this virus completely protected mice of three ages from lethal disease and effected more-rapid virus clearance. Compared to rU-ΔE, rMA15-ΔE immunization resulted in significantly greater neutralizing antibody and SARS-CoV-specific CD4 and CD8 T cell responses. After challenge, inflammatory cell infiltration, edema, and lung destruction were decreased in the lungs of rMA15-ΔE-immunized mice compared to those in rU-ΔE-immunized 12-month-old mice. Collectively, these results show that immunization with a species-adapted attenuated coronavirus lacking E protein expression is safe and provides optimal immunogenicity and long-term protection against challenge with lethal virus. This approach will be generally useful for development of vaccines protective against human coronaviruses as well as against coronaviruses that cause disease in domestic and companion animals.
Imabing mass spectrometry and molecular network guided genome mining of microbial systems (2012)

In this lecture I will describe the latest mass spectrometry based tools and genome mining approaches we have developed to study the metabolic exchange of microbes.1–8 The goal for visualizing molecules microbes and bridging this with genome mining is to enable the functional translation to understand their molecular language. The presentation will highlight microbial imaging mass spectrometry, the development of mass spectrometry based genome mining tools, including the utility of peptidogenomics and glycogenomics tools that will be explained by Brad Moore in the next talk, in conjunction with live colony mass spectrometry, molecular networking, molecular dendrograms, and ambient mass microscopy to study metabolic exchange and ecology of microbial communities for applications in agriculture, diagnostics and therapeutic discovery. Finally, perhaps most significantly, this lecture will introduce the development of a molecular “Genbank” and its search engines that are being co-developed with the Bandeira laboratory at the NIH Center for Computational Mass Spectrometry that will merge natural product analysis with modern genome mining.
Full-scale self-emissive blue and green microdisplays based on GaN micro-LED arrays (2011)

Micro-size light emitting diode (μLED) arrays based on III-nitride semiconductors have emerged as a promising technology for a wide range of applications. If InGaN μLED arrays can be integrated on to Si complementary metal-oxide-semiconductor (CMOS) substrates for active driving, these devices could play crucial roles in ultra-portable products such as next generation pico-projectors, as well as in emerging fields such as biophotonics and optogenetics. Here we present a demonstration of, and methods for, creating a highresolution solid-state self-emissive microdisplay based on InGaN/GaN semiconductors. An energy efficient active drive scheme is accomplished by integrating micro-emitter arrays with CMOS active matrix drivers that are flip-chip bonded together via indium metal bumps.