gebhart/patrepeval huggingface dataset:
Structural Correlates of the Temperature Sensitive Phenotype Derived from Saturation Mutagenesis Studies of CcdB (2008)

Temperature sensitive (ts) mutants are widely used to reversibly modulate protein function in vivo and to understand functions of essential genes. Despite this, little is known about the protein structural features and mechanisms responsible for generating a ts phenotype. Also, such mutants are often difficult to isolate, limiting their use. In this study, a library consisting of 75% of all possible single-site mutants of the 101-residue, homodimeric Escherichia coli toxin CcdB was constructed. Mutants were characterized in terms of their activity at two different temperatures and at six different expression levels. Of the total of 1430 single-site mutants that were screened, 231 (16%) mutants showed a ts phenotype. The bulk of these consisted of 120 ts mutants found at all 22 buried sites and 34 ts mutants at all seven active site residues involved in binding DNA gyrase. Of the remaining ts mutants, 16 were found at residues in van der Waals contact with active site residues, 36 were at partially buried residues, and 30 resulted from introduction of Pro. Thus virtually all ts mutants could be rationalized in terms of the structure of the native protein and without knowledge of folding pathways. Data were analyzed to obtain insights into molecular features responsible for the ts phenotype and to outline structure- and sequence-based criteria for designing ts mutants of any globular protein. The criteria were validated by successful prediction of ts mutants of three other unrelated proteins, TBP, T4 lysozyme, and Gal4.
MR spectroscopy using multi-ring surface coils (1999)

A spatially uniform B(1)-field is preferred for MR imaging and spectroscopy. Unfortunately, volume coils are sometimes unavailable, or do not provide adequate RF power or SNR for some applications. In quantitative MRS, mean metabolite concentration cannot be evaluated when the coil response is nonuniform, unless an assumption is made concerning the metabolite spatial distribution. It is well known that standard single-loop surface coils, although offering high SNR characteristics, have poor B(1) homogeneity. New multi-ring surface coils are proposed which produce a locally uniform B(1) field, with sensitivity and power requirements comparable to those of standard surface coils. MR spectroscopy using two and three-ring versions of this "local volume coil" result in spatial localization essentially identical to that obtained with a volume coil but with much improved RF power and SNR characteristics. When compared to standard surface coils, the multi-ring coil offers much improved water suppression and localization, as well as reduced outer voxel contamination, with only a small loss in SNR and moderate increase in SAR. In summary, the multi-ring coil operates midway between the volume coil and the standard surface coil, retaining the most advantageous properties of both. Magn Reson Med 42:655-664, 1999. Published 1999 Wiley-Liss, Inc.
An Ultra-Low Power Always-On Keyword Spotting Accelerator Using Quantized Convolutional Neural Network and Voltage-Domain Analog Switching Network-Based Approximate Computing (2019)

An ultra-low power always-on keyword spotting (KWS) accelerator is implemented in 22nm CMOS technology, which is based on an optimized convolutional neural network (CNN). To reduce the power consumption while maintaining the system recognition accuracy, we first perform a bit-width quantization method on the proposed CNN to reduce the data/weight bit width required by the hardware computing unit without reducing the recognition accuracy. Then, we propose an approximate computing architecture for the quantized CNN using voltage-domain analog switching network based multiplication and addition unit. Implementation results show that this accelerator can support 10 keywords real time recognition under different noise types and SNRs, while the power consumption can be significantly reduced to 52 μW.
Factors Affecting Ionic Liquids Based Removal of Anionic Dyes from Water (2007)

Liquid--liquid extraction with imidazolium based ionic liquids--[C4mim][PF6], [C6miml][PF6], [C6mim[BF4], and [C8mim][PF6--is proposed for removal of anionic dyes including methyl orange, eosin yellow, and orange G from aqueous solutions. The effects of extraction time, pH of aqueous phase, structure of the ionic liquids, temperature, and KCl concentration on the extraction efficiencies have been studied. Extraction efficiencies of dyes were strongly affected by the pH of the aqueous phase. Under the optimized pH condition, 85-99% of methyl orange, almost 100% eosin yellows, and 69% of orange G in tested water samples were transferred into the ionic liquids in a single extraction. Extraction efficiency for a given dye was found to increase with increasing temperature and increasing alkyl chain length of cation of the ionic liquids. Presence of a small amount of KCl in the aqueous phase did not considerably improve the extraction efficiency of the dyes. Thermodynamic studies revealed that the extraction process was driven by hydrophobic interaction of the anionic dyes and the ionic liquids.
The effects of calcium on smooth muscle mechanics and energetics. (1987)

In smooth muscle isometric force, shortening velocity, the ATP utilization under isometric conditions, and tension cost are all functions of calcium. This suggests that both cross bridge number and cycle rate are dependent on calcium. On the other hand, the series elastic component does not exhibit a significant dependence on calcium under conditions in which Vus can be increased with little change in Fo. And although the data is not as extensive, the efficiency in working producing contractions is not a strong function of calcium. Our challenge is to fit these mechanical and energetic data into a mechanism which fits the ever growing and controversial body of evidence on the biochemical basis for the action of calcium on the contractile apparatus. At present the most striking feature is the observation that calcium can control the velocity in a manner which is independent of isometric force and efficiency. This would appear to favor a mechanism in which calcium directly affected cross bridge cycle rate in the absence of an internal load.
Automatic Construction Algorithm for Multi-class Support Vector Machines with Binary Tree Architecture (2006)

Multi-class support vector machines with binary tree architecture (SVM-BTA) have the fastest decision-making speed in the existing multi-class SVMs. But SVM-BTA usually has bad classification capability. According to internal characteristics of feature samples, this paper uses resemblance coefficient method to construct automatically binary tree to incorporate multiple binary SVMs. The multi-class SVMs with constructed binary tree have good classification capability and fast decision-making speed. Experimental results of yeast protein localization site prediction and radar emitter signal recognition show that the introduced multi-class SVMs with binary tree architectures are superior to several popular multi-class SVMs including one-against-all, one-against-one, directed acyclic graph, bottom-up binary tree and several classification methods in the recent literatures. Key words: Support vector machines, Resemblance coefficient, Radar emitter, Binary tree architecture
Cancer-Related Axonogenesis and Neurogenesis in Prostate Cancer (2008)

This is the first description of cancer-related neurogenesis and its putative regulatory mechanism.
Limiting the number of dirty cache lines (2009)

Caches often employ write-back instead of write-through, since write-back avoids unnecessary transfers for multiple writes to the same block. For several reasons, however, it is undesirable that a significant number of cache lines will be marked dirty. Energy-efficient cache organizations, for example, often apply techniques that resize, reconfigure, or turn off (parts of) the cache. In such cache organizations, dirty lines have to be written back before the cache is reconfigured. The delay imposed by these write-backs or the required additional logic and buffers can significantly reduce the attained energy savings. A cache organization called the clean/dirty cache (CD-cache) is proposed that combines the properties of write-back and write-through. It avoids unnecessary transfers for recurring writes, while restricting the number of dirty lines to a hard limit. Detailed experimental results show that the CD-cache reduces the number of dirty lines significantly, while achieving similar or better performance. We also use the CD-cache to implement cache decay. Experimental results show that the CD-cache attains similar or higher performance than a normal decay cache, while using a significantly less complex design.
Perforin expression in cytotoxic lymphocytes from patients with hemophagocytic lymphohistiocytosis and their family members (2002)

Mutations in the perforin gene have been described in some patients with hemophagocytic lymphohistiocytosis (HLH), but the role of perforin defects in the pathogenesis of HLH remains unclear. Four-color flow cytometric analysis was used to establish normal patterns of perforin expression for control subjects of all ages, and patterns of perforin staining in cytotoxic lymphocytes (natural killer [NK] cells, CD8(+) T cells, CD56(+) T cells) from patients with HLH and their family members were studied. Eleven unrelated HLH patients and 19 family members were analyzed prospectively. Four of the 7 patients with primary HLH showed lack of intracellular perforin in all cytotoxic cell types. All 4 patients showed mutations in the perforin gene. Their parents, obligate carriers of perforin mutations, had abnormal perforin-staining patterns. Analysis of cytotoxic cells from the other 3 patients with primary HLH and remaining family members had normal percentages of perforin-positive cytotoxic cells. On the other hand, the 4 patients with Epstein-Barr virus-associated HLH typically had depressed numbers of NK cells but markedly increased proportions of CD8(+) T cells with perforin expression. Four-color flow cytometry provides diagnostic information that, in conjunction with evidence of reduced NK function, may speed the identification of life-threatening HLH in some families and direct further genetic studies of the syndrome.
Providing convincing evidence for psychological influences on health constitutes a tremendous scientific challenge (2018)

Lazarus comments on the problems of providing "unequivocal" demonstrations of the effects of psychosocial factors on health. Because I find it difficult to demonstrate anything "unequivocally," I search for something a little less ambitious--convincing evidence.
The effects of exogenous lactate and pyruvate on the recovery of coronary flow in the rat heart after ischaemia (1993)

Exogenous substrates modify the recovery of flow after ischaemia. In the presence of exogenous lactate, severe disturbances of flow are already obvious after 30 minutes of ischaemia in the inner layers of the left ventricle. Exogenous pyruvate delays impairment of flow in the inner layers compared with exogenous lactate.
Towards a robust rescue network: Wireless communication is the choice (2017)

This paper examines the limitations of conventional communication systems during disaster recovery and discusses alternative wireless solutions that can assist with post-disaster relief operations. Factors such as network infrastructure, deployment requirements, localization and tracking architecture, and autonomous control are considered. One of the biggest challenges is that conventional communications infrastructure collapses or becomes out of order after a major disaster. Wireless communication could offer an opportunity to rapidly restore communications which is critical for minimizing loss of life and property. It can reduce deployment time and ensure the timely flow of information to meet the immediate needs of first responders. Since wired networks act as a backhaul to most wireless systems, the collapse of their infrastructure such as towers may severely limit their use. Consequently, infrastructure-less, self-organizing, internally-powered, and easily deployable networks could be the method of choice. However, the lack of sufficient coverage range in such networks may hinder initial efforts to collect, manage, and circulate information. This problem is made worse by the operational constraints associated with the disaster operations area. While wireless service is available in open areas, in partially obstructed or indoor environments, wireless service may not be available or the quality of radio signal may be quite coarse. As an example, factors such as disaster ruins, multipath, reflection and attenuation collectively work to decrease the accuracy of tracking and localization systems in estimating the position of a person trapped under mine or tunnel rubble. In this paper, we review the most recent studies that address the aforementioned challenges and the technical solutions proposed to establish a rapid and cost-effective rescue system.
Bufferbloat (2011)

Networks without effective AQM may again be vulnerable to congestion collapse.
SNAP-Tag Technology Optimized for Use in Entamoeba histolytica (2013)

Entamoeba histolytica is a protozoan parasite responsible for invasive intestinal and extraintestinal amebiasis. The pathology of amebiasis is still poorly understood, which can be largely attributed to lack of molecular tools. Here we present the optimization of SNAP-tag technology via codon optimization specific for E. histolytica. The resultant SNAP protein is highly expressed in amebic trophozoites, and shows proper localization when tagged with an endoplasmic reticulum retention signal. We further demonstrate the capabilities of this system using super resolution microscopy, done for the first time in E. histolytica.
Conestoga launch vehicles (1988)

Several major applications for commercial and government markets have developed recently which will make use of small satellites. A launch vehicle designed specifically for small satellites brings many attendant benefits. Space Services Incorporated has developed the Conestoga family of launch vehicles to meet the needs of five major markets: low orbiting communication satellites, positioning satellites, earth sensing satellites, space manufacturing prototypes, and scientific experiments. The Conestoga provides low cost, rapid schedules, one-stop shopping, flexible launch sites, multiple satellite deplo
An adeno-associated viral vector transduces the rat hypothalamus and amygdala more efficient than a lentiviral vector (2010)

This study showed that AAV1 vectors are better tools to overexpress or knockdown genes in the lateral hypothalamus and amygdala of adult rats, since more cells can be transduced with AAV1 than with LV vectors and the titer of AAV1 vectors can easily be increased to transduce the area of interest.
Directly diode-pumped high-energy Ho:YAG oscillator (2012)

We report on the high-energy laser operation of an Ho:YAG oscillator resonantly pumped by a GaSb-based laser diode stack at 1.9 μm. The output energy was extracted from a compact plano-concave acousto-optically Q-switched resonator optimized for low repetition rates. Operating at 100 Hz, pulse energies exceeding 30 mJ at a wavelength of 2.09 μm were obtained. The corresponding pulse duration at the highest pump power was 100 ns, leading to a maximum peak power above 300 kW. Different pulse repetition rates and output coupling transmissions of the Ho:YAG resonator were studied. In addition, intracavity laser-induced damage threshold measurements are discussed.
Transient vitamin B5 starving improves mammalian cell homeostasis and protein production (2020)

Maintaining a metabolic steady state is essential for an organism's fitness and survival when confronted with environmental stress, and metabolic imbalance can be reversed by exposing the organism to fasting. Here, we attempted to apply this physiological principle to mammalian cell cultures to improve cellular fitness and consequently their ability to express recombinant proteins. We showed that transient vitamin B5 deprivation, an essential cofactor of central cellular metabolism, can quickly and irreversibly affect mammalian cell growth and division. A selection method was designed that relies on mammalian cell dependence on vitamin B5 for energy production, using the co-expression of the B5 transporter SLC5A6 and a gene of interest. We demonstrated that vitamin B5 selection persistently activates peroxisome proliferator-activated receptors (PPAR), a family of transcription factors involved in energy homeostasis, thereby altering lipid metabolism, improving cell fitness and therapeutic protein production. Thus, stable PPAR activation may constitute a cellular memory of past deprivation state, providing increased resistance to further potential fasting events. In other words, our results imply that cultured cells, once exposed to metabolic starvation, may display an improved metabolic fitness as compared to non-exposed cells, allowing increased resistance to cellular stress.
Reversal of Pacific ciguatoxin-1B effects on myelinated axons by agents used in ciguatera treatment (2022)

Ciguatera fish poisoning is a distinctive form of ichthyosarcotoxism characterised mainly by gastrointestinal and neurological disturbances. The ciguatoxins, responsible for this poisoning, are complex polyethers produced by toxic strains of the dinoflagellate Gambierdiscus toxicus. These toxins are increased to dangerous levels for man during their transmission through herbivorous and carnivorous fish, various species being contaminated. The known molecular target of ciguatoxins is the voltage-gated Na+ channel. During the action of these toxins, the permanent opening of channels, at the resting membrane potential, produces a continuous entry of Na+ ions in excitable cells causing a marked increase in membrane excitability and in cellular volume. To precise the neurocellular basis of the efficacy of some agents used in clinical and traditional treatments of ciguatera, their effects were studied on frog myelinated axons exposed to Pacific ciguatoxin-1B (CTX-1B). During the action of this toxin, the increase in axonal volume and membrane excitability was reversed by lidocaine (a local anaesthetic), by CaCl2 and by hyperosmotic external solutions (containing D-mannitol, sucrose tetramethylammonium chloride). The CTX-1B induced hyperexcitability of the membrane was also reversed by extracts of Argusia argentea leaves or Davallia solida rhizomes, used traditionally in New Caledonia. It is concluded that the various agents studied are able to counteract the neurocellular effects of CTX-1B in myelinated axons. These results are of particular interest since they provide a scientific basis to understand the beneficial action of therapeutic agents used in the treatment of ciguatera fish poisoning.
Duplex Molecular Assay Intended for Point-of-Care Diagnosis of Influenza A/B Virus Infection (2013)

Early diagnosis and management of influenza virus infection directly correlates with the effectiveness in disease control. Current molecular influenza virus tests were designed for use in diagnostic testing facilities, where sophisticated equipment and highly trained technicians are available. A longer turnaround time for the centralized testing than when testing near the sample source could delay the initiation of medical intervention, thereby reducing the efficacy of antiviral treatment. The new assay, the SAMBA (simple amplification-based assay) Flu duplex test, is a dipstick-based molecular assay developed to provide a simple, accurate, and cost-effective solution for the diagnosis of influenza A/B viruses intended for near-patient testing. The test presents an alternative format of influenza virus molecular testing that utilizes isothermal amplification and visual detection of nucleic acid on a test strip. The entire test procedure (extraction, amplification, and detection) is integrated into an enclosed semiautomated system. Analytically, the SAMBA Flu duplex test detects 95 and 85 copies of viral genomes for influenza A and B viruses, respectively, with no cross-reactivity observed against other common respiratory pathogens. The clinical performance was established by blind testing of 328 nasal/throat and nasopharyngeal swab specimens from the United Kingdom and Belgium and comparing the results with the quantitative reverse transcription-PCR method routinely used in two public health laboratories. The SAMBA Flu duplex test showed a clinical sensitivity and specificity of 100% and 97.9% for influenza virus A and 100% and 100% for influenza virus B. The test provides a new technology that could facilitate simple and timely identification of influenza virus infection, potentially resulting in more efficient control measures.
Energy considerations in a micromagnetic hysteresis model and the Preisach model (2010)

Finding the relations between the microstructural material parameters and the macroscopic hysteresis behavior is indispensable in the design of ferromagnetic materials with minimal (hysteresis) losses. Micromagnetic hysteresis simulations enable a rigorous and structured investigation of these relations since in the numerical model each material parameter can be altered independently. This paper describes a procedure to extract the Preisach distribution function, quantifying the macroscopic hysteresis properties, from micromagnetic simulations incorporating the materials’ microstructure. Furthermore, the instantaneously added, stored and dissipated energy while running through the hysteresis loop as described in the macroscopic Preisach model and in the micromagnetic hysteresis model are compared, evidencing a very good agreement. Moreover, using the micromagnetic model, the energy rearrangements between the different micromagnetic interaction terms is studied at each time point of the hysteresis loop. It is concluded that the micromagnetic hysteresis model is a valuable tool in the study of hysteresis properties and loss mechanisms in ferromagnetic materials.
Fundamentals and applications of microsphere resonator circuits (2009)

Microsphere resonator circuits have emerged as a technology allowing integration of cavities in all three spatial dimensions (3D) in chip-scale structures. This presentation is devoted to fabrication, optical properties and applications of mesoscale structures formed by microspheres. The ldquomesophotonicsrdquo properties of such structures stem from two properties of individual dielectric microspheres with dimensions comparable to the wavelength of light: (i) high quality factors of whispering gallery modes (WGMs) and (ii) subwavelength dimensions of the focused spots termed ldquophotonic nanojetsrdquo. Traditionally, the resonant optical transport properties of such structures have been described by a tight binding approximation for photonic atoms. Recently we showed that the WGM-based transport in 2D and 3D systems with disorder can be understood on the basis of analogy with a percolation theory. Along with these resonant coupling effects very interesting properties of periodical focusing of light were observed in long chains of spheres. These properties were explained due to formation of nanojet-induced modes with small propagation losses. At the device level, these studies stimulate developing designs where coupled cavities are applied to developing narrow spectral filters, delay lines, arrayed-resonator light emitting devices, tight focusing micro-probes, sensors, and compact spectrometers.