gebhart/patrepeval huggingface dataset:
Understanding the Influence of Codon Translation Rates on Cotranslational Protein Folding (2014)

Protein domains can fold into stable tertiary structures while they are synthesized by the ribosome in a process known as cotranslational folding. If a protein does not fold cotranslationally, however, it has the opportunity to do so post-translationally, that is, after the nascent chain has been fully synthesized and released from the ribosome. The rate at which a ribosome adds an amino acid encoded by a particular codon to the elongating nascent chain can vary significantly and is called the codon translation rate. Recent experiments have illustrated the profound impact that codon translation rates can have on the cotranslational folding process and the acquisition of function by nascent proteins. Synonymous codon mutations in an mRNA molecule change the chemical identity of a codon and its translation rate without changing the sequence of the synthesized protein. This change in codon translation rate can, however, cause a nascent protein to malfunction as a result of cotranslational misfolding. In some situations, such dysfunction can have profound implications; for example, it can alter the substrate specificity of an ABC transporter protein, resulting in patients who are nonresponsive to chemotherapy treatment. Thus, codon translation rates are crucial in coordinating protein folding in a cellular environment and can affect downstream cellular processes that depend on the proper functioning of newly synthesized proteins. As the importance of codon translation rates makes clear, a necessary aspect of fully understanding cotranslational folding lies in considering the kinetics of the process in addition to its thermodynamics. In this Account, we examine the contributions that have been made to elucidating the mechanisms of cotranslational folding by using the theoretical and computational tools of chemical kinetics, molecular simulations, and systems biology. These efforts have extended our ability to understand, model, and predict the influence of codon translation rates on cotranslational protein folding and misfolding. The application of such approaches to this important problem is creating a framework for making quantitative predictions of the impact of synonymous codon substitutions on cotranslational folding that has led to a novel hypothesis regarding the role of fast-translating codons in coordinating cotranslational folding. In addition, it is providing new insights into proteome-wide cotranslational folding behavior and making it possible to identify potential molecular mechanisms by which molecular chaperones can influence such behavior during protein synthesis. As we discuss in this Account, bringing together these theoretical developments with experimental approaches is increasingly helping answer fundamental questions about the nature of nascent protein folding on the ribosome.
A high-speed quantum random number generator prototype (2013)

We present a high-speed real-time quantum random number generator prototype by measuring the quantum phase noise of a laser. The simplicity and robustness of our design suggest that it is readily commercialized for practical applications.
<title>Surface-micromachined counter-meshing gears discrimination device</title> (1998)

This paper discusses the design, fabrication and testing of a surface micromachined Counter-Meshing Gears discrimination device which functions as a mechanically coded lock. A 24 bit code is input to unlock the device. Once unlocked, the device provides a path for an energy or information signal to pass through the device. The device is designed to immediately lock up if any portion of the 24 bit code is incorrect. The motivation for the development of this device is based on occurrences referred to as High Consequence Events. A High Consequence Even is an event where an inadvertent operation of a system could result in the catastrophic loss of life, property, or damage to the environment.
Identification of a functional mutation in pp32r1 (ANP32C) (2004)

No mutations or polymorphisms have previously been reported in pp32r1 (ANP32C; GenBank: AF008216.1). pp32r1 is part of the highly conserved ANP32 family, some of whose members are associated with control of histone acetylation, mRNA stability, and specialized forms of apoptosis. Although 87.6% identical at the protein level, pp32r1 is functionally distinct from pp32 (ANP32A) in its failure to suppress oncogenesis in in vitro transformation systems and its tumorigenicity in in vivo assays. The present study found that pp32r1 expression levels vary among human tumor cell lines, with the highest levels found in prostatic adenocarcinoma cell lines. pp32r1 also appears to be polymorphic at nucleotide g.4520 and nucleotide g.4664 in human tobacco-associated oral mucosal lesions, human fibroblast cell lines, and several carcinoma cell lines. PC-3 human prostatic adenocarcinoma cells likewise appear to be polymorphic at these loci, but additionally contain a g.4870T>C transversion mutation. The mutation results in a p.Tyr140His substitution, which lies in a functionally important region of the molecule. In the PC-3 prostate cancer line, the mutation is either homozygous, or hemizygous accompanied by loss of heterozygosity. ACHN cells stably transfected with pp32r1 containing this mutation showed a markedly increased rate of growth. The pp32r1 mutation could thus be causally associated with the neoplastic growth properties of PC-3, and be of potential clinical significance.
Donor-Acceptor Complexes in Copolymerization. XVIII. Alternating Diene–Dienophile Copolymers. 1. Conjugated Diene–Maleic Anhydride Copolymers through Radical-Catalyzed Polymerization (1971)

Abstract The copolymerization of isoprene, butadiene, and other conjugated dienes with maleic anhydride was readily initiated in polar solvents by conventional free radical catalysts, including peroxides, hydroperoxides, and azobisisobutyronitrile, at high concentrations or at temperatures at which the catalyst had a half-life of 1 hr or less and the total reaction time was 0.5-1 hr. Decreasing the reaction temperature or the rate of catalyst addition resulted in increased yields of Diels-Alder adduct and decreased yields of copolymer. The molecular weight decreased as the temperature increased. Dioxane and tetrahydrofuran peroxides, obtained by the passage of oxygen or UV irradiation in air, also initiated the copolymerization. The soluble diene-maleic anhydride copolymers were equimolar and alternating, had [n] 0.1-6 (cyclohexanone) and contained 75-95% 1,4 structure according to ozonolysis, titration with IC1 and NMR. The IR spectrum of the butadiene–maleic anhydride copolymer indicated 75-95% cis-1,4, 5-20% trans-1,4 and 0-5% 1,2-vinyl unsaturation. The proposed mechanism of polymerization involves a donor-acceptor (diene-dienophile) interaction generating a ground-state charge transfer complex which is readily converted to the cyclic adduct. Under the influence of radicals the ground-state complex is transformed into an excited complex which undergoes polymerization. High concentrations of radicals are necessary to generate polymerizable excited complexes in competition with adduct formation.
Evidence that DNA damage triggers interleukin 10 cytokine production in UV-irradiated murine keratinocytes. (1996)

UV irradiation interferes with the induction of T cell-mediated immune responses, in part by causing cells in the skin to produce immunoregulatory cytokines. Recent evidence implicates UV-induced DNA damage as a trigger for the cascade of events leading to systemic immune suppression in vivo. However, to date, there has been no direct evidence linking DNA damage and cytokine production in UV-irradiated cells. Here we provide such evidence by showing that treatment of UV-irradiated murine keratinocytes in vitro with liposomal T4 endonuclease V, which accelerates the repair of cyclobutylpyrimidine dimers in these cells, inhibits their production of immunosuppressive cytokines, including interleukin 10. Application of these liposomes to murine skin in vivo also reduced the induction of interleukin 10 by UV irradiation, whereas liposomes containing heat-inactivated T4 endonuclease V were ineffective. These results support our hypothesis that unrepaired DNA damage in the skin activates the production of cytokines that down-regulate immune responses initiated at distant sites.
Development of Thermal Fatigue Resistant Austenitic Cast Alloys for High Temperature Engine Exhaust Gas Systems (2003)

As trends of automobile engine exhaust gas temperature are reducing emissions, the material for the exhaust components have been changed from ductile irons to ferritic cast alloys or stainless steel, further to austeniticcast alloys for higher performance engines. The current austenitic alloys, however, have thermal fatigue failure over 1273K. The authors developed excellent thermal fatigue resistant austenitic cast alloys, by investigating the effects of alloying elements on strength and thermal expansion, which correlate with thermal fatigue property. Developed alloys are expected to apply to exhaust components at gas temperatures over 1273K.
Evaluation of a prototype small-animal PET detector with depth-of-interaction encoding (2004)

We report on the evaluation of a prototype small-animal positron emission tomography (PET) detector with depth-of-interaction (DOI) encoding. The detector consisted of an 8/spl times/8 array of scintillator crystals that were read out on the top and bottom by position sensitive avalanche photodiodes (PSAPD). Each scintillator crystal had dimensions of 1.65 mm/spl times/1.65 mm/spl times/22.00 mm, and the array had a pitch of 1.75 mm. The 14/spl times/4 mm PSAPDs were coupled to compact, discrete transimpedance preamplifiers. The DOI response was measured by illuminating the detector module from the side with an electronically collimated fan beam of 511 keV gamma rays. The signals from the corner contacts of the PSAPDs were used to identify the crystal of interaction, and the ratio of the total signals from the two PSAPDs was used to calculate the depth z at which the interaction took place. By stepping the crystal array in the z direction (perpendicular to the fan beam), we were able to determine the DOI resolution for each individual crystal. For measurements made at 10/spl deg/C, the average DOI resolution was better than 3 mm. Energy resolution and timing resolution (versus a fast plastic scintillator coupled to a photomultiplier tube) were made under the same operating conditions. The average energy resolution across the array was 16.6% at 511 keV, and the average timing resolution was 3.9 ns. Importantly, the detector performance was maintained all the way out to the crystals at the edges of the PSAPDs.
Prompt neutrons from photofission and its use in homeland security applications (2010)

Photofission is the process in which a nucleus disintegrates into two daughter products after absorbing a photon. Photofission near threshold in actinides is very similar to spontaneous fission in terms of the number of emitted decay neutrons and their energy distribution. Most of the neutrons are in the ~2 MeV energy range, and can be efficiently detected with liquid scintillator detectors. Thus, Prompt Neutrons from Photofission (PNPF) near threshold can be used as an excellent tool for the detection of actinides. Since the photofission cross section for most fissionable materials drops to near zero for incident photon energies of less than 6 MeV, a source of photons with a higher energy is needed, for example 9 MeV. At this energy interference from (γ, n) processes is minimal. Photon sources in this energy range are well suited for other non-intrusive inspection applications as well as searching for fissionable materials. Passport Systems, Inc. is currently operating a continuous wave (CW) 9 MeV electron accelerator and an array of liquid scintillator detectors to achieve this goal. Pulse shape discrimination (PSD) techniques are used determine the particle type. The remaining neutrons are also filtered through an in-house developed pileup rejection algorithm. The resulting neutron count is compared with the known background to determine the confidence level for possible shielded Special Nuclear Material identification. Initial testing of this system has been performed and the results will be presented. The results show the utility of a CW photon source as well as the ability to fuse the PNPF data with other data to reduce the dose to cargo, or scan times.
Identification of In Vivo-Induced Bacterial Protein Antigens during Human Infection with <i>Salmonella enterica</i> Serovar Typhi (2006)

We applied an immunoscreening technique, in vivo-induced antigen technology (IVIAT), to identify immunogenic bacterial proteins expressed during human infection with Salmonella enterica serovar Typhi, the cause of typhoid fever. We were able to assign a functional classification to 25 of 35 proteins identified by IVIAT. Of these 25, the majority represent proteins with known or potential roles in the pathogenesis of S. enterica. These include proteins implicated in fimbrial structure and biogenesis, antimicrobial resistance, heavy metal transport, bacterial adhesion, and extracytoplasmic substrate trafficking as well as secreted hydrolases. The 10 remaining antigens represent proteins with unknown functions. Of the 35 identified antigens, four had no immunoreactivity when probed with control sera from individuals never exposed to serovar Typhi organisms; these four included PagC, TcfB, and two antigens of unknown function encoded by STY0860 and STY3683. PagC is a virulence factor known to be upregulated in vivo in S. enterica serovar Typhimurium infection of mice. TcfB is the major structural subunit of a fimbrial operon found in serovar Typhi with no homolog in serovar Typhimurium organisms. By examining differential immunoreactivities in acute- versus convalescent-phase human serum samples, we found specific anti-PagC and anti-TcfB immunoglobulin G responses in patients with serovar Typhi bacteremia. Serovar Typhi antigens identified by IVIAT warrant further evaluation for their contributions to pathogenesis, and they may have diagnostic, therapeutic, or preventive uses.
In VivoEffects of Leptin-Related Synthetic Peptides on Body Weight and Food Intake in Female ob/obMice: Localization of Leptin Activity to Domains Between Amino Acid Residues 106–140* (1997)

In C57BL/6J ob/ob mice, a single base mutation of the ob gene in codon 105 results in the replacement of arginine by a premature stop codon and production of a truncated inactive form of leptin. These observations suggest that leptin activity may be localized, at least in part, to domains distal to amino acid residue 104. To investigate this possibility, we synthesized six overlapping peptide amides corresponding to residues 106-167 of leptin, and examined their effects on body weight and food intake in female C57BL/6J ob/ob mice. When compared with vehicle-injected control mice, weight gain by mice receiving 28 daily 1-mg i.p. injections of LEP-(106-120), LEP-(116-130), or LEP-(126-140) was significantly (P < 0.01) reduced with no apparent toxicity. Weight gain by mice receiving LEP-(136-150), LEP-(146-160), or LEP-(156-167) was not significantly different from that of vehicle-injected control mice. The effects of LEP-(106-120), LEP-(116-130), or LEP-(126-140) were most pronounced during the first week of peptide treatment. Within 7 days, mice receiving these peptides lost 12.3%, 13.8%, and 9.8%, respectively, of their initial body weights. After 28 days, mice given vehicle alone, LEP-(136-150), LEP-(146-160), or LEP-(156-167) were 14.7%, 20.3%, 25.0%, and 24.8% heavier, respectively, than they were at the beginning of the study. Mice given LEP-(106-120) or LEP-(126-140) were only 1.8% and 4.2% heavier, respectively, whereas mice given LEP-(116-130) were 3.4% lighter. Food intake by mice receiving LEP-(106-120), LEP-(116-130), or LEP-(126-140), but not by mice receiving LEP-(136-150), LEP-(146-160), or LEP-(156-167), was reduced by 15%. The results of this study indicate 1) that leptin activity is localized, at least in part, in domains between residues 106-140; 2) that leptin-related peptides have in vivo effects similar to those of native leptin; and 3) offer hope for development of peptide analogs of leptin having potential application in human or veterinary medicine.
Packet selection technique for clock recovery over packet networks (2014)

The primary challenge in the design of a clock recovery system for packet networks is to deal with Packet Delay Variations (PDVs) - that is, the variation of the packet transit delays introduced by queuing process in Network Elements (NEs) such as switches and routers. In order to obtain clean signal from recovered clock various techniques are employed to mitigate the effect of the PDVs. One of such mechanisms, referred to as Packet Selection Algorithm (PSA), reduces recovered clock noise variance by filtering incoming timing packets in such a way that only packets complying with predefined selection criteria are passed to the clock recovery algorithm. Since it is a non-trivial task to find optimal PSA criteria analytically using output variance minimization, this paper introduces a probabilistic approach for the PSA optimality analysis. Based on this probabilistic analysis a new packet selection technique is proposed, which outperforms prior art when compared in simulation by means of Time Deviation (TDEV) standardized metric.
Multi-frame super resolution robust to local and global motion (2017)

Super resolution (SR) is to produce a higher resolution image from one or a sequence of low resolution images of a scene. It is essential in medical image analysis as a zooming of a specific area of interest is often required. This paper presents a new multi-frame super resolution (SR) method that is robust to both global and local motion. One of major challenges in multi-frame SR is concurrent global and local motion emergent in the sequence of low resolution images. It poses difficulties in aligning the low resolution images, resulting in artifacts or blurred pixels in the computed high resolution image. We solve the problem via a series of new methods. We first align the upscaled images from bicubic interpolation, and analyze the pixel distribution for the presence of local motion. If local motion is identified, we conduct the local image registration using dense SIFT features. Based on the local registration of images, we analyze pixel locations whose cross-frame variation is high and adaptively select subset of frame pixels in those locations. The adaptive selection of frame pixels is based on a clustering analysis of luminance values of pixels aligned at the same position, such that noise and motion biases are excluded. At the end, a median filter is applied for the selected pixels at each pixel location for super resolution image. We conduct experiments for multi-frame SR, where the proposed method delivers favorable results, especially better than state-of-the-art in dealing with concurrent local and global motions across frames.
A Compliant, Underactuated Hand for Robust Manipulation (2013)

This paper introduces the i-HY Hand, an underactuated hand driven by 5 actuators that is capable of performing a wide range of grasping and in-hand manipulation tasks. This hand was designed to address the need for a durable, inexpensive, moderately dexterous hand suitable for use on mobile robots. The primary focus of this paper will be on the novel minimalistic design of i-HY, which was developed by choosing a set of target tasks around which the design of the hand was optimized. Particular emphasis is placed on the development of underactuated fingers that are capable of both firm power grasps and low- stiffness fingertip grasps using only the passive mechanics of the finger mechanism. Experimental results demonstrate successful grasping of a wide range of target objects, the stability of fingertip grasping, as well as the ability to adjust the force exerted on grasped objects using the passive finger mechanics.
Effects of xylulokinase activity on ethanol production from d-xylulose by recombinant Saccharomyces cerevisiae (2003)

Overexpression of the XKS1 gene made xylulose fermentation process accelerated to produce ethanol through the pentose phosphate pathway.
Thermal Synthesis of Perchlorinated Oligosilanes: A Fresh Look at an Old Reaction (2017)

A combined experimental and theoretical study of the high-temperature reaction of SiCl<sub>4</sub> and elemental silicon is presented. The nature and reactivity of the product formed upon rapid cooling of the gaseous reaction mixture is investigated by comparison with the defined model compounds cyclo-Si<sub>5</sub> Cl<sub>10</sub> , n-Si<sub>5</sub> Cl<sub>12</sub> and n-Si<sub>4</sub> Cl<sub>10</sub> . A DFT assessment provides mechanistic insight into the oligosilane formation. Experimental <sup>29</sup> Si NMR investigations, supported by quantum-chemical <sup>29</sup> Si NMR calculations, consistently show that the reaction product is composed of discrete molecular perchlorinated oligosilanes. Low-temperature chlorination is an unexpectedly selective means for the transformation of cyclosilanes to acyclic species by endocyclic Si-Si bond cleavage, and we provide a mechanistic rationalization for this observation. In contrast to the raw material, the product obtained after low-temperature chlorination represents an efficient source of neo-Si<sub>5</sub> Cl<sub>12</sub> or the amine-stabilized disilene EtMe<sub>2</sub> N⋅SiCl<sub>2</sub> Si(SiCl<sub>3</sub> )<sub>2</sub> through reaction with aliphatic amines.
Time-to-digital converter for RF frequency synthesis in 90 nm CMOS (2005)

We propose and demonstrate a 20 ps time-to-digital converter (TDC) in 90 nm digital CMOS. It is used as a phase/frequency detector and charge pump replacement in an all-digital PLL for a fully-compliant GSM transceiver. The TDC core is based on a pseudo-differential digital architecture that makes it insensitive to NMOS and PMOS mismatches. The time conversion resolution is equal to an inverter propagation delay, which is the finest logic-level regenerative timing in CMOS. The TDC is self calibrating with estimation accuracy better than 1%. Measured INL is 0.7 LSB. The TDC consumes 1.3 mA from a 1.3 V supply.
DIFFICULTY IN DISLODGING IN VIVO FIXED RADIOSTRONTIUM (2004)

Many trials based on the basic phenomena of isotopic dilution, adsorption, ion exchange, chelation, etc., have been attempted for the decorporation of radiostrontium, particularly Sr, after its entry in the in vivo system. We have recently demonstrated a non-isotopic carrier effect of some common calcium salts (calcium = 9 mg mL) to reduce the whole body retention of radiostrontium, if administered within 2 h after radiostrontium exposure and furthermore once daily, in rats, supplemented with calcium fortified diet. However, 25-30% of radiostrontium (compared to 50-60% in untreated animals) was still found to be retained in the animal even after 2 wk of treatment. Trial of some simple interventional measures, which would not adversely affect the animal metabolism, like pyrophosphate and magnesium sulfate, sodium citrate, chitin (a bio-absorbent), crown ether (a metal-chelator), and ammonium chloride, was therefore attempted to dislodge this remaining radiostrontium by switching over these animals to normal diet and subjecting them to different lines of treatment with these simple interventions through diet and drinking water separately for a further 4 wk. However, this remaining portion of radiostrontium is fixed in the bone and is difficult to dislodge.