gebhart/patrepeval huggingface dataset:
Single-Cell and Bulk Fluorescence Excitation Signatures of Seven Phytoplankton Species During Nitrogen Depletion and Resupply (2018)

Phytoplankton play a vital role as primary producers in aquatic ecosystems. One common approach to classifying phytoplankton is fluorescence excitation spectroscopy, which leverages the variation in types and concentrations of pigments among different phytoplankton taxonomic groups. Here, we used a fluorescence imaging photometer to measure excitation ratios ("signatures") of single cells and bulk cultures of seven differently pigmented phytoplankton species as they progressed from nitrogen N-replete to N-depleted conditions. Our objective was to determine whether N depletion alters the fluorescence excitation signature of each species and, if so, how quickly they recover when N (as nitrate) was resupplied, because these factors affect our ability to classify the species correctly. Of the seven species studied, only Proteomonas sulcata, a marine cryptophyte, showed measurable changes in single-cell fluorescence excitation ratios and bulk fluorescence excitation spectra. These changes were likely due to decreases in the cellular concentration of phycoerythrin, a N-rich pigment, as N became scarce. Within 3 h of resupply of N, fluorescence signatures began returning to pre-depletion values and were indistinguishable from N-replete cells by 80 h after resupply. These data suggest that our classification approach is robust for non-PE containing phytoplankton. PE-containing phytoplankton might exhibit systematic changes in their signatures depending on their level of N depletion, but this could be detected and the phytoplankton re-classified following a few hours of incubation in N replete conditions.
Ribosome recycling step in yeast cytoplasmic protein synthesis is catalyzed by eEF3 and ATP (2010)

After each round of protein biosynthesis, the posttermination complex (PoTC) consisting of a ribosome, mRNA, and tRNA must be disassembled into its components for a new round of translation. Here, we show that a Saccharomyces cerevisiae model PoTC was disassembled by ATP and eukaryotic elongation factor 3 (eEF3). GTP or ITP functioned with less efficiency and adenosine 5gamma'-(beta,gamma-imido)triphosphate did not function at all. The k(cat) of eEF3 was 1.12 min(-1), which is comparable to that of the in vitro initiation step. The disassembly reaction was inhibited by aminoglycosides and cycloheximide. The subunits formed from the yeast model PoTC remained separated under ionic conditions close to those existing in vivo, suggesting that they are ready to enter the initiation process. Based on our experimental techniques used in this paper, the release of mRNA and tRNA and ribosome dissociation took place simultaneously. No 40S*mRNA complex was observed, indicating that eEF3 action promotes ribosome recycling, not reinitiation.
Thought-Based Authenticated Key Exchange (2019)

Identity authentication techniques based on password-authenticated key exchange (PAKE) protocols rely on weak secrets shared between users and host systems. In PAKE, a symmetric key is derived from the shared secret, used to mutually authenticate communicating parties, and then used to establish a secure channel for subsequent communications. A common source of PAKE weak secrets are password and passphrase strings. Though easily recalled by a user, these inputs typically require keyboard entry, limiting their utility in achieving universal access. This paper describes authentication techniques based on weak secrets derived from knowledge extracted from biometric sensors and brain-actuated control systems. The derived secrets are converted into a format suitable for use by a PAKE protocol. When combined with other authentication factors, PAKE protocols can be extended to provide strong, two-factor identity authentication that is easy to use by persons living in assistive environments.
Bone Formation in Cervical Total Disk Replacement (CTDR) up to the 6-Year Follow-up (2013)

Background: Bone formation or so-called heterotopic ossification (HO) has been recognized as a complication of cervical total disk replacement (CTDR), potentially decreasing the range of motion (ROM) or even fusing the operated level. The purposes were to evaluate HO occurrence after CTDR with the PCM device and to determine the corresponding clinical significance. Methods: A prospective functional study and a retrospective radiographic review were performed. Two hundred seventy-two levels with CTDR using PCM device were enrolled. The follow-up average was 4.5 years (±1.37; range, 1 to 6). Radiographic images and clinical outcomes were collected. Results: Of the 272 levels studied, 21 (7.7%) revealed some degree of HO. Of these 21 levels, 10 (47.6%) levels were rated to be grade I, 7 (33.3%) were rated as grade II, 3 (14.28%) as grade III, and 1 (4.76%) as grade IV. Whereas 16.9% of the single-level cases developed HO, only 4.4% of the multilevel cases had some bone formation. Surprisingly, the HO patient group did not demonstrate a worsening of the clinical outcome. In 90.5% of patients with HO, preoperative radiographs showed an incipient osteophyte. The mean ROM in flexion-extension images was 11.2 degrees postoperatively, decreasing to 8.3 degrees at 12 months postoperatively and to 6.0 degrees at 72 months. Conclusions: The incidence of HO has a low rate in our series and does not seem to adversely affect clinical outcomes up to this point. Nevertheless, it is an important event that influenced the mean ROM after 72 months and may be further studied for assessment of any late consequences.
Flow Aware Transport of MPLS Pseudowires (2009)

Where the payload carried over a pseudowire carries a number of
identifiable flows it can in some circumstances be desirable to carry
those flows over the equal cost multiple paths that exist in the
packet switched network. This draft describes two methods of achieving
that, the one by including an additional label in the label stack, the
other by using a block of alternative pseudowire labels.
Human angiogenin fused to human CD30 ligand (Ang-CD30L) exhibits specific cytotoxicity against CD30-positive lymphoma. (2001)

A number of different immunotoxins composed of cell-specific targeting structures coupled to plant or bacterial toxins have increasingly been evaluated for immunotherapy. Because these foreign proteins are highly immunogenic in humans, we have developed a new CD30 ligand-based fusion toxin (Ang-CD30L) using the human RNase angiogenin. The completely human fusion gene was inserted into a pET-based expression plasmid. Transformed Escherichia coli BL21(DE3) were grown under osmotic stress conditions in the presence of compatible solutes. After isopropyl beta-D-thiogalactoside induction, the M(r) 37,000 His(10)-tagged Ang-CD30L was directed into the periplasmic space and functionally purified by a combination of metal ion affinity followed by enterokinase cleavage of the His(10)-Tag and molecular size chromatography. The characteristics of the recombinant protein were assessed by ELISA, flow cytometry, and toxicity assays showing specific activity against CD30(+) Hodgkin-derived cells. Specific binding activity of Ang-CD30L was verified by competition with anti-CD30 monoclonal antibody Ki-4 and commercially available CD30L-CD8 chimeric protein. Ang-CD30L showed RNase activity in vitro. The human recombinant immunotoxin showed significant toxicity toward several CD30-positive cell lines (HDLM-2, L1236, KM-H2, and L540Cy) and exhibited highest cytotoxicity against L540 cells (IC(50) = 8 ng/ml) as determined by cell proliferation assays. CD30 specificity was confirmed by competitive toxicity assays. This is the first report on the specific cytotoxicity of a recombinant completely human fusion toxin with possibly largely reduced immunogenicity for the treatment of CD30-positive malignancies.
Modeling and Analysis of Automatic Transmission Engagement Dynamics-Linear Case (2005)

Abstract A control-oriented model of a typical four-speed automatic transmission is developed by using the bond graph modeling method. The planetary gear set model utilizes the Karnopp friction model for hydraulic and one-way clutches, in order to provide a favorable computing efficiency. The full gear set model is reduced for various phases of the park/reverse and park/drive engagements. The reduced gear set models and linearized torque converter model are used as a basis for an algebraic analysis of the engagement dynamics. The analysis is originally conducted for the basic case of fully applied brake, and it is then extended by an analysis of the influence of wheel dynamics in the brake-off case. The analysis results are verified by computer simulations and experiments.
Overproduction of Heterologous Proteins in Escherichia coli (2020)

One of the biggest achievements of recombinant DNA technology is the ability to ensure the overproduction of a desired gene product. In this chapter, the authors provide an overview of the general considerations for gene overexpression and some examples. However, the constitutive overproduction of potentially toxic proteins by the elevated gene dosage is usually detrimental to host cell growth. The authors present a method for achieving the high-level expression of the human interleukin-6 (hIL-6) gene as an example of designing for overproduction. On the basis of an analysis of previous attempts to express hIL-6 cDNA, the main strategy the readers employed to increase the production level was improvement of translation efficiency through the installation of dual Shine-Dalgarno sequences and the adoption of a modified nucleotide sequence for encoding hIL-6. Besides gene manipulation to achieve overexpression, both the fementation technology and the downstream processing (including the purification and renaturation of gene products) are also very important.
Polymerase chain reaction amplification of naphthalene-catabolic and 16S rRNA gene sequences from indigenous sediment bacteria (1993)

We report the amplification of bacterial genes from uninoculated surface and subsurface sediments by the polymerase chain reaction (PCR). PCR amplification of indigenous bacterial 16S ribosomal DNA genes was unsuccessful when subsurface sediment containing approximately 10(7) cells.g-1 was added directly to a PCR mixture. However, when 10 mg of sediment was inoculated with approximately 10(5) cells of Pseudomonas putida G7, the nahAc naphthalene dioxygenase gene characteristic of the P. putida G7 NAH7 plasmid was detected by PCR amplification. Southern blotting of the PCR amplification product improved sensitivity to 10(3) to 10(4) cells from samples inoculated with P. putida G7, but controls with no sediment added showed that the PCR was partially inhibited by the sediments. Lysozyme-sodium dodecyl sulfate-freeze-thaw DNA extraction was combined with gel electrophoretic partial purification in the presence of polyvinylpyrrolidone to render DNA from indigenous bacteria in surface or subsurface sediment samples amplifiable by PCR using eubacterial 16S ribosomal DNA primers. The nahAc gene could also be amplified from indigenous bacteria by using nahAc-specific primers when PCR conditions were modified by increasing Taq and primer concentrations. Restriction digests of the nahAc amplification products from surface and subsurface sediments revealed polymorphism relative to P. putida G7. The procedures for DNA extraction, purification, and PCR amplification described here demonstrate that the PCR is a potentially useful tool in studies of function- and taxon-specific DNA from indigenous microbial communities in sediment and groundwater environments.
Evaluation of strength of porous aluminum by aluminum alloy powder addition (2016)

Open-cell porous aluminum (Al) was fabricated by spark plasma sintering process. In this process, a mixture of pure Al powder, 6061 aluminum alloy powder and sodium chloride (NaCl) powder as spacer particle was used as starting materials. The powder mixture was sintered by spark plasma sintering process. NaCl was removed by placing the sintered mixture in water, and pores were formed. In this study, pore structures of obtained porous Al were nondestructively observed by X-ray computing tomography (CT). It was shown that strength of porous Al was improved by 6061 aluminum alloy powder addition.
Nonobstructive septal hypertrophy in a young adult provoking recurrent polymorphic ventricular tachycardia successfully treated with transaortic and transventricular septal myectomy: A case report (2015)

Tabled 1KEY TEACHING POINTS•Septal myectomy may be an effective treatment for ischemia-induced ventricular arrhythmia in hypertrophic cardiomyopathy (HCM) patients.•Coronary ischemia due to myocardial bridging is a potentially reversible and possibly underrecognized cause of ventricular arrhythmias in HCM patients.•Septal myectomy is a mainstay of treatment for symptomatic left ventricular outflow tract obstruction refractory to medical therapy. Open table in a new tab
<title>Improving stigmation control of the CD-SEM</title> (2000)

Production fads currently rely on CD-SEM metrology for linewidth control in lithography and etch. The quality of the measurement data is therefore directly tied to the quality of the SEM imaging and that of the electron beam. Experience has shown that even within a 12 hour period, the beam alignment can drift sufficiently to cause a shift of several nanometers in the measured CD. Furthermore, the alignment of the electron beam has traditionally been performed manually, with the quality of the SEM image then being dependent on the judgement of the operator. While this has been adequate in the past, the drive towards ever smaller geometries means that even slight changes in the beam spot can lead to unacceptable variation in the CD measurements. In this paper, we will describe how a more consistent electron beam can be achieved by obtaining quantitative feedback on its sharpness and eccentricity. Using this quantitative information removes the subjective nature of the manual beam alignment and requires less training on part of the users. Furthermore, this procedure results in beam conditions that are at least as good as the alignment performed by an experienced operator, and in fact generally improves the alignment when compared to that obtained by subjective judgement of the image quality. Once a baseline is established, SPC charts for the sharpness and eccentricity values can be used to track tool performance. If either value falls out of a specified range, the system can be flagged as having a problem and efforts to restore the image resolution can begin immediately, reducing the risk of erroneous measurements and thus preventing lots from being misprocessed or mistakenly reworked.
Kinetic theory for electrostatic waves due to transverse velocity shears (1988)

A kinetic theory in the form of an integral equation is provided to study the electrostatic oscillations in a collisionless plasma immersed in a uniform magnetic field and a nonuniform transverse electric field. In the low temperature limit the dispersion differential equation is recovered for the transverse Kelvin-Helmholtz modes for arbitrary values of K parallel, where K parallel is the component of the wave vector in the direction of the external magnetic field assumed in the z direction. For higher temperatures the ion-cyclotron-like modes described earlier in the literature by Ganguli, Lee and Plamadesso are recovered. In this article, the integral equation is reduced to a second-order differential equation and a study is made of the kinetic Kelvin-Helmholtz and ion-cyclotron-like modes that constitute the two branches of oscillation in a magnetized plasma including a transverse inhomogeneous dc electric field.
Samarium Diiodide-Promoted Reductive Coupling of Imines (1990)

Abstract Aromatic aldimines are reductively coupled to 1,2-diamines by treatment with samarium diiodide. Cross-coupling of aromatic ketimines with ketones to 2-aminoalcohols is also promoted by the same reagent.
Photoluminescence and Scintillation Properties of Tb:GdTaO4 Crystals (2021)

Tb-doped GdTaO 4 crystals were synthesized to investigate their photoluminescence and scintillation properties. Tb:GdTaO 4 exhibits photo-and radioluminescence characterized by several sharp peaks due to 4f-4f transitions of Tb 3+ . The photo-and radioluminescence decay time constants are 500-900 s. The values become short with increasing Tb concentration and are typical for the 4f-4f transitions of Tb 3+ . From the quantum yield (QY), radioluminescence spectra, and pulse height under 137 Cs -rays, the 1% Tb:GdTaO 4 crystal shows the highest scintillation output among the samples.
Safe Carrier Sensing Range in CSMA Network under Physical Interference Model (2009)

In this paper, we study the setting of carrier-sensing range in 802.11 networks under the (cumulative) physical interference model. Specifically, we identify a carrier-sensing range that will prevent collisions in 802.11 networks due to carrier-sensing failure under the physical interference model. We find that the carrier-sensing range required under the physical interference model must be larger than that required under the protocol (pairwise) interference model by a multiplicative factor. For example, if the SINR requirement is 10dB and the path-loss exponent is 4, the factor is 1.4. Furthermore, given a fixed pathloss exponent of 4, the factor increases as the SINR requirement increases. However, the limit of the factor is 1.84 as the SINR requirement goes to infinity.
Pragmatic mAb lead molecule engineering from a developability perspective (2021)

As the number of antibody drugs being approved and marketed increases, our knowledge of what makes potential drug candidates a successful product has increased tremendously. One of the critical parameters that have become clear in the field is the importance of mAb "developability." Efforts are being increasingly focused on simultaneously selecting molecules that exhibit both desirable biological potencies and manufacturability attributes. In the current study mutations to improve the developability profile of a problematic antibody that inconsistently precipitates in a batch scale-dependent fashion using a standard platform purification process are described. Initial bioinformatic analysis showed the molecule has no obvious sequence or structural liabilities that might lead it to precipitate. Subsequent analysis of the molecule revealed the presence of two unusual positively charged mutations on the light chain at the interface of VH and VL domains, which were hypothesized to be the primary contributor to molecule precipitation during process development. To investigate this hypothesis, straightforward reversion to the germline of these residues was carried out. The resulting mutants have improved expression titers and recovered stability within a forced precipitation assay, without any change to biological activity. Given the time pressures of drug development in industry, process optimization of the lead molecule was carried out in parallel to the "retrospective" mutagenesis approach. Bespoke process optimization for large-scale manufacturing was successful. However, we propose that such context-dependent sequence liabilities should be included in the arsenal of in silico developability screening early in development; particularly since this specific issue can be efficiently mitigated without the requirement for extensive screening of lead molecule variants.
Endotherapy including temporary stenting of fistulas of the upper gastrointestinal tract after laparoscopic bariatric surgery (2007)

Endoscopic treatment using SEMSs for complications of bariatric surgery is feasible. Healing of severe leaks was obtained in 81 % (17/21) of patients, avoiding high-risk reintervention. Gastrocutaneous fistulas on a sleeve suture are the most difficult condition to treat.
Evolution of Tertiary Carbinamine BACE‐1 Inhibitors: Aβ Reduction in Rhesus CSF upon Oral Dosing (2008)

Turning up the BACE: Incorporation of an isonicotinic core into oxadiazolyl tertiary carbinamine-based inhibitors of BACE-1 has led to the identification of an exquisitely potent inhibitor, which displays good Papp and low susceptibility to the P-gp efflux pump. Upon twice daily oral administration to monkeys, co-dosed with ritonavir, this inhibitor was shown to penetrate the CNS and lower Aβ42 levels in the CSF by >40 % over the 3 day course of the experiment. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
The Effect of A Whey-Protein and Galacto-Oligosaccharides Based Product on Parameters of Sleep Quality, Stress, and Gut Microbiota in Apparently Healthy Adults with Moderate Sleep Disturbances: A Randomized Controlled Cross-Over Study (2021)

People experiencing sleep problems may benefit from nutrients supporting serotonin metabolism and stress reduction. We studied the effect of a dairy-based product (DP) containing protein, galacto-oligosaccharides, vitamins and minerals, on sleep quality, stress, and gut-microbiota. In a cross-over RCT (three weeks intervention; three weeks washout), adults (<i>n</i> = 70; 30-50 y) with sleep disturbances (Pittsburgh Sleep Quality Index (PSQI) ≥ 9) consumed products 1 h before bed-time. Sleep quality (PSQI) was measured weekly, stress at base- and end-line (Depression Anxiety Stress Scale and saliva cortisol). Fecal samples were collected in the 1st intervention period only. Compared to placebo (skimmed milk), PSQI was only lower at day 14 in the 2nd intervention period in intention-to-treat (ITT) (<i>p</i> = 0.017; <i>n</i> = 69) and per-protocol (PP) (<i>p</i> = 0.038; <i>n</i> = 64) analyses. Post-hoc analysis (modified-PP: n=47, with baseline PSQI ≥ 9, and endline day 14), however, showed a decrease in PSQI (-1.60 ± 2.53; <i>p</i> = 0.034). Early morning saliva cortisol decreased versus placebo (<i>p</i> = 0.045). Relative abundance of <i>Bifidobacterium</i> increased (<i>p</i> = 0.02). Redundancy analysis showed an inverse relationship between baseline microbiota composition and baseline PSQI (<i>p</i> = 0.046). Thus, although DP did not improve sleep quality in ITT and PP populations, it did in the modPP. DP reduced salivary cortisol and stimulated <i>Bifidobacterium</i>, which possibly is important for sleep improvement.