gebhart/patrepeval huggingface dataset:
Strategies for Undertaking Expressed Sequence Tag (EST) Projects (2009)

Complementary DNA (cDNA) sequencing can be used to sample an organism's transcriptome, and the generated EST sequences can be used for a variety of purposes. They are especially important for enhancing the utility of a genome sequence or for providing a gene catalog for a genome that has not or will not be sequenced. In planning and executing a cDNA project, several criteria must be considered. One should clearly define the project purpose, including organism tissue(s) choice, whether those tissues should be pooled, ability to acquire adequate amounts of clean and well-preserved tissue, choice of type(s) of library, and construction of a library (or libraries) that is compatible with project goals. In addition, one must possess the skills to construct the library (or libraries), keeping in mind the number of clones that will be necessary to meet the project requirements. If one is inexperienced in cDNA library construction, it might be wise to outsource the library production and/or sequence and analysis to a sequencing center or to a company that specializes in those activities. One should also be aware that new sequencing platforms are being marketed that may offer simpler protocols that can produce cDNA data in a more rapid and economical manner. Of course, the bioinformatics tools will have to be in place to de-convolute and aid in data analysis for these newer technologies. Possible funding sources for these projects include well-justified grant proposals, private funding, and/or collaborators with available funds.
High-dynamic-range cascaded-focus optical limiter (2000)

We report experimental results of using an f/5 , cascaded-focus optical geometry for a high-dynamic-range optical limiter. The device consists of a 2-cm-thick CS(2) cell at the first focus and a reverse saturable-absorber dye in a thin cell (0.1 mm) at the second focus. The strong self-focusing in the CS(2) that is due to the ac Kerr effect and electrostriction keeps the energy at the second cell below its damage threshold. Using lead phthalocyanine in chloroform as the reverse saturable-absorption material, we clamped the maximum output energy below 1muJ for input energies up to 14.5 mJ without damage. We used a frequency-doubled, Q -switched 5-ns (FWHM) Nd:YAG laser operating at a 10-Hz repetition rate. The measured dynamic range of the device is at least 7500.
Activation of oxoglutarate dehydrogenase in the kidney in response to acute acidosis (1980)

1. Activation by H+ and by Ca2+ of 2-oxoglutarate dehydrogenase extracted from mitochondria of normal or acidotic rat kidney is described. This effect, first shown for the enzyme from heart by McCormack & Denton [Biochem. J. (1979) 180, 533--544], is of a regulatory importance in kidney, in which organ, in contrast with heart, increased flux occurs during acute acidosis. 2. In renal-cortical tubules, 2-oxoglutarate concentration fell within 1 min of decreasing the pH and rose again 1--3 min after increasing the pH of the medium. The extent of the decrease in 2-oxoglutarate was directly related to the decrease in pH. A similar fall in the oxoglutarate concentration in the whole perfused kidney was noted within 5 min of inducing acidosis. 3. In tubules, the rates of gluconeogenesis and ammoniagenesis from 1 mM-glutamine were increased by 64 and 33% respectively on decreasing pH to 7.0, the increase in rates being proportional to the fall in pH between 7.4 and 7.0. 4. The increased rates of renal ammoniagenesis and gluconeogenesis seen in acute acidosis in vitro can be accounted for by the increased activity of 2-oxoglutarate dehydrogenase and the tissue concentrations of 2-oxoglutarate when calculated from the Km determined at normal and acidotic pH. 5. The decrease in 2-oxoglutarate concentration seen in acute acidosis implies a fall in intramitochondrial pH in kidney, and is the result of two phenomena, accelerated disposal via 2-oxoglutarate dehydrogenase and maintenance of near equilibrium of glutamate dehydrogenase.
A Layered Lattice Coding Scheme for a Class of Three User Gaussian Interference Channels (2008)

The paper studies a class of three user Gaussian interference channels. A new layered lattice coding scheme is introduced as a transmission strategy. The use of lattice codes allows for an "alignment" of the interference observed at each receiver. The layered lattice coding is shown to achieve more than one degree of freedom for a class of interference channels and also achieves rates which are better than the rates obtained using the Han-Kobayashi coding scheme.
Impact of the elevation angle in the coherence time as a function of the sea wave height (2015)

For a given geometry, the coherence time of a GNSS-R waveform can be initially related to the significant wave height. However, when the coherence time is analyzed, several issues shall be considered, such as the geometry (i.e altitude, elevation angle). This work presents a review of the coherence time and its dependence on the geometry. In addition, the impact that the SWH has on both the coherence time and elevation angles is analyzed. Real data from different scenarios (spaceborne, airborne, and ground based) are used in this study.
Acute severe memory impairment as a presenting symptom of multiple sclerosis: a clinical case study with 3D double inversion recovery MR imaging (2010)

We present the case of a 21-year-old woman with acute memory impairment. It was initially not recognized as organic in nature. Repeated neuropsychological testing confirmed severely disturbed encoding and recall. Three-dimensional double inversion recovery (3D-DIR) MRI confirmed hippocampal and cortical lesions. Further clinical symptoms, visual evoked potential and MRI suggested a diagnosis of multiple sclerosis (MS). The amnestic syndrome has remained for 5 years. This case illustrates that MS can present with acute cortical symptoms which can be difficult to recognize. The hippocampus can be acutely affected and DIR MRI imaging can help to demonstrate cortical lesions that explain the clinical picture.
E4 allele of apolipoprotein gene was associated with lower blood pressure (2001)

Apolipoprotein E4 allele (apoE/E4) increases the plasma cholesterol level and the risk for the late onset type of Alzheimer's disease. However, the correlation between hypertension and apoE/E4 has not been clarified yet. To examine the apoE/E4 effect in a Japanese general population, we demonstrated a large genetic epidemiological survey (the Suita Study). The Suita Study was a cohort study based on a random sample of 14,200 Japanese residents of Suita city. The subjects who gave the informed consent for genetic analysis recruited in the current study (n=3,997). ApoE polymorphism was clearly determined by TaqMan PCR method. All statistical analyses were conducted using JMP 3.1.5 (SAS). Subjects with apoE/E4 were significantly (p<0.03) more frequent (19.7%) in normotensive subjects (SBP/DBP<140/90mmHg and without antihypertensive therapy) than those in hypertensive subjects (16.9%), the estimated odds ratio for hypertension (with apoE/E4 vs. without apoE/E4) being 0.82 (95% CI: 0.67-0.96). Even after the adjustment of confounding factors (age, gender, and BMI), its association with hypertension and with systolic blood pressure remained (both p<0.05). ApoE/E4 also contributes to the 2.5% increase of total cholesterol and 10% increase of triglyceride levels. We concluded that apoE/E4 was associated with increase of plasma lipid level and with decrease of systolic blood pressure. The final conclusion whether apoE/E4 contributes to the risk for cardiovascular disease will be clarified in the analysis of the cumulative incidence to be obtained in the future Suita Study.
Long‐term follow‐up of patients with resected pancreatic cancer following vaccination against mutant K‐ras (2010)

K-ras mutations are frequently found in adenocarcinomas of the pancreas and can elicit mutation-specific immune responses. Targeting the immune system against mutant Ras may thus influence the clinical course of the disease. Twenty-three patients who were vaccinated after surgical resection for pancreatic adenocarcinoma (22 pancreaticoduodenectomies, one distal resection), in two previous Phase I/II clinical trials, were followed for more than 10 years with respect to long-term immunological T-cell reactivity and survival. The vaccine was composed of long synthetic mutant ras peptides designed mainly to elicit T-helper responses. Seventeen of 20 evaluable patients (85%) responded immunologically to the vaccine. Median survival for all patients was 27.5 months and 28 months for immune responders. The 5-year survival was 22% and 29%, respectively. Strikingly, 10-year survival was 20% (four patients out of 20 evaluable) versus zero (0/87) in a cohort of nonvaccinated patient treated in the same period. Three patients mounted a memory response up to 9 years after vaccination. The present observation of long-term immune response together with 10-year survival following surgical resection indicates that K-ras vaccination may consolidate the effect of surgery and represent an adjuvant treatment option for the future.
Stephania tetrandra prevents and regresses liver fibrosis induced by carbon tetrachloride in rats (2009)

Stephania tetrandra safely and effectively prevents and reverses hepatic fibrosis through activating HSC apoptosis in rats.
Feasibility of Continuous Sub-criticality Monitoring using a Digital Reactivity Meter to Overcome the Criticality Accident (2006)

In the foregoing studies, it has been proved that the digital reactivity meter can be used for not only sub-criticality measurement but also continuous sub-criticality monitoring during criticality approach. Based on these studies, we investigated the applicability of a digital reactivity meter for continuous sub-criticality monitoring to intervene before a criticality accident occurs that is similar to the Tokai-mura accident in 1999. In our mock up numerical simulation, there are three calculation steps that are (1) reactivity transient calculation, (2) neutron transient calculation and (3) sub-criticality monitoring calculation. The reactivity transient was calculated using two-group diffusion nuclear constants and the neutron transient was calculated using the one-point reactor kinetics. In sub-criticality monitoring, three algorithms for reactivity evaluation were compared. We have investigated which algorithm is the most suitable to use in an actual system. In practice, we also advise use of some filtering algorithm to reduce the neutron transient fluctuation and a warning reactivity to know estimated sub-criticality as earlier as possible.
Search for long-lived particles using displaced jets in proton-proton collisions at s=13  TeV (2021)

An inclusive search is presented for long-lived particles using displaced jets. The search uses a data sample collected with the CMS detector at the CERN LHC in 2017 and 2018, from proton-proton collisions at a center-of-mass energy of 13 TeV. The results of this search are combined with those of a previous search using a data sample collected with the CMS detector in 2016, yielding a total integrated luminosity of 132 fb -1 . The analysis searches for the distinctive topology of displaced tracks and displaced vertices associated with a dijet system. For a simplified model, where pair-produced long-lived neutral particles decay into quark-antiquark pairs, pair production cross sections larger than 0.07 fb are excluded at 95% confidence level (C.L.) for long-lived particle masses larger than 500 GeV and mean proper decay lengths between 2 and 250 mm. For a model where the standard model-like Higgs boson decays to two long-lived scalar particles that each decays to a quark-antiquark pair, branching fractions larger than 1% are excluded at 95% C.L. for mean proper decay lengths between 1 mm and 340 mm. A group of supersymmetric models with pair-produced long-lived gluinos or top squarks decaying into various finalstate topologies containing displaced jets is also tested. Gluino masses up to 2500 GeV and top squark masses up to 1600 GeV are excluded at 95% C.L. for mean proper decay lengths between 3 and 300 mm. The highest lower bounds on mass reach 2600 GeV for long-lived gluinos and 1800 GeV for long-lived top squarks. These are the most stringent limits to date on these models.
Smart modular lighting control system with dual-beam luminaires (2014)

We consider a smart lighting system with multiple dual-beam luminaires, with co-located occupancy and light sensors. A dual-beam luminaire emits a hollow beam and a narrow beam, suitable, respectively, for providing ambient and task lighting both controllable independently. We consider an occupancy- and daylight-adaptive lighting system, wherein the luminaire controller determines the dimming levels of the dual beams such that the lighting system provides a desired illuminance based on local occupancy and light sensor inputs. We present a method for calibrating the light sensors to obtain control set-points and a controller design so that the set-points may be attained. The proposed system performance is compared with a standard-beam lighting system using lighting simulations. We find that the dual-beam lighting system provides higher illumination and power saving in comparison to the standard-beam lighting system, given the additional degree of freedom provided by the two optical beams.
Reactive ion beam etching of ZnSe and ZnS epitaxial films using Cl2 electron cyclotron resonance plasma (1990)

Reactive ion beam etching of ZnSe and ZnS epitaxial films was carried out using pure Cl2 as an etching gas. Electron cyclotron resonance plasma was excited at pressures of 2.5×10−4 –2.5×10−3 Torr. Chlorine ions were extracted with voltages of 0–400 V. Sputtering yields were strongly dependent on the extraction voltage and the gas pressure. The etching mechanism starts with the generation of chloride compounds, mainly ZnClx, by the chemical reaction of the surface and chlorine radicals, mainly Cl atoms. The chloride compounds are subsequently sputtered off by the accelerated ion beam. The crystalline quality of etched ZnSe films was characterized by photoluminescence measurements. We found that high quality etched films, which have almost no damage and no Cl contamination, can be obtained at an extraction voltage of about 300 V.
In-situ grafted amine functionalized metal-organic frameworks for CO2 capture: Preparation and bench-scale performance evaluation (2023)

The work includes the preparation of zirconium fumarate (ZrFu) metal-organic framework (MOF) and investigation of the CO2 capture performance of the material. The CO2 adsorption experiments were performed in a bench-scale flow reactor with a simulated flue gas mixture. To enhance the CO2 capture capacity of the ZrFu material, two polydentate amines, namely diethylenetriamine (DETA) and tetraethylenepentamine (TEPA) were incorporated into the ZrFu by an in-situ grafting method. The effects of adsorption temperature, pressure, amine loading, and CO2 concentration in the feed gas mixture on CO2 capture were examined. The obtained value of the CO2 uptake capacity of the pristine ZrFu is 73 g CO2/kg sorbent at 30 ºC under atmospheric pressure. Among the amine-modified MOFs, the DETA-modified ZrFu (10-DETA-ZrFu) showed a maximum adsorption capacity of 86 g CO2/kg sorbent. It is also noted that at 90 °C, the CO2 adsorption capacity of the material is 57 g CO2/kg sorbent, which is about 67% of the capture capacity at 30 °C. This demonstrates that the MOFs can capture and retain the CO2 molecules inside the MOF moiety even at higher temperatures. The study also revealed that the synthesized MOFs are chemically stable with about 10% moisture environment. The prepared MOFs exhibited admirable thermo-chemical stability up to around 150 °C. Among the studied isotherm models, the Langmuir model showed a good agreement with the experimental data for lower values of adsorption pressure. The estimated value of adsorption energy for the adsorption of CO2 on ZrFu is 6.9 kJ/mol at 30 °C.
Molecular evidence of anteroposterior patterning in adult echinoderms (2023)

Abstract The origin of the pentaradial body plan of echinoderms from a bilateral ancestor is one of the most enduring zoological puzzles. Since echinoderms are defined by morphological novelty, even the most basic axial comparisons with their bilaterian relatives are problematic. Here, we used conserved antero-posterior (AP) axial molecular markers to determine whether the highly derived adult body plan of echinoderms masks underlying patterning similarities with other deuterostomes. To revisit this classical question, we used RNA tomography and in situ hybridizations in the sea star Patiria miniata to investigate the expression of a suite of conserved transcription factors with well-established roles in the establishment of AP polarity in bilaterians. We find that the relative spatial expression of these markers in P. miniata ambulacral ectoderm shows similarity with other deuterostomes, with the midline of each ray representing the most anterior territory and the most lateral parts exhibiting a more posterior identity. Interestingly, there is no ectodermal territory in the sea star that expresses the characteristic bilaterian trunk genetic patterning program. This suggests that from the perspective of ectoderm patterning, echinoderms are mostly head-like animals, and prompts a reinterpretation of the evolutionary trends that made echinoderms the most derived animal group.
Search for heavy particles decaying into a top-quark pair in the fully hadronic final state in pp collisions at s=13  TeV with the ATLAS detector (2019)

final state in pp collisions at ffiffi s p = 13 TeV with the ATLAS detector M. Aaboud et al.
SiGe EAM-Based Transceivers for Datacenter Interconnects and Radio Over Fiber (2020)

Silicon photonics is a key-enabling technology leveraging decades of effort and infrastructure of the microelectronics CMOS industry resulting in high yield, low cost and potential high volume manufacturing. Furthermore, due to the high index contrast of the platform, very compact, high-complexity photonic integrated circuits can be devised. To benefit from these advantages, high-speed modulators should also be compatible with silicon technology. In this respect, SiGe electro-absorption modulators (EAM) are considered as a promising candidate since they are CMOS-compatible and offer high-speed, compact, low-loss and low-power modulation. In this paper, we discuss SiGe EAM-based transceivers for next-generation datacenter interconnects (DCI) and radio-over-fiber (RoF) fronthaul in next-generation cellular networks.
Monitoring the Health to Disease Continuum with Global Metabolic Profiling and Systems Biology (2006)

Global metabolic profiling, which includes both metabolomics and metabonomics studies, is the latest 'omics' research platform that is being applied to understand the health and disease continuum. Metabolic profiling analyses have been demonstrated for the investigation of inborn errors of metabolism, organ transplant rejection, drug toxicity, disease diagnosis and prognosis, drug efficacy and nutritional status. Combining information generated from a metabolic profiling platform with that obtained based on genetics, transcriptomics and proteomics research paradigms will pave the way for a better understanding of the mechanisms of disease and toxicity. Metabolomics and nutrition will lay the groundwork for the application of personalized medicine in the 21st century.
pH-sensitive Assembly of Light-Harvesting Dendrimer Zinc Porphyrin Bearing Peripheral Groups of Primary Amine with Poly(ethylene glycol)-b-poly(aspartic acid) in Aqueous Solution (2003)

The light-harvesting dendrimer zinc porphyrin [NH2CH2CH2NHCO]32DPZn, a potential photosensitizer in photodynamic therapy, was synthesized and successfully assembled with poly(ethylene glycol)-b-poly(aspartic acid) to form micelles in PBS buffer (10 mM) following the concept of polyion complex micelle. The coupling reaction between the [CO2H]32DPZn and N-trifluoroacetylethylene-1,2-diamine using the DCC/HOBt method afforded the protected dendrimer [CF3CONHCH2CH2NHCO]32DPZn, which was then mildly hydrolyzed to remove all the trifluoroacetyl protecting groups. Light-scattering measurements showed that the [NH2CH2CH2NHCO]32DPZn has the ability to assemble with poly(ethylene glycol)-b-poly(aspartic acid) to form a spherical micelle with a diameter of about 55 nm, having a narrow size polydispersity in PBS. The micelles were stable both in size and composition up to a 0.90 M (NaCl) salt concentration. The high salt stability is associated with a hydrogen-bonding network formed in the micellar core among the amide groups of the dendrimers and those of poly(aspartic acid) moieties, which could be destroyed by urea, a typical hydrogen-bonding cleaver. Furthermore, the pH range for the stable micelles in physiological saline (0.15 M NaCl) is from 6.2 to 7.4, suggesting the potential of the pH-triggered release of the entrapped dendrimers in the acidic pH environment (pH ∼ 5.0) of the intracellular endosomal compartment.
Dielectric waveguide with transverse index variation that support a zero group velocity mode at a non-zero longitudinal wavevector (2023)

Optical components including a laser based on a dielectric waveguide extending along a waveguide axis and having a refractive index cross-section perpendicular to the waveguide axis, the refractive index cross-section supporting an electromagnetic mode having a zero group velocity for a non-zero wavevector along the waveguide axis.
Interim data analysis of the ADAPT trial using the modified intent to treat (mITT) population re-evaluates Rocapuldencel-T for clinical benefit over standard of care. (2018)

4557 Background: The Phase 3 ADAPT trial evaluates overall survival (OS) of Rocapuldencel-T (Roca) in combination (combo) with standard-of-care (SoC) for the treatment of newly diagnosed mRCC compared to SoC alone. At a February 2017 interim analysis, the study was judged unlikely to demonstrate statistically significant improvement in OS. However, the ITT patients included 39 patients (combo) that did not receive Roca and 14 SoC patients not treated. Therefore, additional analyses for the modified ITT (mITT) was evaluated for OS and immune response (IR) in patients receiving therapy. Methods: The mITT includes 268 combo patients who received ≥1 dose of Roca + sunitinib and 141 SoC patients that received ≥1 cycle of sunitinib. Median OS was calculated by log-rank analysis and correlated with IR measured over 1 year Roca dosing. Also, the potency of Roca product administered (measured by level of IL-12 secretion) was correlated with OS. IR and IL-12 levels were assayed by flow cytometry and correlations were analyzed by the Spearman’s rank correlation coefficient method. Results: The mITT combo arm had a median OS of 30.4 months (mo) vs. 32.4 mo in the SoC arm (HR 0.97 95%Cl 0.72, 1.33), however, > 50% of patients were censored at the time of analysis. To test for delayed effects of Roca, we stratified patients based on follow-up time from randomization. For patients in the 1st quartile (longest follow-up time), OS was 35.5 mo for the combo arm (n = 66, 32% censored) and 22.5 mo for SoC (n = 35, 15% censored). As the percentage of censored subjects increased and follow-up time decreased, the OS advantage in the combo arm diminished (3.5 months, 1st 50% randomized and 3.1 months, 1st 75% randomized). Also, the magnitude of anti-tumor IR after 7 doses of Roca correlated with OS (r = 0.4, p < 0.0001) and IL-12 levels correlated with both IR (r = 0.4, p < 0.0001) and OS (r = 0.27, p < 0.0002). Conclusions: The mITT combo subjects, all of whom received Roca therapy, are anticipated to be the population that could benefit from this treatment. This analysis demonstrated correlations between Roca mechanism of action and OS and longer follow-up time is warranted to assess potential efficacy of Roca. Clinical trial information: NCT01582672.
Blue thermally activated delayed fluorescence emitters with a δ-pyridoindole donor moiety (2018)

Blue TADF emitters with δ-carboline as the donor.