gebhart/patrepeval huggingface dataset:
An artificial chromosome ylAC enables efficient assembly of multiple genes in Yarrowia lipolytica for biomanufacturing (2020)

The efficient use of the yeast Yarrowia lipolytica as a cell factory is hampered by the lack of powerful genetic engineering tools dedicated for the assembly of large DNA fragments and the robust expression of multiple genes. Here we describe the design and construction of artificial chromosomes (ylAC) that allow easy and efficient assembly of genes and chromosomal elements. We show that metabolic pathways can be rapidly constructed by various assembly of multiple genes in vivo into a complete, independent and linear supplementary chromosome with a yield over 90%. Additionally, our results reveal that ylAC can be genetically maintained over multiple generations either under selective conditions or, without selective pressure, using an essential gene as the selection marker. Overall, the ylACs reported herein are game-changing technology for Y. lipolytica, opening myriad possibilities, including enzyme screening, genome studies and the use of this yeast as a previous unutilized bio-manufacturing platform.
A new complementary approach to endoscopy for esophageal cancer diagnosis. (2017)

42 Background: For esophageal cancer, no viable non-invasive detection technologies are available today. In earlier investigations, Cancer Differentiation Analysis (CDA) Technology which measures information relating to both protein fragments and cellular signals in blood samples in a single test has showed a significant advantage in esophageal cancer diagnosis. Methods: Blood samples from 105 individuals in EDTA tubes were collected from Shanghai Changhai Hospital, China, between July and December 2014, CDA and endoscopy tests were carried out on all samples before clinically diagnosed. A performance predication model of CDA and endoscopy test results was built using pROC package in R Language for the data of Area Under the Curve (AUC) and CDA threshold values. Further analysis was carried out based on the CDA threshold values. Results: Out of the 105 individuals, samples from 6 individuals diagnosed as esophageal benign diseases were selected as control group. 99 samples from individuals diagnosed as esophageal cancer, of which 3 and 82 cases were adenocarcinoma and squamous carcinoma, 2, 26, 33, 31 and 7 cases were classified as stage 0,I,II, III, IV, respectively. Details of AUC results of endoscopy, and CDA plus endoscopy for each group were given in Table 1 below. Conclusions: Even though the sensitivity of the endoscopy is usually high due to its pathological examination, this investigation showed that CDA technology could further enhance the diagnosis sensitivity of endoscope, especially for early stage of esophageal cancer, and it (CDA) can be an effective complementary tool to clinical diagnosis and operation determination while obtaining the pathological information via endoscopy. In conclusion, CDA technology is of great value in esophageal diagnosis and therapeutic decision-making. [Table: see text]
Extrinsic Signature Embedding in Text Document Using Exposure Modulation for Information Hiding and Secure Printing in Electrophotography (2005)

Printer identification based on a printed document can provide forensic information to protect copyright and verify authenticity. In addition to intrinsic features (intrinsic signatures) of the printer, modulating the printing process to embed specific signature (extrinsic signatures) will further extend the encoding capacity. Some features generated by modulating EP process such like raggedness of the edge in the text, can be designed and utilized to help develop the extrinsic signature. By increasing the level of modulation, which increase reliability of detection and thus capacity, we can drive the extrinsic signature to a point without perceptual degradation of the image quality. In this paper, we will investigate embedding extrinsic signature in text documents using laser intensity as a signal modulation source and develop extrinsic signatures using both frequency as well as amplitude modulation. Preliminary experimental results showed that it is feasible to embed detectable extrinsic signatures in text characters without degrading perceptual text quality.
Fast on-chip mean filter requiring only integer operations (2007)

This paper presents a novel formulation of the classical mean filtering, which has been shown to stem from the theory of continued fractions as well as from the rules of binomial expansion. Such an alternative formulation of mean filtering is marked by its sufficiency of only a few primitive operations, namely binary shifts and addition (subtraction), in the integer domain. Subsequently, the resultant process of smoothing a digital image using the mean filter is devoid of any floating-point computation, and can be implemented by a simple hardware, thereof. In addition, the formulation has the ability of yielding an approximate solution using fewer operations, which can bring the hardware cost further down. We have tested our method for various images, and have reported some relevant results to demonstrate its elegance, versatility, and effectiveness, specially when an approximate solution is called for.
Supplementary Legends from SLAMF6 as a Regulator of Exhausted CD8<sup>+</sup> T Cells in Cancer (2023)

&lt;p&gt;Supplementary Figure legends&lt;/p&gt;
ChemInform Abstract: 2‐Benzamidoethyl Group — A Novel Type of Phosphate Protecting Group for Oligonucleotide Synthesis. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Preliminary Studies of the Impact of CXCL12 on the Foreign Body Reaction to Pancreatic Islets Microencapsulated in Alginate in Nonhuman Primates: Erratum (2019)

[This corrects the article DOI: 10.1097/TXD.0000000000000890.].
Sufficiently premixed compression ignition of a gasoline-like fuel using three different nozzles in a diesel engine (2011)

Fuels that are more resistant to autoignition allow more time for mixing before combustion occurs and help to reduce nitrogen oxides (NO x ) and smoke in a diesel engine. However, hydrocarbon (HC) and carbon monoxide (CO) emissions are high at low loads because combustion is more likely to take place in lean mixture packets with better mixing caused by longer ignition delays. These problems can be significantly alleviated by managing the mixture strength by changing the injection pressure and the nozzle geometries. A single-cylinder diesel engine is run on a mixture of gasoline and diesel with a research octane number of 91, at different speeds, loads, and exhaust gas recirculation levels using three different nozzles. It is much easier to obtain low NO x and low smoke emissions with this fuel than with a European diesel fuel using the standard nozzle. Larger injector holes and lower injection pressures help to reduce the HC and CO emissions at low loads and also enable the gasoline-like fuel to run at a higher speed of 4000 r/min at a reasonably high load (indicated mean effective pressure) of 10 bar.
A New Method For Measuring Cortical Folding In A 3D Space From MR Images (2006)

Development of technologies in the field of neuroimaging brought an increase interest in the quantification of cortical folding (gyrification), notably for neurogenetic and psychiatric disorders that may result from an early abnormal cortical development. For example, gyrification has been reported altered in schizophrenia (Kulynych, 1997; Harris, 2004), autism (Hardan, 2004), and Williams syndrome (Schmitt, 2002). Algorithms traditionally used to quantify gyrification measure the cortical perimeter on two-dimensional coronal sections of the brain, as first proposed by Zilles (Zilles, 1988). We propose here a new method inspired of the classical equation that takes into account the inherent 3-dimensional nature of the cortex. Brain MRI images were acquired for 30 typically developing individuals (6-30 years old) using a 1.5T scanner. Images were subsequently imported into the software Freesurfer (http://surfer.nmr.mgh.harvard.edu/), for removal of extra-cerebral structures, tissue segmentation and reconstruction of the cortical surface. Resulting cortical surfaces were analyzed using Matlab (http://www.mathworks.com/). For each brainÂs lobe, 3D Gyrification Index (3D-GI) was defined as the ratio of the area of the total folded cortical surface over its convex hull. 3D-GI were then analyzed on two bases. First, we compared 3D-GI to those obtained with classical 2D algorithms for each subject. Then, we analyze the relationship between 3D-GI with variables that are known not to be correlated with GI, like age, weight, gender (Armstrong, 1995). We propose that the three-dimensional method will better detect small change in gyrification. Ultimately, such tools may improve our comprehension of cortical complexity in neurogenetic and psychiatric disorders.
The effect of different criteria on the number of patients blind from open-angle glaucoma (2011)

Excluding visual field status will seriously underestimate the prevalence of glaucoma blindness. In our patient population, 30% more patients were classified as blind by the US than by the WHO definition. Also, 60% more were identified as visually impaired by the US SSA criterion than by the WHO criteria. Visual field assessment is vital to determine visual impairment caused by glaucoma.
Impact of circulating endothelial progenitor cells on the growth of viable tumor rim after treatment with a vascular disrupting agent. (2006)

Proc Amer Assoc Cancer Res, Volume 47, 2006

5710 

Unlike most antiangiogenic drugs, vascular disrupting agents (VDAs) can cause an acute shutdown in tumor blood flow, leading to a subsequent rapid cytotoxic-like process of extensive tumor necrosis. However, the impact of this therapeutic effect is compromised by a remaining viable tumor rim, from which the tumors can rapidly re-grow, a process accompanied by robust angiogenesis. This suggests that the use of a VDA with an antiangiogenic agent e.g., anti-VEGFR-2 antibodies, could be a very effective combination vascular targeting treatment, for which there is some evidence. The basis for rapid and robust angiogenesis at the viable tumor rim after VDA treatment is unclear. We hypothesized that in addition to exploiting the vasculature of the surrounding normal tissue, angiogenesis at the viable rim after VDA treatment must be facilitated by a compensatory host process. We present evidence that the immediate influence of bone marrow derived endothelial progenitor cells (CEPs) homing to the rim, may indeed represent such a contributory mechanism. Thus we found the following: i) administration of a VDA (CA4P or Oxi-4503) to normal (non tumor bearing) mice leads to a marked (3 fold) increase in CEP levels in peripheral blood within 4 hours - in contrast to antiangiogenic agents such as anti-VEGFR-2 antibody (e.g. DC101), which suppress CEPs levels; ii) the CEPs ‘home’ to the viable tumor rim after VDA treatment in two distinct tumor models (human melanoma xenograft and Lewis lung mouse carcinoma); iii) administration of DC101 24 hours prior to the VDA prevents the spike in CEPs which leads to virtually complete obliteration of the viable tumor rim; iv) administration of Oxi-4503 to Id mutant tumor-bearing mice, which cannot mobilize CEPs, leads to a powerful anti-tumor effect, compared to wild type control mice. Overall, our results suggest a compelling role for CEPs in the response to VDAs, and hence, a strategy to maximize the therapeutic potential of both VDAs and antiangiogenic drugs.
Search for physics beyond the standard model in multilepton final states in proton-proton collisions at $$ \sqrt{s} $$ = 13 TeV (2020)

A bstract A search for physics beyond the standard model in events with at least three charged leptons (electrons or muons) is presented. The data sample corresponds to an integrated luminosity of 137 fb − 1 of proton-proton collisions at $$ \sqrt{s} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msqrt> <mml:mi>s</mml:mi> </mml:msqrt> </mml:math> = 13 TeV, collected with the CMS detector at the LHC in 2016–2018. The two targeted signal processes are pair production of type-III seesaw heavy fermions and production of a light scalar or pseudoscalar boson in association with a pair of top quarks. The heavy fermions may be manifested as an excess of events with large values of leptonic transverse momenta or missing transverse momentum. The light scalars or pseudoscalars may create a localized excess in the dilepton mass spectra. The results exclude heavy fermions of the type-III seesaw model for masses below 880 GeV at 95% confidence level in the scenario of equal branching fractions to each lepton flavor. This is the most restrictive limit on the flavor-democratic scenario of the type-III seesaw model to date. Assuming a Yukawa coupling of unit strength to top quarks, branching fractions of new scalar (pseudoscalar) bosons to dielectrons or dimuons above 0.004 (0.03) and 0.04 (0.03) are excluded at 95% confidence level for masses in the range 15–75 and 108–340 GeV, respectively. These are the first limits in these channels on an extension of the standard model with scalar or pseudoscalar particles.
Terminal Deoxynucleotidyl Transferase Activity in Human Leukemic Cells and in Normal Human Thymocytes (1975)

Peripheral leukocytes from patients with and without leukemia were assayed for presence of terminal deoxynucleotidyl transferase. Activity of this enzyme was detected in circulating leukemic cells from 11 to 13 patients with acute lymphoblastic leukemia, and in one of four with chronic myelogenous leukemia in blast crisis, but not in leukocytes from patients with other kinds of leukemia or in normal leukocytes. Its presence in a patient with chronic myelogenous leukemia in blast crisis lends biochemical support to the suggestion that some patients with chronic myelogenous leukemia undergo a lymphoblastic rather than a myeloblastic crisis. The thymocyte and leukemic-cell enzyme have the same substrate and primer preference. Normal thymocytes and leukemic cells contain two forms of terminal deoxynucleotidyl transferase that can be separated by phosphocellulose chromatography. The enzyme may provide a means for classifying leukemic cells on a biochemical basis independently of classic morphologic and clinical criteria.
MEMS Based Dual-axes Confocal Reflectance Handheld Microscope for in vivo Imaging (2006)

We demonstrate a dual-axes confocal reflectance microscope in a 10-mm diameter handheld package. Miniaturization is achieved by using a barbell-shaped, gimbaled, two-dimensional MEMS scanner that is actuated by self-aligned vertical comb actuators. The maximum DC optical scan angles are plusmn3.3deg on the inner axis and plusmn1.0deg on the outer axis, and the corresponding resonance frequencies are 3.54 kHz and 1.1 kHz. The imaging rate is 30 frames/second, and the microscope achieves full-width-half-maximum (FWHM) transverse and axial resolutions of 8 mum and 10 mum, respectively
Association between Maternal and Infant Class I and II HLA Alleles and of Their Concordance with the Risk of Perinatal HIV Type 1 Transmission (2002)

We aimed to investigate the influence of class I and class II HLA specificities and of the concordance between maternal and infant HLA on vertical HIV-1 transmission. HLA typing of samples from mothers and infants enrolled in the Ariel study, a perinatal HIV-1 transmission cohort including 203 mother-infant pairs, was performed by serological and molecular methods. HLA effects were evaluated alone and by multivariate modeling considering also other known predictors of perinatal HIV-1 transmission (maternal viral load, antiretroviral therapy, duration of rupture of membranes, and histological chorioamnionitis). Modest associations were seen with specific HLA markers (increased risk with infant B67 and B58 and maternal DR1; decreased risk with maternal B12), but these were not statistically significant after adjusting for multiple comparisons. Mother-infant concordance at any class I locus was a strong predictor of transmission (odds ratio [OR], 4.16; p = 0.028). Transmission was not associated with class II concordance. Class I HLA concordance retained its importance after adjusting for maternal viral load, antiretroviral therapy, duration of rupture of membranes or histological chorioamnionitis. In multivariate modeling, only class I concordance (OR, 3.59; p = 0.069) and chorioamnionitis (OR, 3.79; p = 0.030) were retained as independent predictors of transmission. HLA alleles, and in particular the class I concordance between maternal and neonatal HLA, may regulate the risk of perinatal HIV-1 transmission.
Abstract 14581: Vascular Access and Closure Management in Patients With Severe and Morbid Obesity Undergoing Transcatheter Aortic Valve Replacement (2019)

Background: Severe and morbid obesity (S/MO) (Body mass index>=35 Kg/m2) is a current epidemic that poses major challenges in vascular access and closure during transcatheter aortic valve replaceme...
Tympanal hearing in the sarcophagid parasitoid fly Emblemasoma sp.: the biomechanics of directional hearing (1999)

In Diptera, tympanal hearing has evolved at least twice in flies that belong to two different families, the tachinids and the sarcophagids. Common to these flies is their parasitoid reproductive strategy, both relying on the acoustic detection and localization of their hosts, singing insects, by means of tympanal hearing organs. In the present study, the external anatomy of the unusual hearing organs of the sarcophagid fly Emblemasoma sp. is described. The sarcophagid ears bear numerous anatomical similarities with those of ormiine tachinids: they are located on the ventral prosternum and possess a pair of scolopidial mechanoreceptive sense organs. A striking difference, however, resides in the lack of a well-defined presternum in the sarcophagid tympanal system. Instead, a deep longitudinal fold, the tympanal fold, spans both hemilateral tympanal membranes across the midline of the animal. Measured using laser Doppler vibrometry, the tympanal mechanical response in the sound field reveals asymmetrical deflection shapes that differ from those of tachinids. Lacking a central fulcrum, the sarcophagid tympanal complex presents different vibrational modes that also result in interaural coupling. The evolutionarily convergent, yet distinct, solutions used by these two small auditory systems to extract directional cues from the sound field and the role of tympanal coupling in this process are discussed.
Noether's variational theorem II and the BV formalism (2002)

We review the basics of the Lagrangian approach to field theory and recast Noether's Second Theorem formulated in her language of dependencies using a slight modernization of terminology and notation. We then present the Cattaneo-Felder sigma model and work out the Noether identities or dependencies for this model. We review the description of the Batalin-Vilkovisky formalism and show explicitly how the anti-ghosts encode the Noether identities in this example.
A Photolabile Ligand for Light-Activated Release of Caged Copper (2008)

A photosensitive caged copper complex has been prepared from a tetradentate ligand (H2cage) composed of two pyridyl-amide arms connected by a photoreactive nitrophenyl group. H2cage binds Cu2+ in aqueous solution with a stability constant (log beta) of 10.8, which corresponds to a KD of 16 pM at pH 7.4. The neutral Cu2+ complex, [Cu(OH2)(cage)], crystallizes as a distorted trigonal bipyramid coordinated by two amide and two pyridyl N atoms, with a water molecule bound in the trigonal plane. Photolysis with 350 nm UV light cleaves the ligand backbone to release photoproducts with significantly diminished affinity for Cu2+, thereby uncaging the metal ion. When coordinated as the caged complex, copper has diminished reactivity to produce hydroxyl radicals from Fenton-like reaction mixtures containing hydrogen peroxide and ascorbic acid. Postphotolysis, uncaged copper promotes hydroxyl radical formation under the same conditions. The strategy of caging copper is promising for applications where light could be used to trigger release of copper as a pro-oxidant to increase oxidative stress or as a tool to release copper intracellularly to study mechanisms of copper trafficking.
Statistical modeling for the minimum standby supply voltage of a full SRAM array (2007)

This paper presents two fast and accurate methods to estimate the lower bound of supply voltage scaling for standby SRAM/cache leakage power reduction of an SRAM array. The data retention voltage (DRV) defines the minimum supply voltage for a cell to hold its state. Within-die variation causes a statistical distribution of DRV for individual cells in a memory array, and cells far out the tail (i.e. >6sigma) limit the array DRV for large memories. We present two statistical methods to estimate the tail of the DRV distribution. First, we develop a new statistical model based on the connection between DRV and static noise margin (SNM). Second, we apply our Statistical Blockade tool to obtain fast Monte-Carlo simulation and a generalized Pareto distribution (GPD) model for comparison. Both the new model and the GPD model offer a high accuracy (<2% error) and a huge speed-up (>10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> times for 1 G-b memory) over Monte-Carlo simulation. In addition, both models show a very close agreement with each other at the tail even beyond 7sigma.
Tricarboxylic Acid Cycle Intermediates in Chronic Renal Failure (1987)

In 21 uraemic subjects not yet requiring dialysis, the serum values of citrate, fumarate, oxalacetate and malate were significantly increased, so that the sum of the concentrations of the TCA-cycle intermediates were increased threefold compared to that of 18 control subjects. The replenishment of TCA intermediates could, in theory, occur by several anaplerotic reactions, mainly those catalysed by pyruvate-carboxylase and malic enzyme. The overall pattern detected in uraemic patients is similar to that observed in rat skeletal muscle during exercise, in which increased acetyl CoA has been found.
Incorporate day-ahead robustness and real-time incentives for electricity market design (2022)

In this paper, we propose a two-stage electricity market framework to explore the participation of distributed energy resources (DERs) in a day-ahead (DA) market and a real-time (RT) market. The objective is to determine the optimal bidding strategies of the aggregated DERs in the DA market and generate online incentive signals for DER-owners to optimize the social-welfare taking into account network operational constraints. Distributionally robust optimization is used to explicitly incorporate data-based statistical information of renewable forecasts into the supply/demand decisions in the DA market. We evaluate the conservativeness of bidding strategies distinguished by different risk aversion settings. In the RT market, a bi-level time-varying optimization problem is proposed to design the online incentive signals to tradeoff the RT imbalance penalty for distribution system operators (DSOs) and the costs of individual DER-owners. This enables tracking their optimal dispatch to provide fast balancing services, in the presence of time-varying network states while satisfying the voltage regulation requirement. Simulation results on both DA wholesale market and RT balancing market demonstrate the necessity of this two-stage design, and its robustness to uncertainties, the performance of convergence, the tracking ability and the feasibility of the resulting network operations.
Noggin haploinsufficiency differentially affects tissue responses in destructive and remodeling arthritis (2006)

Tight spatiotemporal control of BMP signaling appears to be critical in the response of joint tissues in models of arthritis.