gebhart/patrepeval huggingface dataset:
Optimization of Golden Gate assembly through application of ligation sequence-dependent fidelity and bias profiling (2018)

ABSTRACT Modern synthetic biology depends on the manufacture of large DNA constructs from libraries of genes, regulatory elements or other genetic parts. Type IIS restriction enzyme-dependent DNA assembly methods (e.g., Golden Gate) enable rapid one-pot, ordered, multi-fragment DNA assembly, facilitating the generation of high-complexity constructs. The order of assembly of genetic parts is determined by the ligation of flanking Watson-Crick base-paired overhangs. The ligation of mismatched overhangs leads to erroneous assembly, and the need to avoid such pairings has typically been accomplished by using small sets of empirically vetted junction pairs, limiting the number of parts that can be joined in a single reaction. Here, we report the use of a comprehensive method for profiling end-joining ligation fidelity and bias to predict highly accurate sets of connections for ligation-based DNA assembly methods. This data set allows quantification of sequence-dependent ligation efficiency and identification of mismatch-prone pairings. The ligation profile accurately predicted junction fidelity in ten-fragment Golden Gate assembly reactions, and enabled efficient assembly of a lac cassette from up to 24-fragments in a single reaction. Application of the ligation fidelity profile to inform choice of junctions thus enables highly flexible assembly design, with &gt;20 fragments in a single reaction.
Phase-Change Contrast Agents for Imaging and Therapy (2012)

Phase-change contrast agents (PCCAs) for ultrasound-based applications have resulted in novel ways of approaching diagnostic and therapeutic techniques beyond what is possible with microbubble contrast agents and liquid emulsions. When subjected to sufficient pressures delivered by an ultrasound transducer, stabilized droplets undergo a phase-transition to the gaseous state and a volumetric expansion occurs. This phenomenon, termed acoustic droplet vaporization, has been proposed as a means to address a number of in vivo applications at the microscale and nanoscale. In this review, the history of PCCAs, physical mechanisms involved, and proposed applications are discussed with a summary of studies demonstrated in vivo. Factors that influence the design of PCCAs are discussed, as well as the need for future studies to characterize potential bioeffects for administration in humans and optimization of ultrasound parameters.
Magnetic Resonance Imaging of Isolated Skeletal Muscles (1996)

Muscle contraction results in increased T2 relaxation time, but intracellular water hardly contributes to the increase in this value. Therefore, an increase in extracellular water may be the main cause of the increase in T2 relaxation time seen in exercised muscles.
Automatic classification of hand drawn geometric shapes using constructional sequence analysis (2005)

A method for automatically assessing theconstructional sequence from a neuropsychologicaldrawing task using Hidden Markov Models is presented.We also present a method of extracting and identifyingthe position of individual pen strokes relating toindividual sides of a shape within a drawing to formtraining and testing sequences. Our results from twoexperiments using data from patients with visuo-spatialneglect show the HMM classifier is able to generalise onincorrectly extracted sequences and obtain a diagnosticclassification which can be used alongside other forms ofconventional assessment.
Losses in GaAs microstrip (1990)

Newly measured data for the loss of microstrip on 4 mil GaAs from DC to 40 GHz are presented. These data were taken from transmission measurements of lightly coupled, multiple-half-wave-length resonators. A comparison of the loss data with the predicted losses from three popular CAE (computer-aided engineering) tools is provided. The loss models provided by two out of three software vendors agree fairly well with measured data through 40 GHz. Since the measured loss roughly follows a square-law frequency relationship through 20 GHz, it should be possible to adjust the loss below this frequency and above 1 GHz by modifying the resistivity of the conductor in the simulator.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
What's the Gist? Privacy-Preserving Aggregation of User Profiles (2014)

Over the past few years, online service providers have started gathering increasing amounts of personal information to build user profiles and monetize them with advertisers and data brokers. Users have little control of what information is processed and are often left with an all-or-nothing decision between receiving free services or refusing to be profiled. This paper explores an alternative approach where users only disclose an aggregate model -- the "gist" -- of their data. We aim to preserve data utility and simultaneously provide user privacy. We show that this approach can be efficiently supported by letting users contribute encrypted and differentially-private data to an aggregator. The aggregator combines encrypted contributions and can only extract an aggregate model of the underlying data. We evaluate our framework on a dataset of 100,000 U.S. users obtained from the U.S. Census Bureau and show that (i) it provides accurate aggregates with as little as 100 users, (ii) it generates revenue for both users and data brokers, and (iii) its overhead is appreciably low.
Pediatric cardiac xenograft growth in a rhesus monkey‐to‐baboon transplantation model (1996)

Abstract: It is unclear that organs from other species could grow successfully in the environment of another species. We evaluated the growth capacity of a cardiac xenograft in a rhesus monkey‐to‐juvenile baboon orthotopic heart transplantation model where there exists a discrepancy of the organ size and its growth rate between donor and recipient species. Eight recipient baboons who survived over 60 days were followed for body weight (BW) and the size of xenografts (left ventricular end‐diastolic volume, LVEDV; left ventricular mass, LVM; and left ventricular posterior wall thickness, LVPWT) by echocardiography at 1 week and monthly after xenotransplantation. One baboon is growing along the normal growth curve. The other three baboons gained BW in parallel with normal growth curve except for a few months after surgery. LVEDV, LVM, and LVPWT increased constantly in these four baboons. In one baboon, BW increased over 1 year to 5.5 kg (which was almost the same as BW of adult rhesus monkey) and then plateaued. LVEDV, LVM, and LVPWT increased until 1 year posttransplantation, but then stopped when BW plateaued. In the other four baboons who did not gain BW because of infectious complications or side effects by immunosuppressive therapy, LVEDV, LVM, and LVPWT did not change significantly. We conclude that a cardiac xenograft from a rhesus monkey can successfully grow and support normal growth of a juvenile baboon, but whether a recipient can grow beyond the donor size is yet unknown.
Virtue Plane Mapping: A Method of Rendering into Depth Images (2008)

首先推导与归纳了图像三维变换中像素深度场的变换规律,同时提出了基于深度场和极线原则的像素可见性别方法,根据上述理论和方法,提出一种基于深度图像的建模与绘制(image-based modeling and rendering,简称IBMR)技术,称为虚平面映射.该技术可以基于图像空间内任意视点对场景进行绘制.绘制时,先在场景中根据视线建立若干虚拟平面,将源深度图像中的像素转换到虚平面上,然后通过对虚平面上像素的中间变换,将虚平面转换成平面纹理,再利用虚平面的相互拼接,将视点的成像以平面纹理映射的方式完成.新方法还能在深度图像内侧,基于当前视点快速获得该视点的全景图,从而实现视点的实时漫游.新方法视点运动空间大、存储需求小,且可以发挥图形硬件的纹理映射功能,并能表现物体表面的三维凹凸细节和成像视差效果,克服了此前类似算法的局限和不足.
Calibration of Multiple Depth Sensor Network Using Reflective Pattern on Spheres: Theory and Experiments (2020)

SUMMARY The usage of depth data from time-of-flight or any equivalent devices overcomes visual challenges presented under low illumination. For integrating such data from multiple sources, the paper proposes a novel tool for the calibration of sensors. The proposed tool consists of retro-reflective stripped spheres. To correctly estimate these spheres, the paper investigates the performance of spherical estimations from either infrared or depth data. The relationship between sensors is determined by calculating the poses between the calibration tool and each sensor. The paper evaluates and compares the proposed approach against other state-of-the-art approaches in terms of shape reconstruction and spatial consistency.
Coherent contol and readout of a coupled quantum dot-donor in silicon. (2018)

Abstract not provided.
Why do isoluminant stimuli appear slower? (1988)

There is ample evidence that the perception of movement, both real and apparent, is substantially impaired at isoluminance. Models of movement perception require spatial and temporal information about the stimulus. We ask whether changes at isoluminance result from a spatial or a temporal error or uncertainty. Reaction times to three kinds of stimulus were measured: (a) temporal stimuli, such as the onset of a square in a known location; (b) spatial stimuli, a vernier displacement of two squares; and (c) spatiotemporal stimuli, moving squares either starting or stopping. The results suggest that there is relatively little effect of isoluminance on purely temporal tasks (a). Longer reaction times were, however, obtained for detecting vernier offset (b). The reaction times to moving stimuli (c) were also slower at isoluminance to an extent that implies that perceived velocity at isoluminance is approximately 30% less than that seen at 8% contrast. The slowing of reaction times at isoluminance could be mimicked by adding random positional jitter to a nonisoluminant moving stimulus and also by presenting a low-contrast monochromatic stimulus. A simple explanation of the data is given in terms of a motion-detecting unit coupled to a temporal integrator. It is shown how such a unit can encode perceived velocity. The results of these experiments suggest that the neural coding of isoluminant stimuli is similar to that of low-contrast luminance stimuli and therefore that isoluminance may not be an effective method to find out whether specific visual mechanisms are color-blind.
Iron stress and genetic response in cyanobacteria : fur genes from Synechococcus PCC 7942 and Anabaena PCC 7120 (2002)

Fur (Ferric uptake regulator) is a DNA-binding protein which represses the transcription of iron-regulated promoters using Fe2+ as a cofactor. In Gram negative bacteria, fur controls the expression of toxins and virulence factors when facing iron-stress. Iron is a key element limiting the growth and proliferation of phytoplankton. We have cloned the fur-gene from the cyanobacterium Synechococcus PCC 7942, applying the polymerase chain reaction (PCR) technique. The DNA fragments amplified encodes a Fur-type protein, which conserves the main motifs found in the family of Fur proteins. Recombinant Fur protein was successfully overproduced, reaching about 15 % of the total protein content. Also, a Fur protein was identified in the filamentous, nitrogen-fixing cyanobacterium Anabaena PCC 7120.
Supplementary Figure Legends from Assessing Immune-Related Adverse Events of Efficacious Combination Immunotherapies in Preclinical Models of Cancer (2023)

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13C and 1H nuclear magnetic resonance spectroscopy of C-19 and 6β-methyl substituted steroids: long-range shift effects in conformational analysis (1979)

13 C and 1 H nmr spectra were obtained and assigned for nine C-19 substituted cholest-5-enes, three 6β-substituted 19-norcholest-5(10)-enes, and several related steroids. 13 C chemical shift effects have previously not been studied in either C-19 substituted steroids or in cholest-5(10)-enes. In the present study, substituent effects on the 13 C chemical shifts of the α, β, γ, and δ carbons were evaluated in detail. Although the substituent in C-19 substituted and 6β-methyl substituted steroids is less rigidly oriented with respect to the rest of the molecule than in ring-substituted steroids, similar shift effects were observed. In cholest-5-enes the observed 13 C and 1 H shift effects and the temperature dependence of the 13 C shifts indicate that the preferred orientation of the C-19 substituent is anti to C-1. The relative stabilities of the rotamers can be attributed to the orientation of the C-19 substituent with respect to the double bond. This interpretation is supported by the fact that the preferred orientation of the iodine in 6β-iodomethyl-19-norcholest-5(10)-en-3β-ol has the same spacial relationship with respect to the double bond, i.e., gauche to C-5 and C-7.
Remote gestational weight gain monitoring in a large low‐risk US population (2021)

Engagement with the mobile app was associated with increased adherence to the IOM gestational weight gain guidelines and with increased postpartum weight loss. Use of remote patient monitoring in conjunction with mHealth technology may be a strategy to improve adherence to IOM guidelines.
Interfacial modification for an aluminum/epoxy resin laminated composite (1994)

The surface of aluminum plates were modified by coating with a thin layer of copper and subsequently reacting with 2-mercaptobenzimidazole (MBIH) or benzotriazole (BTAH). Chemisorption of an epoxy compound on top of adsorbed MBIH and BTAH on copper metal has been investigated by the use of surface enhanced Raman scattering (SERS). Aluminum-polymer laminated composites were prepared by sandwiching aluminum plates and the epoxy resin reinforced with carbon fabrics. Experimental data show that the laminated composites composed of the Cu-MBIH modified aluminum plates exhibit a higher strength and better water-resistance.
LF Indoor Location and Identification System (2009)

Abstract In this paper, a low-frequency RFID location system based on a matrix of quad antennae placed under a floor surface is described. A prototype system was used for parameterisation and feasibility tests. The results show that it is possible to build a location system using floor quad antennae.
Heat Capacity of β-Manganese. (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHeat Capacity of β-Manganese.R. A. Butera and R. S. CraigCite this: J. Chem. Eng. Data 1965, 10, 1, 38–39Publication Date (Print):January 1, 1965Publication History Published online1 May 2002Published inissue 1 January 1965https://doi.org/10.1021/je60024a015RIGHTS & PERMISSIONSArticle Views36Altmetric-Citations3LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (212 KB) Get e-Alertsclose Get e-Alerts
Association among Vitamin D, Retinoic Acid-Related Orphan Receptors, and Vitamin D Hydroxyderivatives in Ovarian Cancer (2020)

Vitamin D and its derivatives, acting via the vitamin D receptor (VDR) and retinoic acid-related orphan receptors γ and α (RORγ and RORα), show anticancer properties. Since pathological conditions are characterized by disturbances in the expression of these receptors, in this study, we investigated their expression in ovarian cancers (OCs), as well as explored the phenotypic effects of vitamin D hydroxyderivatives and RORγ/α agonists on OC cells. The VDR and RORγ showed both a nuclear and a cytoplasmic location, and their expression levels were found to be reduced in the primary and metastatic OCs in comparison to normal ovarian epithelium, as well as correlated to the tumor grade. This reduction in VDR and RORγ expression correlated with a shorter overall disease-free survival. VDR, RORγ, and RORα were also detected in SKOV-3 and OVCAR-3 cell lines with increased expression in the latter line. 20-Hydroxy-lumisterol3 (20(OH)L<sub>3</sub>) and synthetic RORα/RORγ agonist SR1078 inhibited proliferation only in the OVCAR-3 line, while 20-hydroxyvitamin-D<sub>3</sub> (20(OH)D<sub>3</sub>) only inhibited SKOV-3 cell proliferation. 1,25(OH)<sub>2</sub>D<sub>3</sub>, 20(OH)L<sub>3</sub>, and SR1078, but not 20(OH)D<sub>3</sub>, inhibited spheroid formation in SKOV-3 cells. In summary, decreases in VDR, RORγ, and RORα expression correlated with an unfavorable outcome for OC, and compounds targeting these receptors had a context-dependent anti-tumor activity in vitro. We conclude that VDR and RORγ expression can be used in the diagnosis and prognosis of OC and suggest their ligands as potential candidates for OC therapy.
The Effect of Postural Pelvic Dynamics on the Three-dimensional Orientation of the Acetabular Cup in THA Is Patient Specific (2020)

Future studies concerning THA (in)stability should not only include the initial acetabular cup orientation, but also they need to incorporate the effect of sagittal pelvic dynamics on the individual 3-D acetabular cup orientation. Clinicians can also use the developed tool, www.3d-hip.com, to calculate the acetabular cup's orientation in other instances, such as for patients with spinopelvic imbalance.
Novel Room Temperature Inorganic Ionic Liquids (2004)

Abstract New inorganic ionic liquids (IIL) consisting of an inorganic polyoxometalate anion with the Keggin structure and a sodium cation, that is Na 13 [Ln(TiW 11 O 39 ) 2 ]· x H 2 O [where Ln = lanthanide (type 1)], Na 5 [MTiW 11 O 39 ]· x H 2 O and Na 6 [MTiW 11 O 39 ]· x H 2 O [where M = transition metal (type 2)], were prepared and their physicochemical properties were investigated. These ionic liquids were characterized by NMR and IR spectroscopy and by elemental analysis. Their melting point, viscosity, conductivity, thermal stability, and miscibility with water and organic solvents were determined. When the temperature is below ambient temperature (about 298 K) these ionic liquids are almost immiscible with water. When the temperature is raised, the solubility of the new ionic liquids increases sharply. The influence of the size and of the charge density of both the cations and anions on these properties was examined. The most remarkable feature of IILs is that water is their indispensable component. The role of the water molecule in ionic liquids is similar to that of crystalline water in hydrated compounds. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2004)
A phase I trial of palbociclib in combination with dexamethasone in relapsed or refractory adult B-cell acute lymphoblastic leukemia (ALL). (2019)

TPS7065 Background: c-Myb is a DNA-binding transcription factor that is highly expressed in immature hematopoietic cells. c-Myb and its products are essential in regulating normal hematopoiesis and influencing leukemogenesis. Knockdown of c-Myb causes cell cycle arrest and apoptosis in pre-B-ALL cells. The effects of c-Myb depend on transcriptional regulation of CDK6 and Bcl-2. c-Myb-silenced Ph+ ALL cells exhibit Rb-dependent cell cycle arrest and apoptosis, both of which are rescued by ectopic expression of cyclin D3, CDK6, and Bcl-2 expression. Preclinical studies suggest that the cytotoxic activity of dexamethasone in ALL cells may be due to decreased c-Myb expression and reduced Bcl-2 levels. Thus, the novel combination of palbociclib, a small molecule CDK4/6 inhibitor, and dexamethasone is a logical approach for the treatment of B-cell ALL. Methods: This is a single arm, phase I, dose escalation study with a traditional 3+3 design. Adult patients with relapsed or refractory B-cell ALL are eligible. Patients with Ph+ ALL must be refractory to or intolerant of standard tyrosine kinase inhibitor therapy. Patients receive a 1-week lead-in of palbociclib alone followed by induction with 4 weeks of palbociclib and dexamethasone. If an adequate response is seen, patients move to maintenance therapy, which consists of 1 week of palbociclib plus dexamethasone followed by 3 weeks of palbociclib alone. Treatment continues until disease progression, dose limiting toxicity, or availability of an alternative therapy. The primary endpoints are dose limiting toxicity and maximum tolerated dose of palbociclib and dexamethasone. Correlative studies, which are performed on pretreatment, day +1 and day +8 samples, include RB phosphorylation and FOXM1 expression as measures of palbociclib activity; CD19+ cell gene expression profiling of (1) p21 expression as an indicator of cell cycle activity, (2) S-Phase, Annexin V/Caspase 3 activation as indicators of proliferation and apoptosis and (3) Myb and Bcl-2 expression as indicators of dexamethasone sensitivity. Cohort 1 is currently enrolling. Once a maximum tolerated dose is established, an expansion cohort is planned. Clinical trial information: NCT03472573.
In vitro induction of MUC-1 peptide-specific type 1 T lymphocyte and cytotoxic T lymphocyte responses from healthy multiparous donors (1996)

We have recently provided evidence that there is a natural immunization against human cancer-associated MUC-1 mucin epitopes during pregnancy by studying MUC-1 Ag-specific T cell lines established from multiparous women. Using this experimental model system, we now report that MUC-1 peptide-specific MHC class I-restricted CTLs can be generated in vitro using T cells from multiparous women stimulated with synthetic MUC-1 peptide-loaded, autologous APCs. The complexity of cytokines produced in response to the MUC-1 peptide by anti-MUC-1 T-cells was examined. IFN-gamma was generated by MUC-1-specific T cell lines in long term cultures, whereas in short term cultures, both IFN-gamma and IL-4 were produced. The presence of MUC-1-reactive T cells in multiparous women is consistent with their potential role in immune surveillance and provides a rationale for the use of certain synthetic MUC-1 peptides for active specific immunotherapy of human carcinomas.
Geometric distortion calibration using a pinhole mask (2018)

Adaptive optics (AO) systems deliver high-resolution images that may be ideal for precisely measuring positions of stars (i.e. astrometry) if the system has stable and well-calibrated geometric distortions. Calibration units equipped with back-illuminated pinhole masks are often utilized to measure instrumental distortions. AO systems on the largest ground-based telescopes, such as the W. M. Keck Observatory and the Thirty Meter Telescope, or with large fields of view, such as the ‘imaka ground-layer adaptive optics experiment, require pinhole positions known to 20 nm to achieve astrometric precisions of 0.001 of a resolution element. We characterized the nonlinear geometric distortion of a simple imaging system using a photo-lithographic pinhole reference grid to be 1650 nm RMS with a final residual of 41 nm RMS (20.5 &mu;as for TMT). Our system model uses fourth order polynomials to model the distortion and allows the reference positions of the pinholes to vary. The nonlinear deviations in the pinhole pattern with respect to the manufacturing design of a square pattern are estimated to be 29 nm over a 1200 mm<sup>2</sup>, which reflects the additional error induced in a distortion measurement when assuming the pattern is perfectly manufactured.