gebhart/patrepeval huggingface dataset:
Temperature fluctuations during deep temperature cryopreservation reduce PBMC recovery, viability and T-cell function (2013)

The ability to analyze cryopreserved peripheral blood mononuclear cell (PBMC) from biobanks for antigen-specific immunity is necessary to evaluate response to immune-based therapies. To ensure comparable assay results, collaborative research in multicenter trials needs reliable and reproducible cryopreservation that maintains cell viability and functionality. A standardized cryopreservation procedure is comprised of not only sample collection, preparation and freezing but also low temperature storage in liquid nitrogen without any temperature fluctuations, to avoid cell damage. Therefore, we have developed a storage approach to minimize suboptimal storage conditions in order to maximize cell viability, recovery and T-cell functionality. We compared the influence of repeated temperature fluctuations on cell health from sample storage, sample sorting and removal in comparison to sample storage without temperature rises. We found that cyclical temperature shifts during low temperature storage reduce cell viability, recovery and immune response against specific-antigens. We showed that samples handled under a protective hood system, to avoid or minimize such repeated temperature rises, have comparable cell viability and cell recovery rates to samples stored without any temperature fluctuations. Also T-cell functionality could be considerably increased with the use of the protective hood system compared to sample handling without such a protection system. This data suggests that the impact of temperature fluctuation on cell integrity should be carefully considered in future clinical vaccine trials and consideration should be given to optimal sample storage conditions.
Novel Point Mutation in the Splice Donor Site of Exon-Intron Junction 6 of the Androgen Receptor Gene in a Patient with Partial Androgen Insensitivity Syndrome* (2000)

Androgen receptor (AR) gene mutations have been shown to cause androgen insensitivity syndrome with altered sexual differentiation in XY individuals, ranging from a partial insensitivity with male phenotype and azoospermia to a complete insensitivity with female phenotype and the absence of pubic and axillary sexual hair after puberty. In this study we present an 11-yr-old XY girl, with clinical manifestations peculiar for impaired androgen biological action, including female phenotype, blind-ending vagina, small degree of posterior labial fusion, and absence of uterus, fallopian tubes, and ovaries. At the time of the diagnosis the patient had a FSH/LH ratio according to the puberal stage, undetectable 17beta-estradiol, and high levels of testosterone (80.1 ng/mL). After bilateral gonadectomy, performed at the age of 11 yr, histological examination showed small embryonic seminiferous tubules containing prevalently Sertoli cells and occasional spermatogonia together with abundant fibrous tissue. Molecular study of the patient showed a guanine to thymine transversion in position +5 of the donor splice site in the junction between exon 6 and intron 6 of the AR gene. The result of RT-PCR amplification of the AR messenger ribonucleic acid from cultured genital skin fibroblasts of the patient suggests that splicing is defective, and intron 6 is retained in most of the receptor messenger ribonucleic acid molecules. We show by immunoblotting that most of the expressed protein lacks part of the C-terminal hormone-binding domain, and a small amount of normal receptor is observed. This is probably responsible for the reduced binding capacity in genital skin fibroblasts of the patient. The molecular basis of the alteration in this case is a novel, uncommon mutation, leading to a phenotype indicative of a partial androgen insensitivity syndrome, Quigley's grade 5.
Does Neurorehabilitation Play a Role in the Recovery of Walking in Neurological Populations?a (1998)

This review demonstrates that neurorehabilitation approaches, based on recent neuroscience findings, can enhance locomotor recovery after a spinal cord injury or stroke. Findings are presented from more than 20 clinical studies conducted by numerous research groups on the effect of locomotor training using either body weight support (BWS), functional electrical stimulation (FES), pharmacological approaches or a combination of them. Among the approaches, only BWS-assisted locomotor training has been demonstrated to have a greater effect than conventional or locomotor training alone. However, when study results were combined and weighted for the number of subjects, the results indicated that there is a gradient of effects from small changes with the immediate application of FES or BWS to larger changes when locomotor training is combined with FES or BWS or pharmacological approaches. The findings of these studies suggest that these neurorehabilitation approaches do play a role in the recovery of walking in subjects with spinal cord injury or stroke. Several factors contribute to the potential for recovery including the site, etiology, and chronicity of the injury, as well as the type, duration, and specificity of the intervention and whether interventions are combined. Furthermore, how these neurorehabilitation approaches may take advantage of the plasticity process following neurological lesion is also discussed.
Casing Integrity Study for Heavy-Oil Production in Cold Lake (2010)

Abstract The Cold Lake heavy oil development is located in northeast Alberta, Canada. It began commercial operation in 1985 and uses a thermal recovery process called cyclic steam stimulation (CSS). During steaming cycles, the dilation and re-compaction that occur within the reservoir cause the overburden to deform much like the motion of flexing a thick telephone book. At weak overburden layers, shear slip plane(s) can form due to excessive shear stress overcoming the interlayer cohesion. Over multiple steaming/production cycles, the cyclic flexing and associated shear slip may lead to overburden casing fatigue failures. In this paper, a multi-scale geomechanics modeling methodology is presented to predict the onset of failure due to CSS-related ultra low cyclic fatigue (ULCF). The modeling methodology consists of: (i) converting geological data into a representative finite element model of a single or multiple CSS pads, (ii) constructing a near-well submodel that includes thermal cement and casing, and (iii) constructing a detailed casing and connection submodel to predict the ULCF life of a pipe body or connection. To predict the ULCF life of the casing and connection, an algorithm based on the concept of cyclic void growth is incorporated into the submodel. It provides the capability to predict the number of steam cycles to failure using the concepts of demand and capacity. This enables studying the effects of alternative steaming practices on overburden shear slip and casing/connection life. Based on the learning from the multi-scale modeling, it is found that shear displacements on a shear slip plane can be superimposed using a single-well solution. By applying steaming and production scaling functions, the shear slip can be determined at any location and time. Integration of the single-well solution with ULCF algorithm has facilitated development of a new software tool that can be used to manage CSS operations in Cold Lake.
MagneShape: A Non-electrical Pin-Based Shape-Changing Display (2022)

Pin-based shape-changing displays can present dynamic shape changes by actuating a number of pins. However, the use of many linear actuators to achieve this makes the electrical structure and mechanical construction of the display complicated. We propose a simple pin-based shape-changing display that outputs shape and motions without any electronic elements. Our display consists of magnetic pins in a pin housing, with a magnetic sheet underneath it. The magnetic sheet has a specific magnetic pattern on its surface, and each magnetic pin has a magnet at its lower end. The repulsive force generated between the magnetic sheet and the magnetic pin levitates the pin vertically, and the height of the pin-top varies depending on the magnetic pattern. This paper introduces the basic structure of the display and compares several fabrication methods for the magnetic pins, to highlight the applicability of this method. We have also demonstrated some applications and discussed future possibilities.
Supplementary Figure 2 from Phosphatidylinositol 3-Kinase Hyperactivation Results in Lapatinib Resistance that Is Reversed by the mTOR/Phosphatidylinositol 3-Kinase Inhibitor NVP-BEZ235 (2023)

Supplementary Figure 2 from Phosphatidylinositol 3-Kinase Hyperactivation Results in Lapatinib Resistance that Is Reversed by the mTOR/Phosphatidylinositol 3-Kinase Inhibitor NVP-BEZ235
Abstract 4928: MiR expression profiles can predict response to systemic treatment in patients with advanced colorectal cancer (2016)

Abstract Background and aim: Patients with advanced colorectal cancer (mCRC) are commonly treated with systemic treatment consisting of fluoropyrimidine-based regimens being ineffective in 20-25% of the patients. Currently, selection criteria for patients to predict who will respond to this treatment is lacking. The aim of this study is to identify which patients will respond to first line fluoropyrimidine-based treatment based using microRNA (miR) expression profiles in order to avoid ineffective treatment. Material and methods: Total RNA was isolated from 88 fresh frozen colorectal cancer tissue samples consisting of ≥ 70% tumor cells, collected from patients with mCRC. MiR expression profiles were generated by next generation sequencing using the Illumina High Seq 2000 platform. Of all patients clinical and pathological data, including treatment response based on RECIST criteria, were collected. Class prediction and miR selection were performed using the GRidge package in R. Penalized selection and internal cross validation were used to select miRs predictive for treatment response. RESULTS: Next generation sequencing resulted in a mean of 10.087.107 (range 6.114.932 to 74.313.067) reads per sample corresponding to 2567 unique mature miR sequences, including 457 novel candidate and 2110 known miRs sequences (miRbase version 19). Penalized regression analysis on tumor specific miRs identified an expression profile which was predictive for clinical benefit (defined as response and stable disease) from first line treatment. Conclusion: With miR profiling of CRC tissue samples response prediction to first line fluoropyrimidine-based treatment in patients with mCRC is possible. We foresee that selection of treatment using miR expression profiling will avoid unnecessary treatment related toxicity and improve outcome for patients with mCRC Citation Format: Dennis Poel, Maarten Neerincx, Daoud L.S. Sie, Nicole C.T. van Grieken, R Shankaraiah, F. S.W. van der Wolf, J. H.T.M van Waesberghe, J. D. Burggraaf, Paul P. Eijk, Bauke Ylstra, Cees Verhoef, Mark A. van de Wiel, Henk M.W. Verheul, Tineke E. Buffart. MiR expression profiles can predict response to systemic treatment in patients with advanced colorectal cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4928.
Analytical solutions for steady and non‐steady heat conduction with temperature dependent material values (1990)

A transformation well‐known for a long time is used to transform the differential equation for heat conduction for temperature dependent material values into a differential equation written in a more simplified form. It is investigated how the initial and boundary conditions are transformed and in which cases the problem with variable material values can be solved by applying the solutions known for constant material values. For constant thermal diffusivity, this reduction is possible for boundary conditions of the first and second kind without limitation, for conditions of the third kind only in some cases. The results of different methods of calculation are compared in an example calculation. The series solution with transformation lies generally much closer to the numerically calculated temperature than the solution without transformation. The computing times for the series solution with transformation are reduced by a factor of 100. If the first minutes of the heating period are disregarded, the first term constitutes an excellent approximation. The computing time for the finite‐difference method with transformation is 20% lower than without transformation.
A quantitative analysis of fixed-point LDPC-decoder implementations using hardware-accelerated HDL emulations (2012)

Using hardware-accelerated HDL emulators of fixed-point implementations has several advantages in comparison to C-based simulations: The high degree of parallelism for example of field-programmable gate-array based hardware accelerators promise an increased emulation throughput. Furthermore, the HDL model of the considered circuit can be used in the following design process making an additional verification dispensable. For a system analysis of different low-density parity-check (LDPC) decoders such an emulator is practically inevitable from a throughput perspective: the outstanding error correction capability of those decoders allowing for bit-error rates (BER) of well below 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-10</sup> requires a simulative decoding of billions of blocks. In this work, an HDL-based emulator is used. The designed HDL model is highly parameterizable and includes an LDPC decoder and high-quality Box-Muller-based white Gaussian-noise generators to create rare error-events. Using this emulator a comparison of the decoding capability of different fixed-point decoder implementations has been performed. Additionally, accurate cost-models are used for estimating the hardware costs of the different decoder implementations which enable an identification of Pareto-optimal decoder implementations. Finally, the achievable emulator throughput is discussed and compared to the simulation throughput of a speed optimized C-model.
Variations in the quality of malaria-specific antibodies with transmission intensity in a seasonal malaria transmission area of Northern Ghana (2017)

The data contribute to understanding the underlying mechanism of the acquisition of strain-transcending antibody immunity following repeated exposure to diverse parasite strains.
Research on the Impact of Data Production Factors on China’s Green Transition (2023)

Abstract Since the 21st century, the digital economy has developed by leaps and bounds. As a key factor of production in the digital economy era, data plays an important role in China’s green transformation. Based on the panel data of 282 prefecture-level cities in China from 2011 to 2019, this paper studies the relationship between data elements and green transformation. The results show that data elements can significantly promote green transformation by improving technical efficiency and achieving technological progress. Based on the above conclusions, all regions should speed up the infrastructure construction of digital economy, train digital talents, reduce resource dependence, improve the green, low-carbon and circular development system, formulate a digital economy development strategy considering local economic development levels, improve resource utilization efficiency and labor productivity, and actively promote green transformation.
Degradation of Polyester Polyurethane by Bacterial Polyester Hydrolases (2017)

Polyurethanes (PU) are widely used synthetic polymers. The growing amount of PU used industrially has resulted in a worldwide increase of plastic wastes. The related environmental pollution as well as the limited availability of the raw materials based on petrochemicals requires novel solutions for their efficient degradation and recycling. The degradation of the polyester PU Impranil DLN by the polyester hydrolases LC cutinase (LCC), TfCut2, Tcur1278 and Tcur0390 was analyzed using a turbidimetric assay. The highest hydrolysis rates were obtained with TfCut2 and Tcur0390. TfCut2 also showed a significantly higher substrate affinity for Impranil DLN than the other three enzymes, indicated by a higher adsorption constant <i>K</i>. Significant weight losses of the solid thermoplastic polyester PU (TPU) Elastollan B85A-10 and C85A-10 were detected as a result of the enzymatic degradation by all four polyester hydrolases. Within a reaction time of 200 h at 70 °C, LCC caused weight losses of up to 4.9% and 4.1% of Elastollan B85A-10 and C85A-10, respectively. Gel permeation chromatography confirmed a preferential degradation of the larger polymer chains. Scanning electron microscopy revealed cracks at the surface of the TPU cubes as a result of enzymatic surface erosion. Analysis by Fourier transform infrared spectroscopy indicated that the observed weight losses were a result of the cleavage of ester bonds of the polyester TPU.
Diagnosis and treatment of antibody-mediated kidney allograft rejection (2003)

Evidence of a significant pathogenetic role of donor-reactive antibodies (DRA) in kidney allograft rejection is accumulating. At least, partially owing to the recent discovery of the complement split product C4d as a valuable rejection marker, antibody-mediated rejection (AMR) has regained increasing attention. We review here the value of various diagnostic criteria, including immunohistochemistry (C4d staining), histomorphology and posttransplant serology, for the diagnosis of AMR. Furthermore, the mechanisms underlying alloantibody/complement-mediated allograft injury are discussed in detail. Finally, a thorough discussion of recently proposed "anti-humoral" therapeutic strategies is provided.
Logistic Regression for Automatic Lexical Level Morphological Paradigm Selection for Konkani Nouns. (2015)

Automatic selection of morphological paradigm for a noun lemma is necessary to automate the task of building morphological analyzer for nouns with minimal human interventions. Morphological paradigms can be of two types namely surface level morphological paradigms and lexical level morphological paradigms. In this paper we present a method to automatically select lexical level morphological paradigms for Konkani nouns. Using the proposed concept of paradigm differentiating measure to generate a training data set we found that logistic regression can be used to automatically select lexical level morphological paradigms with an F-Score of 0.957.
P4542Revisiting the obesity paradox in heart failure: percent body fat as predictor of biomarkers and outcome (2019)

Abstract Background Obesity defined by body mass index (BMI) is characterized by better prognosis and lower plasma N-terminal pro-B-type natriuretic peptide (NT-proBNP) in heart failure (HF). We assessed whether another anthropometric measure, percent body fat (PBF), reveals different associations with outcome and HF biomarkers (NT-proBNP, high-sensitivity troponin T [hs-TnT], soluble suppression of tumorigenesis-2 [sST2]). Methods In an individual patient dataset, BMI was calculated as weight (kg)/height (m)2, and PBF through the Jackson-Pollock and Gallagher equations. Results Out of 6468 patients (median 68 years, 78% men, 76% ischaemic HF, 90% reduced EF), 24% died over 2.2 years (1.5–2.9), 17% from cardiovascular death. Median PBF was 26.9% (22.4–33.0%) with the Jackson-Pollock equation, and 28.0% (23.8–33.5%) with the Gallagher equation, with an extremely strong correlation (r=0.996, p&lt;0.001). Patients in the first PBF tertile had the worst prognosis, while patients in the second and third tertile had similar survival. The risks of all-cause and cardiovascular death decreased by up to 36% and 27%, respectively, per each doubling of PBF. Furthermore, prognosis was better in the second or third PBF tertiles than in the first tertile regardless of model variables. Both BMI and PBF were inverse predictors of NT-proBNP, but not hs-TnT. In obese patients (BMI ≥30 kg/m2, third PBF tertile), hs-TnT and sST2, but not NT-proBNP, independently predicted outcome. Conclusion Patient prognosis improves with either BMI or PBF. Obesity, assessed with BMI or PBF, is associated with lower NT-proBNP but not hs-TnT or sST2. hs-TnT or sST2 are stronger prognostic predictors than NT-proBNP among obese patients.
Predictors of Clinical Worsening in Cerebral Autosomal Dominant Arteriopathy With Subcortical Infarcts and Leukoencephalopathy (2015)

Clinical assessment and brain magnetic resonance imaging aid in predicting incident clinical events and clinical deterioration in cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy. There is a bidirectional relationship between dementia and moderate or severe disability in predicting each other's onset. Active smoking is a modifiable risk factor associated with clinical progression in Notch3 mutation carriers.
Construction via polymerase chain reaction of a mouse/human chimeric heavy chain gene of a monoclonal antibody toward human colorectal carcinoma-associated antigen (1993)

Construction via polymerase chain reaction of a mouse/human chimeric heavy chain gene of a monoclonal antibody toward human colorectal carcinoma-associated antigen Get access A. D. Fernando, A. D. Fernando 1Dept. of Microbiol. and Immunol. Med. Univ. of South Carolina, Charleston, SC 29425 Search for other works by this author on: Oxford Academic PubMed Google Scholar Y. Zhang, Y. Zhang 1Dept. of Microbiol. and Immunol. Med. Univ. of South Carolina, Charleston, SC 29425 Search for other works by this author on: Oxford Academic PubMed Google Scholar I. Y. Wang, I. Y. Wang 2Dept. of Biochem. and Mol. Biol. 2, Med. Univ. of South Carolina, Charleston, SC 29425; Search for other works by this author on: Oxford Academic PubMed Google Scholar M. Arlen, M. Arlen 3North Shore Surgical Oncology, 600 Northern Blvd., Great Neck, NY 11021 Search for other works by this author on: Oxford Academic PubMed Google Scholar K. Y. Tsang, K. Y. Tsang 1Dept. of Microbiol. and Immunol. Med. Univ. of South Carolina, Charleston, SC 29425 Search for other works by this author on: Oxford Academic PubMed Google Scholar A. C. Wang A. C. Wang 1Dept. of Microbiol. and Immunol. Med. Univ. of South Carolina, Charleston, SC 29425 Search for other works by this author on: Oxford Academic PubMed Google Scholar Protein Engineering, Design and Selection, Volume 6, Issue Supplement, 1993, Page 88, https://doi.org/10.1093/protein/6.Supplement.88-a Published: 01 January 1993
Faculty Opinions recommendation of Cerebral organoids recapitulate epigenomic signatures of the human fetal brain. (2019)

Organoids derived from human pluripotent stem cells recapitulate the early three-dimensional organization of the human brain, but whether they establish the epigenomic and transcriptional programs essential for brain development is unknown. We compared epigenomic and regulatory features in cerebral organoids and human fetal brain, using genome-wide, base resolution DNA methylome and transcriptome sequencing. Transcriptomic dynamics in organoids faithfully modeled gene expression trajectories in early-to-mid human fetal brains. We found that early non-CG methylation accumulation at super-enhancers in both fetal brain and organoids marks forthcoming transcriptional repression in the fully developed brain. Demethylated regions (74% of 35,627) identified during organoid differentiation overlapped with fetal brain regulatory elements. Interestingly, pericentromeric repeats showed widespread demethylation in multiple types of in vitro human neural differentiation models but not in fetal brain. Our study reveals that organoids recapitulate many epigenomic features of mid-fetal human brain and also identified novel non-CG methylation signatures of brain development.