gebhart/patrepeval huggingface dataset:
Structural variation and its potential impact on genome instability: Novel discoveries in the EGFR landscape by long-read sequencing (2020)

Structural variation (SV) is typically defined as variation within the human genome that exceeds 50 base pairs (bp). SV may be copy number neutral or it may involve duplications, deletions, and complex rearrangements. Recent studies have shown SV to be associated with many human diseases. However, studies of SV have been challenging due to technological constraints. With the advent of third generation (long-read) sequencing technology, exploration of longer stretches of DNA not easily examined previously has been made possible. In the present study, we utilized third generation (long-read) sequencing techniques to examine SV in the EGFR landscape of four haplotypes derived from two human samples. We analyzed the EGFR gene and its landscape (+/- 500,000 base pairs) using this approach and were able to identify a region of non-coding DNA with over 90% similarity to the most common activating EGFR mutation in non-small cell lung cancer. Based on previously published Alu-element genome instability algorithms, we propose a molecular mechanism to explain how this non-coding region of DNA may be interacting with and impacting the stability of the EGFR gene and potentially generating this cancer-driver gene. By these techniques, we were also able to identify previously hidden structural variation in the four haplotypes and in the human reference genome (hg38). We applied previously published algorithms to compare the relative stabilities of these five different EGFR gene landscape haplotypes to estimate their relative potentials to generate the EGFR exon 19, 15 bp canonical deletion. To our knowledge, the present study is the first to use the differences in genomic architecture between targeted cancer-linked phased haplotypes to estimate their relative potentials to form a common cancer-linked driver mutation.
Immunohistological Localization of Regenerating Protein in Ocular Structures (1996)

As in other tissues and organs, the reg protein, in the eye, is found in structures known for their continuous and rapid renewal. This protein seems not to exist (or persist) in eyes from aged donors while it is strongly expressed in young donor eyes (monkey, stillborn baby) as well as in regenerating corneal epithelium. These findings enforce the hypothesis about the involvement of reg protein in cell proliferation and differentiation phenomena and its probable correlation with aging.
Digital Assembly of Spherical Viscoelastic Bio‐Ink Particles (2021)

Abstract 3D bioprinting additively assembles bio‐inks to manufacture tissue‐mimicking biological constructs, but with the typical building blocks limited to 1D filaments. Here, it is developed a voxelated bioprinting technique for the digital assembly of spherical particles (DASP), which are effectively 0D voxels—the basic unit of 3D structures. It is shown that DASP enables on‐demand generation, deposition, and assembly of viscoelastic bio‐ink droplets. A two‐parameter diagram is developed to outline the viscoelasticity of bio‐inks required for printing spherical particles of good fidelity. Moreover, a strategy is developed for engineering bio‐inks with independently controllable viscoelasticity and mesh size, two of the most important yet intrinsically coupled physical properties of biomaterials. Using DASP, mechanically robust, multiscale porous scaffolds composed of interconnected yet distinguishable hydrogel particles are created. Finally, it is demonstrated the application of the scaffolds in encapsulating human pancreatic islets for sustained responsive insulin release. Together with the knowledge of bio‐ink design, DASP might be used to engineer highly heterogeneous, yet tightly organized tissue constructs for therapeutic applications.
Two-wavelength double heterodyne interferometry using a matched grating technique (1991)

Two-wavelength double heterodyne interferometry is applied for topographic measurements on optically rough target surfaces. A two-wavelength He-Ne laser and a matched grating technique are used to improve system stability and to simplify heterodyne frequency generation.
Email Communities of Interest. (2007)

Email has become an integral and sometimes overwhelming part of users ’ personal and professional lives. In this paper, we measure the flow and frequency of user email toward the identification of communities of interest (COI)–groups of users that have a common bond. If detectable, such associations will be useful in automating email management, e.g., topical classification, flagging important missives, and SPAM mitigation. An analysis of a large corpus of university email is used to drive the generation and validation of algorithms for automatically determining COIs. We examine the effect of the structure and transience of COIs with the algorithms and validate algorithms using user-labeled data. Our analysis shows that the proposed algorithms correctly identify email as being sent from the human-identified COI with high accuracy. The structure and characteristics of COIs are explored analytically and broader conclusions about email use are posited. 1.
Preparation of carbon quantum dots based high photostability luminescent membranes (2016)

Urethane acrylate (UA) was used to prepare carbon quantum dots (C-dots) luminescent membranes and the resultants were examined with FT-IR, mechanical strength, scanning electron microscope (SEM) and quantum yields (QYs). FT-IR results showed the polyurethane acrylate (PUA) prepolymer -C = C-vibration at 1101 cm<sup>-1</sup> disappeared but there was strong vibration at1687cm<sup>-1</sup> which was contributed from the-C = O groups in cross-linking PUA. Mechanical strength results showed that the different quantity of C-dots loadings and UV-curing time affect the strength. SEM observations on the cross-sections of the membranes are uniform and have no structural defects, which prove that the C-dots are compatible with the water-soluble PUA resin. The C-dot loading was increased from 0 to 1 g, the maximum tensile stress was nearly 2.67 MPa, but the tensile strain was decreased from 23.4% to 15.1% and 7.2% respectively. QYs results showed that the C-dots in the membrane were stable after 120 h continuous irradiation. Therefore, the C-dots photoluminescent film is the promising material for the flexible devices in the future applications.
Epitaxial ferroelectric oxides on silicon with perspectives for future device applications (2021)

Functional oxides on silicon have been the subject of in-depth research for more than 20 years. Much of this research has been focused on the quality of the integration of materials due to their intrinsic thermodynamic incompatibility, which has hindered the flourishing of the field of research. Nevertheless, growth of epitaxial transition metal oxides on silicon with a sharp interface has been achieved by elaborated kinetically controlled sequential deposition while the crystalline quality of different functional oxides has been considerably improved. In this Research Update, we focus on three applications in which epitaxial ferroelectric oxides on silicon are at the forefront, and in each of these applications, other aspects of the integration of materials play an important role. These are the fields of piezoelectric microelectromechanical system devices, electro-optical components, and catalysis. The overview is supported by a brief analysis of the synthesis processes that enable epitaxial growth of oxides on silicon. This Research Update concludes with a theoretical description of the interfaces and the possibility of manipulating their electronic structure to achieve the desired coupling between (ferroelectric) oxides and semiconductors, which opens up a remarkable perspective for many advanced applications.
[T lymphocyte receptors after allogenic bone marrow transplantation]. (1988)

Following allogeneic bone marrow transplantation, prominent expansion of peripheral T cells (40%) bearing gamma T cell receptor was observed in some patients. Biochemical, functional and molecular analyses were performed to characterize this T cell receptor and to understand its role in the immunodeficient state after transplantation.
Efficient design space exploration via statistical sampling and AdaBoost learning (2016)

Design space exploration (DSE) has become a notoriously difficult problem due to the exponentially increasing size of design space of microprocessors and time-consuming simulations. To address this issue, machine learning techniques have been widely employed to build predictive models. However, most previous approaches randomly sample the training set leading to considerable simulation cost and low prediction accuracy. In this paper, we propose an efficient and precise DSE methodology by combining statistical sampling and Adaboost learning technique. The proposed method includes three phases. (1) Firstly, orthogonal design based feature selection is employed to prune design space. (2) Sencondly, an orthogonal array based training data sampling method is introduced to select the representative configurations for simulation. (3) Finally, a new active learning approach ActBoost is proposed to build predictive model. Evaluations demonstrate that the proposed framework is more efficient and precise than state-of-art DSE techniques.
Distributed strain sensing optical guidance for epidural anesthesia (2019)

Epidural anesthesia is the most diffused clinical practice described as a placement of a medical needle into an epidural space, an insertion of a catheter through the needle and an injection of anesthetic in order to numb the nerves. A skilled anesthesiologist penetrates the needle through tissue layers such as subcutaneous fat, interspinous ligament, intraspinous ligament, ligamentum flavum and reaches the target space. Currently, methods of positioning of the needle tip into the epidural space are based on subjective perception, which are not safe and accurate. In order to improve the effectiveness of the epidural space identification, this work proposes a sensorized optical fiber mounted externally on the needle. This medical device provides continuous and real-time measurements with the help of an optical backscattered reflectometry. When the needle is exposed to strain variations during its advancement, the intensity of backscattered light changes. By correlating the spectrum with the reference one, strain patterns can be produced. Obtained data can detect the needle passage from one tissue to the other in a custom made phantom, which mimics a human spinal anatomy. Specifically, needle passage from the stiff ligamentum flavum to the soft epidural space results in a significant strain drop and a consequent increase, which is considered as a crucial indicator of epidural space identification. The proposed device is advantageous over existing optical guidance: it does not obstruct the flow of a liquid in the inner side of the needle; the needle from the tip to the tail performs as a sensor.
SIGNIFICANCE OF PLATELET FUNCTION AND THROMBOXANE B2 LEVELS ACROSS THE HUMAN MYOCARDIAL VASCULAR BED (1981)

ABSTRACT There is an intense interest in the role of platelets in the pathogenesis of myocardial ischemia. To determine platelet function in coronary circulation and the influence of various platelet‐active drugs, we have studied large number of patients with coronary disease (CD) defined as &gt;50 % luminal narrowing and subjects with normal coronary arteries (NCA). Blood samples were collected from aorta (Ao) and coronary sinus (CS) at rest, during and following atrial‐pacing induced tachycardia characterized by ECG changes and symptoms. Platelet aggregation (PAg) using epinephrine (E) and adenosine diphosphate (ADP) as stimulating agents and platelet counts were performed. In CD patients CS blood had lower (Pd&lt;0.01) PAg (E‐59 ± 8, ADP‐49 ± 7 %) than Ao blood (E‐74 ± 6, ADP‐68 ± 7 %). Platelet counts in CS blood (173,000 ± 16,000/mm 3 ) were lower (P&lt;0.01) than in Ao blood (233,000 + 30,000/mm 3 ). In NCA patients, the CS and Ao platelet counts and PAg were not significantly different. During tachycardia stress PAg and counts were unaltered in NCA patients. In contrast in CD patients PAg increased significantly (P&lt;0.05) in CS but not in Ao blood during stress and returned to baseline following tachycardia implying platelet activation during stress‐induced myocardial ischemia. Oral aspirin 650 mg abolished the differences in Ao and CS blood PAg (CS‐E 51 ± 8, ADP 54 ± 7%; Ao‐E 45 ± 8, ADP 55 ± 8 %), and in counts (CS‐221,000 ± 8,000/mm 3 ; Ao‐230,000 ± 71,000/mm 3 ) in CD patients. Aspirin also significantly decreased tachycardia‐related increase in PAg in CS blood. Administration of intravenous dipyridamole 25 mg in 8 other CD patients, resulted in increase in platelet counts in CS from 255,000 ± 29,000 to 286 ± 34,000/mm 3 and in PAg from 30 ± 8 to 52 ± 9 %, while Ao blood counts and PAg were unchanged, so that the differences in Ao and CS platelet counts and aggregation were abolished. In other studies, we compared CD patients treated with and without propranolol. Propranolol‐treated patients had lower PAg in Ao as well as CS blood compared to non‐treated patients, but the gradients in PAg and counts between Ao and CS blood was still present. However, tachycardia‐related increase in CS PAg was markedly less in CS blood in propranolol‐treated patients compared to non‐treated patients. These data show that 1) gradient in platelet counts from Ao to CS exists related probably to platelet aggregate formation in atherosclerotic vessels, 2) activation of platelets leads to low PAg activity in CS blood, 3) tachycardia stress is associated with platelet activation at the level of myocardial vascular bed, 4) aspirin and dipyridamole modify these gradients, 5) aspirin blunts tachycardia‐related increase in CS PAg, 6) propranolol has potent PAg inhibitory effects and modifies platelet response to tachycardia stress.
Supplementary Figure Legends 1-7 from Identification of a Novel Pathway That Selectively Modulates Apoptosis of Breast Cancer Cells (2023)

Supplementary Figure Legends 1-7 from Identification of a Novel Pathway That Selectively Modulates Apoptosis of Breast Cancer Cells
ChemInform Abstract: Photoconductor Fatigue. Part 1. Photochemistry of Hydrazone‐Based Hole‐ Transport Molecules in Organic Layered Photoconductors: Spectroscopic Characterization and Effect on Electrical Properties. (1991)

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.
Experiments of continuously and stably flowing lithium limiter in EAST towards a solution for the power exhaust of future fusion devices (2018)

Liquid lithium (Li) can partly ameliorate lifetime and power-exhaust issues of plasma facing components (PFCs) by enabling a self-healing, self-replenishing surface with a reduced susceptibility to neutron damage in future fusion devices. To assess operational stability and heat-exhaust capability under tokamak exposure, two generations of continuously flowing liquid Li (FLiLi) limiters on the concept of a thin flowing Li film have been successfully designed and tested in high performance discharges in EAST. The design uses a circulating Li layer with a thickness of <0.1 mm and a flow rate ∼2 cm3s−1. In addition, the limiter employs a novel electro-magnetic pump to drive liquid Li flow from a collector at the bottom of the limiter into a distributor at its top. Free surface gravitational flow closes the loop for a continuously flowing liquid Li film on the wetted PFC. Here we summarize key FLiLi limiter development and experimental results in H-mode plasmas. Keywords: Limiter, Lithium, Plasma facing component, EAST
Depth of anaesthesia monitoring: a clinical study comparing BIS and AAI during heart surgery (2004)

Background and Goal of Study: Developing a reliable depth of anaesthesia monitor, which quantifies with a simple numerical index the complex interaction between depressant anaesthetics/analgesics and noxious stimulation, has proven difficult. This study compares the anaesthetic depth indices BIS (bispectral index of passive EEG) and the A-line monitor based on the mid-latency-auditory evoked response (AAI) in patients undergoing heart surgery with cardio-pulmonary bypass (CPB). Materials and Methods: Ten patients (age 44-83, weight 72-96). Induction with fentanyl/midazolam, maintained with sevoflurane until CPB when propofol was infused. BIS and AAI were registered every 5 minutes during CPB (BIS Aspect 2000 version 3.3; A-line AEP monitor version 1.4, Danmeter), the anaesthetist being blinded as to the registration. BIS and AAI indices were classified as “good”, “moderate” or “poor” agreement. Results and Discussions: A total of 126 duplicate recordings were made during CPB. AAI index showed a higher occurrence of low values while BIS is more evenly distributed over the full range (Figure 1). A majority (65%) of measurements showed “good”, while 31 (25%) “moderate” and 13 (10%) “poor” agreement (Table 1).Figure 1.Table 1Conclusion: When BIS and AAI are recorded simultaneously during CPB, a high proportion of readings give contradictory information.
GaInNAs long-wavelength lasers: progress and challenges (2002)

Research to realize long-wavelength, GaInNAs quantum well lasers has been intense in the past three years. The results have been very promising considering the relative immaturity and challenges of this new materials system. This paper reviews both the materials challenges and progress in growth of the metastable GaInNAs alloys required to reach the 1.3–1.55 μm communication wavelengths and the challenges and progress in device design for both vertical-cavity surface-emitting lasers and higher power edge-emitting lasers.
The kielin/chordin-like protein (KCP) attenuates high-fat diet-induced obesity and metabolic syndrome in mice (2017)

Obesity and its associated complications such as insulin resistance and non-alcoholic fatty liver disease are reaching epidemic proportions. In mice, the TGF-β superfamily is implicated in the regulation of white and brown adipose tissue differentiation. The kielin/chordin-like protein (KCP) is a secreted regulator of the TGF-β superfamily pathways that can inhibit both TGF-β and activin signals while enhancing bone morphogenetic protein (BMP) signaling. However, KCP's effects on metabolism and obesity have not been studied in animal models. Therefore, we examined the effects of KCP loss or gain of function in mice that were maintained on either a regular or a high-fat diet. KCP loss sensitized the mice to obesity and associated complications such as glucose intolerance and adipose tissue inflammation and fibrosis. In contrast, transgenic mice that expressed KCP in the kidney, liver, and adipose tissues were resistant to developing high-fat diet-induced obesity and had significantly reduced white adipose tissue. Moreover, KCP overexpression shifted the pattern of SMAD signaling <i>in vivo</i>, increasing the levels of phospho (P)-SMAD1 and decreasing P-SMAD3. Adipocytes in culture showed a cell-autonomous effect in response to added TGF-β1 or BMP7. Metabolic profiling indicated increased energy expenditure in KCP-overexpressing mice and reduced expenditure in the KCP mutants with no effect on food intake or activity. These findings demonstrate that shifting the TGF-β superfamily signaling with a secreted protein can alter the physiology and thermogenic properties of adipose tissue to reduce obesity even when mice are fed a high-fat diet.
Geomechanics of Lost-Circulation Events and Wellbore-Strengthening Operations (2015)

Summary Lost circulation, a major complication of drilling operations, is commonly treated by adding materials of various types, shapes, and particle-size distributions to the drilling mud. Generally known as wellbore strengthening, this technique often helps the operator to drill with higher mud gradients compared with that suggested by the conventional fracture-gradient or borehole-fracture-limit analysis. The underlying mechanisms through which a wellbore is strengthened, however, are not yet fully understood. This study explores these wellbore-strengthening mechanisms through an analytical solution to the related solid-mechanics model of the wellbore and its adjacent fractures. The provided solution is generic in that it takes into account the mechanical interaction of multiple fractures between one another and the wellbore under an arbitrary state of in-situ stress anisotropy. An additional generality in this solution arises from its unification and quantification of some solid-mechanics aspects of the previous hypotheses that have been published on the subject—i.e., stress cage, as well as the tip isolation and its effect on the fracture-propagation resistance. In relation to the stress-cage theory, the study investigates the wellbore-hoop-stress enhancement upon fracturing. The findings indicate that the induced hoop stress is significant at some regions near the wellbore, especially in the general vicinity of the fracture(s). However, given the strong dependency of wellbore stress on the mechanical and geometrical parameters of the problem, generalizing these results to the entire region around the wellbore may not always be trivial. The study also examines tip isolation, a common feature of fracture-closure and propagation-resistance hypotheses, through the analysis of partially reduced fracture pressures and a breakdown criterion, defined by the critical stress-intensity factor of the formation rock.
17.8 A 190nW 33kHz RC oscillator with ±0.21% temperature stability and 4ppm long-term stability (2014)

In wireless networks with a low duty cycle, the radio is operational for only a small percentage of the time. A sleep timer is used to synchronize the data transmission and reception. The total system power is then limited by the sleep power and the sleep timer frequency stability. Low-frequency crystal oscillators are a common choice for sleep timers due to their excellent long-term stability, frequency stability over temperature, and very low power consumption. However, the external crystal cost and board area are undesired. If an integrated oscillator is used as an alternative, the frequency variation must be minimized so the sleep time can be maximized.
Functional 4-D clustering for characterizing intratumor heterogeneity in dynamic imaging: evaluation in FDG PET as a prognostic biomarker for breast cancer (2021)

Our findings suggest that imaging markers of FTH add independent value beyond standard PET imaging metrics in predicting recurrence-free survival in breast cancer and thus merit further study.
ChemInform Abstract: BIS(TRIMETHYLPHOSPHORANYLIDENE)METHANE, (CH3)3PCP(CH3)3 (1976)

Abstract Die Titelverbindung (V) wird durch Erhitzen des Fluorphosphoranylmethylenphosphorans (III), erhalten aus Difluortrimethylphosphoran (I) und den Methylentrimethylphosphoranen (II), mit NaH als äußerst reaktive und luftempfindliche Substanz dargestellt.