gebhart/patrepeval huggingface dataset:
Abstract 1564: A computational framework for removing mouse contamination in tumors sequenced from patient-derived xenografts (2017)

Abstract Introduction: Using patient derived xenograft (PDX) models has become an effective way for investigating response to standard or new therapeutics in cancer. Human cancer cells injected in mice are allowed to establish tumors and subjected to desired treatments. The PDX tumors are later harvested and characterized, often by massive parallel sequencing. However, a major challenge with analyzing these data is the presence of stromal mouse genomic material, frequently resulting in artifacts in downstream variant detection. We present a computational method to eliminate mouse contamination in PDX. Method: We used the Burrows-Wheeler Aligner to map reads obtained from sequencing the PDX samples to a combined human and mouse reference genome . We remove reads that are mapped to the mouse reference. The remaining reads are then processed through standard mutation calling pipelines for somatic mutation detection. To test the efficacy of our method, we created in silico mixtures of human and mouse whole-exome sequencing reads from a melanoma patient’s tumor and an immortalized mouse cell line captured with human exome baits. We then carried out a sensitivity analysis to examine how changing the mean target coverage of sequencing, or mouse contamination levels affects our results. For each of the computational experiments, we evaluated somatic mutations detected from the synthetic samples in comparison to the original human sample. Results: We calculated the sensitivity and specificity of detecting somatic mutations to determine our algorithm’s performance. In all instances, we found greater than 99% for both sensitivity and specificity. Conclusions: Our results demonstrate that our method works accurately towards removing mouse reads in PDX samples. This task could also be applied to separating sequence reads from other species. Citation Format: Ali Amin-Mansour, Judit Jané-Valbuena, Xinmeng Jasmine Mu, Levi Garraway. A computational framework for removing mouse contamination in tumors sequenced from patient-derived xenografts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1564. doi:10.1158/1538-7445.AM2017-1564
Neural Stem Cells and Specification of Cell Fates: Biological and Therapeutical Perspectives (2003)

Stem cells, whether blastocyst or organ/tissue derived, are increasingly becoming of interest to the general public, politicians, and scientists. This is refl ected by the popularity of stem cell research in the media and the dramatic increase of scientifi c productivity in the fi eld. Stem cells provide an exciting opportunity to understand the basic mechanisms involved in histogenesis, mechanisms that may translate into prospective applications in tissue engineering and biomedicine in general. In this chapter, we will be discussing some of the recent advances made toward answering the fascinating questions of how a neural stem cell (NSC) maintains itself and how its progeny choose their fate. We will discuss current principles of cellular differentiation with a particular interest in the generation of dopaminergic neurons from dopaminergic and nondopaminergic sources.
Carbon nanotube in situ TEM large strain and chiral angle analysis enabled by modular coupon and MEMS test platform system (2013)

A modular MEMS-based test platform enables straining of pristine carbon nanotubes inside a transmission electron microscope. The interchangeable coupon is compatible with the high-temperature environment of nanostructure synthesis whereas the metal leads of the micro actuator are not exposed to the harsh synthesis conditions. The actuator of the universal test platform translates its large displacement onto the shuttle of the coupon where the as-grown carbon nanotubes are strained and simultaneously observed by the electron beam passing through the backside hole. Electron diffraction enables assignment of nanotube chirality.
Further Studies on the Effects of Greening on Juice Quality: Do Nutritional Sprays Ameliorate HLB-Induced Off-flavor? (2014)

Citrus groves receiving nutritional sprays were compared with groves in the same areas managed with conventional fertilization treatments.&nbsp; Fruit were harvested from healthy and Huanglongbing (HLB)-affected trees. Within HLB-affected trees, fruit were sorted into asymptomatic (HLB-a) and symptomatic (HLB-s) fruit.&nbsp; Sensory tests were performed using the difference-from-control (DFC) method, where juice from HLB-affected trees was compared with juice from healthy trees.&nbsp; Results show that panelists could detect differences between juice from HLB-affected and healthy trees in the 2009-2010 and 2010-2011 seasons, regardless of nutritional treatments, for Hamlin and Valencia. Like in previous years, those differences were perceived as more bitter or metallic for early harvests of HLB-affected Hamlin, but those differences were less and inconsistently perceived as more bitter, sweeter or more sour for late harvests or Valencia HLB-affected fruit. In the 2011-2012 season, there were much less differences between juice from healthy and HLB trees, possibly due to a season with high Brix/TA ratio, or due to later harvests.&nbsp; Results will be discussed in relation to chemical analysis of sugars, acids, and limonoids.&nbsp; Nutritional treatments that mitigate HLB symptoms on trees did not have a consistent effect on the HLB induced off-flavor of the fruit and juice, necessitating more seasons of study.
Electromagnetic transient simulation of power electronic equipment in power systems: challenges and solutions (2006)

The panel presentation identities requirements for electromagnetic transient simulation programs for simulating large power networks with embedded power electronics. Interpolation based simulation and other methods are discussed which provide precision in simulation of semiconductor switching events without a corresponding penalty in computer time. A method for accurately estimating power semiconductor losses without significant increase in the simulation time is discussed. The use of simulation in design requires multiple runs to explore a wide range of operating scenarios and component tolerances. Intelligent methods, including those based on nonlinear optimization limit the these runs to the most promising areas of the parameter space and considerably reduce the design cycle time
Towards automatic transcription of large spoken archives - English ASR for the MALACH project (2003)

Digital archives have emerged as the pre-eminent method for capturing the human experience. Before such archives can be used efficiently, their contents must be described. The NSF-funded MALACH project aims to provide improved access to large spoken archives by advancing the state-of-the-art in automated speech recognition (ASR), Information Retrieval (IR) and related technologies [1,2] for multiple languages. This paper describes the ASR research for the English speech in the MALACH corpus. The MALACH corpus consists of unconstrained, natural speech filled with disfluencies, heavy accents, age-related coarticulation, uncued speaker and language switching, and emotional speech collected in the form of interviews from over 52000 speakers in 32 languages. In this paper, we describe this new testbed for developing speech recognition algorithms and report on the performance of well-known techniques for building better acoustic models for the speaking styles seen in this corpus. The best English ASR system to date has a word error rate of 43.8% on this corpus.
Design and Assessment of a Single-size Semi-soft Assistive Mitten for People with Cervical Spinal Cord Injuries (2019)

Assistive orthotics have the potential to augment the grasping capabilities of individuals with limited hand functionality. People with a cervical-level spinal cord injury (SCI) lack direct control of semi-flaccid, curled fingers on both hands, which often precludes independent donning and doffing of orthotics, thus limiting their use in daily life. This paper presents a novel orthotic designed to improve hand functionality while facilitating independent daily use for individuals with cervical SCI: the Single-size Semi-soft Assistive Mitten (SSAM). This device utilizes a slim dorsal leaf spring and underactuated cable drive to passively open and actively close the hand, in a way that is robust to variations in hand size. This mitten is intended to improve ease of donning and doffing, as the device is attached to all fingers at once. A prototype is developed based on simulation studies, and grasping performance of the proposed design is validated with five healthy subjects. Successful grasping trials, along with positive user feedback, suggest that the SSAM has a comfortable and intuitive design for long-term, independent use and will enable future studies into feasibility of daily use for people with SCI.
Filling the gap between system conception and silicon/software implementation (2003)

The convergence of silicon and embedded software, accompanied by increasing design complexity, exposes a gap between system conception and silicon/software implementation. Design methodologies are presented that make the connection from high level system specification to integrated system solution. These techniques are demonstrated on a digital audio broadcast application.
Performance evaluation of the isolated mmWave small cell (2015)

In this paper we introduce the performance evaluation of the isolated millimeter-wave (mmWave) small cell. The potential performance of the mmWave small cells is evaluated on the base of PHY layer technique with parameters similar to IEEE 802.11ad standard. Two important practical tasks are addressed in this paper: the efficiency of mmWave spectrum utilization and the small cell optimal coverage. Two approaches for spectrum utilization are considered: frequency reuse-1 (each cell sector operates in three channels) and frequency reuse-3 (each of three cell sectors operates in only one channel). We start from the comparison of these scenarios spectral efficiency. At the next step the interference mitigation techniques are applied in order to improve the system performance for both scenarios. Also we discuss the mmWave small cell coverage and its limits due to the regulator requirements. The impact of small cell radius on MU-MIMO mode performance is addressed and evaluated. Finally, the discussion and recommendations on the small cell size, frequency reuse scenario and interference mitigation techniques are provided.
Inverse‐Tunable Red Luminescence and Electronic Properties of Nitridoberylloaluminates Sr2−xBax[BeAl3N5]:Eu2+ (x=0–2) (2022)

The nitridoberylloaluminate Ba<sub>2</sub> [BeAl<sub>3</sub> N<sub>5</sub> ]:Eu<sup>2+</sup> and solid solutions Sr<sub>2-x</sub> Ba<sub>x</sub> [BeAl<sub>3</sub> N<sub>5</sub> ]:Eu<sup>2+</sup> (x=0.5, 1.0, 1.5) were synthesized in a hot isostatic press (HIP) under 50 MPa N<sub>2</sub> atmosphere at 1200 °C. Ba<sub>2</sub> [BeAl<sub>3</sub> N<sub>5</sub> ]:Eu<sup>2+</sup> crystallizes in triclinic space group <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>P</mml:mi> <mml:mover><mml:mn>1</mml:mn> <mml:mo>‾</mml:mo></mml:mover> </mml:mrow> </mml:math> (no. 2) (Z=2, a=6.1869(10), b=7.1736(13), c=8.0391(14) Å, α=102.754(8), β=112.032(6), γ=104.765(7)°), which was determined from single-crystal X-ray diffraction data. The lattice parameters of the solid solution series have been obtained from Rietveld refinements and show a nearly linear dependence on the atomic ratio Sr : Ba. The electronic properties and the band gaps of M<sub>2</sub> [BeAl<sub>3</sub> N<sub>5</sub> ] (M=Sr, Ba) have been investigated by a combination of soft X-ray spectroscopy and density functional theory (DFT) calculations. Upon irradiation with blue light (440-450 nm), the nitridoberylloaluminates exhibit intense orange to red luminescence, which can be tuned between 610 and 656 nm (fwhm=1922-2025 cm<sup>-1</sup> (72-87 nm)). In contrast to the usual trend, the substitution of the smaller Sr<sup>2+</sup> by larger Ba<sup>2+</sup> leads to an inverse-tunable luminescence to higher wavelengths. Low-temperature luminescence measurements have been performed to exclude anomalous emission.
PRP27–30Is a Normal Soluble Prion Protein Fragment Released by Human Platelets (1996)

Prion diseases are neurodegenerative disorders characterized by the accumulation of abnormal isoforms of prion protein (PrPSc) in the central nervous system. PrPSc isoforms differ from their normal homologue (PrPC), in that they possess increased beta-sheet conformation, are partially protease resistant and may be associated with amyloid deposition. Amyloid proteins are thought to derive from soluble precursors or fragments thereof, present in biological fluids, which in the disease state undergo conformational change leading to aggregation and deposition in target tissues. We report here that platelets carry PrP mRNA and release PrPC, a sialoglycoprotein bound to the cell surface by a glycosylphosphatidylinositol (GPI) anchor. Soluble PrPC, and a N-terminal truncated PrPC isoform starting at position 90 are secreted by resting and agonist-stimulated platelets and are detectable after partial deglycosylation of releasates. N-terminal sequence analysis of the soluble 27-30 kDa isoform, GQGGGTHSQ(W)NKP, revealed homology to scrapie PrP27-30, the protease resistant core derived from PrPSc. These findings indicate that in addition to PrPC, platelets process a soluble PrP27-30 isoform. Whether this isoform can be converted in scrapie PrP27-30 remains to be determined.
Down‐regulation of collagen synthesis and matrix metalloproteinase expression in myofibroblasts from dupuytren nodule using adenovirus‐mediated relaxin gene therapy (2013)

Dupuytren's disease is a fibroproliferative connective tissue disorder characterized by contracture of the palmer fascia of the hand. Relaxin (RLN) is a multifunctional factor which contributes to the remodeling of the pelvic ligament by inhibiting fibrosis and inflammatory activities. The aim of this study was to investigate the effect of the RLN gene on the inhibition of fibrosis in myofibroblastic cells. Myofibroblast cells with adenovirus LacZ (Ad-LacZ) as a marker gene or adenovirus relaxin (Ad-RLN) as therapeutic gene showed transgene expressions in beta-galactosidase assay and Western blot analysis. Myofibroblastic cells with Ad-RLN demonstrated a 22% and 48% reduction in collagen I and III mRNA expressions respectively, a 50% decrease in MMP-1, 70% decrease in MMP-2, 80% decrease in MMP-9, and a 15% reduction in MMP-13 protein expression compared with cultures with viral control and saline control. In addition, myofibroblastic cells with Ad-RLN showed a 40% decrease in TIMP 1 and a 15% increase in TIMP 3 protein expression at 48 h compared to cultures with viral control and saline control. Also, myofibroblastic cell with Ad-RLN demonstrated a 74% inhibition of fibronectin and a 52% decrease in total collagen synthesis at 48 h compared with cultures with viral control and saline control. In conclusion, the RLN gene render antifibrogenic effect on myofibroblastic cells from Dupuytren's nodule via direct inhibition of collagen synthesis not through collagenolytic pathway such as MMP-1, -13, TIMP 1, and 3. Therefore relaxin can be an alternative therapeutic strategy in initial stage of Dupuytren's disease by its antifibrogenic effect.
Supplementary Figure 2 from Targeting the PI3K Pathway in the Brain—Efficacy of a PI3K Inhibitor Optimized to Cross the Blood–Brain Barrier (2023)

&lt;p&gt;PDF file - 77K, Cell viability following treatment with GNE-317&lt;/p&gt;
Developing a Diagnostic Multivariable Prediction Model for Urinary Tract Cancer in Patients Referred with Haematuria: Results from the IDENTIFY Collaborative Study (2022)

We have developed a tool that uses a person's characteristics to determine the risk of cancer if that person develops blood in the urine (haematuria). This can be used to help prioritise patients for further investigation.
Material selection for elastic energy absorption in origami-inspired compliant corrugations (2014)

Elastic absorption of kinetic energy and distribution of impact forces are required in many applications. Recent attention to the potential for using origami in engineering may provide new methods for energy absorption and force distribution. A three-stage strategy is presented for selecting materials for such origami-inspired designs that can deform to achieve a desired motion without yielding, absorb elastic strain energy, and be lightweight or cost effective. Two material indices are derived to meet these requirements based on compliant mechanism theory. Finite element analysis is used to investigate the effects of the material stiffness in the Miura-ori tessellation on its energy absorption and force distribution characteristics compared with a triangular wave corrugation. An example is presented of how the method can be used to select a material for a general energy absorption application of the Miura-ori. Whereas the focus of this study is the Miura-ori tessellation, the methods developed can be applied to other tessellated patterns used in energy absorbing or force distribution applications.
Data from Detection of Therapeutically Targetable Driver and Resistance Mutations in Lung Cancer Patients by Next-Generation Sequencing of Cell-Free Circulating Tumor DNA (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; The expanding number of targeted therapeutics for non–small cell lung cancer (NSCLC) necessitates real-time tumor genotyping, yet tissue biopsies are difficult to perform serially and often yield inadequate DNA for next-generation sequencing (NGS). We evaluated the feasibility of using cell-free circulating tumor DNA (ctDNA) NGS as a complement or alternative to tissue NGS.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; A total of 112 plasma samples obtained from a consecutive study of 102 prospectively enrolled patients with advanced NSCLC were subjected to ultra-deep sequencing of up to 70 genes and matched with tissue samples, when possible.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We detected 275 alterations in 45 genes, and at least one alteration in the ctDNA for 86 of 102 patients (84%), with &lt;i&gt;EGFR&lt;/i&gt; variants being most common. ctDNA NGS detected 50 driver and 12 resistance mutations, and mutations in 22 additional genes for which experimental therapies, including clinical trials, are available. Although ctDNA NGS was completed for 102 consecutive patients, tissue sequencing was only successful for 50 patients (49%). Actionable &lt;i&gt;EGFR&lt;/i&gt; mutations were detected in 24 tissue and 19 ctDNA samples, yielding concordance of 79%, with a shorter time interval between tissue and blood collection associated with increased concordance (&lt;i&gt;P&lt;/i&gt; = 0.038). ctDNA sequencing identified eight patients harboring a resistance mutation who developed progressive disease while on targeted therapy, and for whom tissue sequencing was not possible.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Therapeutically targetable driver and resistance mutations can be detected by ctDNA NGS, even when tissue is unavailable, thus allowing more accurate diagnosis, improved patient management, and serial sampling to monitor disease progression and clonal evolution. &lt;i&gt;Clin Cancer Res; 22(23); 5772–82. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
High-Frequency Hippocampal Oscillations Activated by Optogenetic Stimulation of Transplanted Human ESC-Derived Neurons (2012)

After transplantation, individual stem cell-derived neurons can functionally integrate into the host CNS; however, evidence that neurons derived from transplanted human embryonic stem cells (hESCs) can drive endogenous neuronal network activity in CNS tissue is still lacking. Here, using multielectrode array recordings, we report activation of high-frequency oscillations in the β and γ ranges (10-100 Hz) in the host hippocampal network via targeted optogenetic stimulation of transplanted hESC-derived neurons.
The Treatment of Lumbar Spinal Pain Syndromes Diagnosed by Discography (1994)

Based on the results of this study, it appears that discogenic pain syndromes can be treated by arthrodesis.
Autopoietic Computing Systems and Triadic Automata: The Theory and Practice (2020)

Physical world contains many complex sentient structures. They have evolved to learn how to organize themselves and optimally use the resources available to them while interacting with their environment. These complex adaptive systems (CAS) sustain their continued existence in the face of external forces causing large fluctuations. The study of CAS functions, structures and their dynamics under the influence of fluctuations has thrown light into self-organizing patterns that are common among these disparate systems. Common theme among these structures is that a system encodes and processes information to organize and manage its components interacting with each other and their environment. The self-organizing patterns also sense and counteract fluctuations to maintain their stability. They become autopoietic and maintain homeostasis. Digital Computing structures composed of distributed and communicating software and hardware components also fall into the category of a complex system where fluctuations in the demand for, or the availability of, resources required to execute the computations disturb their stability and performance. The fluctuations impact the resiliency and efficiency of the structure as the scale of components increase. This paper describes the theory and practice of applying the self-organizing and self-managing patterns to distributed digital computing structures and making them autopoietic machines.
Electrically pumped, waveguide-coupled Si light emitting diodes (2017)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text S. M. Buckley, M. J. Stevens, S. W. Nam, R. P. Mirin, and J. M. Shainline, "Electrically pumped, waveguide-coupled Si light emitting diodes," in Conference on Lasers and Electro-Optics, OSA Technical Digest (online) (Optica Publishing Group, 2017), paper SM3O.6. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Transplantation of human hematopoietic repopulating cells: mechanisms of regeneration and differentiation using human???mouse xenografts (2008)

This review focuses on recent progress in HSC ex-vivo manipulation and transplant biology, and the potential improvements arising from identification of molecular players and cellular components of the microenvironment niche.
Slotted Circularly Polarized Microstrip Antenna for RFID Application (2017)

A single layer coaxial fed rectangular microstrip slotted antenna for circular polarization (CP) is proposed for radio frequency identification (RFID) application. Two triangular shaped slots and one rectangular slot along the diagonal axis of a square patch have been embedded. Due to slotted structure along the diagonal axis and less surface area, good quality of circular polarization has been obtained with the reduction in the size of microstrip antenna by 4.04%. Circular polarization radiation performance has been studied by size and angle variation of diagonally slotted structures. The experimental result found for 10 dB return loss is 44 MHz with 10 MHz of 3 dB Axial Ratio (AR) bandwidth respectively at the resonant frequency 910 MHz. The overall proposed antenna size including the ground plane is 80 80 4.572 mm 3 .