gebhart/patrepeval huggingface dataset:
Abstract 3296: KLF9, a differentiation-associated transcription factor, suppresses Notch1 signaling and inhibits glioblastoma-initiating stem cells (2011)

Abstract Tumor-initiating stem cells (alternatively called cancer stem cells, CSCs) are a subpopulation of tumor cells that plays unique roles in tumor propagation, therapeutic resistance and tumor recurrence. It is becoming increasingly important to understand the molecular signaling that regulates the self-renewal and differentiation of CSCs. Transcription factors are critical for the regulation of normal and neopolastic stem cells. The Krüppel-like family of transcription factors (KLFs) consists of 17 evolutionarily conserved zinc finger containing proteins with diverse regulatory functions. KLFs bind to GC-GT rich sites in gene promoter and enhancer regions and are known to contextually regulate the growth, proliferation, and differentiation of cells including non-neoplastic stem cells and cancer cells. Here, we examined the expression and function of KLF transcription factors in human glioblastoma (GBM)-drived neurosphere lines and low passage primary GBM-derived neurospheres that are enriched for tumor-initiating stem cells. We identify KLF9 as a relatively unique differentiation-induced transcription factor in GBM-derived neurospheres. KLF9 knockdown rescues GBM-derived neurospheres from Retinoic -acid-induced growth inhibition and differentiation. KLF9 induction is shown to induce neurosphere cell differentiation, inhibit neurosphere formation and deplete neurospheres of CD133+ stem-like cells. KLF9 induction also inhibits the growth of tumor xenografts established from GBM-derived neurospheres. We also show that KLF9 regulates GBM neurosphere cells by binding to the Notch1 promoter and suppressing Notch1 expression and downstream signaling. We compared the KLF9 expression between human GBM tumors and non-neoplastc human specimens. KLF9 is down regulated in human GBM tumors relative to normal brain. Our findings expand the role of KLF family members in stem cell and cancer biology, support KLF9 as a regulator of GBM malignancy, and as a potential biomarker and target for cancer therapeutics. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3296. doi:10.1158/1538-7445.AM2011-3296
Fog at the Edge: Experiences Building an Edge Computing Platform (2018)

Technology advancement has pushed computation to the network edge, paving the way for a class of IoT applications that leverage CPU, storage and communications in edge devices. Building these new IoT applications is not an easy task however. Two key challenges are supporting the dynamic nature of the edge network and the context-dependent characteristics of application logic. In this paper we report our experience in building an edge computing platform called Distributed Node-RED (DNR) that uses a distributed data flow programming model based on the popular open source Node-RED tool. We describe some of the challenges we faced as well as some novel solutions that were implemented in our platform. A new approach in applying the concept of exogenous coordination is also presented and shown to be necessary in building large-scale IoT applications across the edge, fog and cloud.
Adaptive loss of field protection based on phasor measurements (2011)

Loss of field protection is of great importance for the security of large-scale generators. With the development of large-scale generators and corresponding loss of field protection, the complicated structure leads to the high possibility of loss of field faults. According to the statistical data, more than sixty percentages of the synchronous generator faults are the excitation system faults, which might cause loss of load, tie-line tripping, instability, collapse and etc. Therefore, it is crucial to identify loss of field as early as possible and take countermeasures. In loss of field protection, the impedance boundary criterion of steady state stability limit is widely used to distinguish loss of field and normal condition. However, the steady state stability limit circle is affected by the system operating modes, which might result in mis-operation of the relay. In this paper, an approach for on-line identifying system equivalent impedance is presented based on PMU measurements. The steady state stability limit circle can be adaptively fit for operating modes. The computer simulation results demonstrate that the proposed method works well.
Role of laparoscopy in the diagnosis and treatment of prostate cancer (1996)

Laparoscopic surgical techniques were originally applied to the staging of prostate cancer in the form of laparoscopic pelvic lymph node dissection. The efficiency of laparoscopic pelvic lymph node dissection has proven to be comparable to open lymphadenectomy in tissue yield and also shows a considerable decrease in postoperative morbidity. Subsequently, laparoscopy has been used as an adjuvant to perineal prostatectomy for preliminary dissection of the seminal vesicles. Laparoscopic radical prostatectomy has been performed but the long-term efficacy of this treatment is unknown at this point. Future clinical applications of laparoscopic surgical techniques in the diagnosis and treatment of prostate cancer include harvesting of primary and metastatic prostatic tissue for adjuvant gene therapies for prostate cancer. © 1996 Wiley-Liss, Inc.
Rectangular Selection of Components in Large 3D Models on the Web (2019)

We introduce a novel method for rectangular selection of components in large 3D models on the web. Our technique provides an easy to use solution that is developed for renderers with partial fragment shader support such as embedded systems running WebGL. This method was implemented using the Unity 3D game engine within the 3D Repo open source framework running on a web browser. A case study with industrial 3D models of varying complexity and object count shows that such a solution performs within reasonable rendering expectations even on underpowered devices without a dedicated graphics card.
Approximate frequency domain analysis for linear damped space structures (1990)

A method is presented for the analysis of damped structures in which the structural components are represented by impedance models and analyzed in the frequency domain. Methods are presented to assemble and condense system impedance matrices and then to identify approximate mass, stiffness, and viscous damping matrices for systems whose impedances are complicated functions of frequency. Formulas are derived for determination of approximate values for the natural frequencies and damping of systems represented by mass, stiffness, and viscous damping matrices. The sensitivities of these approximate values to system parameter changes are analyzed. The implementation of these analysis tools is discussed and applied to a simple mechanical system. Nomenclature C = damping matrix E = Young's modulus F = vector of global forces K — stiffness matrix M = mass matrix P = real power T = transformation matrix for reduction of coordinates v = vector of global velocities dv ?= first variation of the velocity mode shape W(s) — complex weighting function X = reactive power Z = impedance matrix &m,pn = viscoelastic material parameters f = damping ratio rj = loss factor a>n = natural frequency Subscripts. E = eliminated degrees of freedom (DOF) EXT = external / = imaginary L = linear NL — nonlinear R = real or retained DOF V = viscoelastic
Controlled Release of Vancomycin and Tigecycline from an Orthopaedic Implant Coating Prevents <i>Staphylococcus aureus</i> Infection in an Open Fracture Animal Model (2019)

Vancomycin and tigecycline can be encapsulated in a polymer coating and released over time to maintain therapeutic levels during the perioperative period. Our results suggest that antibiotic coatings can be used to prevent implant infection and osteomyelitis in the setting of open fracture. This novel open fracture mouse model can be used as a powerful <i>in vivo</i> preclinical tool to evaluate and optimize the treatment of open fractures before further studies in humans.
Analytical investigation of modulated spin-torque oscillators in the framework of coupled differential equations with variable coefficients (2012)

Modulation of spin torque oscillators (STOs) is investigated by analytically solving the time-dependent coupled equations of an auto-oscillator. A Fourier-series solution is proposed, leading to the coefficients being determined with a linear set of equations, from which a nonlinear amplitude and frequency modulation (NFAM) scheme is obtained. In this framework, the NFAM features are related to the intrinsic STO parameters, revealing a frequency dependence of the harmonic-dependent modulation index that allows a modulation bandwidth to be defined for these devices. The presented results expose a rich parameter space, where the modulation and the STO's operation conditions define the observed modulation features. The Fourier-series representation of the time signal is suitable for studying periodic perturbations on the auto-oscillator equation.
Development of a large-area, light-weight module using the MALTA monolithic pixel detector (2022)

The MALTA pixel chip is a 2 cm x 2 cm large monolithic pixel detector developed in the Tower 180 nm imaging process. The chip contains four CMOS transceiver blocks at its sides which allow chip-to-chip data transfer. The power pads are located mainly at the side edges on the chip which allows for chip-to-chip power transmission. The MALTA chip has been used to study module assembly using different interconnection techniques to transmit data and power from chip to chip and to minimize the overall material budget. Several 2-chip and 4-chip modules have been assembled using standard wire bonding, ACF (Anisotropic Conductive Films) and laser reflow interconnection techniques. These proceedings will summarize the experience with the different interconnection techniques and performance tests of MALTA modules with 2 and 4 chips tested in a cosmic muon telescope. They will also show first results on the effect of serial power tests on chip performance as well as the impact of the different interconnection techniques and the results of mechanical tests. Finally, a conceptual study for a flex based ultra-light weight monolithic pixel module based on the MALTA chip with minimum interconnections is presented.
The Biological Basis of the Bone-Muscle Inter-relationship in the Algorithm of Fracture Healing (2008)

The biological cascade of fracture healing is intimately linked to the muscle envelope. It further depends on the preservation of stable, perpetual axial micromovements. The current study was designed to demonstrate that high molecular weight bioactive substances diffuse from the muscle envelope to initiate osteoinductive activity at experimental fracture sites. Forty-eight rats underwent an experimental fracture of the left tibia and stabilization with an intramedullary 20-gauge needle. The animals were divided into 4 groups (A-D) of 12 rats each according to the post-fracture treatment. In group A (control) no additional treatment was applied following fracture and intramedullary fixation. In groups B, C, and D, a nitrocellulose membrane of various sizes was wrapped around the fracture, separating the periosteum from the muscle envelope. The groups differed by the membrane pore size, allowing passage of the following molecular sizes: 50 kilodaltons (kDa), 12 to 14 kDa, and 3.5 kDa in groups B, C, and D, respectively. Four animals in each group were sacrificed 2, 5, and 10 weeks after the procedure for radiographic and histological evaluation of fracture healing. Radiographic evaluation revealed a decreased rate of bone synthesis that correlated with the nitrocellulose pore size. Morphological and functional analysis of the bone explants indicated poorly healed fractures in groups B, C, and D. Direct contact between fractured bone and its muscle envelope is essential for the biological sequence of new bone formation. The extent of obstruction between the fracture and its muscle envelope correlates with the delay in fracture healing.
Behandlungskosten auf einer medizinischen Intensivstation: Ein Vergleich von 1992 und 1997 (2008)

The costs of a stay in the ICU has greatly increased over the last 5 years, the main causes being a change to new forms of treatment, especially in patients with myocardial infarction and those with haemophilia.
The Three Steps of Clustering In The Post‐Genomic Era (2013)

This chapter considers three clustering steps: choice of a distance function; choice of a clustering algorithm; and choice of a methodology to assess the statistical significance of clustering solutions. First, the chapter discusses the experimental set-up used for the results that are presented here. Next, it deals with distance functions; in particular, new approaches to assess the intrinsic separation ability of many standard distance functions and their use in conjunction with clustering algorithms. A section is devoted to clustering algorithms, in particular to nonnegative matrix factorization (NMF). The chapter further discusses the assessment of the statistical significance of a clustering solution. It explains the identification of the correct number of clusters in a given data set. This class of statistical methods is usually referred to as internal validation measures. Finally, the chapter deals with consensus clustering highlighting its paradigmatic nature for stability-based validation measures and its excellent discriminative power.
Dietary sodium enhances the expression of SLC4 family transporters, IRBIT, L-IRBIT, and PP1 in rat kidney: Insights into the molecular mechanism for renal sodium handling (2023)

The kidney plays a central role in maintaining the fluid and electrolyte homeostasis in the body. Bicarbonate transporters NBCn1, NBCn2, and AE2 are expressed at the basolateral membrane of the medullary thick ascending limb (mTAL). In a previous study, NBCn1, NBCn2, and AE2 are proposed to play as a regulatory pathway to decrease NaCl reabsorption in the mTAL under high salt condition. When heterologously expressed, the activity of these transporters could be stimulated by the InsP3R binding protein released with inositol 1,4,5-trisphosphate (IRBIT), L-IRBIT (collectively the IRBITs), or protein phosphatase PP1. In the present study, we characterized by immunofluorescence the expression and localization of the IRBITs, and PP1 in rat kidney. Our data showed that the IRBITs were predominantly expressed from the mTAL through the distal renal tubules. PP1 was predominantly expressed in the TAL, but is also present in high abundance from the distal convoluted tubule through the medullary collecting duct. Western blotting analyses showed that the abundances of NBCn1, NBCn2, and AE2 as well as the IRBITs and PP1 were greatly upregulated in rat kidney by dietary sodium. Co-immunoprecipitation study provided the evidence for protein interaction between NBCn1 and L-IRBIT in rat kidney. Taken together, our data suggest that the IRBITs and PP1 play an important role in sodium handling in the kidney. We propose that the IRBITs and PP1 stimulates NBCn1, NBCn2, and AE2 in the basolateral mTAL to inhibit sodium reabsorption under high sodium condition. Our study provides important insights into understanding the molecular mechanism for the regulation of sodium homeostasis in the body.
Golgi architecture in the malaria parasite Plasmodium falciparum (2007)

Plasmodium falciparum, the causative agent of malaria, relies on a sophisticated protein secretion system for host cell invasion and transformation. Although the parasite displays a secretory pathway similar to those of all eukaryotic organisms, it possesses a rather unique Golgi apparatus. In order to get a better understanding of Golgi morphology in Plasmodium we identified and characterized the Golgi matrix protein PfGRASP, a homologue of the Golgi re‐assembly stacking protein (GRASP) family. Our analysis revealed that although the genome of the parasite encodes only one grasp gene, two splice variants exist. This might be reminiscent of the two GRASP proteins present in other eukaryotic systems. Using GFP‐fusion proteins we visualized the subcellular distribution of the two PfGRASP proteins. To further dissect the spatial organization of the Golgi and its relationship with the ER we used the luminal ER marker protein BiP and the COPII marker protein Sec13p. We show that ER export competence lies within well‐defined specialized ER compartments adjacent to the Golgi apparatus.
Synthesis of Morpholine-2,5-dione Monomers for the Preparation of Polydepsipeptides (2010)

Biomaterials derived from synthetic polymers have traditionally been used for a variety of tissue engineering applications, however current research focuses on biologically functionalizing materials to improve various physical characteristics. Our laboratory has investigated the synthesis and characterization of polydepsipeptides (PDPs), which combine both synthetic and biologically relevant chemical groups. PDPs are prepared from a cyclic intermediate, the morpholine dione (MD). Here, we describe the synthesis of MDs using solid phase synthesis in an attempt to control racemization and improve purity with respect to prior solution phase synthesis methods.
Pseudo-field effects in type II semimetals: new probes for over-tilted Weyl cones (2020)

We study the effects of pseudo-magnetic fields on Weyl semimetals with over-tilted Weyl cones, or type II cones. We compare the phenomenology of the resulting pseudo-Landau levels in the type II Weyl semimetal to the known case of type I cones. We predict that due to the nature of the chiral Landau level resulting from a magnetic field, a pseudo-magnetic field, or their combination, the optical conductivity can be utilized to detect a type II phase and deduce the direction of the tilt. Finally, we discuss ways to engineer homogeneous and inhomogeneous type II semimetals via generalizations of known layered constructions in order to create controlled pseudo-magnetic fields and over-tilted cones.
Separating Speech from Speech Noise Annual Report 2006 (2007)

The main work at Columbia this year has been the development of algorithms for extracting and recognizing speech in nonstationary, noisy environments when only a single microphone channel is available. Our particular approach is based on using trained models to distinguish regions of time-frequency containing speech from nonspeech areas [2], and we have pursued this along several directions: One approach is to use trained models of the speech signal and to find the best set of model parameters that are consistent with the noisy speech observations. An alternative approach is to treat the labeling of each time-frequency cell as a simple classification task, and to train pattern recognition classifiers to perform this task. In that work, the challenge is to find the best classifier architecture and the most effective representation of the context. When more than one microphone channel is available, some different approaches to source separation become possible. The two-channel case is particularly interesting because this is the number of ears possessed by the typical listener. We have been looking at ways to separate sources in recordings made
Large‐Area Vapor‐Phase Growth and Characterization of MoS<sub>2</sub> Atomic Layers on a SiO<sub>2</sub> Substrate (2012)

Atomic-layered MoS(2) is synthesized directly on SiO(2) substrates by a scalable chemical vapor deposition method. The large-scale synthesis of an atomic-layered semiconductor directly on a dielectric layer paves the way for many facile device fabrication possibilities, expanding the important family of useful mono- or few-layer materials that possess exceptional properties, such as graphene and hexagonal boron nitride (h-BN).
Psychoactive Substances Taken with Mephedrone and HCV Infection (2021)

HCV infection is a statistically significant factor affecting the increase in liver enzymes levels in the group of patients taking mephedrone.
Structural design and modelling of the zigzag wingbox for span morphing wing (2012)

This paper presents the Zigzag wingbox concept that allows the wing span to be varied. The wingbox consists of a rigid part and a morphing part. The rigid part is a semi-monocoque construction that houses the fuel tank. The morphing part consists of various morphing partitions where in each partition there are two spars each consisting of two C-beams hinged together. Each morphing partition is bounded by two ribs through which the spars are connected. The ribs transfer the loads between the spars of adjacent morphing partition and serves as the main structure to which the flexible skins are to be attached. The Zigzag wingbox concept is to be incorporated on a medium altitude long endurance (MALE) UAV to enhance operational performance and provide roll control. Equivalent modelling and preliminary sizing of the concept are performed to assess its feasibility and quantify its potential benefits.
Effect of uncoordinated network interference on UWB autocorrelation receiver (2009)

Over the last few years there has been an emerging interest in ultrawideband (UWB) communications in wireless sensor networks, mainly due to their low-complexity and low-power consumption. In particular, auto-correlation receiver (AcR) is a potential candidate for such applications. However, the presence of network interference, especially interference between uncoordinated UWB networks, will severely degrade the performance of such receiver. In this paper, we analyze the bit error probability performance of the AcR in the presence of UWB interference. We model the network interference as an aggregate UWB interference, generated by elements of uncoordinated UWB networks scattered according to a spatial Poisson process. Our analytical framework allows a tractable performance analysis and still provides sufficient insight into the effect of uncoordinated network interference on UWB systems.
Seq-ing the SINEs of central nervous system tumors in cerebrospinal fluid (2023)

It is often challenging to distinguish cancerous from non-cancerous lesions in the brain using conventional diagnostic approaches. We introduce an analytic technique called Real-CSF (repetitive element aneuploidy sequencing in CSF) to detect cancers of the central nervous system from evaluation of DNA in the cerebrospinal fluid (CSF). Short interspersed nuclear elements (SINEs) are PCR amplified with a single primer pair, and the PCR products are evaluated by next-generation sequencing. Real-CSF assesses genome-wide copy-number alterations as well as focal amplifications of selected oncogenes. Real-CSF was applied to 280 CSF samples and correctly identified 67% of 184 cancerous and 96% of 96 non-cancerous brain lesions. CSF analysis was considerably more sensitive than standard-of-care cytology and plasma cell-free DNA analysis in the same patients. Real-CSF therefore has the capacity to be used in combination with other clinical, radiologic, and laboratory-based data to inform the diagnosis and management of patients with suspected cancers of the brain.
All-Dielectric Metasurfaces: Optical Nonlinearities and Emission Control (2019)

In this work we show our results on the harmonic generation and nonlinear frequency mixing enhanced by Mie modes in GaAs metasurfaces. Moreover, we show enhancement and directionality control of the quantum dot emission embedded in the metasurface.