gebhart/patrepeval huggingface dataset:
Multiple Testing. Part III. Procedures for Control of the Generalized Family-Wise Error Rate and Proportion of False Positives (2004)

The accompanying articles by Dudoit et al. (2003b) and van der Laan et al. (2003) provide single-step and step-down resampling-based multiple testing procedures that asymptotically control the family-wise error rate (FWER) for general null hypotheses and test statistics. The proposed procedures fundamentally differ from existing approaches in the choice of null distribution for deriving cut-offs for the test statistics and are shown to provide asymptotic control of the FWER under general data generating distributions, without the need for conditions such as subset pivotality. In this article, we show that any multiple testing procedure (asymptotically) controlling the FWER at level alpha can be augmented into: (i) a multiple testing procedure (asymptotically) controlling the generalized family-wise error rate (i.e., the probability, gFWER(k), of having more than k false positives) at level alpha and (ii) a multiple testing procedure (asymptotically) controlling the probability, PFP(q), that the proportion of false positives among the rejected hypotheses exceeds a user-supplied value q in (0,1) at level alpha. Existing procedures for control of the proportion of false positives typically rely on the assumption that the test statistics are independent, while our proposed augmentation procedures control the PFP and gFWER for general data generating distributions, with arbitrary dependence structures among variables. Applying our augmentation methods to step-down multiple testing procedures that asymptotically control the FWER at exact level alpha (van der Laan et al., 2003), yields multiple testing procedures that also asymptotically control the gFWER and PFP at exact level alpha. Finally, the adjusted p-values for the gFWER and PFP-controlling augmentation procedures are shown to be simple functions of the adjusted p-values for the original FWER-controlling procedure.
The capacity region of broadcast channels with intersymbol interference and colored Gaussian noise (2001)

We derive the capacity region for a broadcast channel with intersymbol interference (ISI) and colored Gaussian noise under an input power constraint. The region is obtained by first defining a similar channel model, the circular broadcast channel, which can be decomposed into a set of parallel degraded broadcast channels. The capacity region for parallel degraded broadcast channels is known. We then show that the capacity region of the original broadcast channel equals that of the circular broadcast channel in the limit of infinite block length, and we obtain an explicit formula for the resulting capacity region. The coding strategy used to achieve each point on the convex hull of the capacity region uses superposition coding on some or all of the parallel channels and dedicated transmission on the others. The optimal power allocation for any point in the capacity region is obtained via a multilevel water-filling. We derive this optimal power allocation and the resulting capacity region for several broadcast channel models.
Online Calibration of MOSFET On-State Resistance for Precise Current Sensing (2004)

An approach for online current sensing calibration is presented where an auxiliary switch and a precision sense resistor are connected in parallel with a main power switch to achieve accuracy comparable to the sense resistor method, together with the advantage of essentially no additional power loss. The proposed current-sensing circuit and the calibration methods are particularly well suited for digital controller implementations where the required control and calibration functions can be easily accomplished. Experimental results with a digitally controlled 1.5-V 15-A synchronous buck converter demonstrate functionality of the online calibration approach, showing a significant improvement in accuracy over voltage sensing across the power MOSFET on-resistance.
Influence of sintering conditions on low-temperature degradation of dental zirconia (2012)

status: Published
Multifunctional roles of urokinase plasminogen activator (uPA) in cancer stemness and chemoresistance of pancreatic cancer (2013)

Pancreatic ductal adenocarcinoma (PDAC) is almost always lethal. One of the underlying reasons for this lethality is believed to be the presence of cancer stem cells (CSC), which impart chemoresistance and promote recurrence, but the mechanisms responsible are unclear. Recently the poor prognosis of PDAC has been correlated with increased expression of urokinase plasminogen activator (uPA). In the present study we examine the role of uPA in the generation of PDAC CSC. We observe a subset of cells identifiable as a side population (SP) when sorted by flow cytometry of MIA PaCa-2 and PANC-1 pancreatic cancer cells that possess the properties of CSC. A large fraction of these SP cells are CD44 and CD24 positive, are gemcitabine resistant, possess sphere-forming ability, and exhibit increased tumorigenicity, known characteristics of cancer stemness. Increased tumorigenicity and gemcitabine resistance decrease after suppression of uPA. We observe that uPA interacts directly with transcription factors LIM homeobox-2 (Lhx2), homeobox transcription factor A5 (HOXA5), and Hey to possibly promote cancer stemness. uPA regulates Lhx2 expression by suppressing expression of miR-124 and p53 expression by repressing its promoter by inactivating HOXA5. These results demonstrate that regulation of gene transcription by uPA contributes to cancer stemness and clinical lethality.
Polyvinylidene fluoride (PVDF) elastic, piezoelectric, pyroelectric, and dielectric coefficients and their non-linearities (1993)

This work presents a set of material coefficients for a uniaxially 4x stretched 25 μm thick PVDF film. Calculations of the type d = se, where d and e are piezoelectric coefficients and s is the compliance, are used to compare independent measurements of piezoelectric coefficients. The piezoelectric coefficient e333 is found to be constant to strains over 25%. The non-linearities in the dijk coefficients are due to non-linearities in the elastic moduli that are typical of polymers above their glass transition temperature, i.e. strain rate dependent, viscoelastic, temperature dependent.
Real-world data in retinal diseases treated with anti-vascular endothelial growth factor (anti-VEGF) therapy – a systematic approach to identify and characterize data sources (2019)

The study provides a comprehensive list of RWD sources for patients with retinal disease, many of which will be useful for conducting real-world studies in the field of ophthalmology.
The functional annotation and exploration the SOX11 enhanceosome (2021)

Background/Introduction Neuroblastoma (NB) is the most common extra cranial solid tumor during early childhood, arising from progenitors of the sympathetic nervous system. We identified the adrenergic specific transcription factor SOX11 as a lineage dependency factor and a putative master regulator of epigenetic plasticity in NB. The expression of lineage identity genes is typically regulated by cell type specific enhancers thereby acting as putative cell-specific vulnerabilities that may be targeted while minimizing harm to the normal development of tissues. Aims We aimed to gain insight into the long-range control of SOX11 expression in NB cells as a first step towards cell type specific therapeutic targeting of SOX11-driven neuroblastoma. Methods/Materials We analyzed H3K27ac data to map noncoding regulatory enhancer regions in the vicinity of the SOX11 locus. Chromatin conformation analysis (4C-seq) additionally shows evidence for looping contacts between the SOX11 promotor region and the SILC1 locus, a lncRNA downstream of SOX11. For further exploration of the function of SILC1, chromatin isolation by RNA purification (ChIRP) is performed to identify lncRNA bound DNA sequences. Functional inhibition of the SILC1 locus is explored using dCas9-KRAB silencing in NB cells. Results We identified a super-enhancer in a large gene poor region, 1.1 Mb distal to the SOX11 locus. This region coincides with the previously annotated lncRNA coined SILC1 which was shown to be implicated in neurite outgrowth and neuron regeneration. SILC1 was found to be strongly expressed in adrenergic NB cells while absent in mesenchymal NB cells and highly correlated to SOX11 expression levels in both NB cell lines and tumors. Also, in the normal developing sympathetic lineage, SILC1 expression pattern closely resembled that of SOX11. Using 4C-seq, we observed looping in this highly active region between the SOX11 and SILC1 promoter in adrenergic NB cells while absent in the mesenchymal NB cell line SH-EP. We are currently unraveling the role of SILC1 using ChIRP sequencing and a dCas9-KRAB silencing system. Summary/conclusion In conclusion, our data suggests that SILC1 plays a crucial role in assisting the function of the transcription factor SOX11 thus offering an entry point for targeted therapy for SOX11-driven neuroblastoma.
Transverse flow measurement using photoacoustic Doppler bandwidth broadening: phantom and in vivo studies (2010)

In photoacoustic (PA) imaging of microvascular networks, the transverse component of the blood flow that is perpendicular to the acoustic probing beam is usually dominant. We propose a new method to measure the transverse flow, based on the Doppler bandwidth broadening. The bandwidth broadening is inversely proportional to the transit time spent by the absorbers passing through the focus. Because the photoacoustic signal in one A-scan has a wide band, multiple successive A-scans are used to estimate the relatively small signal variance. Then the bandwidth broadening can be calculated from the standard derivation of the Doppler spectrum. By exploiting the pulse excitation and bidirectional raster motor scanning, threedimensional structural and flow information can be obtained simultaneously. From a flow of a suspension of carbon particles (diameter: 6 &mu;m), transverse flow speeds from 0 to 2.5 mm/s were measured using optical-resolution photoacoustic microscopy. The bandwidth broadening at each speed was in good agreement with the theoretical prediction. The blood flow in a mouse brain was also imaged.
DMD-encoded spectral photoacoustic microscopy (2012)

We present a spectrally encoded photoacoustic microscope based on a digital mirror device (DMD). It enables fast spatially resolved spectral measurements of optical absorption. The imaging system can quickly tune the laser illumination spectrum at the laser pulse repetition rate of 2 kHz. To demonstrate multi-wavelength absorption measurements, we imaged optically absorbing solution phantom. Compared with spectral scanning, spectral encoding recovers chromophore absorption spectra with improved accuracy by enhancing photoacoustic amplitude signal-to-noise ratio.
New MR imaging methods for metallic implants in the knee: Artifact correction and clinical impact (2011)

SEMAC and MAVRIC correct for metal artifact, noninvasively providing high-resolution images with superb bone and soft tissue contrast.
Belief in Transmigration of the Soul and Psychopathology in Israeli Druze (1998)

One of the central tenets of the Druze religion is the transmigration of the soul. In rare cases this belief may be related to psychopathology or cause a temporary inability to function normally. We report on 5 Druze patients whose preoccupation with transmigration was the basis of their pathological behavior. These cases illustrate the interaction between cultural and religious beliefs, and psychopathology, and emphasize the importance of employing a culture-specific psychiatric approach in the management of this type of patients.
Characteristics of lung cancer among patients with idiopathic pulmonary fibrosis and interstitial lung disease – analysis of institutional and population data (2018)

Lung cancer is approximately 3.34 times more frequently diagnosed in IPF patients compared to general population, and associated with worse prognosis compared with IPF without lung cancer, with squamous cell carcinoma and lower lobe predilection. The causality between non-smoking IPF patients and lung cancer is to be determined.
Questions to Chemical Educators from the Chemistry Community (2008)

This chapter poses twenty questions whose answers are of vital importance in teaching chemistry to beginning students at the college or university level. These questions are addressed primarily to those who carry out research in chemical education, but the argument is made that the answers provided by this community of scholars will have little impact unless chemists and chemical education researchers can communicate clearly to one another and gain not only each other's respect but also the attention and respect of the wider chemistry community.
Acoustic Array Systems: Theory, Implementation, and Application (2013)

Presents a unified framework of far-field and near-field array techniques for noise source identification and sound field visualization, from theory to application. Acoustic Array Systems: Theory, Implementation, and Application provides an overview of microphone array technology with applications in noise source identification and sound field visualization. In the comprehensive treatment of microphone arrays, the topics covered include an introduction to the theory, far-field and near-field array signal processing algorithms, practical implementations, and common applic
Structural and Electrical Properties of Solution-Processed Gallium-Doped Indium Oxide Thin-Film Transistors (2011)

We fabricated solution-processed gallium-doped indium oxide (GIO) thin-film transistors (TFTs). The electrical property, crystallinity, and transmittance were investigated as a function of gallium content. Varying the gallium/indium ratio is found to have a significant effect on structural and electrical properties of thin films. The shrinkage of the lattice of a GIO film originates from substitution of Ga on In sites in the In2O3 lattice, which was verified by X-ray diffraction (XRD) analysis. By increasing the gallium ratio of the channel material, the GIO film shows an amorphous phase. The optimized GIO film (Ga/In= 0.35) has an electron mobility of 3.59 cm2 V-1 s-1, a threshold voltage of 0.1 V, an on/off current ratio of 8.2×107, and a subthreshold slope of 0.9 V/decade, and is highly transparent (∼92%) in the visible region.
Reduced Cladding Diameter Fibers for High-Density Optical Interconnects (2019)

Data centers are continually striving to meet the challenge of delivering more bandwidth, and this will require higher capacity optical switches and servers. One proposal for achieving this higher bandwidth density is to use embedded optical transceivers, which have arrays of VCSEL or silicon-photonic lasers integrated into on-board and co-packaged optics. The capacities of these transceivers are limited by the densities of the arrays, which in turn depend on the physical dimensions of the optical fibers that are coupled to the chip. This size constraint is motivating component manufacturers to consider using optical fibers with reduced cladding (RC) and coating diameters to enable higher density interconnects. In this paper, we introduce bend-insensitive single-mode and multimode RC fibers that have low attenuation, low bend loss, and are backward-compatible with the installed base of standard optical fibers. We also discuss how these RC fibers can be integrated into fiber array units to create a high-density fiber-chip connectivity solution.
17.4 A 14nm 1.1Mb embedded DRAM macro with 1ns access (2015)

IBM introduced trench capacitor eDRAM into its high performance microprocessors beginning with 45nm and Power 7 [1] to provide a higher density cache without chip crossings. Whereas the 45 and 32nm designs employ a micro sense amplifier [2] and three-level bitline hierarchy, the design implemented for 22nm utilizes a higher gain sense amplifier and two-level bitline architecture that together provide significant reductions in area, latency, and power. This 22nm design style has been migrated into a 14nm FinFET [3] learning vehicle, complete with an ABIST engine, wordline charge pumps (VPP and VWL), and padcage interface circuitry.
YBa2Cu3O7 thin-film step junctions on MgO substrates (1992)

Josephson junctions have been made by the evaporation of epitaxial YBa2Cu3O7 over steps etched in (001) MgO. Such junctions differ from those grown on perovskite substrates in that the c-axis of the film grows approximately normal to the local substrate surface, so the junction comprises two tilt grain boundaries. Results are reported for junctions formed by this process which showed Josephson currents at temperatures up to 89 K and resistively shunted junctionlike current-voltage curves. A weak magnetic field applied normal to the substrate gave Fraunhofer patterns indicative of good current uniformity across the junction. The dc SQUIDs show deep modulation, and promising noise performance.
Multicast Using Bit Index Explicit Replication (BIER) (2017)

This document specifies a new architecture for the forwarding of
multicast data packets. It provides optimal forwarding of multicast
packets through a domain. However, it does not require a
protocol for explicitly building multicast distribution trees, nor
does it require intermediate nodes to maintain any per-flow state.
This architecture is known as Bit Index Explicit Replication (BIER).
When a multicast data packet enters the domain, the ingress router
determines the set of egress routers to which the packet needs to be
sent. The ingress router then encapsulates the packet in a BIER
header. The BIER header contains a bit string in which each bit
represents exactly one egress router in the domain; to forward the
packet to a given set of egress routers, the bits corresponding to
those routers are set in the BIER header. The procedures for
forwarding a packet based on its BIER header are specified in this
document. Elimination of the per-flow state and the explicit tree-
building protocols results in a considerable simplification.
Enzymes as Catalysts in Carbohydrate Synthesis (1991)

The discovery of the myriad roles of carbohydrates in biological recognition phenomena has led to an increased demand for practical routes to gram-scale quantities of unnatural carbohydrate structures. We have investigated the applicability of enzymes as catalysts for mono-oligo-, and polysaccharide synthesis. Here, we review our progress in the area, in particular the use of aldolases for monosaccharide synthesis, the synthesis of the activated sugar nucleosides required for Leloir-pathway glycosidic bond formation, and the use of both Leloir-and non-Leloir-pathway enzymes for the synthesis of carbohydrate polymers.
Low-overhead mechanism to detect address faults in ECC-protected memories (2023)

Embodiments are generally directed to a low-overhead mechanism to detect address faults in ECC-protected memories. An embodiment of an apparatus includes a memory array; an error correction code (ECC) encoder for the memory array to encode ECC values based on a data value and a respective address value for the data value; and an ECC decoder for the memory array to decode ECC values that are based on data values and respective addresses for the data values; wherein the apparatus is to detect and correct an error in an address value based on an ECC value, address value, and data value stored in the memory.
Dynamic Exhaust Valve Flow 1-D Modelling During Blowdown Conditions (2019)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;To conduct system level studies on internal combustion engines reduced order models are required in order to keep the computational load below reasonable limits. By its nature a reduced order model is a simplification of reality and may introduce modeling errors. However what is of interest is the size of the error and if it is possible to reduce the error by some method. A popular system level study is gas exchange and in this paper the focus is on the exhaust valve. Generally the valve is modeled as an ideal nozzle where the flow losses are captured by reducing the flow area. As the valve moves slowly compared to the flow the process is assumed to be quasi-steady, i.e. interpolation between steady-flow measurements can be used to describe the dynamic process during valve opening. These measurements are generally done at low pressure drops, as the influence of pressure ratio is assumed to be negligible. As it is very difficult to measure time-resolved mass flow it is hard to test validity of these modeling assumptions. Experimental data indicates that the model overestimates valve flow during the blowdown event. As the blowdown pulse contains a significant portion of the energy in the cylinder at exhaust valve opening, it is therefore of importance to model this correctly. In this paper experimental results from previously published research have been compared to simulation results and the deviation from quasi-steady behavior has been quantified. The deviation appears to be a function of pressure ratio over the valve and valve opening speed. A model is proposed to compensate for the observed effects.&lt;/div&gt;&lt;/div&gt;
ChemInform Abstract: f‐Element‐Crown Ether Complexes. Part 9. The Role of Solvent Hydrogen Bonding: Synthesis and Crystal Structure of Aquotetrachlorotris(ethanol)thorium(IV)‐1,4,7,10,13,16‐Hexaoxacyclo‐octadecane‐Water (1/1/1). (1988)

Abstract The interaction of hydrated ThCl 4 with 18‐crown‐6 in EtOH gives the title complex (no yield given), which crystallizes in the space group P1 with Z=2.
Design, Synthesis and Biological Evaluation of Novel HIF1α Inhibitors. (2015)

Elevated levels of hypoxia inducible factor-1 (HIF1) are linked to tumor metastasis, angiogenesis, poor patient prognosis and response to chemotherapy. HIF1α is a master regulator of the hypoxic response, including in cancer cells, through transcriptional activation of several target genes. Previously, we identified compound CJ-3k with high anti-HIF1α activity based on the structure of a well-known HIF1α inhibitor, YC-1. In this study, the CJ-3k scaffold was systematically modified to explore the structure-activity relationships. Fifty-three new CJ-3k analogs were synthesized and screened for their anti-HIF-1α activity in a luciferase-transfected human breast cancer cell line (MDA-MB-231). Some of these new analogs have a significantly greater activity than that of CJ-3k and hold potential for development as new therapeutic agents for the treatment of cancer.
Clinical, Hematologic, Biologic and Molecular Characteristics of Patients with Myeloproliferative Neoplasms and a Chronic Myelomonocytic Leukemia-Like Phenotype (2020)

Patients with a myeloproliferative neoplasm (MPN) sometimes show a chronic myelomonocytic leukemia (CMML)-like phenotype but, according to the 2016 WHO classification, a documented history of an MPN excludes the diagnosis of CMML. Forty-one patients with an MPN (35 polycythemia vera (PV), 5 primary myelofibrosis, 1 essential thrombocythemia) and a CMML-like phenotype (MPN/CMML) were comprehensively characterized regarding clinical, hematologic, biologic and molecular features. The white blood cell counts in MPN/CMML patients were not different from CMML patients and PV patients. The hemoglobin values and platelet counts of these patients were higher than in CMML but lower than in PV, respectively. MPN/CMML patients showed myelomonocytic skewing, a typical in vitro feature of CMML but not of PV. The mutational landscape of MPN/CMML was not different from JAK2-mutated CMML. In two MPN/CMML patients, development of a CMML-like phenotype was associated with a decrease in the JAK2 V617F allelic burden. Finally, the prognosis of MPN/CMML (median overall survival (OS) 27 months) was more similar to CMML (JAK2-mutated, 28 months; JAK2-nonmutated 29 months) than to PV (186 months). In conclusion, we show that patients with MPN and a CMML-like phenotype share more characteristics with CMML than with PV, which may be relevant for their classification and clinical management.