gebhart/patrepeval huggingface dataset:
Measurable residual disease in chronic lymphocytic leukemia: expert review and consensus recommendations (2021)

Assessment of measurable residual disease (often referred to as "minimal residual disease") has emerged as a highly sensitive indicator of disease burden during and at the end of treatment and has been correlated with time-to-event outcomes in chronic lymphocytic leukemia. Undetectable-measurable residual disease status at the end of treatment demonstrated independent prognostic significance in chronic lymphocytic leukemia, correlating with favorable progression-free and overall survival with chemoimmunotherapy. Given its utility in evaluating depth of response, determining measurable residual disease status is now a focus of outcomes in chronic lymphocytic leukemia clinical trials. Increased adoption of measurable residual disease assessment calls for standards for nomenclature and outcomes data reporting. In addition, many basic questions have not been systematically addressed. Here, we present the work of an international, multidisciplinary, 174-member panel convened to identify critical questions on key issues pertaining to measurable residual disease in chronic lymphocytic leukemia, review evaluable data, develop unified answers in conjunction with local expert input, and provide recommendations for future studies. Recommendations are presented regarding methodology for measurable residual disease determination, assay requirements and in which tissue to assess measurable residual disease, timing and frequency of assessment, use of measurable residual disease in clinical practice versus clinical trials, and the future usefulness of measurable residual disease assessment. Nomenclature is also proposed. Adoption of these recommendations will work toward standardizing data acquisition and interpretation in future studies with new treatments with the ultimate objective of improving outcomes and curing chronic lymphocytic leukemia.
Transcriptional network underlying Caenorhabditis elegans vulval development (2005)

The vulval development of Caenorhabditis elegans provides an opportunity to investigate genetic networks that control gene expression during organogenesis. During the fourth larval stage (L4), seven vulval cell types are produced, each of which executes a distinct gene expression program. We analyze how the expression of cell-type-specific genes is regulated. Ras and Wnt signaling pathways play major roles in generating the spatial pattern of cell types and regulate gene expression through a network of transcription factors. One transcription factor (lin-29) primarily controls the temporal expression pattern. Other transcription factors (lin-11, cog-1, and egl-38) act in combination to control cell-type-specific gene expression. The complexity of the network arises in part because of the dynamic nature of gene expression, in part because of the presence of seven cell types, and also because there are multiple regulatory paths for gene expression within each cell type.
Table S1 from Cobomarsen, an Oligonucleotide Inhibitor of miR-155, Slows DLBCL Tumor Cell Growth <i>In Vitro</i> and <i>In Vivo</i> (2023)

&lt;p&gt;Supplementary table S1&lt;/p&gt;
Zero-shot Multi-Domain Dialog State Tracking Using Descriptive Rules (2020)

In this work, we present a framework for incorporating descriptive logical rules in state-of-the-art neural networks, enabling them to learn how to handle unseen labels without the introduction of any new training data. The rules are integrated into existing networks without modifying their architecture, through an additional term in the network's loss function that penalizes states of the network that do not obey the designed rules. As a case of study, the framework is applied to an existing neural-based Dialog State Tracker. Our experiments demonstrate that the inclusion of logical rules allows the prediction of unseen labels, without deteriorating the predictive capacity of the original system.
Comparative investigation of third- and fifth-harmonic generation in atomic and molecular gases driven by midinfrared ultrafast laser pulses (2011)

We report on the comparative experimental investigation on third- and fifth-harmonic generation (THG and FHG) in atomic and molecular gases driven by midinfrared ultrafast laser pulses at a wavelength of \ensuremath{\sim}1500 nm. We observe that the conversion efficiencies of both the THG and FHG processes saturate at similar peak intensities close to \ensuremath{\sim}1.5 \ifmmode\times\else\texttimes\fi{} 10${}^{14}$ W/cm${}^{2}$ for argon, nitrogen, and air, whose ionization potentials are close to each other. Near the saturation intensity, the ratio of yields of the FHG and THG reaches \ensuremath{\sim}10${}^{\ensuremath{-}1}$ for all the gases. Our results show that high-order Kerr effect seems to exist; however, contribution from the fourth-order Kerr refractive index coefficient alone is insufficient to balance the Kerr self-focusing without the assistance of plasma generation.
Combining 2G and 3G (4G) BTS outputs sharing the same frequency band (2012)

This work faces the problem of combining the outputs of two co-siting BTS, one operating with 2G networks and the other with 3G (or 4G) networks. This requirement is becoming more and more frequent because many operators, for increasing the capacity for data and voice signal transmission, have overlaid the new network in 3G or 4G technology to the existing 2G infrastructure. The solution here proposed is constituted by a low loss combiner realized through a directional double single-sided filtering system, which manages both TX and RX signals from each BTS output. The design approach for the combiner architecture is described with a particular emphasis on the synthesis of the double single-sided filters (realized by means of extracted pole technique). A prototype of the low-loss combiner has been designed and fabricated for validating the proposed approach. The results obtained are here discussed making into evidence the pros & cons of the proposed solution.
Transcriptional program activated by R1881 exposure in LNCaP cells (2011)

<b>Copyright information:</b>Taken from "Transcriptional programs activated by exposure of human prostate cancer cells to androgen"Genome Biology 2002;3(7):research0032.1-research0032.12.Published online 14 Jun 2002PMCID:PMC126237.Copyright © 2002 DePrimo et al., licensee BioMed Central Ltd Hierarchical cluster analysis of androgen-responsive genes in LNCaP cells treated with R1881. This is a scaled-down overview of the cluster diagram generated by querying microarray data against the list of genes generated by SAM analysis (see text). The complete image with all gene names is viewable at [12]. Each column represents data from microarray analysis of a single RNA sample from LNCaP cells corresponding to a given time; the columns under the green heading show data in which RNA from R1881-treated and control cells were hybridized on the same microarray, while those under the black heading show experiments in which RNA from treated cells was hybridized against a common reference and normalized to the '0' time point. Numbers above each column denote specific time points. The dose of R1881 was 1 nM in all experiments. Red squares indicate transcripts with expression levels higher than that of ethanol-treated control cells; green squares, levels lower than that of controls; black, levels approximately equal to those in controls; gray, data of insufficient quality. Representative androgen-regulated genes measured in microarray analysis of LNCaP cells treated with 1 nM R1881. Expression profiles of transcripts representing previously published androgen target genes are depicted. Genes listed more than once indicate that the microarray contained multiple elements representing that gene. As indicated by the scale bar, color saturation reflects magnitude of expression ratio.
Machine Learning, Reasoning, and Intelligence in Daily Life: Directions and Challenges (2006)

Technical developments and trends are providing a fertile substrate for creating and integrating machine learning and reasoning into multiple applications and services. I will review several illustrative research efforts on our team, and focus on challenges, opportunities, and directions with the streaming of machine intelligence into daily life. 1 Reflections on Trends and Directions Over the last decade, technical and infrastructural developments have come together to create a nurturing environment for developing and fielding applications of machine learning and reasoning—and for harnessing automated intelligence to provide value to people in the course of their daily lives. These developments include (1) technical advancements in machine learning and reasoning, (2) the growth in CPU and memory capabilities within commonly available devices and platforms, (3) the connectivity, content, and services provided by the evolving Web, and (4) the increasing availability of data resources, including corpora of behavioral data collected via inexpensive sensors, and through ongoing interaction with software and services. 1.1 Panoply of Applications and Services Opportunities for integrating applications of machine intelligence into the daily lives of people are growing with the increasing popularity of computing systems, the widening diversity of web services, the growing popularity of portable devices that contain general-purpose operating systems, and ongoing innovations in human-computer interaction— including the increasing prowess of speech recognition, handwriting, and sketch-understanding interfaces. Various examples of the integration of automated learning and reasoning into daily life have been appearing as implicit and explicit extensions to traditional systems and services, and also in prototypes and systems that provide qualitatively new kinds of experiences. I will review several projects and efforts undertaken by our team that highlight directions and approaches to introducing potentially valuable machine learning and reasoning into the daily lives of people.
A snapshot multispectral imager with integrated tiled filters and optical duplication (2013)

Although the potential of spectral imaging has been demonstrated in research environments, its adoption by industry has so far been limited due to the lack of high speed, low cost and compact spectral cameras. We have previously presented work to overcome this limitation by monolithically integrating optical interference filters on top of standard CMOS image sensors for high resolution pushbroom hyperspectral cameras. These cameras require a scanning of the scene and therefore introduce operator complexity due to the need for synchronization and alignment of the scanning to the camera. This typically leads to problems with motion blur, reduced SNR in high speed applications and detection latency and overall restricts the types of applications that can use this system. This paper introduces a novel snapshot multispectral imager concept based on optical filters monolithically integrated on top of a standard CMOS image sensor. By using monolithic integration for the dedicated, high quality spectral filters at its core, it enables the use of mass-produced fore-optics, reducing the total system cost. It overcomes the problems mentioned for scanning applications by snapshot acquisition, where an entire multispectral data cube is sensed at one discrete point in time. This is achieved by applying a novel, tiled filter layout and an optical sub-system which simultaneously duplicates the scene onto each filter tile. Through the use of monolithically integrated optical filters it retains the qualities of compactness, low cost and high acquisition speed, differentiating it from other snapshot spectral cameras based on heterogeneously integrated custom optics. Moreover, thanks to a simple cube assembly process, it enables real-time, low-latency operation. Our prototype camera can acquire multispectral image cubes of 256x256 pixels over 32 bands in the spectral range of 600-1000nm at a speed of about 30 cubes per second at daylight conditions up to 340 cubes per second at higher illumination levels as typically used in machine vision applications.
Infrared phased-array sensor (2011)

Metal-oxide-metal (MOM) tunnel diode detectors when integrated with phased-array antennas provide determination of the angle of arrival and degree of coherence of received infrared radiation. Angle-of-arrival measurements are made with a pair of dipole antennas coupled to a MOM diode through a coplanar strip transmission line. The direction of maximum angular response is altered by varying the position of the MOM diode along the transmission line connecting the antenna elements. Phased-array antennas can also be used to measure the degree of coherence of a partially coherent infrared field. With a two-element array, the degree of coherence is a measure of the correlation of electric fields received by the antennas as a function of the element separation. Antenna-coupled MOM diode devices are fabricated using electron beam lithography and thin-film deposition through a resist shadow mask. Measurements at 10.6 &#956;m are substantiated by electromagnetic simulations and compared to analytic results.
Quenching of Tris(2,2'-bipyridine)ruthenium(II) Luminescence by Cobalt(III) Polypyridyl Complexes in Different Sites in and on Clays (1995)

The effect of quenching of tris(2,2'-bipyridine)ruthenium(II) [Ru(bpy)_3^(2+)] luminescence by Co(phen)_3^(3+) in various locations in and on bentolite-H clay has been investigated. Ru(bpy)_3^(2+) incorporated into the interlayer region of bentolite-H by ion exchange exhibited spectral properties that were distinct from the Ru(bpy)_3^(2+) incorporated by incipient wetness methods. For example, the samples showed different diffraction, luminescence emission, and lifetime decays. The method of preparation, the nature of counterion (chloride or cyanide), and the presence of a quencher [Co(phen)_3^(3+) influence the emission properties. For example, incipient wetness methods allow deposition on outer surfaces (OUT) of the clay whereas ion-exchange leads to deposition primarily in the interlayer spacing (IN) based on spectroscopic and diffraction data. The luminescence intensities and lifetimes decrease in the order Ru(0UT) &gt; Ru(IN) &gt; Ru(OUT)/Co(IN) &gt; Ru(IN)/Co(0UT) &gt; Ru(OUT)/Co(OUT) ≃ Ru(IN)/Co(IN). Different methods of preparation and treatment result in location of Ru(bpy)_3^(2+) at different internal or external sites in the clay which give different luminescence and lifetime properties. By controlling the locations of Ru(II) and Co(III) (inside or outside), the quenching rates could be modulated. The location of the Ru(II) complex seems to control both the photophysical properties and the efficiency and rate of quenching by Co(III). The Ru(IN) and Co(IN) sample is very similar to the Ru(OUT) and Co(OUT) sample. These two samples are considerably different from the Ru(IN)/Co(OUT) sample and the Ru(OUT)/Co(IN) sample.
Secondary motions of the knee during weight bearing and non‐weight bearing activities (2003)

The objective of this study was to test the hypothesis that during a weight bearing activity such as walking, a dynamic range (envelope of motion) exists in the relationship between the secondary knee motions (anterior-posterior (AP) translation, internal-external (IE) rotation, and abduction-adduction (Ab-Adduction)) and knee flexion angle. In addition differences in the envelope of motion between a weight bearing and non-weight bearing activity were tested. The hypothesis was evaluated by testing for differences (offsets) in secondary displacements at specific knee flexion angles during the walking cycle and seated leg extension (non-weight bearing). Kinematic measurements were obtained using a previously developed point cluster technique to analyze the six-degrees of freedom movement of the knee. During walking, phase plots of the IE rotation and AP translation versus knee flexion demonstrated significant offsets from one phase of the gait cycle to another at the same flexion angle. During the non-weight bearing activity, no significant offset in the secondary movement was found; the knee followed the same pathway of motion during the flexion and extension phase of this activity. The characteristics of the secondary motions during walking indicated that secondary knee movements are caused by the external forces (muscle, inertial and gravitational) that act on the knee during the various phases of the walking cycle. The boundaries of the envelope appear to reflect the characteristics of the passive restraints. The weight bearing secondary motion AP and IE rotation seen during a walking activity demonstrated an envelope of dynamic laxity that could potentially be used to evaluate functional instabilities at the knee.
Supplementary Figure 6 from Inhibition of Glutaminase Preferentially Slows Growth of Glioma Cells with Mutant IDH1 (2023)

Supplementary Figure 6 from Inhibition of Glutaminase Preferentially Slows Growth of Glioma Cells with Mutant IDH1
Mesenchymal Stem Cells (2013)

Mesenchymal stem cells (MSCs) are multipotent adult stem cells, prototypically found in the bone marrow, which are undergoing investigation as a cell-based therapeutic for several clinical disorders. This potential of MSCs is due to their ability for self renewal, to be immune privileged and immunosuppressive, and to give rise to different specialized cells from the mesoderm lineage, such as adipocytes, chondrocytes, osteocytes, cardiocytes, or myocytes, and from nonmesoderm lineage, such as neurons (ectoderm) or hepatocytes (endoderm). Several animal studies (e.g. swine) have shown that bone marrow derived MSCs restore cardiac function and regenerate cardiac tissue in settings of both acute and chronic injury. Based on rigorous preclinical results, there are numerous ongoing Phase I/II clinical trials addressing the safety, cell dose, delivery technique, and efficacy of MSCs in patients with chronic heart failure. Here we describe the procedures for the isolation, expansion and cryopreservation of MSCs from harvested bone marrow for cardiac delivery.
SODA (2006)

The physical layer of most wireless protocols is traditionally implemented in custom hardware to satisfy the heavy computational requirements while keeping power consumption to a minimum. These implementations are time consuming to design and difficult to verify. A programmable hardware platform capable of supporting software implementations of the physical layer, or software defined radio, has a number of advantages. These include support for multiple protocols, faster time-to-market, higher chip volumes, and support for late implementation changes. The challenge is to achieve this without sacrificing power. In this paper, we present a design study for a fully programmable architecture, SODA, that supports software defined radio a high-end signal processing application. Our design achieves high performance, energy efficiency, and programmability through a combination of features that include single-instruction multiple- data (SIMD) parallelism, and hardware optimized for 16bit computations. The basic processing element is an asymmetric processor consisting of a scalar and SIMD pipeline, and a set of distributed scratchpad memories that are fully managed in software. Results show that a four processor design is capable of meeting the throughput requirements of theW-CDMA and 802.11a protocols, while operating within the strict power constraints of a mobile terminal.
Modulation Squeezing of a 10 Gb/s RZ and NRZ Signal with a Single SOA (2009)

A characterisation of a SOA-based modulation suppressor for 10Gb/s RZ and NRZ signals is performed. Its effectiveness in colourless WDM PON is demonstrated obtaining error-free operation in a 20km-long link.
Data center asset tracking using a mobile robot (2013)

Management and monitoring of data centers is a growing field of interest, with much current research, and the emergence of a variety of commercial products aiming to improve performance, resource utilization and energy efficiency of the computing infrastructure. Despite the large body of work on optimizing data center operations, few studies actually focus on discovering and tracking the physical layout of assets in these centers. Such asset tracking is a prerequisite to faithfully performing administration and any form of optimization that relies on physical layout characteristics.
Large-Scale Synthesis of Freestanding Layer-Structured PbI2 and MAPbI3 Nanosheets for High-Performance Photodetection (2017)

Recently, due to the possibility of thinning down to the atomic thickness to achieve exotic properties, layered materials have attracted extensive research attention. In particular, PbI2 , a kind of layered material, and its perovskite derivatives, CH3 NH3 PbI3 (i.e., MAPbI3 ), have demonstrated impressive photoresponsivities for efficient photodetection. Herein, the synthesis of large-scale, high-density, and freestanding PbI2 nanosheets is demonstrated by manipulating the microenvironment during physical vapor deposition. In contrast to conventional two-dimensional (2D) growth along the substrate surface, the essence here is the effective nucleation of microplanes with different angles relative to the in-plane direction of underlying rough-surfaced substrates. When configured into photodetectors, the fabricated device exhibits a photoresponsivity of 410 mA W-1 , a detectivity of 3.1 × 1011 Jones, and a fast response with the rise and decay time constants of 86 and 150 ms, respectively, under a wavelength of 405 nm. These PbI2 nanosheets can also be completely converted into MAPbI3 materials via chemical vapor deposition with an improved photoresponsivity up to 40 A W-1 . All these performance parameters are comparable to those of state-of-the-art layered-material-based photodetectors, revealing the technological potency of these freestanding nanosheets for next-generation high-performance optoelectronics.
An illuminating retractor for intracranial microneurosurgery (1998)

During certain microneurosurgical procedures, the illumination provided by current coaxial microscope light sources is suboptimal. One potential solution is the surgical light blade (SLB), a malleable retractor incorporating a flat fiberoptic bundle along its surface. The SLB provides intense illumination within the surgical field without decreasing the amount of limited operating space. A prototype of the SLB was tested in six patients. Results suggest that with further development the SLB could become useful for intracranial microneurosurgery.
Photochemical origins of burn-in degradation in small molecular weight organic photovoltaic cells (2015)

Using a combination of Fourier transform infrared (FTIR) spectroscopy and physics-based degradation models, we find that the early aging of small molecular weight organic photovoltaic (OPV) cells is due to photochemical degradation of the C<sub>60</sub>acceptor layer.
DOEs for color correction in broad band optical systems: validity and limits of efficiency approximations (2010)

Diffractive optical elements (DOE) are well-suited for the correction of longitudinal and transverse chromatic aberrations in broadband optical systems such as photographic lenses, HMDs or infrared lenses. Unfortunately, the diffraction efficiency &eta; for the working order of DOEs is often clearly below 100% which causes stray light from unwanted diffraction orders and prevents a more frequent use of DOEs in practice. The main reasons for the decrease of diffraction efficiency &eta; are spectral bandwidth, variation of the incidence angle of impinging light and manufacturing errors of the DOE. In the present paper, several scalar approximations for the diffraction efficiency &eta; as a function of these parameters are compared with rigorous electromagnetic calculations. The validity of these formulae are shown to extend over a surprisingly large range of parameters.