gebhart/patrepeval huggingface dataset:
IDDF2019-ABS-0131 Algorithms using noninvasive tests can accurately identify patients with advanced fibrosis due to NASH: data from the STELLAR clinical trials (2019)

<h3>Background</h3> There is a major unmet need for accurate, readily available, noninvasive tests (NITs) to identify patients with advanced fibrosis due to NASH. Our goal was to evaluate sequential NIT algorithms to minimize the requirement for biopsy and improve accuracy overuse of single tests. <h3>Methods</h3> The STELLAR studies (NCT03053050, NCT03053063) enrolled NASH patients with bridging fibrosis (F3) or compensated cirrhosis (F4). Baseline liver biopsies were read using the NASH CRN fibrosis classification and noninvasive fibrosis markers: FIB-4 index, ELF test, and FibroScan® (FS). The performance of these tests to discriminate advanced fibrosis was evaluated using AUROCs with 5-fold cross-validation repeated 100x. Thresholds were obtained by maximizing specificity given ≥85% sensitivity. The cohort was divided (80%/20%) into evaluation/validation sets. The evaluation set was further stratified 250x into training and test sets (66%/33%). Optimal thresholds were derived as the average across training sets, and applied sequentially (FIB-4 followed by ELF and/or FS) to the validation set. Data are from an interim analysis on 26 July 2018. <h3>Results</h3> All patients with available liver histology (N=3202, 71% F3-F4) and NIT results were included. While single tests were able to discriminate advanced fibrosis (AUROCs of 0.78, 0.80, and 0.80 for FIB-4, ELF, and FS in validation cohort), up to 32% of patients had an indeterminate result. Using thresholds derived from STELLAR data, FIB-4 followed by FS or ELF in those with indeterminate FIB-4 values (1.23 to 2.1) reduced indeterminate results to as low as 13% (table 1). Published NIT thresholds yielded similar results (data not shown). Adding a third test (FIB-4 then ELF then FS) reduced the rate of indeterminate results to 8%. Misclassification occurred at rates similar to biopsy (15–21%). The majority of misclassifications (63–81%) were false negatives; among false positive cases (19–27% of misclassifications) up to 70% had F2 fibrosis. <h3>Conclusions</h3> FIB-4 followed by ELF and/or FS nearly eliminated the need for liver biopsy and accurately identified patients with advanced fibrosis due to NASH with misclassification rates similar to liver biopsy.
NIR Photodynamic Destruction of PDAC and HNSCC Nodules Using Triple-Receptor-Targeted Photoimmuno-Nanoconjugates: Targeting Heterogeneity in Cancer (2020)

Receptor heterogeneity in cancer is a major limitation of molecular targeting for cancer therapeutics. Single-receptor-targeted treatment exerts selection pressures that result in treatment escape for low-receptor-expressing tumor subpopulations. To overcome this potential for heterogeneity-driven resistance to molecular targeted photodynamic therapy (PDT), we present for the first time a triple-receptor-targeted photoimmuno-nanoconjugate (TR-PIN) platform. TR-PIN functionalization with cetuximab, holo-transferrin, and trastuzumab conferred specificity for epidermal growth factor receptor (EGFR), transferrin receptor (TfR), and human epidermal growth factor receptor 2 (HER-2), respectively. The TR-PINs exhibited up to a 24-fold improvement in cancer cell binding compared with EGFR-specific cetuximab-targeted PINs (Cet-PINs) in low-EGFR-expressing cell lines. Photodestruction using TR-PINs was significantly higher than the monotargeted Cet-PINs in heterocellular 3D in vitro models of heterogeneous pancreatic ductal adenocarcinoma (PDAC; MIA PaCa-2 cells) and heterogeneous head and neck squamous cell carcinoma (HNSCC, SCC9 cells) containing low-EGFR-expressing T47D (high TfR) or SKOV-3 (high HER-2) cells. Through their capacity for multiple tumor target recognition, TR-PINs can serve as a unique and amenable platform for the effective photodynamic eradication of diverse tumor subpopulations in heterogeneous cancers to mitigate escape for more complete and durable treatment responses.
Illumination Design Process (2022)

Now that we have discussed some theory, defined the most important quantities and analysis tools, and set up a few example problems, we are ready to discuss how optical design for illumination actually works.
High-capacity data hiding in text documents (2009)

In today's digital world securing different forms of content is very important in terms of protecting copyright and verifying authenticity. One example is watermarking of digital audio and images. We believe that a marking scheme analogous to digital watermarking but for documents is very important. In this paper we describe the use of laser amplitude modulation in electrophotographic printers to embed information in a text document. In particular we describe an embedding and detection process which has the capability to embed 14 bits into characters that have a left vertical edge. For a typical 12 point document this translates to approximately 12000 bits per page.
Comparative study of three recursive parameter estimation algorithms with application to acoustic echo cancellation (2004)

Comparative study of three recursive parameter estimation algorithms with application to acoustic echo cancellation
Spermiogenesis and DNA Repair: A Possible Etiology of Human Infertility and Genetic Disorders (2008)

This paper reviews the possible origin of sperm DNA fragmentation and focuses on the nuclear events associated with spermiogenesis as a potential source of genetic instability and reduced fertilizing potential of the mature male gamete. Recent findings suggest a programmed DNA fragmentation and DNA damage response during the chromatin remodeling steps in spermatids. We also discuss the spermatid DNA repair mechanisms and the possible involvement of condensing proteins, such as transition proteins and protamines, in the process, as this DNA fragmentation is normally not found in late spermatids. We propose that alterations in the chromatin remodeling steps or DNA repair in elongating spermatids may lead to persistent DNA breaks. This vulnerable step of spermiogenesis may provide a clue to the etiology of sperm DNA fragmentation associated with infertility in humans. This vulnerability is further emphasized given the haploid character of spermatids that must resolve programmed double-stranded breaks by an error-prone DNA repair mechanism. Therefore, spermiogenesis has probably been overlooked as an important source of genetic instability.
Renal osteodystrophy in patients on hemodialysis for more than 10 years. (1986)

We performed bone biopsies on 13 patients who had been on dialysis from 11.1 to 17.6 years (mean 14.5 +/- 2.1 years) to evaluate renal osteodystrophy in long-term dialysis patients. Seven patients had osteitis fibrosa and 6 had a mineralization defect. Stainable bone aluminum was present in 9 of the patients. Serum phosphorus and parathyroid hormone levels were higher and bone aluminum lower in patients with osteitis fibrosa compared to those with a mineralization defect. Those seriously disabled with decreased mobility due to bone pain (7 of 13) had more bone aluminum than those patients with minimal or no disability (1.55 +/- 1.0 mm/mm2 vs. 0.11 +/- 0.18, respectively, p less than 0.01). A history of fractures during the years on dialysis was also associated with elevated stainable bone aluminum (p = 0.04). We conclude that in long-term dialysis patients aluminum-related osteodystrophy results in greater morbidity than osteitis fibrosa. We recommend that aluminum-containing phosphate binders be used sparingly in patients who are to remain indefinitely on dialysis.
The Evolution of Extracellular Matrix (2010)

We present a perspective on the molecular evolution of the extracellular matrix (ECM) in metazoa that draws on research publications and data from sequenced genomes and expressed sequence tag libraries. ECM components do not function in isolation, and the biological ECM system or "adhesome" also depends on posttranslational processing enzymes, cell surface receptors, and extracellular proteases. We focus principally on the adhesome of internal tissues and discuss its origins at the dawn of the metazoa and the expansion of complexity that occurred in the chordate lineage. The analyses demonstrate very high conservation of a core adhesome that apparently evolved in a major wave of innovation in conjunction with the origin of metazoa. Integrin, CD36, and certain domains predate the metazoa, and some ECM-related proteins are identified in choanoflagellates as predicted sequences. Modern deuterostomes and vertebrates have many novelties and elaborations of ECM as a result of domain shuffling, domain innovations and gene family expansions. Knowledge of the evolution of metazoan ECM is important for understanding how it is built as a system, its roles in normal tissues and disease processes, and has relevance for tissue engineering, the development of artificial organs, and the goals of synthetic biology.
Supplementary Table 2 from Combining ABCG2 Inhibitors with IMMU-132, an Anti–Trop-2 Antibody Conjugate of SN-38, Overcomes Resistance to SN-38 in Breast and Gastric Cancers (2023)

&lt;p&gt;Functional activity of ABCB1 shown for HCT15, but not for NCI-N87 or NCI-N87-S120&lt;/p&gt;
Micro-fluid Channel Based on Ultralow-loss Silicon Crossing Waveguide for Various Sensing (2014)

We experimentally demonstrate a new type of micro-fluid channel design with crossing optical waveguides that not only block any gaps in the microfluidic channels in one fabrication step but also enable nearly lossless optical propagation in the primary waveguides on a chip. Such designs are critical for all sensing applications where the analyte must be flowed over the sensor.
Application of FLiP Method for Differentiation of Mycobacterium tuberculosis Strains in Comparison to Commonly Used Methods, Spoligotyping and MIRU-VNTR Typing (2013)

The current "gold standard" in molecular epidemiological studies of Mycobacterium tuberculosis is IS6110 RFLP based on IS6110 polymorphism. However PCR-based methods are becoming increasingly important. Recently, fast ligation-mediated PCR (FLiP), based on IS6110 polymorphism was proposed. In this study, the discriminatory power of FLIP, spoligotyping and MIRU-VNTR typing, in differentiation of M. tuberculosis isolates was compared. The discriminatory index (HGI) of spoligotyping, MIRU-VNTR analysis, and FLiP was 0.653, 0.837, and 0.917, respectively. This indicates that FLiP allows a high level of differentiation among M. tuberculosis strains and it might be a valuable alternative to the other typing methods.
On design criteria and construction of noncoherent space~time constellations (2003)

We consider the problem of digital communication in a Rayleigh flat-fading environment using a multiple-antenna system, when the channel state information is available neither at the transmitter nor at the receiver. It is known that at high signal-to-noise ratio (SNR), or when the coherence interval is much larger than the number of transmit antennas, a constellation of unitary matrices can achieve the capacity of the noncoherent system. However, at low SNR, high spectral efficiencies, or for small values of coherence interval, the unitary constellations lose their optimality and fail to provide an acceptable performance. In this work, inspired by the Stein's lemma, we propose to use the Kullback-Leibler (KL) distance between conditional distributions to design space-time constellations for noncoherent communication. In fast fading, i.e., when the coherence interval is equal to one symbol period and the unitary construction provides only one signal point, the new design criterion results in pulse amplitude modulation (PAM)-type constellations with unequal spacing between constellation points. We also show that in this case, the new design criterion is equivalent to design criteria based on the exact pairwise error probability and the Chernoff information. When the coherence interval is larger than the number of transmit antennas, the resulting constellations overlap with the unitary constellations at high SNR, but at low SNR they have a multilevel structure and show significant performance improvement over unitary constellations of the same size. The performance improvement becomes especially more significant when an appropriately designed outer code or multiple receive antennas are used. This property, together with the facts that the proposed constellations eliminate the need for training sequences and are most suitable for low SNR, makes them a good candidate for uplink communication in wireless systems.
Two-point probability function for distributions of oriented hard ellipsoids (1990)

The macroscopic properties of two-phase random heterogeneous media depend upon an infinite sequence of n-point functions S(i)n(x1,x2,...,xn) giving the joint probability of finding n points with positions x1,x2,...,xn all in phase i. This paper reports the first study and calculation of the two-point probability function S(i)2 for distributions of oriented, hard spheroids with eccentricity ε in a matrix. This is a useful model of statistically anisotropic two-phase media, enabling one to examine the special limiting cases of oriented disks (ε=0), spheres (ε=1), and oriented needles (ε=∞).
ChemInform Abstract: NEUE REDOX‐RK. VON DIAZONIUMFLUOROBORATEN, BLDG. VON KUPFERSALZ‐AZOVERBINDUNG‐KOMPLEXEN, WASSERINDUZIERTE AROMATISCHE RADIKALARYLIERUNG (1973)

Abstract Die Diazoniumsalze (II) bilden in Benzol‐Aceton in Gegenwart äquivalenter Mengen an Cu‐Puder Komplexe aus ionischem Cu und den entsprechenden Azoverbindungen.
A deep convolutional neural network approach for astrocyte detection (2018)

Astrocytes are involved in various brain pathologies including trauma, stroke, neurodegenerative disorders such as Alzheimer's and Parkinson's diseases, or chronic pain. Determining cell density in a complex tissue environment in microscopy images and elucidating the temporal characteristics of morphological and biochemical changes is essential to understand the role of astrocytes in physiological and pathological conditions. Nowadays, manual stereological cell counting or semi-automatic segmentation techniques are widely used for the quantitative analysis of microscopy images. Detecting astrocytes automatically is a highly challenging computational task, for which we currently lack efficient image analysis tools. We have developed a fast and fully automated software that assesses the number of astrocytes using Deep Convolutional Neural Networks (DCNN). The method highly outperforms state-of-the-art image analysis and machine learning methods and provides precision comparable to those of human experts. Additionally, the runtime of cell detection is significantly less than that of other three computational methods analysed, and it is faster than human observers by orders of magnitude. We applied our DCNN-based method to examine the number of astrocytes in different brain regions of rats with opioid-induced hyperalgesia/tolerance (OIH/OIT), as morphine tolerance is believed to activate glia. We have demonstrated a strong positive correlation between manual and DCNN-based quantification of astrocytes in rat brain.
Focal plane reduction of large aperture optical systems (1998)

The size of the focal plane of an optical system is shown to be reduced through the use of re-imaging optics. The general principles of image segmentation and relay optics are discussed as well as trade-offs that must be performed to develop a practical system. A system of re-imaging optics is designed that reduces the necessary detector area of a proposed air shower detector by almost an order of magnitude.
Out-of-band distortion analysis of envelope tracking technique for power amplifiers (2009)

This paper presents an analysis of out-of-band distortion components generated by waveform clipping in an envelope tracking technique for the transmitter power amplifier of mobile base stations. Numerical investigations show that the out-of-band distortion components are dependent on the bandwidth and clipped level of the envelope signal of the input signal to the transmitter power amplifier. Based on this dependency, the bandwidth and clipped level are appropriately set in order to suppress the out-of-band distortion components. When the envelope bandwidth is restricted to 60% at the output backoff of 4 dB, the out-of-band distortion components are suppressed by more than approximately 30 dB.
Abstract 85: CCAAT/enhancer binding protein beta facilitates castrate-resistant prostate cancer cell growth and sensitivity to mTOR inhibitors (2015)

Abstract Adaptive changes that frequently occur in castrate-resistant prostate cancer (CRPC) cells are genomic mutations which enhance the activity of the PI3K-mTOR signaling pathway. Although there have been several promising clinical trials for the treatment of CRPC utilizing inhibitors of mTOR, these efforts failed to show significant improvement of patient outcomes. Thus, identifying potential mechanisms of resistance to these agents could improve their therapeutic efficacy. CCAAT/enhancer binding protein beta (C/EBPβ) is a broadly expressed transcription factor, with three isoforms that are differentially translated by mTOR activity. T reatment of cells with mTOR inhibitors increases the translation of the larger C/EBPβ LAP isoforms and decreases the truncated LIP isoform. The function of C/EBPβ LAP has been previously associated with survival and cellular senescence, while the LIP isoform facilitates cell cycle progression. Our central hypothesis was that the differential translation of LAP and LIP C/EBPβ isoforms was essential for the survival of CRPC cells treated with mTOR inhibitors. We found that treatment of PC3 cells with mTOR inhibitors unexpectedly increased the protein levels of all three C/EBPβ isoforms, while androgen-sensitive LNCaP cells largely showed decreased C/EBPβ protein levels. However, the PI3K inhibitor LY294002, decreased the LIP isoform of C/EBPβ without affecting LAP expression in LNCaP and PC3 cells. C/EBPβ gene expression decreased in both LNCaP and PC3 cells in response to treatment with mTOR inhibitors. We next evaluated whether C/EBPβ facilitated cell survival during mTOR inhibition. We found that PC3 cells deficient in C/EBPβ, via shRNA knockdown or TALEN gene editing, were less sensitive to the mTORC1/2 inhibitor, INK128, as assessed by a significant increase in IC50 value determined by the WST-1 assay. Further, suppression of C/EBPβ through shRNA KD or TALEN targeting dramatically decreased the rate of PC3 cell growth, clonogenic potential and induced a senescent phenotype. Intriguingly, loss of C/EBPβ in LNCaP cells increased clonogenic potential. Collectively, these data suggest that C/EBPβ has a differential role for cell growth in androgen-sensitive versus castrate-resistant prostate cancer and that C/EBPβ levels inversely correlate with mTOR inhibitor resistance. Citation Format: David J. Barakat, Jing Zhang, Alan D. Friedman, Samuel R. Denmeade, Ido Paz-Priel. CCAAT/enhancer binding protein beta facilitates castrate-resistant prostate cancer cell growth and sensitivity to mTOR inhibitors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 85. doi:10.1158/1538-7445.AM2015-85
Evaluation of Cost and Parental Satisfaction in Type B Polydactyly Excision Completed in Office Vs. Operating Room (2023)

Background/Objective:One in 500 children in the US are born with polydactyly, extra digits on hands or feet. Out of those children, 95% of cases comprise of type B polydactyly, in which the extra digit is attached by neurovascular bundle without bones. Surgeries to remove type B polydactylies by excision have been traditionally performed in operating rooms. Even though operating room surgeries are successful, they can be expensive and time consuming. In contrast, the surgeries performed in physician’s office, while non-traditional, can minimize expenses and save time and effort. We hypothesize that excisions conducted in offices are safe alternatives to operating room excision and are associated with definitive financial savings for patients’ families and hospitals, while increasing satisfaction of parents. Methods:Using CPT codes and reviewing electronic medical records, we identified all patients from 2019 to 2022 who had been treated for Type B Polydactyly with either office procedures or OR procedures, all of which had been performed at Riley Children’s Hospital. Patient billing data were obtained from Indiana University Hospital billing department. Average charge to patients for total cost of procedure and estimated removal of one digit were analyzed and compared. A 9-question parental satisfaction questionnaire was administered to patient’s parents over phone call. Results:Thus far, out of 93 patients who underwent type B polydactyly removal, 36 patients received procedures in physician’s offices, and 57 patients received procedures in ORs. Average charge to patients per digit removed for in-office group was around $500 cheaper than that of OR group. Average total charge to patients for in-office group was around $600 cheaper than that of OR group. Parental satisfaction data are pending. Conclusion and Potential Impact:This study shows the cost effectiveness of type B polydactyly excision in office. With analysis of future satisfaction survey data, we hope to gauge parental satisfaction associated with in-office excisions and promote in-office excisions as effective alternative to OR excisions.
Comparison of MR and Contrast Venography of the Cervical Venous System in Multiple Sclerosis (2011)

IJ caliber changes were seen in characteristic locations on both MRV and CV in MS patients. Agreement between modalities was higher for stenosis than for collaterals. If CV is considered a standard, MRV performance is good but may require additional improvement before MRV can be used for screening.
The Next Generation of Beam Hopping Satellite Systems: Dynamic Beam Illumination With Selective Precoding (2022)

Beam Hopping (BH) is a popular technique considered for next-generation multi-beam satellite communication system which allows a satellite focusing its resources on where they are needed by selectively illuminating beams. While beam illumination plan can be adjusted according to its needs, the main limitation of convectional BH is the adjacent beam avoidance requirement needed to maintain acceptable levels of interference. With the recent maturity of precoding technique, a natural way forward is to consider a dynamic beam illumination scheme with selective precoding, where large areas with high-demand can be covered by multiple active precoded beams. In this paper, we mathematically model such beam illumination design problem employing an interference-based penalty function whose goal is to avoid precoding whenever possible subject to beam demand satisfaction constraints. The problem can be written as a binary quadratic programming (BQP). Next, two convexification frameworks are considered namely: (i) A Semi-Definition Programming (SDP) approach particularly targeting BQP type of problems, and (ii) Multiplier Penalty and Majorization-Minimization (MPMM) based method which guarantees to converge to a local optimum. Finally, a greedy algorithm is proposed to alleviate complexity with minimal impact on the final performance. Supporting results based on numerical simulations show that the proposed schemes outperform the relevant benchmarks in terms of demand matching performance while minimizing the use of precoding.