gebhart/patrepeval huggingface dataset:
The Specific Regulation Of Immune Responses By CD8<sup>+</sup>T Cells Restricted By The MHC Class Ib Molecule, Qa-1 (2000)

Over the last three decades considerable evidence has accumulated that CD8(+) T cells regulate peripheral immune responses, in part, by specifically controlling the outgrowth of antigen-triggered CD4(+) T cells. This regulatory function of CD8(+) T cells has been shown, in vivo, to control the emergence of autoreactive CD4(+) T cells as well as CD4(+) T cells reactive to conventional antigens, including alloantigens. In this review, we summarize the evidence that this immune suppression mediated by CD8(+) T cells is dependent, in part, on specific cognate interactions between MHC class I-restricted regulatory CD8(+) cells and antigen-activated CD4(+) T cells. Moreover, we review the evidence that regulatory CD8(+) T cells recognize antigen-activated CD4(+) T cells in a TCR specific manner restricted by the MHC class Ib molecule, Qa-1. The Qa-1 molecule may be uniquely qualified to serve this MHC restrictive function because, unlike conventional MHC molecules, it is preferentially and transiently expressed on activated and not resting CD4(+) T cells. This may assure that only recently antigen-activated CD4(+) T cells expressing Qa-1/TCR peptide complexes will induce regulatory CD8(+) T cells and subsequently become susceptible to regulation. Because Qa-1 also binds to self Qdm peptides that trigger NK (CD94/ NKG2) receptors on CD8(+) T cells, the machinery for homeostatic regulation of regulatory CD8(+) T cells can be envisioned. Finally, we propose a model by which these TCR specific, Qa-1-restricted regulatory CD8(+) T cells selectively downregulate antigen-activated T cells expressing TCRs of certain affinities. Ultimately these regulatory CD8(+) T cells control the peripheral TCR repertoire during the course of immune responses to both self and foreign antigens.
Abstract 4866: Development and characterization of novel CD40 antibody agonists for cancer immunotherapy (2016)

Abstract CD40 is a key molecule in the regulation of immune responses and its activity can be modulated using antibodies. In particular, agonist CD40 antibodies are highly effective in preclinical tumor models either through direct interaction with CD40-expressing lymphomas, or indirectly through the activation of an adaptive anti-tumor immune response. To date, limited clinical data have been reported with strong CD40 agonist antibodies; nonetheless it seems likely that targeting this pathway will require a balance between the benefits of immune stimulation to drive anti-tumor responses, and the damage that can result from non-specific immune cell activation. We set out to develop novel human anti-CD40 antibodies with different levels of agonist activity to identify a lead candidate for systemic application. Anti-CD40 monoclonal antibodies (mAbs) were generated by immunization of human Ig transgenic mice with recombinant and cell surface expressed human CD40. Hybridomas developed from these mice were screened using CD40 binding assays and activity on a reporter cell line engineered to express CD40 and NFêB-responsive luciferase. The variable regions of lead antibodies that displayed differential activity were cloned into vectors containing human IgG1 or IgG2 constant domains and expressed in CHO cells. These human CD40 mAbs were further characterized by analysis of binding affinity, CD40L blocking activity, B cell and dendritic cell activation, and anti-tumor activity in xenograft tumor models. We found a wide range of activities among the CD40 mAbs that is linked to epitope specificity as well as the isotype. In general, the IgG2 isotype mAbs had greater signaling activity than their IgG1 counterparts. The lead candidate mAbs are undergoing additional testing related to functional and toxicity parameters before a final candidate is nominated for clinical development. Citation Format: Laura A. Vitale, Thomas O’Neill, Jenifer Widger, Andrea Crocker, Li-Zhen He, Jeffrey Weidlick, Karuna Sundarapandiyan, James Storey, Lawrence Thomas, Joel Goldstein, Henry C. Marsh, Tibor Keler. Development and characterization of novel CD40 antibody agonists for cancer immunotherapy. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4866.
<title>Table structure recognition and its evaluation</title> (2000)

Tables are an important means for communicating information in written media, and understanding such tables is a challenging problem in document layout analysis. In this paper we describe a general solution to the problem of recognizing the structure of a detected table region. First hierarchial clustering is used to identify columns and then spatial and lexical criteria to classify headers. We also address the problem of evaluating table structure recognition. Our model is based on a directed acyclic attribute graph, or table DAG. We describe a new paradigm, 'random graph probing,' for comparing the results returned by the recognition system and the representation created during ground-truthing. Probing is in fact a general concept that could be applied to other document recognition tasks and perhaps even other computer vision problems as well.
Correlation of elevated level of blood midkine with poor prognostic factors of human neuroblastomas (2003)

The heparin-binding growth factor midkine (MK) is the product of a retinoic acid-responsive gene, and is implicated in neuronal survival and differentiation, and carcinogenesis. We previously reported that MK mRNA expression is elevated in neuroblastoma specimens at all stages, whereas pleiotrophin, the other member of the MK family, is expressed at high levels in favourable neuroblastomas. As MK is a secretory protein, it can be detected in the blood. Here, we show a significant correlation of the plasma MK level with prognostic factors of neuroblastomas. The plasma MK level was determined in 220 patients with neuroblastomas, and compared with that in children without malignant tumors (n=17, <500 pg ml(-1)). The plasma MK level became significantly elevated with advancing stages (stage 1: 445 pg ml(-1) (median), n=73; stage 2: 589, n=39; stage 3: 864, n=40; stage 4: 1445, n=56; and stage 4S: 2439, n=12). More importantly, a higher MK level was strongly correlated with poor prognostic factors: over 1 year of age (P=0.0299), MYCN amplification (P<0.0001), low TrkA expression (P=0.0005), nonmass screening, sporadic neuroblastomas (P<0.0001), and diploidy/tetraploidy (P=0.0007). Thus, these results demonstrate that the plasma MK level is a good marker for evaluating the progression of neuroblastomas. Moreover, considering the ability of antisense MK oligodeoxyribonucleotide to suppress tumour growth of colorectal carcinoma cells in nude mice, as recently reported, the present study suggests that MK is a possible candidate molecular target for therapy for neuroblastomas.
Spectral Properties of Yb3+-Doped Crystals for Laser Applications (1992)

Since the advent of AlGaAs laser diodes, many Nd-doped materials have been pumped by these sources and demonstrated great promise as efficient, dependable laser systems. Analogously, the recent availability of InGaAs laser diodes has provided a means by which to pump the Yb impurity. Following the suggestion of Krupke and Chase,1 Fan has recently demonstrated that Yb in Y3Al5O12 can be effectively pumped by InGaAs laser diodes.2 In this paper, we report our spectroscopic investigations of numerous Yb-doped crystals, and our assessment of the potential InGaAs-pumped laser performance of these systems.
Effective Radii of On-Chip Decoupling Capacitors (2008)

Decoupling capacitors are widely used to reduce power supply noise. On-chip decoupling capacitors have traditionally been allocated into the white space available on a die or placed inside the rows in standard cell circuit blocks. The efficacy of on-chip decoupling capacitors depends upon the impedance of the power/ground lines connecting the capacitors to the current loads and power supplies. A design methodology for placing on-chip decoupling capacitors is presented in this paper. A maximum effective radius is shown to exist for each on-chip decoupling capacitor. Beyond this effective distance, a decoupling capacitor is ineffective. Depending upon the parasitic impedance of the power distribution system, the maximum voltage drop seen at the current load is caused either by the first droop (determined by the rise time) or by the second droop (determined by the transition time). Two criteria to estimate the minimum required on-chip decoupling capacitance are developed based on the critical parasitic impedance. In order to provide the required charge drawn by the load, the decoupling capacitor has to be charged before the next switching cycle. For an on-chip decoupling capacitor to be effective, both effective radii criteria should be simultaneously satisfied.
Efficient Measurement of Aircraft Quality Factor for Evaluation and Prototyping of Wireless Systems (2018)

A measurement technique for fast and efficient calculation of quality factor (Q) in arbitrary cavities is presented. The technique has the advantage over other methods in that the calculation is independent of cavity volume estimates, which are often hard to compute in complex cavities with arbitrary shapes and a large number of apertures. A comparison of the technique with accepted methods is made, showing good agreement and wide applicability to a number of platforms and vehicle compartments. Through application of this technique, a method is proposed to tune a reverberation chamber through matching of Q so that the aircraft environment is adequately emulated from a radio frequency (RF) stand point. This provides a controlled and reproducible test environment for evaluation and prototyping of wireless systems in a relevant environment.
UWB-Assisted Fast mmWave Beam Alignment (2021)

Due to their large bandwidth and impressive data speed, millimeter-wave (mmWave) radios are expected to play a key role in the 5G and beyond (e.g., 6G) communication networks. Yet, to release mmWave’s true power, the highly directional mmWave beams need to be aligned perfectly. Most existing beam alignment methods adopt an exhaustive or semi-exhaustive space scanning, which introduces up to seconds of delays.To eliminate the need of a complex space scanning, this paper presents an Ultra-wideband (UWB)-assisted mmWave communication framework, which leverages the co-located UWB antennas to estimate the best angles for mmWave beam alignment. One major challenge to apply this idea in real-world is the barrier of limited antenna numbers. Commercial-Off-The-Shelf (COTS) devices are usually equipped with only a few number of UWB antennas, which are not enough for the existing algorithms to provide an accurate angle estimation. To solve this challenge, we design a novel Multi-Frequency MUSIC (MF-MUSIC) algorithm, which extends the classic MUSIC algorithm to the frequency domain and overcomes the antenna limitation barrier in the spatial domain. By doing this, our framework uses only 3 antennas to achieve an accurate angle estimation, which is merely 0.15° different from the state-of-the-art 16-antenna method.
A study of electronic ballast for electrodeless fluorescent lamps with dimming capabilities (2002)

The electrodeless fluorescent lamp has the features of extremely long life and rapid power switching response without the delay associated with electrode warm-up and cooling since they do not have electrodes. The authors aimed at the feature of the quick response, and then adopted intermittent operation, which means that ON/OFF of the lamp is repeated rapidly, in order to dim the lamp operated at 13.56 MHz. The dimming ballast was developed and was able to dim the lamp by 5% smoothly.
Polarization-maintaining fiber Fabry–Perot tunable filters (1994)

We report what are to our knowledge the first high-performance polarization-maintaining single-mode fiber Fabry-Perot tunable filters. These filters simultaneously exhibited a loss of <2.5 dB, a finesse between 150 and 310, and an extinction ratio of >30 dB. A unique fabrication technique is developed that utilizes the tunability and the polarization resonance splitting inside the filter to align the birefringent axes at a pigtail-cavity joint. A general criterion is established for aligning polarization-maintaining fibers with elliptical inputs.
Serologic Response to Cell Wall Mannoproteins and Proteins of<i>Candida albicans</i> (1998)

The cell wall of Candida albicans not only is the structure in which many biological functions essential for the fungal cells reside but also is a significant source of candidal antigens. The major cell wall components that elicit a response from the host immune system are proteins and glycoproteins, the latter being predominantly mannoproteins. Both the carbohydrate and protein moieties are able to trigger immune responses. Although cell-mediated immunity is often considered to be the most important line of defense against candidiasis, cell wall protein and glycoprotein components also elicit a potent humoral response from the host that may include some protective antibodies. Proteins and glycoproteins exposed at the most external layers of the wall structure are involved in several types of interactions of fungal cells with the exocellular environment. Thus, coating of fungal cells with host antibodies has the potential to influence profoundly the host-parasite interaction by affecting antibody-mediated functions such as opsonin-enhanced phagocytosis and blocking the binding activity of fungal adhesins for host ligands. In this review, the various members of the protein and glycoprotein fraction of the C. albicans cell wall that elicit an antibody response in vivo are examined. Although a number of proteins have been shown to stimulate an antibody response, for some of these species the response is not universal. On the other hand, some of the studies demonstrate that certain cell wall antigens and anti-cell wall antibodies may be the basis for developing specific and sensitive serologic tests for the diagnosis of candidasis, particularly the disseminated form. In addition, recent studies have focused on the potential for antibodies to cell wall protein determinants to protect the host against infection. Hence, a better understanding of the humoral response to cell wall antigens of C. albicans may provide the basis for the development of (i) effective procedures for the serodiagnosis of disseminated candidiasis and (ii) novel prophylactic (vaccination) and therapeutic strategies for the management of this type of infection.
Development of fluridil, a topical suppressor of the androgen receptor in androgenetic alopecia (2003)

Abstract Nonsteroidal antiandrogens (AA) cannot be topically used for androgenetic alopecia (AGA) because of systemic resorption. A new class of androgen receptor (AR) suppressors designed for safe topical treatment of AGA was synthesized from (3‐amino‐2‐hydroxy‐2‐methyl‐ N ‐(4‐nitro‐3‐trifluoromethyl)phenyl) propanamide (BP‐34), to contain perfluoroalkyl moieties. The trifluoromethyl derivative (fluridil) at 10 μM decreased expression of the AR in LNCaP human cells by 95%, its serum half‐life was 6 h; it decomposes hydrolytically to BP‐34 and trifluoroacetic acid. Acute intraperitoneal maximum tolerated dose (MTD) of fluridil in mice is 270–300 mg/kg/d and the subacute MTD is 450 mg/kg/d. The oral LD 50 in mice was 2,872 mg/kg in males, 2,232 mg/kg in females, and >2,500 mg/kg in rats. Fluridil solution in isopropanol was not cutaneously absorbed in rabbits, did not sensitize or show any phototoxic or photoallergic effects on guinea pig skin, and demonstrated no skin irritation potential in rabbits and humans. Fluridil solid induced only slight and reversible eye irritancy in rabbits and displayed no cytotoxicity to rabbit corneal fibroblasts in vitro . Fluridil demonstrated no significant mutagenicity potential by Ames method. In a double‐blind study, 43 males with AGA, Norwood grade II to Va, used topical 2% fluridil in isopropanol or the vehicle daily for 12 months. Anagens (growing hairs) increased in the fluridil group from 76% to 89%. All hematological and biochemistry values remained within normal range, including testosterone, which varied but seasonally. No fluridil or its decomposition product (BP‐34) was detected in serum. No adverse side effects were reported. Drug Dev. Res. 59:292–306, 2003. © 2003 Wiley‐Liss, Inc.
Insoluble starch xanthate: Use in heavy metal removal (1975)

Abstract Water‐insoluble starch xanthates were prepared by xanthation of highly crosslinked starches under various conditions. After isolation of the products by solvent dehydration, freeze drying, or spray drying, their properties were determined. These products were very effective in removing heavy metals from water.
Industrial yeasts strains for biorefinery solutions: Constructing and selecting efficient barcoded xylose fermenting strains for ethanol (2014)

Abstract There have been intense efforts in the scientific community and industry to engineer S. cerevisiae strains to co‐consume xylose and glucose. In this context, this paper describes a process for introducing a barcode into an industrial xylose fermenting yeast strains to ensure quick and reliable identification of patented industrial strains. Furthermore, this work presents a novel procedure for screening and selecting the clones that reflects the characteristics of the industrial process. The key points of efficient selection of high‐performing clones are elaborated and discussed. In spite of the unforeseen effects on yeast physiology after the introduction of a new sequence into the genome, we obtained barcoded clones with the same xylose consumption rates and ethanol yields as the cells without the barcode. © 2014 Society of Chemical Industry and John Wiley & Sons, Ltd
O-125 Development of an artificial intelligence embryo witnessing system to accurately track and identify patient specific embryos in a human IVF laboratory (2021)

Abstract Study question Can convolutional neural networks (CNN) be used as a witnessing system to accurately track and identify patient specific embryos at the cleavage stage of development? Summary answer We developed the first artificial intelligence driven witnessing system to accurately track cleavage and blastocyst stage embryos in a human ART laboratory. What is known already There are reports of human errors in embryo tracking that have led to the births of children with different genetic makeup than their birth parents. Clinical practices rely on manual identification, barcodes or radio-frequency identification technology to track embryos. These systems are designed to track culture dishes but are unable to monitor developing embryos within the dish to help ensure an error-free patient match. Previously, we developed an AI witnessing system to track blastocysts with 100% accuracy. The goal of this study was to determine whether an AI witnessing system could be developed that accurately tracks cleavage stage embryos. Study design, size, duration A pre-developed deep neural network technology was first trained and tested on 4944 embryos images. The algorithm processed embryo images for each patient and produced a unique key that was associated with the patient ID at 60 hpi, which formed our library. When the algorithm evaluated embryos at 64 hpi it generated another key that was matched with the patient’s unique key available in the library. Participants/materials, setting, methods A total of 3068 embryos from 412 patients were examined by the CNN at both 60 hpi and 64 hpi. These timepoints were chosen as they reflect the time our laboratory evaluates Day 3 embryos (60 hpi) and the time we move them to another dish and prepare them for transfer (64 hpi). The patient cohorts ranged from 3-12 embryos per patient. Main results and the role of chance The accuracy of the CNN in correctly matching the patient identification with the patient embryo cohort was 100% (CI: 99.1% to 100.0%, n = 412). Limitations, reasons for caution Limitations of this study include that all embryos were imaged under identical conditions and within the same EmbryoScope. Additionally, this study only examined fresh Day 3 embryos cultured over a span of 4 hours. Future studies should include images of fresh and frozen/thawed embryos captured using different imaging systems. Wider implications of the findings This study describes the first artificial intelligence-based approach for cleavage stage embryo tracking and patient specimen identification in the IVF laboratory. This technology offers a robust witnessing step based on unique morphological features that are specific to each individual embryo. Trial registration number This work was partially supported by the Brigham Precision Medicine Developmental Award (Brigham Precision Medicine Program, Brigham and Women’s Hospital), Partners Innovation Discovery Grant (Partners Healthcare), and R01AI118502, and R01AI138800.
Enhancing Docetaxel Delivery to Multidrug-Resistant Cancer Cells with Albumin-Coated Nanocrystals (2018)

Intravenous delivery of poorly water-soluble anticancer drugs such as docetaxel (DTX) is challenging due to the low bioavailability and the toxicity related to solubilizing excipients. Colloidal nanoparticles are used as alternative carriers, but low drug loading capacity and circulation instability limit their clinical translation. To address these challenges, DTX nanocrystals (NCs) were prepared using Pluronic F127 as an intermediate stabilizer and albumin as a functional surface modifier, which were previously found to be effective in producing small and stable NCs. We hypothesize that the albumin-coated DTX NCs (DTX-F-alb) will remain stable in serum-containing medium so as to effectively leverage the enhanced permeability and retention effect. In addition, the surface-bound albumin, in its native form, may contribute to cellular transport of NCs through interactions with albumin-binding proteins such as secreted protein acidic and rich in cysteine (SPARC). DTX-F-alb NCs showed sheet-like structure with an average length, width, and thickness of 284 ± 96, 173 ± 56, and 40 ± 8 nm and remained stable in 50% serum solution at a concentration greater than 10 μg/mL. Cytotoxicity and cellular uptake of DTX-F-alb and unformulated (free) DTX were compared on three cell lines with different levels of SPARC expression and DTX sensitivity. While the uptake of free DTX was highly dependent on DTX sensitivity, DTX-F-alb treatment resulted in relatively consistent cellular levels of DTX. Free DTX was more efficient in entering drug-sensitive B16F10 and SKOV-3 cells than DTX-F-alb, with consistent cytotoxic effects. In contrast, multidrug-resistant NCI/ADR-RES cells took up DTX-F-alb more than free DTX with time and responded better to the former. This difference was reduced by SPARC knockdown. The high SPARC expression level of NCI/ADR-RES cells, the known affinity of albumin for SPARC, and the opposing effect of SPARC knockdown support that DTX-F-alb have exploited the surface-bound albumin-SPARC interaction in entering NCI/ADR-RES cells. Albumin-coated NC system is a promising formulation for the delivery of hydrophobic anticancer drugs to multidrug-resistant tumors.
Tunable wavelength filters with Bragg gratings in polymer waveguides (1998)

Tunable wavelength filters are demonstrated based on the thermo-optic refractive index change of the polymer waveguide with Bragg reflection grating. For the low-loss waveguide operating around 1.55 μm, fluorinated polymers are incorporated. Bragg reflection gratings are fabricated using a phase mask and a high-index polymer. The Bragg reflector exhibits a narrow bandwidth of less than 1.0 nm, a crosstalk of −20 dB, an insertion loss of 3.2 dB, and a flat-top passband. The peak wavelength of Bragg reflection is shifted over 11 nm with a slight insertion loss change. The thermo-optic tuning efficiency is 22 nm/W and the peak shift is linearly proportional to the heating power.