gebhart/patrepeval huggingface dataset:
Abstract 4055: Enhancing anti-PD-1 immune blockade in melanoma through selective inhibition of histone deacetylase 6 (2017)

Abstract Histone deacetylases (HDACs), were originally described in a limited context as histone modifiers. New evidence has demonstrated that HDACs are also involved in a diverse range of cellular processes that are not restricted to the chromatin environment, such as the regulation of the cell cycle/apoptosis and, more recently, a modulator of immune response. However, much remains unknown about the mechanism of action of HDACs and their roles in the immune-biology of cancer. The non-specific nature of pan-HDAC inhibitors results in a narrow therapeutic window of use, limiting the dose and duration due to toxicity. Our group has focused in one specific HDAC, HDAC6, and shown that both the genetic abrogation and pharmacological inhibition of this HDAC modulates the expression of a variety of immune-regulatory proteins in the tumor microenvironment, including PD-L1, PD-L2, MHC class I, B7-H4 and TRAIL-R1. In particular, we have previously demonstrated that both pharmacological inhibition and/or genetic abrogation of HDAC6 plays a critical role in the immune check point blockade by down-regulating the expression of PD-L1 and other check-point modulators such as PD-L2, B7-H4, etc. Moreover, we have also observed that in vivo inhibition of HDAC6 reduces tumor growth in B16 and SM1 murine melanoma models within syngeneic immunocompetent hosts. Additionally, we have found that the combination of low doses of the HDAC6i Nexturastat A and checkpoint immune blockade, including anti-PD-1 and anti-CTLA4, results in an important improvement in anti-tumor immune responses as evidenced by the reduction of tumor growth when compared to treatment with individual stand-alone agents. In these studies we also evidenced an increased production of IFNγ and IL-2 in the stand-alone check-point inhibitor treatments, which leads to an upregulation of PD-L1 and PD-L2. Similar levels of IFNγ and IL-2 were found in the combination groups. However, the expression level of PD-L1 and PD-L2 were comparable to the non-treated group. Taking all together, we have found that HDAC6i could be used as a potential adjuvant in ongoing therapeutic options involving immune check-point blockade. Citation Format: Tessa Knox, Eva Sahakian, Jayakumar Nair, Jennifer Kim, Debarati Banik, Melissa Hadley, John Powers, Fengdong Cheng, Sida Shen, Javier Pinilla, Jeffrey Weber, Alan Kozikowski, Eduardo Sotomayor, Alejandro Villagra. Enhancing anti-PD-1 immune blockade in melanoma through selective inhibition of histone deacetylase 6 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4055. doi:10.1158/1538-7445.AM2017-4055
ChemInform Abstract: Sonochemical Hydrolysis of Ga3+ Ions: Synthesis of Scroll‐Like Cylindrical Nanoparticles of Gallium Oxide Hydroxide. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Hot-topic debate on tolerance: Immunosuppression withdrawal (2011)

1. Liver allografts exhibit intrinsic tolerogenic properties that result in their spontaneous acceptance in many experimental animal models. 2. In clinical transplantation, liver allografts require milder immunosuppression regimens than other organs, are relatively resistant to antibody-mediated rejection, and only very rarely are lost because of immunological insults. 3. A fraction of stable liver transplant recipients can withdraw from all immunosuppression therapy and then maintain normal graft function and not experience rejection. This phenomenon is known as spontaneous operational tolerance (SOT). 4. The intentional discontinuation of immunosuppression in stable liver transplant recipients has led to successful weaning in almost 20% of recipients, but the true prevalence of SOT in unselected recipients is still unknown. 5. The prevalence could be higher in pediatric recipients undergoing transplantation before 1 year of age and in adult recipients with more than 10 years of posttransplant follow-up. 6. Rejection occurring during medically supervised immunosuppression weaning trials tends to be mild and, in the overwhelming majority of cases, can be easily resolved without the administration of high-dose immunosuppression. 7. Tolerant liver recipients exhibit specific transcriptional patterns in peripheral blood and liver tissue that may constitute future diagnostic markers of tolerance. 8. There is still no formal proof that the discontinuation of low-dose immunosuppression in long-term survivors of liver transplantation improves the morbidity and mortality rates associated with immunosuppression therapy.
ChemInform Abstract: ASYMMETRIC INDUCTION ARISING FROM Σ/Π INTERACTIONS (1984)

Abstract Aus dem Dien (I) entsteht dem Schema entsprechend ein Gemisch der isomeren Isodicyclopentadiene (I) und (II).
Multi-layered stacked patch-antennas on electro-Optic material for optical modulation (2016)

Multi-layered stacked patch-antennas on an electro-optic (EO) material are proposed for optical modulation. By using multi-layered structures, larger antenna gain can be obtained to induce stronger millimeter-wave electric fields. The induced millimeter-wave electric field can be used for optical modulation through the Pockels effects of the EO crystal. Since the antenna gain is enhanced by using multi-layered stacked patch-antennas, the modulation index improvement can be obtained.
Distinct sequence elements in a napin promoter interact in vitro with DNA‐binding proteins from Brassica napus (1991)

Nuclear extracts obtained from developing seeds of oilseed rape, Brassica napus cv. Svalöv Karat K 20516, were shown to contain several distinct DNA‐binding proteins as evidenced by gel retardation experiments. Four of the proteins were capable of interacting in vitro with oligonucleotide probes containing sequences related to motives in a napin gene promoter and its upstream region. Another protein interacted with an A/T‐rich repeated sequence present at the 3’end of the gene. The proteins appear to be present also in leaf nuclei and do not show any detectable variations that correlate with napin expression during seed development. Thus, analogous with many transcription factors, the DNA‐binding proteins that we have identified are present in both expressing and non‐expressing cells.
High‐Resolution Observations of the Cosmic Microwave Background Power Spectrum with ACBAR (2004)

We report the first measurements of anisotropy in the cosmic microwave background (CMB) radiation with the Arcminute Cosmology Bolometer Array Receiver (ACBAR). The instrument was installed on the 2.1 m Viper telescope at the South Pole in 2001 January; the data presented here are the product of observations up to and including 2002 July. We present two deep differential maps produced by subtracting leading and trailing observations from the main field. The differential maps cover approximately 24 deg2 of sky selected for low dust contrast. These results represent the highest signal-to-noise ratio observations of CMB anisotropy to date; in the deepest 150 GHz band map, we reached an rms of ~8.0 ?K per 5' beam. The 3
Supplementary Figure 2 from 6-Bromoindirubin-3′-Oxime Inhibits JAK/STAT3 Signaling and Induces Apoptosis of Human Melanoma Cells (2023)

Supplementary Figure 2 from 6-Bromoindirubin-3′-Oxime Inhibits JAK/STAT3 Signaling and Induces Apoptosis of Human Melanoma Cells
Precise hand segmentation from a single depth image (2016)

We propose a new approach to segmenting a hand accurately from a single depth image. Given a depth image, we extract first a rough hand region of interest (RoI) including a hand and a part of an arm. Then, the RoI is partitioned into triangles by using a constrained Delaunay triangulation (CDT) approach from which hand segmentation proposals are generated. Each segmentation proposal is evaluated by a shallow convolutional neural network (CNN) which is trained as a regression function to predict a confidence score for each proposal. Finally, the segmentation proposal with the highest confidence score is selected as our hand segmentation result. To evaluate the effectiveness of our approach, we use a set of real data containing more than 370,000 frames of hand depth images collected from 40 subjects with large variations in pose, orientation and sensing distance. Compared with segmentation results achieved by a random decision forest (RDF) based approach, our approach achieves much higher accuracy.
The etiology and evolution of magnetic resonance imaging-visible perivascular spaces: Systematic review and meta-analysis (2023)

https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=346564, identifier CRD42022346564.
Microdialysis and SPECT measurements of amphetamine-induced dopamine release in nonhuman primates (1997)

The competition between endogenous transmitters and radiolabeled ligands for in vivo binding to neuroreceptors might provide a method to measure endogenous transmitter release in the living human brain with noninvasive techniques such as positron emission tomography (PET) or single photon emission computerized tomography (SPECT). In this study, we validated the measure of amphetamine-induced dopamine release with SPECT in nonhuman primates. Microdialysis experiments were conducted to establish the dose-response curve of amphetamine-induced dopamine release and to document how pretreatment with the dopamine depleter alpha-methyl-para-tyrosine (alpha MPT) affects this response. SPECT experiments were performed with two iodinated benzamides, [123I]IBZM and [123I]IBF, under sustained equilibrium condition. Both radio-tracers are specific D2 antagonists, but the affinity of [123I]IBZM (KD-0.4 nM) is lower than that of [123I]IBF (KD 0.1 nM). With both tracers, we observed a prolonged reduction in binding to D2 receptors following amphetamine injection. [123I]IBZM binding to D2 receptors was more affected than [123I]IBF by high doses of amphetamine, indicating that a lower affinity increases the vulnerability of a tracer to endogenous competition. With [123I]IBZM, we observed an excellent correlation between reduction of D2 receptor binding measured with SPECT and peak dopamine release measured with microdialysis after various doses of amphetamine. Pretreatment with alpha MPT significantly reduced the effect of amphetamine on [123I]IBZM binding to D2 receptors, confirming that this effect was mediated by intrasynaptic dopamine release. Together, these results validate the use of this SPECT paradigm as a noninvasive measurement of intrasynaptic dopamine release in the living brain.
How Small Scale Tests may be useful to predict Large Scale Behavior of Materials (2017)

The objective of this study is to develop a small scale test allowing to (i) evaluate the performances of materials in extreme conditions representative of a jet fire, (ii) better understand the materials behavior when exposed to such type of fire and (iii) correlate the parameters of the fire scenario (e.g. heat flux profile, temperature profile, pressure…) on the behavior and performances of the materials. An independent set of the levels of each parameter will allow studying the influence of the constraints separately or in combination. The bench will also be instrumented to measure and control adequately the constraints (e.g. measurements of the radiative part of the flame, of the erosion force applied to the sample, of the nature of the flame…).
AutoLoss: Learning Discrete Schedules for Alternate Optimization (2018)

Many machine learning problems involve iteratively and alternately optimizing different task objectives with respect to different sets of parameters. Appropriately scheduling the optimization of a task objective or a set of parameters is usually crucial to the quality of convergence. In this paper, we present AutoLoss, a meta-learning framework that automatically learns and determines the optimization schedule. AutoLoss provides a generic way to represent and learn the discrete optimization schedule from metadata, allows for a dynamic and data-driven schedule in ML problems that involve alternating updates of different parameters or from different loss objectives. We apply AutoLoss on four ML tasks: d-ary quadratic regression, classification using a multi-layer perceptron (MLP), image generation using GANs, and multi-task neural machine translation (NMT). We show that the AutoLoss controller is able to capture the distribution of better optimization schedules that result in higher quality of convergence on all four tasks. The trained AutoLoss controller is generalizable -- it can guide and improve the learning of a new task model with different specifications, or on different datasets.
Dynamic Analysis of Vertebrate Cardiogenesis (2009)

Vertebrate heart morphogenesis is a complex process that integrates different structures and cell types driven to interact by genetic and epigenetic factors. We have taken an interdisciplinary approach to studying heart formation by combining the power of molecular genetics with advanced optical imaging within living embryos. We have developed a Tie1‐H2B.eYFP transgenic quail and novel imaging methods that permit dynamic observation and manipulation of vascular development. Avian embryos are ideal for imaging because they are accessible at all stages of development outside of their vertebrate mother, unlike mammals, yet they develop a heart that has four chambers. Our over‐arching goal is to analyze heart morphogenesis and assess the relative roles of epigenetic and genetic mechanisms. Our experimental plan directly tests the hypothesis that flow is a major determinant of cardiac development and offers experimental tools that can be applied in a variety of experimental settings. Grant Funding Source NIH Cardio
A Mouse Model for the Carney Complex Tumor Syndrome Develops Neoplasia in Cyclic AMP–Responsive Tissues (2005)

Carney complex is an autosomal dominant neoplasia syndrome characterized by spotty skin pigmentation, myxomatosis, endocrine tumors, and schwannomas. This condition may be caused by inactivating mutations in PRKAR1A, the gene encoding the type 1A regulatory subunit of protein kinase A. To better understand the mechanism by which PRKAR1A mutations cause disease, we have developed conventional and conditional null alleles for Prkar1a in the mouse. Prkar1a(+/-) mice developed nonpigmented schwannomas and fibro-osseous bone lesions beginning at approximately 6 months of age. Although genotype-specific cardiac and adrenal lesions were not seen, benign and malignant thyroid neoplasias were observed in older mice. This spectrum of tumors overlaps that seen in Carney complex patients, confirming the validity of this mouse model. Genetic analysis indicated that allelic loss occurred in a subset of tumor cells, suggesting that complete loss of Prkar1a plays a key role in tumorigenesis. Similarly, tissue-specific ablation of Prkar1a from a subset of facial neural crest cells caused the formation of schwannomas with divergent differentiation. These observations confirm the identity of PRKAR1A as a tumor suppressor gene with specific importance to cyclic AMP-responsive tissues and suggest that these mice may be valuable tools not only for understanding endocrine tumorigenesis but also for understanding inherited predispositions for schwannoma formation.
In vitro analysis of inhibition of interactions of VEGF-A and its receptors by proximity ligation (2006)

Proximity ligation is a recently established technique that can provide answers to questions about the concentration, localization, interactions, modifications and functions of proteins. The method enables sensitive protein measurements with a detection limit in the low femtomolar range in complex biological samples. In proximity ligation, the challenge of detecting specific proteins is converted to the analysis of specific DNA sequences. Proximity probes containing oligonucleotide extensions are designed to bind pairwise to target proteins, and to form amplifiable tag sequences upon ligation when brought in proximity. Protocols for the conversion of monoclonal or polyclonal antibodies into proximity probes through the attachment of oligonucleotide sequences are described in the thesis. In addition, the thesis describes the adaptation of the proximity ligation technology for detection of microbial pathogens, analysis of interactions between proteins and nucleic acids, and of inhibition of receptor-ligand interactions. Nucleic acid amplification allows specific detection of pathogens with single-copy sensitivity. There are many circumstances, however, when analysis of pathogen surface antigens or the antibody response can provide increased diagnostic value. Proximity ligation reactions were used to measure numbers of virus and bacteria by detection of viral or bacterial surface proteins. Detection sensitivities similar to those of nuclear acid-based detection reactions were achieved directly in infected samples for a parvovirus and for an intracellular bacterium. Biological processes are orchestrated by interactions of proteins with molecules in their environment, and investigations of interactions between proteins and other biomolecules are thus of great importance. Protocols were established for very specific and sensitive homogeneous-phase analysis of interactions between proteins and specific nucleic acid sequences. Finally, the proximity ligation mechanism was used to monitor interactions between VEGF-A and two of its receptors, VEGFR-1 and VEGFR-2, and to characterize the effects of agents disrupting this interaction.
Inter-organellar Communication in Parkinson's and Alzheimer's Disease: Looking Beyond Endoplasmic Reticulum-Mitochondria Contact Sites (2022)

Neurodegenerative diseases (NDs) are generally considered proteinopathies but whereas this may initiate disease in familial cases, onset in sporadic diseases may originate from a gradually disrupted organellar homeostasis. Herein, endolysosomal abnormalities, mitochondrial dysfunction, endoplasmic reticulum (ER) stress, and altered lipid metabolism are commonly observed in early preclinical stages of major NDs, including Parkinson's disease (PD) and Alzheimer's disease (AD). Among the multitude of underlying defective molecular mechanisms that have been suggested in the past decades, dysregulation of inter-organellar communication through the so-called membrane contact sites (MCSs) is becoming increasingly apparent. Although MCSs exist between almost every other type of subcellular organelle, to date, most focus has been put on defective communication between the ER and mitochondria in NDs, given these compartments are critical in neuronal survival. Contributions of other MCSs, notably those with endolysosomes and lipid droplets are emerging, supported as well by genetic studies, identifying genes functionally involved in lysosomal homeostasis. In this review, we summarize the molecular identity of the organelle interactome in yeast and mammalian cells, and critically evaluate the evidence supporting the contribution of disturbed MCSs to the general disrupted inter-organellar homeostasis in NDs, taking PD and AD as major examples.
Preparation of membranes using solvent-less vapor deposition followed by in-situ polymerization (2023)

A system of fabricating a composite membrane from a membrane substrate using solvent-less vapor deposition followed by in-situ polymerization. A first monomer and a second monomer are directed into a mixing chamber in a deposition chamber. The first monomer and the second monomer are mixed in the mixing chamber providing a mixed first monomer and second monomer. The mixed first monomer and second monomer are solvent-less vapor deposited onto the membrane substrate in the deposition chamber. The membrane substrate and the mixed first monomer and second monomer are heated to produce in-situ polymerization and provide the composite membrane.
CIXB-1: combined input-one-cell-crosspoint buffered switch (2002)

Buffered crossbars have been considered as an alternative for non-buffered crossbars to improve switching throughput. The drawback of a buffered crossbar is the memory amount that is proportional to the square of the number of ports (O(N/sup 2/)). This is not the main limitation when the buffer size is kept to a minimum size such that implementation is feasible. For a small buffer size, the number of ports of a switch module is not limited by the memory amount but by the pin count. We propose a novel architecture: a combined input-one-cell-crosspoint buffer crossbar (CIXB-1) with virtual output queues (VOQs) at the inputs and round-robin arbitration. We show that the proposed architecture can provide 100% throughput under uniform traffic. A CIXB-1 offers several advantages for a feasible implementation such as scalability and timing relaxation. With the currently available memory technology, a one-cell-crosspoint buffered switch is feasible for a 32/spl times/32 fabric module.
Impact of Lactobacillus reuteri colonization on gut microbiota, inflammation, and crying time in infant colic (2017)

Infant colic is a distressing condition of unknown etiology. An aberrant gastrointestinal microbiota has been associated, and Lactobacillus reuteri supplementation has been shown to reduce crying and/or fussing time ('crying time') in some infants with colic. The relationship between L. reuteri gut colonization and crying time has not been examined. We investigated the relationship between L. reuteri colonization and fecal microbiota (microbial diversity and Escherichia coli), intestinal inflammation, and crying time in infants with colic, using a subset of 65 infants from the Baby Biotics trial, which randomized healthy term infants aged <13 weeks with infant colic to receive probiotic L. reuteri DSM 17938 (1 × 10<sup>8</sup> colony forming units) or placebo daily for 28 days. We observed an overall reduction in median crying time, regardless of L. reuteri colonization status (n = 14 colonized). There were no differences in E. coli colonization rates or densities, microbial diversity or intestinal inflammation by L. reuteri colonization status. We found that L. reuteri density positively correlated with crying time, and E. coli density negatively correlated with microbial diversity. As density of L. reuteri was associated with increased crying time, L. reuteri supplementation may not be an appropriate treatment for all infants with colic.
Minimally invasive extracavitary approach for thoracic discectomy and interbody fusion: 1-year clinical and radiographic outcomes in 13 patients compared with a cohort of traditional anterior transthoracic approaches (2011)

Compared with transthoracic procedures, MIECTDF effectively decompressed the spinal canal, yielding identical 1-year radiographic and clinical outcomes to those seen in controls, while producing superior clinical scores in the interim. Thus, MIECTDF is the authors' treatment of choice for TDH.
Radar CFAR Thresholding in Clutter and Multiple Target Situations (1983)

Radar detection procedures involve the comparison of the received signal amplitude to a threshold. In order to obtain a constant false-alarm rate (CFAR), an adaptive threshold must be applied reflecting the local clutter situation. The cell averaging approach, for example, is an adaptive procedure. A CFAR method is discussed using as the CFAR threshold one single value selected from the so-called ordered statistic (this method is fundamentally different from a rank statistic). This procedure has some advantages over cell averaging CFAR, especially in cases where more than one target is present within the reference window on which estimation of the local clutter situation is based, or where this reference window is crossing clutter edges.