gebhart/patrepeval huggingface dataset:
Transfection of Rat Pancreatic Islet Tissue by Polymeric Gene Vectors (2009)

These results suggest that the gene delivery efficacy to isolated islets can be improved by manipulating the transfection conditions. Polymeric vectors will broaden the options for islet transfection, which is currently limited to viral vectors.
Supplementary Methods, Figure Legends 1-5 from Inactivation of Junctional Adhesion Molecule-A Enhances Antitumoral Immune Response by Promoting Dendritic Cell and T Lymphocyte Infiltration (2023)

Supplementary Methods, Figure Legends 1-5 from Inactivation of Junctional Adhesion Molecule-A Enhances Antitumoral Immune Response by Promoting Dendritic Cell and T Lymphocyte Infiltration
Magnetic Latex Particles in Nanobiotechnologies for Biomedical Diagnostic Applications: State of the Art (2009)

Abstract Summary: The main objective of this short state‐of‐the art is to report on the preparation of reactive magnetic latexes for biomedical applications. The main advantage of colloidal magnetic particles is their separation upon applying an external permanent magnetic field. Then magnetic particles bearing reactive groups or specific receptors are used in biomedical diagnosis such as immunoassay, molecular diagnosis for specific capture and detection of nucleic acids, viruses extraction and detection, cell sorting and more recently in numerous biotechnological applications. The preparation of magnetic latexes requires the use of well‐defined iron oxide nanoparticles in appropriate medium. In this direction, aqueous ferrofluids were largely used to prepare functional magnetic latexes, whereas few approaches have been devoted to the use of organic ferrofluids.
Anti-Müllerian hormone Bruxelles: a nonsense mutation associated with the persistent Müllerian duct syndrome. (1991)

The persistent Müllerian duct syndrome (PMDS) is characterized by the persistence of Müllerian derivatives, uterus and tubes, in otherwise normally virilized males. In a previous study, we showed that this syndrome is heterogeneous, with lack of production of anti-Müllerian hormone (AMH) by testicular tissue accounting for only some, AMH-negative, cases of this disorder. We have characterized the point mutation responsible for an AMH-negative PMDS in three siblings: a guanine to thymine transversion at position 2096 in the fifth exon changes a GAA triplet, coding for glutamic acid, to a TAA stop codon. The mutation could also be recognized, using the polymerase chain reaction, on RNA produced in trace amounts by a lymphoblastic cell line. The translation product, although undetectable in testicular tissue, could be visualized in culture medium of cells transfected with the mutant gene.
Arbitrary factorisation of decimation ratio for efficient multistage realisation (2004)

Multistage implementation of decimators is in many cases more efficient than single-stage one. However, if the decimation ratio is prime, it cannot be factorised into a product of smaller integer factors. Previously it has been proposed that a rational decimation stage can be used to enable arbitrary selection of the decimation ratios. This way the advantages of multistage decimation and special filter structures such as halfband filters become available regardless of the overall decimation ratio. In this paper, we propose a method for optimising the overall response of such multistage decimators. Imaging and aliasing phenomena in such decimators are analysed, an iterative design method is introduced, and design examples are given. The proposed method can also be used for non-prime decimation ratios when their prime factors are not favourable for multistage implementation. 1.
Detection of Human Bodypart Abnormalities by Microwaves – A New Approach (2019)

We present modified antenna-like devices - applicators - for direct detection of internal inhomogeneities such as breast tumours and brain haemorrhages, at a frequency about 1 GHz. This direct detection provides the possibility of using a simple microwave generator and simple rectification and position registration of the received signals. Direct readouts are thus possible, without any massive computing resources as with tomographic imaging. The transmitting applicator is noncontacting and in free air close to the object. It generates an essentially quasistatic axial magnetic field which induces a circular electric field in the tissue. The receiving 3D contacting applicator contains a high-permittivity ceramic and is resonant. Its mode field provides the desired polarisation sensitivity and filters out the main electric field. The overall system sensitivity for detection of internal inhomogeneities is accomplished by optimised use of the orthogonality of the primary magnetic, induced electric, and diffracted electric fields. When developments are completed, the system will replace or complement existing commercial technologies at a low cost.
Next-generation transgenic mice for optogenetic analysis of neural circuits (2013)

Here we characterize several new lines of transgenic mice useful for optogenetic analysis of brain circuit function. These mice express optogenetic probes, such as enhanced halorhodopsin or several different versions of channelrhodopsins, behind various neuron-specific promoters. These mice permit photoinhibition or photostimulation both in vitro and in vivo. Our results also reveal the important influence of fluorescent tags on optogenetic probe expression and function in transgenic mice.
Parametric control of a diffractive axicon beam rider (2021)

A laser beam rider is a large-scale optical structure designed so that it is attracted toward the optical axis, while also affording forward propulsion via radiation pressure along the beam path. Such structures form the basis of laser-driven light sails. Experimental measurements are described whereby a thin diffractive axicon film is shown to exhibit a natural restoring force when its axis is displaced from the optical axis. This effect is attributed to the optical momentum change of diffracted light. Whereas continuous illumination supports harmonic motion, modulated illumination is shown to support both parametric gain and parametric damping. The 12.7µ<i>m</i> period photopolymer axicon grating was suspended in a vacuum torsion oscillator and irradiated with a 1.5 W near-infrared laser modulated at a period of 38 s.
Silver nanoparticles embedded in zeolite membranes: release of silver ions and mechanism of antibacterial action (2011)

These results indicate that AgNP-ZM provide a novel matrix for gradual release of Ag(+).
Crystal structure of (1-ethoxyethylidene)dimethylazanium tetraphenylborate (2015)

In the cation of the title salt, C6H14NO(+)·C24H20B(-), the C-N bond lengths are 1.297 (2), 1.464 (2) and 1.468 (2) Å, indicating double- and single-bond character, respectively. The C-O bond length of 1.309 (2) Å shows double-bond character, pointing towards charge delocalization within the NCO plane of the iminium ion. In the crystal, C-H⋯π inter-actions between the iminium H atoms and the phenyl C atoms of the anion are present. The phenyl rings form aromatic pockets, in which the iminium ions are embedded.
Effects of gonadotropin releasing hormone agonists and antagonists on reproductive functions (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEffects of gonadotropin releasing hormone agonists and antagonists on reproductive functionsCatherine Rivier, Wylie Vale, and Jean RivierCite this: J. Med. Chem. 1983, 26, 11, 1545–1550Publication Date (Print):November 1, 1983Publication History Published online1 May 2002Published inissue 1 November 1983https://pubs.acs.org/doi/10.1021/jm00365a001https://doi.org/10.1021/jm00365a001research-articleACS PublicationsRequest reuse permissionsArticle Views69Altmetric-Citations28LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Structural Basis for Agonism and Antagonism for a Set of Chemically Related Progesterone Receptor Modulators (2011)

The progesterone receptor is able to bind to a large number and variety of ligands that elicit a broad range of transcriptional responses ranging from full agonism to full antagonism and numerous mixed profiles inbetween. We describe here two new progesterone receptor ligand binding domain x-ray structures bound to compounds from a structurally related but functionally divergent series, which show different binding modes corresponding to their agonistic or antagonistic nature. In addition, we present a third progesterone receptor ligand binding domain dimer bound to an agonist in monomer A and an antagonist in monomer B, which display binding modes in agreement with the earlier observation that agonists and antagonists from this series adopt different binding modes.
Restrained activation of CYFIP2-containing WAVE complexes controls membrane protrusions and cell migration (2020)

Abstract Branched actin networks polymerized by the Arp2/3 complex are critical for cell migration. The WAVE complex is the machinery that activates Arp2/3 in a RAC1-dependent manner at the leading edge of migrating cells. Multiple WAVE complexes are assembled in a cell through various combinations of paralogous subunits. Here we report the surprising phenotype associated with loss-of-function of CYFIP2, a subunit of the WAVE complex. In three different human mammary cell lines and in prechordal plate cells of gastrulating zebrafish embryos, CYFIP2 depletion promoted, rather than impaired, membrane protrusions and migration persistence. CYFIP2, however, assembled WAVE complexes that polymerize branched actin at the cell cortex and rescued membrane protrusions of CYFIP1/2 double knock-out cells, although less efficiently than CYFIP1. Point mutations of CYFIP2 associated with intellectual disability in children were gain-of-function, as they made CYFIP2 as active as CYFIP1 in this rescue experiment. Biochemical reconstitutions of CYFIP2-containing WAVE complexes showed that they bound equally well to active RAC1 as CYFIP1-containing WAVE complexes, yet they were poorly activated in response to RAC1 binding. Together these results suggest that CYFIP2-containing WAVE complexes titrate active RAC1 and thereby prevent efficient CYFIP1-containing complexes from being activated. In this context, where cell migration is governed by the balance of CYFIP1/2 expression, releasing the restrained activity of CYFIP2-containing WAVE complexes leads to pathology.
IBD-Associated TL1A Gene (TNFSF15) Haplotypes Determine Increased Expression of TL1A Protein (2009)

These findings suggest that TL1A gene variation exacerbates induction of TL1A in response to FcgammaR stimulation in Jewish CD patients and this may lead to chronic intestinal inflammation via overwhelming T cell responses. Thus, TL1A may provide an important target for therapeutic intervention in this subgroup of IBD patients.
A Mean Field Theory of Batch Normalization (2019)

We develop a mean field theory for batch normalization in fully-connected feedforward neural networks. In so doing, we provide a precise characterization of signal propagation and gradient backpropagation in wide batch-normalized networks at initialization. Our theory shows that gradient signals grow exponentially in depth and that these exploding gradients cannot be eliminated by tuning the initial weight variances or by adjusting the nonlinear activation function. Indeed, batch normalization itself is the cause of gradient explosion. As a result, vanilla batch-normalized networks without skip connections are not trainable at large depths for common initialization schemes, a prediction that we verify with a variety of empirical simulations. While gradient explosion cannot be eliminated, it can be reduced by tuning the network close to the linear regime, which improves the trainability of deep batch-normalized networks without residual connections. Finally, we investigate the learning dynamics of batch-normalized networks and observe that after a single step of optimization the networks achieve a relatively stable equilibrium in which gradients have dramatically smaller dynamic range. Our theory leverages Laplace, Fourier, and Gegenbauer transforms and we derive new identities that may be of independent interest.
The Latest in Surgical Management of Stage IIIA Non–Small Cell Lung Cancer: Video-Assisted Thoracic Surgery and Tumor Molecular Profiling (2015)

Stage IIIA non-small cell lung cancer (NSCLC) remains a treatment challenge and requires a multidisciplinary care team to optimize survival outcomes. Thoracic surgeons play an important role in selecting operative candidates and assisting with pathologic mediastinal staging via cervical mediastinoscopy, endobronchial ultrasound, or esophageal ultrasound with fine needle aspiration. The majority of patients with stage IIIA disease will receive induction therapy followed by repeat staging before undergoing lobectomy or pneumonectomy; occasionally, a patient with an incidentally found, single-station microscopic IIIA tumor will undergo resection as the primary initial therapy. Multiple large clinical trials, including SWOG-8805, EORTC-8941, INT-0139, and ANITA, have shown 5-year overall survival rates of up to 30% to 40% using triple-modality treatments, and the best outcomes repeatedly are seen among patients who respond to induction treatment or who have tumors amenable to lobectomy instead of pneumonectomy. The need for a pneumonectomy is not a reason to deny patients an operation, because current operative mortality and morbidity rates are acceptably low at 5% and 30%, respectively. In select patients with stage IIIA disease, video-assisted thoracic surgery and open resections have been shown to have comparable rates of local recurrence and long-term survival. New developments in genetic profiling and personalized medicine are exciting areas of research, and early data suggest that molecular profiling of stage IIIA NSCLC tumors can accurately stratify patients by risk within this stage and predict survival outcomes. Future advances in treating stage IIIA disease will involve developing better systemic therapies and customizing treatment plans on the basis of an individual tumor's genetic profile.
Machine Learning Aided Design of Sub-Array MIMO Antennas for CubeSats Based on 3D Printed Metallic Ridge Gap Waveguides (2022)

In this paper, a machine learning-assisted approach is presented for the design of a 3D Printed Metallic Ridge Gap Waveguide-Based array MIMO antenna for inter-cube satellite (CubeSat) communication. The designed antenna has a total dimension of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$\boldsymbol{15.5 \times 10.5 \times 5.78} \mathbf{mm}^3$</tex> and is based on aluminum alloy powder (AlSi10Mg) with a conductivity of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$\boldsymbol{2.04\times 10^{7}}\ \mathbf{S}/\mathbf{m}$</tex> . The antenna exhibits wideband operation in V-band (59.3-66.6 GHz) with a stable realized gain of 10.5 dBi and radiation efficiency of 90% over the operating frequency.
Abstract 110: Clinical Characteristics and Anticoagulant Transition Patterns of Hospitalized Patients with Venous Thromboembolism: A Retrospective Analysis Using Electronic Health Record Data (2019)

Objective: Describe the clinical characteristics and anticoagulant use of patients with venous thromboembolism (VTE) transitioning from a hospital setting using an electronic health care (EHR) database. Methods: This retrospective EHR study analyzed adults (18+ years) with a VTE diagnosis code during a hospital encounter (emergency department [ED], observation [OBS] area, or inpatient [IP] stay) between 1/1/2012-8/31/2017 (ID period). The first VTE hospital encounter (from admission to discharge) during the ID period was defined as the index VTE encounter. Patients with evidence of atrial fibrillation/flutter, pregnancy, or multiple oral anticoagulants during the index VTE encounter were excluded. Clinical characteristics and anticoagulants administered during the index VTE encounter and ordered on the discharge date were reported descriptively. Results: Among the 282,978 patients identified, the mean age (SD) age was 61 (17) years; 48% (136,155 of 282,978) were male; 78% (221,120 of 282,978) were Caucasian; 59% (167,628 of 282,978) had deep vein thrombosis without a pulmonary embolism; 18% (49,596 of 282,978) had evidence of cancer; and 7% (19,447 of 282,978) had evidence of a provoked etiology (hormonal therapy, lower extremity fracture/trauma, pelvic/orthopedic surgery) during the index VTE encounter. Nearly three-quarters (199,568 of 282,978) were admitted for an IP stay with a median length of stay of 6 days; the remaining 29% (83,410 of 282,978) were treated in an ED or OBS area only. Overall, 73% (207,640 of 282,978) were discharged home, 19% (54,283 of 282,978) were discharged to another IP facility, and 7% (21,055 of 282,978) had other or unknown discharge status. During the index VTE encounter, 67% (188,271 of 282,978) received heparin (low molecular weight or unfractionated), 34% (95,090 of 282,978) received warfarin, 12% (34,540 of 282,978) received a non-vitamin K oral anticoagulant (DOAC), and 27% (76,877 of 282,978) had no record of anticoagulant administration. Of those with heparin, 41% (76,471 of 188,271) received heparin only. More than half of those with an order for a DOAC or warfarin on the discharge date had received the same anticoagulant during the index VTE encounter, namely, 65% (22,344 of 34,540) with a DOAC during the index VTE encounter received a discharge order for a DOAC and 58% (55,369 of 95,090) with warfarin during the index VTE encounter received a discharge order for warfarin. Among those with heparin only during the index VTE encounter, approximately 18% (13,759 of 76,471) received an order for heparin, 6% (4,217 of 76,471) received an order for a DOAC, and 5% (3,810 of 76,471) received an order for warfarin on discharge. Conclusion: This EHR study observed that a sizable proportion of hospitalized patients with VTE were either prescribed a different anticoagulant on discharge or discharged without an anticoagulant prescription.
FATE: a FrameNet-Annotated Corpus for Textual Entailment. (2008)

Several studies indicate that the level of predicate-argument structure is relevant for modeling prevalent phenomena in current textual entailment corpora. Although large resources like FrameNet have recently become available, attempts to integrate this type of information into a system for textual entailment did not confirm the expected gain in performance. The reasons for this are not fully obvious; candidates include FrameNet’s restricted coverage, limitations of semantic parsers, or insufficient modeling of FrameNet information. To enable further insight on this issue, in this paper we present FATE (FrameNet-Annotated Textual Entailment), a manually crafted, fully reliable frame-annotated RTE corpus. The annotation has been carried out over the 800 pairs of the RTE-2 test set. This dataset offers a safe basis for RTE systems to experiment, and enables researchers to develop clearer ideas on how to effectively integrate frame knowledge in semantic inferenence tasks like recognizing textual entailment. We describe and present statistics over the adopted annotation, which introduces a new schema based on full-text annotation of so called relevant frame evoking elements. 1.
029 Mitochondrial correlates of signaling processes involved with the cellular response to Eimeria infection in broiler chickens (2017)

Host cellular responses to coccidiosis infection are consistent with elements of apoptosis, autophagy, and necrosis. These processes are enhanced in the cell through cell-directed signaling or repressed through parasite-derived inhibitors of these processes favoring the survival of the parasite. Across all 3 of these cell-based responses, one common factor at the origins of response-initiating signaling is the perturbation of the mitochondria and mitochondria-derived release of superoxide anion and nitric oxide. These reactants can interact to form the potent tyrosine-nitrating reactant peroxynitrite. The objective of our investigation was to determine how mitochondrial dysfunction might arise during the infection-response process and how endogenous biochemical reactions derived from this mitochondrial dysfunction might affect the cell. In the mitochondria, ATP is generated by Complex V ATP synthase, specifically in what is termed the P-loop, a highly ordered hydrophilic pocket. Based on literature citations suggesting that mitochondrial proteins are dysfunctionally nitrated during oxidative stress, we accessed the 3-dimensional structure of the P-loop (PMID: 11509182) and used a computational chemistry algorithm (HyperProtein version 1.0) to model how the nitration of a tyrosine residue (Y-345), significant to the orientation of the ADP, Pi, and Mg+2, might affect the spatial structure of the domain. Analysis revealed that nitration of this specific residue reordered hydrogen bonding and electrostatic charges in the P-loop where the ADP, Pi, and Mg+2 were disfavored from interacting. To test if this nitration could be identified during an oxidative stress in vivo, we developed a highly specific mouse monoclonal anti-nitroY-345 P-loop antibody and performed high-resolution fluorescent imaging on duodenal tissues obtained from broilers infected with coccidiosis parasite Eimeria acervulina. Imaging revealed that this specific nitration event did occur (P < 0.05 vs. noninfected chickens) in villus enterocytes as early as 1 d after infection. This specific P-loop nitration colocalized directly with mitochondria (rabbit-anti-Complex V, C subunit) on d 1 after infection but became more generalized throughout the affected enterocytes as the infection progressed and mitochondria appeared to decrease (P < 0.04) in numbers and condense into tight clumps. The nitration mirrored the progression from d 1 to d 3 to d 6 after infection of the parasites down the villus to the crypts, with the nuclei of both the trophozoites and the schizonts showing evidence of strong generalized protein nitration (P < 0.01; detected with anti-nitrotyrosine antibody) and membrane disruption. The data suggest that post-translational mitochondrial autonitration of Complex V P-loop may participate in cellular responses to coccidiosis.
Synthesis, Stereochemistry and Molecular Structures of Chiral-at-Metal (Cycloheptatrienyl)molybdenum Complexes Containing the Diphosphane Prophos (2002)

The synthesis of a series of 18-electron chiral-at-metal (cycloheptatrienyl)molybdenum complexes [(η7-C7H7)Mo(prophos)X] [prophos = (R)-1,2-bis(diphenylphosphanyl)propane; X = NCMeBF4, Cl, I, CN, H, Me] is reported, which consist of diastereomers differing only in the metal configuration. Diastereomer enrichments have been achieved and the configurational stability of the compounds [(η7-C7H7)Mo(prophos)X] has been studied and compared with the isoelectronic ruthenium complexes [(η5-C5H5)Ru(prophos)X]. The stereochemistry of the substitution reactions has been investigated, and X-ray analysis and NMR spectroscopy were used to determine the absolute configuration of the complexes. (© Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002)