gebhart/patrepeval huggingface dataset:
Supplementary Figure 5B from Molecular Triage of Premalignant Lesions in Liquid-Based Cervical Cytology and Circulating Cell-Free DNA from Urine, Using a Panel of Methylated Human Papilloma Virus and Host Genes (2023)

&lt;p&gt;AlignScape - Pairwise alignment of the HPV16 genome with reads obtained from urine ccfDNA from seven clinical samples: TrDNA-445, TrDNA-455, TrDNA-456, TrDNA-481, TrDNA-504, TrDNA-513, and TrDNA-571. The "close-up" HPV DNA computes and displays nucleotide-level ('close-up') multiple alignments of sequences in a 1Kb region starting at a user-specified address or gene in the reference genome.&lt;/p&gt;
Post-quantum hash functions using $\mathrm{SL}_n(\mathbb{F}_p)$ (2022)

We define new families of Tillich-Zémor hash functions, using higher dimensional special linear groups over finite fields as platforms. The Cayley graphs of these groups combine fast mixing properties and high girth, which together give rise to good preimage and collision resistance of the corresponding hash functions. We justify the claim that the resulting hash functions are post-quantum secure.
Nuclear magnetic resonance studies of hydrogen-loaded and uv-exposed germanosilicate preforms (1999)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text M. A. Hubbard, E. M. Gill, S. L. Gilbert, J. Xiong, H. Lock, G. E. Maciel, T. Taunay, and M. A. Putnam, "Nuclear magnetic resonance studies of hydrogen-loaded and uv-exposed germanosilicate preforms," in Bragg Gratings, Photosensitivity, and Poling in Glass Waveguides, T. Erdogan, E. Friebele, and R. Kashyap, eds., Vol. 33 of OSA Trends in Optics and Photonics Series (Optica Publishing Group, 1999), paper CC5. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
[Genetic aspects of the 46, XX male]. (1998)

The XX males represent a proportion of 1/25 of all patients suffering of the Klinefelter syndrome. From a clinical and endocrinological point of view, they exhibit a hypogonadotropic hypogonadism. Isolated cases are rare and familial forms are exceptional. The XX males may be divided in 3 subgroups: 46, XX males with the SRY gene; 46, XX males without the SRY gene and XX/XY mosaics.
RNAi feeding bioassay: development of a non‐transgenic approach to control Asian citrus psyllid and other hemipterans (2017)

Abstract RNA interference ( RNA i) involves a natural mechanism of gene regulation and an antiviral defense system in eukaryotic cells, resulting in sequence‐specific degradation of RNA s. Recent studies demonstrated the feasibility of using RNA i‐based strategies to reduce insect pests or increase the health of beneficial insects. This technology permits the development of strategies to control a single insect species, with possibly no negative effects on non‐target species, like honey bees or parasitoids. Focus on the development of topically applied RNA i‐based approaches to manage insect pests and pathogens may provide environmentally sound products for use across all agriculture production systems. Herein presented are methods to develop RNA i‐based control to the Asian citrus psyllid ( ACP ), D iaphorina citri K uwayama ( H emiptera: P syllidae), vector of citrus H uanglongbing ( HLB ). Described is an RNA i feeding bioassay, called in plant system ( iPS ), which uses vegetative new‐growth citrus flush to deliver double‐strand RNA (ds RNA ) to ACP during natural feeding. The iPS demonstrated delivery of non‐specific ds RNA in ACP 72 h post feeding. Feeding on flushes treated with ds RNA targeting ACP Arginine Kinase (ds AK ), caused relative transcript knockdown and psyllid mortality. Increasing the dose of ds AK or use of ds RNA triggers made to different regions of the AK mRNA did not increase psyllid mortality. The iPS bioassay provides an easy system for use across many plants to successfully deliver ds RNA to ACP and other hemipteran insects for research or RNA i development.
Vascular dysfunction—The disregarded partner of Alzheimer's disease (2019)

Increasing evidence recognizes Alzheimer's disease (AD) as a multifactorial and heterogeneous disease with multiple contributors to its pathophysiology, including vascular dysfunction. The recently updated AD Research Framework put forth by the National Institute on Aging-Alzheimer's Association describes a biomarker-based pathologic definition of AD focused on amyloid, tau, and neuronal injury. In response to this article, here we first discussed evidence that vascular dysfunction is an important early event in AD pathophysiology. Next, we examined various imaging sequences that could be easily implemented to evaluate different types of vascular dysfunction associated with, and/or contributing to, AD pathophysiology, including changes in blood-brain barrier integrity and cerebral blood flow. Vascular imaging biomarkers of small vessel disease of the brain, which is responsible for >50% of dementia worldwide, including AD, are already established, well characterized, and easy to recognize. We suggest that these vascular biomarkers should be incorporated into the AD Research Framework to gain a better understanding of AD pathophysiology and aid in treatment efforts.
Stochastic Analysis of Flooding in PEM Fuel Cells by Electrochemical Impedance Spectroscopy (2007)

Steady-state and impedance measurements were correlated to gain insight into flooding of a single PEM fuel cell with interdigitated flow channels. While the values of the impedance can be related to the onset of flooding, the stochastic character of the formation of water droplets and subsequent removal by gas flow gives rise to a significant increase in the noise level of the impedance measurement. The standard deviation of the impedance measurements was compared to a base-noise level evaluated using a measurement model analysis for cells operated at minimal levels of flooding. The increase in stochastic noise associated with flooding is more apparent at low frequencies, due to the closer match to the characteristic frequency associated with the growth and removal of water droplets. The present work demonstrates how the stochastic character of flooding may be exploited to detect onset of flooding without the need to regress impedance spectra.
Long‐term outcomes of thalidomide in refractory Crohn's disease (2014)

Thalidomide appears to be safe and effective in some patients with refractory Crohn's disease. Although side effects may limit long-term use, thalidomide has potential to induce significant clinical responses.
Magneto (2017)

Software-defined networking (SDN) provides fine-grained network control and monitoring that simplifies network management. Unfortunately, upgrading existing enterprise networks, comprised of numerous "legacy" switches, to SDN is often cost-prohibitive. We argue that it is possible to achieve most of the benefits of a fully deployed SDN at a fraction of the cost by strategically replacing only few legacy switches with -- or introducing a few -- new SDN-capable switches in a legacy network, thus creating a hybrid network.
Ultra Wide-Band Inductive Peaking VCO with Cascode Noise Reduction (2018)

A ring-based inductive peaking VCO with a novel noise reduction technique is reported in this paper. An extra cascode transistor is used to bias the switching transistor into the deep triode region where the noise performance is better than that in the saturation region. A differential structure with a full custom symmetrical inductor demonstrates the benefits of the concept. The highest operational frequency reached was 39GHz with a tuning range of more than 4 octaves. The figure of merit (≈189) indicates that better overall combination of frequency and phase noise is obtained when compared with previous work.
INFLUENCE OF THE CONSTRUCTION PROCESSIN THE MULTILAYER LIGHTWEIGHT CONCRETE BEAM BEHAVIOUR (2019)

When a multilayer concrete beam is built, several concrete mixtures could be poured sequentially. Usually concrete used in external layers are higher resistance than those placed in internal layers. Time between the pouring of the different layers could have influence on the beam behaviour. The goal of this paper is to study how temporary offset on manufacturing the multilayer concrete beams has influence on their mechanical behaviour. Some has test have been run out to some beams which let us know the different behavior between each other. Finally it has been determinate if the construction process is the cause or other factors lead to produce the founded differences.
ChemInform Abstract: A BINUCLEAR NICKEL(II) ENCAPSULATING AGENT FOR CHLORIDE AND BROMIDE IONS (1980)

Abstract Die Verbindungen (I) wurden durch Zugabe des Liganden zu den Ni‐halogeniden in MeOH dargestellt und nach Zugabe von KPFÖ isoliert.
AN ASSESSMENT OF A METRIC SPACE DATABASE INDEX TO SUPPORT SEQUENCE HOMOLOGY (2005)

Hierarchical metric-space clustering methods have been commonly used to organize proteomes into taxonomies. Consequently, it is often anticipated that hierarchical clustering can be leveraged as a basis for scalable database index structures capable of managing the hyper-exponential growth of sequence data. M-tree is one such data structure specialized for the management of large data sets on disk. We explore the application of M-trees to the storage and retrieval of peptide sequence data. Exploiting a technique first suggested by Myers, we organize the database as records of fixed length substrings. Empirical results are promising. However, metric-space indexes are subject to "the curse of dimensionality" and the ultimate performance of an index is sensitive to the quality of the initial construction of the index. We introduce new hierarchical bulk-load algorithm that alternates between top-down and bottom-up clustering to initialize the index. Using the Yeast Proteomes, the bi-directional bulk load produces a more effective index than the existing M-tree initialization algorithms.
Monte Carlo solution of antiferromagnetic quantum Heisenberg spin systems (1984)

A Monte Carlo method is introduced that overcomes the problem of alternating signs in Handscomb's method of simulating antiferromagnetic quantum Heisenberg systems. The scheme is applied to both bipartite and frustrated lattices. Results of internal energy, specific heat, and uniform and staggered susceptibilities are presented suggesting that quantum antiferromagnets may now be studied as extensively as classical spin systems using conventional Monte Carlo techniques.
Topological Subspace-Induced Bound State in the Continuum (2017)

We propose and experimentally realize a new kind of bound states in the continuum (BICs) in a class of systems constructed by coupling multiple identical one-dimensional chains, each with inversion symmetry. In such systems, a specific separation of the Hilbert space into a topological and a nontopological subspace exists. Bulk-boundary correspondence in the topological subspace guarantees the existence of a localized interface state which can lie in the continuum of extended states in the nontopological subspace, forming a BIC. Such a topological BIC is observed experimentally in a system consisting of coupled acoustic resonators.
Expression and significance of caudal-related homeobox transcription factor 2 in placenta of patients with preeclampsia (2018)

Objective
To investigate the expression of caudal-related homeobox transcription factor 2 (CDX2) and its role in placenta of patients with preeclampsia (PE).


Methods
Thirty cases of PE women who delivered in our hospital from September 2015 to April 2016 were recruited. Thirty cases of the first trimester and 30 cases of full-term birth women at the same period were also recruited. Reverse transcription (RT)-PCR was used to detect the expression of CDX2 mRNA in placenta. Western blotting was used to detect the expression of CDX2 protein in placenta. Immunohistochemistry SP method was applied to detect the expression and the location of CDX2 in placenta.


Results
①RT-PCR showed that the CDX2 mRNA expression was significantly lower in PE (0.385±0.065) than that in the first trimester (1.880±0.235) and full-term birth (1.015±0.184) women groups. There was a significant difference (P<0.05). ②Western blotting showed that the CDX2 protein expression was significantly lower in the placenta of PE (0.276±0.029) than in the first trimester (0.658±0.059) and full-term birth women (0.478±0.136) (P<0.05). ③Immunohistochemical detection showed that the CDX2 protein was expressed in the placentas of full-term birth women and PE women of the first trimester. The expression of CDX2 in placenta mainly distributed in the cytoplasm of placental syncytiotrophoblasts. The expression of CDX2 was significantly decreased in PE group.


Conclusion
The down-regulation of CDX2 may be involved in the pathogenesis of PE, suggesting that it may be involved in trophoblast proliferation, invasion and placental formation.


Key words: 
Caudal-related homeobox transcription factor 2 (CDX2); Placenta; Trophoblast; Preeclampsia (PE)
The PI3-Kinase/mTOR-Targeting Drug NVP-BEZ235 Inhibits Growth and IgE-Dependent Activation of Human Mast Cells and Basophils (2012)

The phosphoinositide 3-kinase (PI3-kinase) and the mammalian target of rapamycin (mTOR) are two major signaling molecules involved in growth and activation of mast cells (MC) and basophils (BA). We examined the effects of the dual PI3-kinase/mTOR blocker NVP-BEZ235 on growth of normal and neoplastic BA and MC as well as immunoglobulin E (IgE)-dependent cell activation. Growth of MC and BA were determined by measuring (3)H-thymidine uptake and apoptosis. Cell activation was determined in histamine release experiments and by measuring upregulation of CD63 and CD203c after challenging with IgE plus anti-IgE or allergen. We found that NVP-BEZ235 exerts profound inhibitory effects on growth of primary and cloned neoplastic MC. In the MC leukemia cell line HMC-1, NVP-BEZ235 showed similar IC(50) values in the HMC-1.1 subclone lacking KIT D816V (0.025 µM) and the HMC-1.2 subclone expressing KIT D816V (0.005 µM). Moreover, NVP-BEZ235 was found to exert strong growth-inhibitory effects on neoplastic MC in a xenotransplant-mouse model employing NMR1-Foxn1(nu) mice. NVP-BEZ235 also exerted inhibitory effects on cytokine-dependent differentiation of normal BA and MC, but did not induce growth inhibition or apoptosis in mature MC or normal bone marrow cells. Finally, NVP-BEZ235 was found to inhibit IgE-dependent histamine release in BA and MC (IC(50) 0.5-1 µM) as well as anti-IgE-induced upregulation of CD203c in BA and IgE-dependent upregulation of CD63 in MC. In summary, NVP-BEZ235 produces growth-inhibitory effects in immature neoplastic MC and inhibits IgE-dependent activation of mature BA and MC. Whether these potentially beneficial drug effects have clinical implications is currently under investigation.
Genetic Causes, Clinical Manifestations and Diagnosis of Central Nervous System Malformations with Emphasis on Corpus Callosum (2022)

The pathological processes of the central nervous system, intrinsic or extrinsic, occurring during the embryonic period are the most common cause of pregnancy termination. The defects of the neural tube which is primitive form of brain and spinal cord are the most common central nervous system (CNS) malformations. In some defects the fetus continues to develop and results in the birth of a child with sever mental and physical deficiencies. The corpus callosum is the largest white matter tract connecting the two cerebral hemispheres and permits the transfer of information between the two cerebral hemispheres. Its partial or complete agenesis is caused by abnormalities during embryonic development. The severity of symptoms varies widely depending on the degree of dysgenesis. Hypotonia, visual impairment, seizures, spasticity, motor co-ordination issues, and atypical facial features are common symptoms. In this review we focus on genetic causes, clinical manifestations and diagnosis of various malformations of central nervous system with special emphasis on Corpus Callosum.
Learning stable pushing locations (2013)

We present a method by which a robot learns to predict effective push-locations as a function of object shape. The robot performs push experiments at many contact locations on multiple objects and records local and global shape features at each point of contact. The robot observes the outcome trajectories of the manipulations and computes a novel push-stability score for each trial. The robot then learns a regression function in order to predict push effectiveness as a function of object shape. This mapping allows the robot to select effective push locations for subsequent objects whether they are previously manipulated instances, new instances from previously encountered object classes, or entirely novel objects. In the totally novel object case, the local shape property coupled with the overall distribution of the object allows for the discovery of effective push locations. These results are demonstrated on a mobile manipulator robot pushing a variety of household objects on a tabletop surface.
Viral Decay Kinetics in the Highly Active Antiretroviral Therapy-Treated Rhesus Macaque Model of AIDS (2010)

To prevent progression to AIDS, persons infected with human immunodeficiency virus type 1 (HIV-1) must remain on highly active antiretroviral therapy (HAART) indefinitely since this modality does not eradicate the virus. The mechanisms involved in viral persistence during HAART are poorly understood, but an animal model of HAART could help elucidate these mechanisms and enable studies of HIV-1 eradication strategies. Due to the specificity of non-nucleoside reverse transcriptase (RT) inhibitors (NNRTIs) for HIV-1, we have used RT-SHIV, a chimeric virus of simian immunodeficiency virus with RT from HIV-1. This virus is susceptible to NNRTIs and causes an AIDS-like disease in rhesus macaques. In this study, two groups of HAART-treated, RT-SHIV-infected macaques were analyzed to determine viral decay kinetics. In the first group, viral loads were monitored with a standard TaqMan RT-PCR assay with a limit of detection of 50 viral RNA copies per mL. Upon initiation of HAART, viremia decayed in a bi-phasic manner with half-lives of 1.7 and 8.5 days, respectively. A third phase was observed with little further decay. In the second group, the macaques were followed longitudinally with a more sensitive assay utilizing ultracentrifugation to concentrate virus from plasma. Bi-phasic decay of viral RNA was also observed in these animals with half-lives of 1.8 and 5.8 days. Viral loads in these animals during a third phase ranged from 2-58 RNA copies/mL, with little decay over time. The viral decay kinetics observed in these macaques are similar to those reported for HIV-1 infected humans. These results demonstrate that low-level viremia persists in RT-SHIV-infected macaques despite a HAART regimen commonly used in humans.
PET Imaging of Tumor Uptake of a Biocompatible C60 Fullerene Drug Delivery Vector (2018)

Traditional chemotherapy is one of the standards in cancer treatment, but the delivery of drugs and biologics is hindered by various barriers throughout the cancer microenvironment. Recently, nanoparticles have been of great interest as drug vectors because they can be tailored for specific functions to increase the amount of administered drug in the tumor microenvironment. In particular, biocompatible C 60 fullerene has potential as a drug delivery scaffold since it has been shown to penetrate very restrictive physiological membranes (e.g. blood-brain-barrier and nuclear membrane) 1 . Our long-term goal is to determine the biodistribution of a biocompatible C 60 material, as well as other pharmacokinetic data in both small and large animal models in order to evaluate its potential as a clinical drug vector for anti-cancer drugs. In this work, we have synthesized a C 60 derivative with a metal chelating agent covalently bound to the C 60 cage. The chelating agent of this material can be easily radiolabeled with 64 Cu 2+ (β + emitter; t 1/2 = 12 h) and tracked in vivo using positron emission tomography (PET) imaging. Because of its extreme sensitivity and routine clinical use, PET is an ideal imaging technique for studying pharmacokinetic properties and tumor accumulation of a C 60 fullerene delivery vector, for both preclinical and possible future clinical studies. The material has been synthesized following an optimized six-step synthesis and the stability of the 64 Cu 2+ ion in the chelate has been evaluated by challenge with biological media. Animal biodistribution data will be determined using PET imaging in tumor- and non-tumor-bearing murine models. Acknowledgements: We gratefully acknowledge The Welch Foundation (C-0627) for support of this work, as well as the Department of Chemistry and the Smalley-Curl Institute at Rice University and the Department of Cancer Systems Imaging at UT MD Anderson Cancer Center. Additionally, the work is supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. 1450681 (N.G.Z.). References: (1) Raoof, M.; Mackeyev, Y.; Cheney, M. A.; Wilson, L. J.; Curley, S. A. Biomaterials 2012 , 33 (10), 2952–2960.
Evaluation of laboratory parameters in 1587 COVID-19 patients admitted to metropolitan hospital area of Bologna, Italy. (2023)

Since the outbreak of the 2019 pandemic coronavirus disease (COVID-19), great attention has been given to identifying the main clinical features of the disease. Identification of laboratory parameters able to classify patients based on their risk is mandatory to improve their clinical management. We retrospectively evaluated twenty-six laboratory tests measured in COVID-19 positive patients admitted to the hospital in March and April 2020 to find any correlation between their changes and the risk of death. We divided them into surviving and non-surviving patients. A total of 1587 patients were recruited, 854 males with median age of 71 (IQR 56-81) and 733 females with median age of 77 (IQR 61-87). On admission, death was found to be positively correlated with age (p=0.001), but not with sex (p=0.640) or with hospitalization in days (p=0.827). Brain natriuretic peptide (BNP), creatinine, C-reactive protein (CRP), INR, leukocyte count, lymphocyte count, neutrophil count, and procalcitonin (PCT) demonstrated a statistically significant difference between the two groups (p<0.001), suggesting their role as markers of disease severity; only lymphocyte count resulted as an independent risk factor for death.
Phenotypical ontology driven framework for multi-task learning (2021)

Despite the large number of patients in Electronic Health Records (EHRs), the subset of usable data for modeling outcomes of specific phenotypes are often imbalanced and of modest size. This can be attributed to the uneven coverage of medical concepts in EHRs. We propose OMTL, an Ontology-driven Multi-Task Learning framework, that is designed to overcome such data limitations.The key contribution of our work is the effective use of knowledge from a predefined well-established medical relationship graph (ontology) to construct a novel deep learning network architecture that mirrors this ontology. This enables common representations to be shared across related phenotypes, and was found to improve the learning performance. The proposed OMTL naturally allows for multi-task learning of different phenotypes on distinct predictive tasks. These phenotypes are tied together by their semantic relationship according to the external medical ontology. Using the publicly available MIMIC-III database, we evaluate OMTL and demonstrate its efficacy on several real patient outcome predictions over state-of-the-art multi-task learning schemes. The results of evaluating the proposed approach on six experiments show improvement in the area under ROC curve by 9% and by 8% in the area under precision-recall curve.