gebhart/patrepeval huggingface dataset:
Improved well-log classification using semisupervised label propagation and self-training, with comparisons to popular supervised algorithms (2019)

Machine-learning techniques allow geoscientists to extract meaningful information from data in an automated fashion, and they are also an efficient alternative to traditional manual interpretation methods. Many geophysical problems have an abundance of unlabeled data and a paucity of labeled data, and the lithology classification of wireline data reflects this situation. Training supervised algorithms on small labeled data sets can lead to overtraining, and subsequent predictions for the numerous unlabeled data may be unstable. However, semisupervised algorithms are designed for classification problems with limited amounts of labeled data, and they are theoretically able to achieve better accuracies than supervised algorithms in these situations. We explore this hypothesis by applying two semisupervised techniques, label propagation (LP) and self-training, to a well-log data set and compare their performance to three popular supervised algorithms. LP is an established method, but our self-training method is a unique adaptation of existing implementations. The well-log data were made public through an SEG competition held in 2016. We simulate a semisupervised scenario with these data by assuming that only one of the 10 wells has labels (i.e., core samples), and our objective is to predict the labels for the remaining nine wells. We generate results from these data in two stages. The first stage is applying all the algorithms in question to the data as is (i.e., the global data), and the results from this motivate the second stage, which is applying all algorithms to the data when they are decomposed into two separate data sets. Overall, our findings suggest that LP does not outperform the supervised methods, but our self-training method coupled with LP can outperform the supervised methods by a notable margin if the assumptions of LP are met.
HEPATOPROTECTION BY A PGI2 ANALOGUE IN COMPLETE WARM ISCHEMIA OF THE PIG LIVER (1994)

We examined the hepatoprotective effect of a prostaglandin (PG)I2 analogue by analyzing the endogenous release of prostanoid from the pig liver. Fourteen female pigs underwent 1 hr complete hepatic vascular exclusion (HVE); the portal and vena caval circulation was actively decompressed. The animals were divided into one of two groups (n = 7, each) according to pretreatment with the prostacyclin analogue (OP 2507, OP) administered via a mesenteric vein branch for 30 min at a rate of 2 micrograms/kg/min immediately prior to HVE. The plasma levels of prostaglandin E2 (PGE2), 6-keto-prostaglandin F1-alpha (6-keto-PGF1 alpha), and thromboxane B2 (TXB2), from the blood samples from the aorta, the hepatic vein, and the portal vein were serially compared for 60 min after the restoration of blood flow. Other parameters included 7-day survival rate, serum biochemistry, and endotoxin assay. A significant improvement in 7-day survival rate (6/7 vs. 1/7 for the control, P < 0.02) was observed in the OP-treated animals, associated with amelioration of serum transaminase activities but with no differences in plasma endotoxin levels. The reperfused liver progressively and substantially released PGE2 but did not generate other prostanoids (TXB2 and 6-keto-PGF1 alpha). OP pretherapy substantially suppressed hepatic generation of the PGE2 postreflow, correlating with serum transaminase levels (rs = 0.80; P < 0.01, at 60 min). We conclude that the PGI2 analogue ameliorates hepatic ischemia/reperfusion injury by down-regulating PGE2 production from the reperfused liver.
Does Granular Activated Carbon with Chlorination Produce Safer Drinking Water? From Disinfection Byproducts and Total Organic Halogen to Calculated Toxicity (2019)

Granular activated carbon (GAC) adsorption is well-established for controlling regulated disinfection byproducts (DBPs), but its effectiveness for unregulated DBPs and DBP-associated toxicity is unclear. In this study, GAC treatment was evaluated at three full-scale chlorination drinking water treatment plants over different GAC service lives for controlling 61 unregulated DBPs, 9 regulated DBPs, and speciated total organic halogen (total organic chlorine, bromine, and iodine). The plants represented a range of impacts, including algal, agricultural, and industrial wastewater. This study represents the most extensive full-scale study of its kind and seeks to address the question of whether GAC can make drinking water safer from a DBP perspective. Overall, GAC was effective for removing DBP precursors and reducing DBP formation and total organic halogen, even after >22 000 bed volumes of treated water. GAC also effectively removed preformed DBPs at plants using prechlorination, including highly toxic iodoacetic acids and haloacetonitriles. However, 7 DBPs (mostly brominated and nitrogenous) increased in formation after GAC treatment. In one plant, an increase in tribromonitromethane had significant impacts on calculated cytotoxicity, which only had 7-17% reduction following GAC. While these DBPs are highly toxic, the total calculated cytotoxicity and genotoxicity for the GAC treated waters for the other two plants was reduced 32-83% (across young-middle-old GAC). Overall, calculated toxicity was reduced post-GAC, with preoxidation allowing further reductions.
To Compose: Teaching Writing in High School and College (1989)

The essays in this volume study the writing process and show ways in which a classroom can be set up to treat students as writers. The central issues are: how writers find topics, how teachers respond to writing, how writing and literature can be combined, and how writing can be used (and learned) in all subjects.
Proximity RNA labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules (2018)

Abstract Diverse ribonucleoprotein complexes control messenger RNA processing, translation, and decay. Transcripts in these complexes localize to specific regions of the cell and can condense into non-membrane-bound structures such as stress granules. It has proven challenging to map the RNA composition of these large and dynamic structures, however. We therefore developed an RNA proximity labeling technique, APEX-Seq, which uses the ascorbate peroxidase APEX2 to probe the spatial organization of the transcriptome. We show that APEX-Seq can resolve the localization of RNAs within the cell and determine their enrichment or depletion near key RNA-binding proteins. Matching the spatial transcriptome, as revealed by APEX-Seq, with the spatial proteome determined by APEX-mass spectrometry (APEX-MS) provides new insights into the organization of translation initiation complexes on active mRNAs, as well as exposing unanticipated complexity in stress granule composition, and provides a powerful and general approach to explore the spatial environment of macromolecules.
MTG FCI visible detector detection chain description and preliminary results (2017)

The next generation of geostationary meteorological satellites is being developed in the frame of Meteosat Third Generation (MTG) ESA program The novel Flexible Combined Imager (FCI) instrument exhibit in particular a detection block including 17 channels from the visible to the far infrared working in snapshot mode at high frame rate (~2.65kHz) with a ground resolution between 0.5 -2km. The full description of FCI optical design and performance features can be found in paper referenced A functional diagram is presented in Fig 1 . The optical signal is spectrally separated in two at the telescope output to be driven to a warm assembly maintained at ambient temperature for the five visible channels, and to another assembly cooled down at 60K for the three NIR and nine infrared ones. The infrared block composed of 4 detectors assemblies based on HgCdTe material hybridized on CMOS ROIC circuit while the visible block contained a CMOS image sensor working at high pixel frequency (~4MHz). Each detector assemblies exhibits one unique analogue output. The video signals are sent to Video Control Units (VCU) to be buffered and digitalized.
Further Evidence of the Clinical, Hormonal, and Genetic Heterogeneity of Klinefelter Syndrome: A Study of 216 Infertile Egyptian Patients (2012)

This study aims to provide further insight into the phenotypic heterogeneity of Klinefelter syndrome (KS) by presenting clinical, hormonal, and genetic data from a large series of Egyptian infertile patients with KS. A retrospective case series of KS patients was studied over a period from January 2003 to April 2010. All patients underwent a complete history and physical examination; color duplex examination; semen analysis; measurement of total testosterone (T), follicle-stimulating hormone (FSH), luteinizing hormone (LH), estradiol (E2), and prolactin (PRL); and chromosomal typing. Mosaic KS diagnosis was confirmed by fluorescence in situ hybridization. The series included 216 KS patients (198 nonmosaic, 16 mosaic, and 2 KS variants). Typical clinical signs of hypoandrogenism were observed in 86% of patients. Gynecomastia affected 20.8% of the patients. Eunuchoidal body proportions, with arm span exceeding height and lower segment length exceeding upper segment length, were detected in 43.9% and 64.4% of the patients, respectively. In all patients, a reduction in testicular size and azoospermia were detected. Normal levels of T, FSH, LH, E2, and PRL were detected in 44.5%, 3.7%, 3.3%, 93.5%, and 91.2% of patients, respectively. Differences were not significant between patients with classic KS and those with mosaic KS in terms of the frequency of clinical signs of hypoandrogenism, gynecomastia, low T concentrations, or high concentrations of FSH, LH, E2, and PRL (all P > .05). The results of the current study emphasize the heterogeneous clinical, hormonal, and genetic phenotype of infertile KS patients. Our findings support the usefulness of cytogenetic studies in infertile patients showing small testicular size and azoospermia, regardless of the presence of other clinical or endocrine findings.
G. Clemente † , W. Barth, L. Groening, S. Mickat, B. Schlitt, W. Vinzenz, GSI, Darmstadt, Germany (2012)

H-mode cavities offer outstanding shunt impedances at low beam energies and enable the acceleration of intense protons and ion beams. Crossed-bar H-cavities extend these properties to energies even beyond 100 MeV. Thus, the designs of the new injector linacs for FAIR, i.e. a 70 MeV, 70 mA proton driver for pbar-production and a cw intermediate mass, superconducting ion linac are based on these novel cavities. Several prototypes (normal and super- conducting) have been built and successfully tested. More- over, designs for a replacement of the 90 MV Alvarez sec- tion of the GSI - Unilac will be discussed to improve the capabilities as the future FAIR heavy ion injector.
Association with the Cellular Export Receptor CRM 1 Mediates Function and Intracellular Localization of Epstein-Barr Virus SM Protein, a Regulator of Gene Expression (1999)

Splicing and posttranscriptional processing of eukaryotic gene transcripts are linked to their nuclear export and cytoplasmic expression. Unspliced pre-mRNAs and intronless transcripts are thus inherently poorly expressed. Nevertheless, human and animal viruses encode essential genes as single open reading frames or in the intervening sequences of other genes. Many retroviruses have evolved mechanisms to facilitate nuclear export of their unspliced mRNAs. For example, the human immunodeficiency virus RNA-binding protein Rev associates with the soluble cellular export receptor CRM 1 (exportin 1), which mediates nucleocytoplasmic translocation of Rev-HIV RNA complexes through the nuclear pore. The transforming human herpesvirus Epstein-Barr virus (EBV) expresses a nuclear protein, SM, early in its lytic cycle; SM binds RNA and posttranscriptionally activates expression of certain intronless lytic EBV genes. Here we show that both the trans-activation function and cytoplasmic translocation of SM are dependent on association with CRM 1 in vivo. SM is also shown to be associated in vivo with other components of the CRM 1 export pathway, including the small GTPase Ran and the nucleoporin CAN/Nup214. SM is shown to be present in the cytoplasm, nucleoplasm, and nuclear envelope of transfected cells. Mutation of a leucine-rich region (LRR) of SM inhibited CRM 1-mediated cytoplasmic translocation and SM activity, as did leptomycin B, an inhibitor of CRM 1 complex formation. Surprisingly, however, leptomycin B treatment and mutation of the LRR both led to SM becoming more tightly attached to intranuclear structures. These findings suggest a model in which SM is not merely a soluble carrier protein for RNA but rather is bound directly to intranuclear proteins, possibly including the nuclear pore complex.
Allergenicity Risks Associated with Novel Proteins and Rapid Methods of Detection (2021)

Novel protein sources require a comprehensive risk assessment as directed in EC regulation no. 258/97. Potential allergenic response from the ingestion or contact with novel proteins is a significant public health concern. Therefore, risk assessment of novel proteins is key to creating awareness and to reducing the risk of allergic reactions. The development of quick and effective allergen detection methods is essential for novel protein manufacturing to ensure accurate labelling and hazards or cross-interaction of these proteins. Techniques currently available for identifying novel protein risks are based on the detection of either protein(s) or their nucleic acids. Those techniques that are based on protein detection include immunoassays, spectroscopic and chromatographic analyses. In this chapter, several sources and the risks involved with the different alternative and novel proteins are discussed. Common and fast techniques for allergen detection are discussed with the focus on their advantages and limitations.
W12c_spewave “Source Physics Experiment modeling” [Posters] (2013)

Abstract not provided.
Abstract O-03: DIURNAL PATTERN OF MELATONIN SECRETION IS HETEROGENEOUSLY MAINTAINED IN CRITICALLY ILL CHILDREN (2018)

Aims & Objectives: Melatonin secretion patterns in critically ill children are poorly understood. This study examined whether diurnal variation of melatonin secretion was maintained during the early phase of PICU admission. Methods Prospective, observational study of children (3 months to 18 years) within 24 hours of PICU admission with access for urinary sampling and PRISM III of ≥1. Urine samples collected at 4-hour intervals for 24 hours, stored at -80oC, and 6-sulfatoxymelatonin (aMT6s) was determined in duplicate by direct ELISA. Results Fifty patients, heterogeneous for diagnosis, median age of 97.2 (IQR = 73.2) months, and median PRISM III of 10 (IQR=8). Mean (SD) total daily aMT6s production was higher than literature normal values (p<0.01) in the age <3 year group (13.6[10.2]mcg, n=14) and similar (p=0.86) for the 3–18 years group (37.7[27.5], n=30). Mean aMT6s production fit a periodic function, with amplitude 326ng/hour, peak excretion 1568ng/hour from 04:00 to 08:00, and nadir from 16:00 to 20:00 (F=4.43, p=0.01). Patients with respiratory failure requiring intubation and deep sedation (n=8) demonstrated a non-reliable amplitude of 117ng/hour (p=0.36), and model fit for a periodic function was poor (F=0.44, p=0.67), Figure 1. Similar results were demonstrated for patients with neurologic injury (n=6; amplitude 586ng/hour, p=0.22; F=0.74, p=0.49; Figure 2), and with sepsis (n=14; amplitude 147ng/hour, p=0.41; F=0.33, p=0.72; Figure 3)Conclusions Diurnal variation of aMT6s production and excretion is heterogeneously maintained early in pediatric critical illness, though this may not hold true for specific diagnostic categories.
Transparent encryption for HEVC using bit-stream-based selective coefficient sign encryption (2014)

We propose a selective encryption scheme for HEVC which allows for transparent encryption in a wide range of quantization parameters. Our approach focusses on the AC coefficient signs, since they can be altered directly in the bit stream without entropy reencoding. This allows for fast encryption and decryption while retaining full format-compliance and length-preservation. Furthermore, we show our approach's applicability for a number of use cases by evaluating the quality degradation and robustness against attacks.
Guidelines for Mass Screening of Congenital Hypothyroidism (2014 revision) (2015)

Purpose of developing the guidelines: Mass screening for congenital hypothyroidism started in 1979 in Japan, and the prognosis for intelligence has been improved by early diagnosis and treatment. The incidence was about 1/4000 of the birth population, but it has increased due to diagnosis of subclinical congenital hypothyroidism. The disease requires continuous treatment, and specialized medical facilities should make a differential diagnosis and treat subjects who are positive in mass screening to avoid unnecessary treatment. The Guidelines for Mass Screening of Congenital Hypothyroidism (1998 version) were developed by the Mass Screening Committee of the Japanese Society for Pediatric Endocrinology in 1998. Subsequently, new findings on prognosis and problems in the adult phase have emerged. Based on these new findings, the 1998 guidelines were revised in the current document (hereinafter referred to as the Guidelines). Target disease/conditions: Primary congenital hypothyroidism. Users of the Guidelines: Physician specialists in pediatric endocrinology, pediatric specialists, physicians referring patients to pediatric practitioners, general physicians, laboratory technicians in charge of mass screening, and patients.
Cathepsin E generates a sumoylated intracellular fragment of the cell adhesion molecule L1 to promote neuronal and Schwann cell migration as well as myelination (2013)

The cell adhesion molecule L1 regulates cellular responses in the developing and adult nervous system. Here, we show that stimulation of cultured mouse cerebellar neurons by a function-triggering L1 antibody leads to cathepsin E-mediated generation of a sumoylated 30 kDa L1 fragment (L1-30) and to import of L1-30 into the nucleus. Mutation of the sumoylation site at K1172 or the cathepsin E cleavage site at E1167 abolishes generation of L1-30, while mutation of the nuclear localization signal at K1147 prevents nuclear import of L1-30. Moreover, the aspartyl protease inhibitor pepstatin impairs the generation of L1-30 and inhibits L1-induced migration of cerebellar neurons and Schwann cells as well as L1-dependent in vitro myelination on axons of dorsal root ganglion neurons by Schwann cells. L1-stimulated migration of HEK293 cells expressing L1 with mutated cathepsin E cleavage site is diminished in comparison to migration of cells expressing non-mutated L1. In addition, L1-stimulated migration of HEK293 cells expressing non-mutated L1 is also abolished upon knock-down of cathepsin E expression and enhanced by over-expression of cathepsin E. The findings of the present study indicate that generation and nuclear import of L1-30 regulate neuronal and Schwann cell migration as well as myelination. Cell adhesion molecule L1 regulates cellular responses in the developing and adult nervous system. L1 stimulation triggers sumoylation and cleavage of L1, thus generating the L1-70 fragment (1) which is cleaved by cathepsin E (2) yielding the L1-30 fragment that is imported to the nucleus (3), may bind to DNA and/or nuclear proteins (4), to regulate diverse cellular functions.
A Unified Approach to the Modeling and Control of Multi-Scale Dynamical Systems (2012)

In this paper, a unified methodology for modeling and control of complex multi-scale mechanical systems is presented. The method utilizes recent results in analytical dynamics adapted to general complex multibody systems. The term multi-scale is employed to denote those mechanical systems whose equations of motion are highly nonlinear, non-autonomous, and can yield motions at multiple time and distance scales. These types of problems can easily become difficult to model and control and the complexity of the equations of motion grows rapidly as the number of component bodies in the system increases. The approach considered herein opens up new routes for modeling and control of general multibody systems by explicitly developing closed form expressions in terms of any desirable number of generalized coordinates that may appropriately describe the configuration of the multi-scale system. The approach is simple in implementation and it poses no restrictions on the total number and nature of modeling constraints to construct the explicit equations of motion of the system. Likewise, no restrictions are placed on the nature and number of the feasible tracking control requirements to obtain explicit expressions for the requisite generalized control forces. Conceptually, the method relies on a simple six-step procedure. It utilizes in a pivotal manner the the explicit equations of motion for constrained mechanical systems with singular mass matrices. The simplicity of the unified method is highlighted by illustrating its use in the modeling and control of a dumbbell made of two unequal masses which is required to be controlled so that one of the masses follows a prescribed time-varying trajectory.
Optimal Solution of Dynamic Matrix Control with Linear Programing Techniques (LDMC) (1985)

LDMC is an optimal multivariable control algorithm which combines linear programming method of optimization with the Dynamic Matrix Control. The LP formulation of DMC allows for the optimum calculation of the future moves in L1 sense. In this work 9 claims are reported with respect to this approach. It will be shown how to formulate the claims made into a LP frame work. Some examples are then presented to show the application of LDMC to any complex linear dynamic system.