gebhart/patrepeval huggingface dataset:
A critical analysis of the biological impacts of plasticizers on wildlife (2009)

This review provides a critical analysis of the biological effects of the most widely used plasticizers, including dibutyl phthalate, diethylhexyl phthalate, dimethyl phthalate, butyl benzyl phthalate and bisphenol A (BPA), on wildlife, with a focus on annelids (both aquatic and terrestrial), molluscs, crustaceans, insects, fish and amphibians. Moreover, the paper provides novel data on the biological effects of some of these plasticizers in invertebrates, fish and amphibians. Phthalates and BPA have been shown to affect reproduction in all studied animal groups, to impair development in crustaceans and amphibians and to induce genetic aberrations. Molluscs, crustaceans and amphibians appear to be especially sensitive to these compounds, and biological effects are observed at environmentally relevant exposures in the low ng l(-1) to microg l(-1) range. In contrast, most effects in fish (except for disturbance in spermatogenesis) occur at higher concentrations. Most plasticizers appear to act by interfering with the functioning of various hormone systems, but some phthalates have wider pathways of disruption. Effect concentrations of plasticizers in laboratory experiments coincide with measured environmental concentrations, and thus there is a very real potential for effects of these chemicals on some wildlife populations. The most striking gaps in our current knowledge on the impacts of plasticizers on wildlife are the lack of data for long-term exposures to environmentally relevant concentrations and their ecotoxicity when part of complex mixtures. Furthermore, the hazard of plasticizers has been investigated in annelids, molluscs and arthropods only, and given the sensitivity of some invertebrates, effects assessments are warranted in other invertebrate phyla.
EVELIO SKIN EXPLANTS UNOER NEURO-INFLAMMATORY STRESS: SYNERGISTIC PROTECTION BY ESCINE ANO OEXTRAN SULFATE (2007)

Summary Human eyelid skin explants can be maintained in an appropriate culture medium in vitro far severa! days while retaining most of the histological features of normai skin. It thus represents a valu able tool to investigate the potentiall y damaging effects of biological, chemical or even physical stress that might alter their integrity. lt is also a useful model to stud y the ability of various ingredients a nd products to prevent such damages and/or im prove the morphological integrity of the skin. We obser­ ved here that a multi-stress inducing preparation including Substance P, Arachidoni c Acid a nd Tu­ rnar Necrosis Factor could alter eyeli d skin morphology. Dilation of superficial plexus microvascu­ lature of the epidermis and an increase in water retenti o n between coll agen bundles of the extracel­ lular matrix were the most reproducible histological alterations observed. We furthermore evide nced that topica! appli cation of esci ne a nd dextran sulfate synergistically protected eyelid ski n explants in culture against the neuro-inflammatory stress preparati on when appli ed prior to ne uro- inflammatory stress conditions, It is thus predictable that not only these two ingredients wi ll be well tolerated in vivo but also that they may, to some extent, protect eye skin outline against the major en vironmental extem al insults encountered day to day.
Utilising the effect of reaction concentration to tune the physical properties of hyperbranched polymers synthesised using transfer-dominated branching radical telomerisation (TBRT) (2023)

TBRT allows the control of cyclisation within branched polymer architectures by simply changing dilution. Increased cyclisation leads to changes in physical properties, therefore, tunig of behaviour is available without changing starting materials.
Characterization of variant subclasses of cell lines derived from small cell lung cancer having distinctive biochemical, morphological, and growth properties. (1985)

We have described the establishment and biochemical characterization of 50 small cell lung carcinoma (SCLC) cell lines. Further analysis of these data, combined with studies of morphology and growth characteristics, indicates that 35 (70%) of the lines retained typical morphology (SCLC, intermediate subtype), growth characteristics (growth as tightly packed floating cellular aggregates, long doubling times and low colony-forming efficiencies), and biochemical profile (presence of L-dopa decarboxylase, bombesin-like immunoreactivity, neuron-specific enolase, and high concentrations of brain isoenzyme of creatine kinase). They are referred to as classic SCLC lines. The remaining 15 (30%) lines had discordant expression of the biochemical markers; they retained high concentrations of brain isozyme of creatine kinase, but had significantly lower concentrations of neuron-specific enolase and lacked L-dopa decarboxylase and bombesin-like immunoreactivity. These cell lines are called variants. SCLC variant lines could further be divided into (a) biochemical variant lines having variant biochemical profile but retaining typical SCLC morphology and growth characteristics; and (b) morphological variant (SCLC-MV) lines having variant biochemical profile, altered morphology (features of large cell undifferentiated carcinoma) and altered growth characteristics (growth as loosely attached floating aggregates, relatively short doubling times and cloning efficiencies). Fifty-five clones derived from the three SCLC subclasses retained their parental phenotypes. In SCLC-MV lines there was a near constant relationship between variant morphology, altered growth characteristics and amplification of the c-myc oncogene; classic SCLC and biochemical variant SCLC lines were not amplified. Variant morphologies frequently are present in SCLC tumors at autopsy, and most SCLC-MV lines reflect changes that had occurred in the tumors from which they were derived. Because SCLC-MV tumors behave more virulently in the patient and are radioresistant in vitro, these findings are of considerable biological and clinical interest.
Stereoselectivity in organometallic catalysis : analysis by means of computational and mathematical chemistry (2009)

Understanding stereoselective binding of chiral organometallic complexes is essential to control the production of a desired stereoisomer. Computational methods are useful predictors of stereoisomers if all conformations that can participate in a reaction are identified. This thesis introduces new strategies for producing and analyzing conformational search data or organometallic complexes, specifically the chirally pure, coordinatively unsaturated [(?5-C5R5)Re(NO)(L)]+ fragment (R=H and Me, L=PPh3 and PMe3), and chiral disophine Rhodium(I) catalyst precursors. A new program, cClus-A, is also introduced to examine conformational clusters of the Rhenium system and for the Rhodium catalyst precursors. cClus-A was tested rigorously on systems containing 2 torsion angles (Rhenium system), and systems that contain 4 torsion angles (Rhodium complexes). Results of the cClus-A show that in both systems more than one conformation exists near the global minimum that can participate in a stereoselective reaction. When compared with literature values of calculated diastereoselectivity, the new techniques put forth in this thesis show exceptional agreement.
From Words to Code: Harnessing Data for Program Synthesis from Natural Language (2023)

Creating programs to correctly manipulate data is a difficult task, as the underlying programming languages and APIs can be challenging to learn for many users who are not skilled programmers. Large language models (LLMs) demonstrate remarkable potential for generating code from natural language, but in the data manipulation domain, apart from the natural language (NL) description of the intended task, we also have the dataset on which the task is to be performed, or the "data context". Existing approaches have utilized data context in a limited way by simply adding relevant information from the input data into the prompts sent to the LLM. In this work, we utilize the available input data to execute the candidate programs generated by the LLMs and gather their outputs. We introduce semantic reranking, a technique to rerank the programs generated by LLMs based on three signals coming the program outputs: (a) semantic filtering and well-formedness based score tuning: do programs even generate well-formed outputs, (b) semantic interleaving: how do the outputs from different candidates compare to each other, and (c) output-based score tuning: how do the outputs compare to outputs predicted for the same task. We provide theoretical justification for semantic interleaving. We also introduce temperature mixing, where we combine samples generated by LLMs using both high and low temperatures. We extensively evaluate our approach in three domains, namely databases (SQL), data science (Pandas) and business intelligence (Excel's Power Query M) on a variety of new and existing benchmarks. We observe substantial gains across domains, with improvements of up to 45% in top-1 accuracy and 34% in top-3 accuracy.
Measuring Annotator Agreement Generally across Complex Structured, Multi-object, and Free-text Annotation Tasks (2022)

When annotators label data, a key metric for quality assurance is inter-annotator agreement (IAA): the extent to which annotators agree on their labels. Though many IAA measures exist for simple categorical and ordinal labeling tasks, relatively little work has considered more complex labeling tasks, such as structured, multi-object, and free-text annotations. Krippendorff’s α, best known for use with simpler labeling tasks, does have a distance-based formulation with broader applicability, but little work has studied its efficacy and consistency across complex annotation tasks.
Acute kidney injury in a preterm infant homozygous for the C3435T polymorphism in the ABCB1 gene given oral morphine (2012)

A 34-week infant born from a mother with a history of drug abuse developed neonatal abstinence syndrome (NAS) in the first hours of life. Urine drug screening was positive for cocaine and heroin. The infant developed acute kidney injury and bilateral hydronephrosis while receiving oral morphine for control of NAS. Cessation of morphine therapy and urinary catheterization resulted in a rapid and complete resolution of the symptoms. Our patient was homozygous for the C3435T polymorphism in the ABCB1 gene, a polymorphism previously associated with impaired P-glycoprotein activity. We hypothesize that acute renal toxicity was related to accumulation of morphine within urothelial cells due to genetically determined impaired P-glycoprotein activity.
Unimolecular thermal decomposition of dimethoxybenzenes (2014)

The unimolecular thermal decomposition mechanisms of o-, m-, and p-dimethoxybenzene (CH3O-C6H4-OCH3) have been studied using a high temperature, microtubular (μtubular) SiC reactor with a residence time of 100 μs. Product detection was carried out using single photon ionization (SPI, 10.487 eV) and resonance enhanced multiphoton ionization (REMPI) time-of-flight mass spectrometry and matrix infrared absorption spectroscopy from 400 K to 1600 K. The initial pyrolytic step for each isomer is methoxy bond homolysis to eliminate methyl radical. Subsequent thermolysis is unique for each isomer. In the case of o-CH3O-C6H4-OCH3, intramolecular H-transfer dominates leading to the formation of o-hydroxybenzaldehyde (o-HO-C6H4-CHO) and phenol (C6H5OH). Para-CH3O-C6H4-OCH3 immediately breaks the second methoxy bond to form p-benzoquinone, which decomposes further to cyclopentadienone (C5H4=O). Finally, the m-CH3O-C6H4-OCH3 isomer will predominantly follow a ring-reduction/CO-elimination mechanism to form C5H4=O. Electronic structure calculations and transition state theory are used to confirm mechanisms and comment on kinetics. Implications for lignin pyrolysis are discussed.
Azo-dye photo-aligning for liquid crystal devices (2006)

Liquid crystal (LC) photo-alignment using azo-dyes is reviewed. It will be shown that this photo-aligning method can provide a controllable pretilt angle and strong anchoring energy of the liquid crystal cell, as well as high thermal and UV stability. The application of this method to the alignment and fabrication of various types of liquid crystal devices for display and photonics applications is also discussed.
The Basophil-Specific Ectoenzyme E-NPP3 (CD203c) as a Marker for Cell Activation and Allergy Diagnosis (2004)

Basophils are effector cells of allergic reactions. These cells produce and store a number of vasoactive and immunomodulatory mediators. During an allergic reaction, basophils can release their mediator substances into the extracellular space and thus contribute to the clinical picture and symptoms in allergy. The phenotypic hallmark of basophils is expression of high-affinity IgE receptors (Fc epsilon RI) on their cell surface together with expression of the activation-linked molecule CD203c. This ectoenzyme is located both on the plasma membrane and in the cytoplasmic compartment of basophils. Cross-linking of the Fc epsilon RI by an allergen or anti-IgE antibody results in a rapid upregulation of intracellular CD203c molecules to the cell surface and is accompanied by mediator release. CD203c is therefore a promising target molecule for a flow cytometry-based test to analyze sensitized individuals and patients with type I allergy. In the present article, we review the current knowledge of CD203c with special regard to its tissue distribution and regulation in basophil activation. In addition, we discuss the application of CD203c in allergy diagnosis.
Pulmonary-Allergy, Dermatological, Gastrointestinal and Arthritis: Cyclooxygenase-2: a novel target for therapeutic intervention (1994)

(1994). Pulmonary-Allergy, Dermatological, Gastrointestinal and Arthritis: Cyclooxygenase-2: a novel target for therapeutic intervention. Expert Opinion on Investigational Drugs: Vol. 3, No. 12, pp. 1323-1325.
Genetically inspired prognostic scoring system (GIPSS) outperforms dynamic international prognostic scoring system (DIPSS) in myelofibrosis patients (2018)

A genetically inspired prognostic scoring system (GIPSS) that stratifies primary myelofibrosis (PMF) patients by genetic variants alone was recently proposed. While non-inferior to the dynamic international prognostic scoring system (DIPSS), the lack of overlapping prognostic variables between the models leads to increased risk for disagreement between two valid prognostic models and presents a challenging clinical situation. In an external cohort of 266 molecularly annotated myelofibrosis (MF) patients, we demonstrated that the GIPSS model significantly differentiated between four risk groups (low, int-1, int-2, high) with median OS that was not reached, not reached, 60.5 and 28.9 months, respectively. High-risk patients had significantly inferior leukemia-free survival (LFS) (P < 0.0001). We identified a cohort of prognostically ambiguous patients (n = 39) in which GIPSS and DIPSS models differed by ≥2 risk groups. Among these patients, a similar proportion were up-staged by DIPSS (n = 19) and GIPSS (n = 20). Patients upstaged by GIPSS (genetically high-risk) had a trend toward inferior OS compared with patients upstaged by DIPSS (clinically high-risk) (P = .08) and significantly worse LFS (P = .04). Patients deemed intermediate-2 and high-risk by GIPSS who underwent allogeneic transplant had improved OS compared with those that did not (P = .04). GIPSS is a valid disease-specific prognostic system and outperforms DIPSS in patients where the two models disagree. Additionally, while GIPSS was developed for PMF; the current study shows, however, that the contemporary genetic model performs equally well for both primary and secondary myelofibrosis.
Parametric fault diagnosis for analog systems using functional mapping (2003)

We propose a new Simulation-After-Test (SAT) methodology for accurate diagnosis of circuit parameters in large analog circuits. Our methodology is based on constructing a non-linear regression model using prior circuit simulation, which relates a set of measurements to the circuit's internal parameters. First, we give algorithms to select measurements that give all the diagnostic information about the Circuit-Under-Test (CUT). From these selected measurements, we solve for the internal parameters of the circuit using iterative numerical techniques. The methodology has been applied to several mixed-signal test benchmark circuits and has applications in process debugging for mixed-signal integrated circuits (ICs) as well troubleshooting and repair of board level systems.
The Equivalence of Two Methods of Parameter Estimation for the Rasch Model (1989)

Two methods of estimating parameters in the Rasch model are compared. It is shown that estimates for a certain loglinear model for the score × item × response table are equivalent to the unconditional maximum likelihood estimates for the Rasch model.
Scenario for large-scale implementation of CCS in Europe (2009)

In the CASTOR project funded by the EU and industry the emission reduction target for CO2 Capture and Storage (CCS) was set at 30% of the CO2 emissions from power plants in Europe, which is to be achieved during the first half of this century. The developed scenario shows that this target can be met, although major uncertainties remain in the timely availability of oil and gas fields and the storage potential of aquifers. Results show that a rapid replacement of power plants after 2011 in northern Europe will give ample opportunity for using CCS.
The mystery of missing heritability: Genetic interactions create phantom heritability (2012)

Human genetics has been haunted by the mystery of "missing heritability" of common traits. Although studies have discovered >1,200 variants associated with common diseases and traits, these variants typically appear to explain only a minority of the heritability. The proportion of heritability explained by a set of variants is the ratio of (i) the heritability due to these variants (numerator), estimated directly from their observed effects, to (ii) the total heritability (denominator), inferred indirectly from population data. The prevailing view has been that the explanation for missing heritability lies in the numerator--that is, in as-yet undiscovered variants. While many variants surely remain to be found, we show here that a substantial portion of missing heritability could arise from overestimation of the denominator, creating "phantom heritability." Specifically, (i) estimates of total heritability implicitly assume the trait involves no genetic interactions (epistasis) among loci; (ii) this assumption is not justified, because models with interactions are also consistent with observable data; and (iii) under such models, the total heritability may be much smaller and thus the proportion of heritability explained much larger. For example, 80% of the currently missing heritability for Crohn's disease could be due to genetic interactions, if the disease involves interaction among three pathways. In short, missing heritability need not directly correspond to missing variants, because current estimates of total heritability may be significantly inflated by genetic interactions. Finally, we describe a method for estimating heritability from isolated populations that is not inflated by genetic interactions.
Combined 3C-ChIP-Cloning (6C) Assay: A Tool to Unravel Protein-Mediated Genome Architecture (2009)

INTRODUCTION Progress in technologies to address long-range chromosomal interactions in vivo has extensively revised concepts about different aspects of transcriptional regulation. These methods allow probing physical proximities between chromatin elements without specifically identifying the protein components that mediate such interactions. Here we describe a detailed protocol for C ombined 3C - C hIP- C loning (6C) technology, which combines multiple techniques to identify the proteins that bridge distant genomic regions, while simultaneously identifying such physical proximities. This method is also useful for determining if a candidate protein might mediate long-range interactions, both in cis and in trans in the nucleus. We discuss how the 6C technique can be incorporated with other techniques to discover all the chromatin regions in the nucleus that interact with a given gene or chromatin region of interest in a specific protein-dependent manner. Such information allows complete, cell-type-specific mapping of all the chromatin interactions mediated by specific proteins. The 6C assay advances our understanding of the three-dimensional aspects of the higher-order folding of chromatin and provides an important tool to examine the role of specific proteins in nuclear organization. In addition to providing a detailed protocol of the 6C technique, we discuss how this technology can be used by investigators working in the area of chromatin biology, with special interest in chromatin long-range interactions.
Atmospheric turbulence characterization using a neuromorphic camera (2022)

The capabilities of neuromorphic (event) based sensors for atmospheric turbulence characterization and refractive index structure parameter ( C<sup>2</sup><sub>n</sub> ) sensing are investigated. The experimental setup used a system that consisted of a telescope with an attached neuromorphic camera that was imaging features of a corner of an installation on the roof of a building in 7 km distance. Synchronously with recording of the event stream from neuromorphic sensor the refractive index structure parameter was measured with a commercial scintillometer along the same propagation path. A processing technique was developed to compare the distribution-width of events generated by the edges of the imaged corner within a given time-span to the measured strength of turbulence from the scintillometer. Spatio-temporal analysis was applied to show the possibility to detect influence of wind flow in the of recorded event stream data.
Design of compact optical systems using multichannel configurations (2016)

Compacting devices is an increasingly demanding requirement for many applications in both nonimaging and imaging optics. “Compacting” means here decreasing the volume of the space between the entry and the exit aperture without decreasing the optical performance. For nonimaging optical systems, compact optics is mainly important for reducing cost. Its small volume means less material is needed for mass-production and small size and light weight save cost in transportation. For imaging optical systems, in addition to the mentioned advantages, compact optics increases portability of devices as well, which contributes a lot to wearable display technologies such as Head Mounted Displays (HMD). After reviewing the different techniques to design compact systems, we analyze here the multichannel strategies. These type of designs split the incoming bundle of rays in different sub-bundles that are optically processed (independently) and then recombined in a single outgoing bundle. The optics volume decreases rapidly with the number of sub-bundles. These designs usually need to be combined with freeform optics in order to get optimum performance.