gebhart/patrepeval huggingface dataset:
Synthesis and Characterization of Polymers: From Polymeric Micelles to Step-Growth Polymerizations (2004)

The benefits of using CO2 in polymer synthesis are numerous, ranging from environmental responsibility to improved materials properties. Carbon dioxide is an inert, nontoxic, nonflammable, and inexpensive reaction and processing medium that is an environmentally benign alternative to the organic solvents or water typically used today. Although the often toxic, carcinogenic, and environmentally hazardous organic solvents are recycled, some release to the environment is inevitable. Replacement of organic solvents with water still requires the costly purification of the wastewater prior to disposal and/or an energy-intensive drying process to remove the water. On the other hand, CO2 can be easily separated from other chemical components and recycled through depressurization and recompression. Although CO2 is a greenhouse gas, the CO2 used as a solvent does not contribute to the greenhouse gases since it is acquired from natural reservoirs or recovered as a by-product from other industrial chemical processes. The more specific environmental benefits of using liquid or supercritical carbon dioxide as a solvent vary depending on the polymerization being considered. The synthesis of fluoropolymers in CO2 is of particular interest since these polymers have historically been prepared in chlorofluorocarbons (CFCs) and other fluorinated solvents, as well as in water. Due to the association of CFCs with ozone-layer depletion, these solvents have been banned and replacement solvents must be found. Alternative fluorinated solvents are expensive and also have environmental concerns. In heterogeneous polymerizations, many polymer latexes produced by emulsion or dispersion polymerization in water or organic solvents can be produced in CO2. To eliminate volatile organic compound (VOC) emissions, more polymer latexes are being synthesized in water. However, for dry polymer applications, the latexes must undergo energy-intensive drying by vacuum or heat to remove the water. For polymer latexes produced in CO2, there are no VOC emissions and the energy-intensive drying step can be significantly reduced since the CO2 has a much lower heat of vaporization in the liquid state and, in fact, has a zero heat of vaporization in the supercritical state. Additionally, the polymer can be shipped dry at 100% solids, thus saving energy and money in shipping the heavy water latex.
Flex Algorithm for BIER (2019)

Bit Index Explicit Replication (BIER) is an architecture that provides
optimal multicast forwarding through a BIER domain without requiring
intermediate routers to run explicit tree-building protocol or to
maintain multicast-related, per-flow state. IGP protocols are extended
to carry BFR-Id and other encapsulation informations that are used by
traditional path computing algorithm using link metric for a loop-free
best path selection. This document defines a constrained based path
selection using IGP flexible Algorithm for BIER.
The Iron Superoxide Dismutase from the Filamentous Cyanobacterium Nostoc PCC 7120 (2004)

The nitrogen-fixing filamentous cyanobacterium Nostoc PCC 7120 (formerly named Anabaena PCC 7120) possesses two genes for superoxide dismutase, a unique membrane-associated manganese superoxide dismutase (MnSOD) and a soluble iron superoxide dismutase (FeSOD). A phylogenetic analysis of FeSODs shows that cyanobacterial enzymes form a well separated cluster with filamentous species found in one subcluster and unicellular species in the other. Activity staining, inhibition patterns, and immunogold labeling show that FeSOD is localized in the cytosol of vegetative cells and heterocysts (nitrogenase containing specialized cells formed during nitrogen-limiting conditions). The recombinant Nostoc FeSOD is a homodimeric, acidic enzyme exhibiting the characteristic iron peak at 350 nm in its ferric state, an almost 100% occupancy of iron per subunit, a specific activity using the ferricytochrome assay of (2040 +/- 90) units mg(-1) at pH 7.8, and a dissociation constant Kd of the azide-FeSOD complex of 2.1 mM. Using stopped flow spectroscopy it was shown that the decay of superoxide in the presence of various FeSOD concentrations is first-order in enzyme concentration allowing the calculation of the catalytic rate constants, which increase with decreasing pH: 5.3 x 10(9) M(-1) s(-1) (pH 7) to 4.8 x 10(6) M(-1) s(-1) (pH 10). FeSOD and MnSOD complement each other to keep the superoxide level low in Nostoc PCC 7120, which is discussed with respect to the fact that Nostoc PCC 7120 exhibits oxygenic photosynthesis and oxygen-dependent respiration within a single prokaryotic cell and also has the ability to form differentiated cells under nitrogen-limiting conditions.
Selectivity profiling and off-target identification of clinically relevant kinase inhibitors for gastrointestinal tumors (2008)

Targeted inhibition of protein kinases by small molecule drugs has evolved into a viable approach for anticancer therapy. These inhibitors are widely used in signal transduction therapy, although the true selectivity of them has remained unclear. Recently several kinase inhibitors have been used for Gastrointestinal tumors.
Learning Brain Dynamics With Coupled Low-Dimensional Nonlinear Oscillators and Deep Recurrent Networks (2021)

Many natural systems, especially biological ones, exhibit complex multivariate nonlinear dynamical behaviors that can be hard to capture by linear autoregressive models. On the other hand, generic nonlinear models such as deep recurrent neural networks often require large amounts of training data, not always available in domains such as brain imaging; also, they often lack interpretability. Domain knowledge about the types of dynamics typically observed in such systems, such as a certain type of dynamical systems models, could complement purely data-driven techniques by providing a good prior. In this work, we consider a class of ordinary differential equation (ODE) models known as van der Pol (VDP) oscil lators and evaluate their ability to capture a low-dimensional representation of neural activity measured by different brain imaging modalities, such as calcium imaging (CaI) and fMRI, in different living organisms: larval zebrafish, rat, and human. We develop a novel and efficient approach to the nontrivial problem of parameters estimation for a network of coupled dynamical systems from multivariate data and demonstrate that the resulting VDP models are both accurate and interpretable, as VDP's coupling matrix reveals anatomically meaningful excitatory and inhibitory interactions across different brain subsystems. VDP outperforms linear autoregressive models (VAR) in terms of both the data fit accuracy and the quality of insight provided by the coupling matrices and often tends to generalize better to unseen data when predicting future brain activity, being comparable to and sometimes better than the recurrent neural networks (LSTMs). Finally, we demonstrate that our (generative) VDP model can also serve as a data-augmentation tool leading to marked improvements in predictive accuracy of recurrent neural networks. Thus, our work contributes to both basic and applied dimensions of neuroimaging: gaining scientific insights and improving brain-based predictive models, an area of potentially high practical importance in clinical diagnosis and neurotechnology.
A Cell-Based High-Throughput Screen for Novel Chemical Inducers of Fetal Hemoglobin for Treatment of Hemoglobinopathies (2014)

Decades of research have established that the most effective treatment for sickle cell disease (SCD) is increased fetal hemoglobin (HbF). Identification of a drug specific for inducing γ-globin expression in pediatric and adult patients, with minimal off-target effects, continues to be an elusive goal. One hurdle has been an assay amenable to a high-throughput screen (HTS) of chemicals that displays a robust γ-globin off-on switch to identify potential lead compounds. Assay systems developed in our labs to understand the mechanisms underlying the γ- to β-globin gene expression switch during development has allowed us to generate a cell-based assay that was adapted for a HTS of 121,035 compounds. Using chemical inducer of dimerization (CID)-dependent bone marrow cells (BMCs) derived from human γ-globin promoter-firefly luciferase β-globin promoter-Renilla luciferase β-globin yeast artificial chromosome (γ-luc β-luc β-YAC) transgenic mice, we were able to identify 232 lead chemical compounds that induced γ-globin 2-fold or higher, with minimal or no β-globin induction, minimal cytotoxicity and that did not directly influence the luciferase enzyme. Secondary assays in CID-dependent wild-type β-YAC BMCs and human primary erythroid progenitor cells confirmed the induction profiles of seven of the 232 hits that were cherry-picked for further analysis.
Theoretical and experimental study of capillary condensation and of its possible application in micro-assembly (2007)

Nowadays, the assembly of small (&lt;1mm) components has become an industrial reality. Many domains like MEMS, surgery, telecommunications, car industry, etc. now have large use of micro-parts. At this scale, predominant forces are different than in macroworld. The pieces often undergo adhesion problems. The adhesion forces can be splitted in different components :van der Waals, electrostatics and capillary condensation. This work focuses on capillary condensation as it often can be the major component of the adhesion force. &lt;p&gt;&lt;p&gt;The first part of this work details a review of literature of different fields involved in capillary condensation. A simulation tool is then implemented and theoretically validated in the second part of the work. Finally, a test bed is presented; this bed is then used to experimentally validate the simulation results.&lt;p&gt;&lt;p&gt;Experiments and simulation results are shown to concord. Therefore, the simulation tool can be used to model the force due to capillary condensation.
Control and switching synchronization of fractional order chaotic systems using active control technique (2013)

This paper discusses the continuous effect of the fractional order parameter of the Lü system where the system response starts stable, passing by chaotic behavior then reaching periodic response as the fractional-order increases. In addition, this paper presents the concept of synchronization of different fractional order chaotic systems using active control technique. Four different synchronization cases are introduced based on the switching parameters. Also, the static and dynamic synchronizations can be obtained when the switching parameters are functions of time. The nonstandard finite difference method is used for the numerical solution of the fractional order master and slave systems. Many numeric simulations are presented to validate the concept for different fractional order parameters.
Transcription patterns of amplified Dytiscus genes coding for ribosomal RNA after injection into Xenopus oocyte nuclei. (1978)

Oocytes of the frog Xenopus were injected with purified circular DNA containing amplified rRNA genes of the water beetle Dytiscus. Nuclear contents of injected oocytes were spread and examined by electron microscopy. Most of the Dytiscus DNA seen in injected nuclei contained regions indensely packed with polymerases and nascent transcripts. Apparently normal, as well as abnormal, patterns of transcription were observed. By this type of experiment, it may become possible to recognize the transcribed regions and immediate transcripts of cloned DNA molecules whose activity cannot be seen by electron microscopy of normal nuclei.
A dominant-negative effect drives selection of TP53 missense mutations in myeloid malignancies (2019)

<i>TP53</i>, which encodes the tumor suppressor p53, is the most frequently mutated gene in human cancer. The selective pressures shaping its mutational spectrum, dominated by missense mutations, are enigmatic, and neomorphic gain-of-function (GOF) activities have been implicated. We used CRISPR-Cas9 to generate isogenic human leukemia cell lines of the most common <i>TP53</i> missense mutations. Functional, DNA-binding, and transcriptional analyses revealed loss of function but no GOF effects. Comprehensive mutational scanning of p53 single-amino acid variants demonstrated that missense variants in the DNA-binding domain exert a dominant-negative effect (DNE). In mice, the DNE of p53 missense variants confers a selective advantage to hematopoietic cells on DNA damage. Analysis of clinical outcomes in patients with acute myeloid leukemia showed no evidence of GOF for <i>TP53</i> missense mutations. Thus, a DNE is the primary unit of selection for <i>TP53</i> missense mutations in myeloid malignancies.
Hong Kong's Growth Synchronisation with China and the U.S.: A Trend and Cycle Analysis (2014)

This paper investigates the synchronisation of Hong Kong's economic growth with mainland China and the US. We identify trends of economic growth based on the permanent income hypothesis. Specifically, we first confirm whether real consumption in Hong Kong and mainland China satisfies the permanent income hypothesis, at least in a weak form. We then identify the permanent and transitory components of income of each economy using a simple state-space model. We use structural vector autoregression models to analyse how permanent and transitory shocks originating from mainland China and the US affect the Hong Kong economy, and how such influences evolve over time. Our main findings suggest that transitory shocks from the US remain a major driving force behind Hong Kong's business cycle fluctuations. On the other hand, permanent shocks from mainland China have a larger impact on Hong Kong's trend growth.
COVID-19 Rehabilitation With Herbal Medicine and Cardiorespiratory Exercise: Protocol for a Clinical Study (Preprint) (2020)

<sec> <title>BACKGROUND</title> Recent studies have revealed that many discharged patients with COVID-19 experience ongoing symptoms months later. Rehabilitation interventions can help address the consequences of COVID-19, including medical, physical, cognitive, and psychological problems. To our knowledge, no studies have investigated the effects of rehabilitation following discharge from hospital for patients with COVID-19. </sec> <sec> <title>OBJECTIVE</title> The specific aims of this project are to investigate the effects of a 12-week exercise program on pulmonary fibrosis in patients recovering from COVID-19. A further aim will be to examine how Chinese herbal medicines as well as the gut microbiome and its metabolites regulate immune function and possibly autoimmune deficiency in the rehabilitation process. </sec> <sec> <title>METHODS</title> In this triple-blinded, randomized, parallel-group, controlled clinical trial, we will recruit adult patients with COVID-19 who have been discharged from hospital in Hong Kong and are experiencing impaired lung function and pulmonary function. A total of 172 eligible patients will be randomized into four equal groups: (1) cardiorespiratory exercise plus Chinese herbal medicines group, (2) cardiorespiratory exercise only group, (3) Chinese herbal medicines only group, and (4) waiting list group (in which participants will receive Chinese herbal medicines after 24 weeks). These treatments will be administered for 12 weeks, with a 12-week follow-up period. Primary outcomes include dyspnea, fatigue, lung function, pulmonary function, blood oxygen levels, immune function, blood coagulation, and related blood biochemistry. Measurements will be recorded prior to initiating the above treatments and repeated at the 13th and 25th weeks of the study. The primary analysis is aimed at comparing the outcomes between groups throughout the study period with an α level of .05 (two-tailed). </sec> <sec> <title>RESULTS</title> The trial has been approved by the university ethics committee following the Declaration of Helsinki (approval number: REC/19-20/0504) in 2020. The trial has been recruiting patients. The data collection will be completed in 24 months, from January 1, 2021, to December 31, 2022. </sec> <sec> <title>CONCLUSIONS</title> Given that COVID-19 and its sequelae would persist in human populations, important findings from this study would provide valuable insights into the mechanisms and processes of COVID-19 rehabilitation. </sec> <sec> <title>CLINICALTRIAL</title> ClinicalTrials.gov NCT04572360; https://clinicaltrials.gov/ct2/show/NCT04572360 </sec> <sec> <title>INTERNATIONAL REGISTERED REPORT</title> PRR1-10.2196/25556 </sec>
Cluster-to-adapt: Few Shot Domain Adaptation for Semantic Segmentation across Disjoint Labels (2022)

Domain adaptation for semantic segmentation across datasets consisting of the same categories has seen several recent successes. However, a more general scenario is when the source and target datasets correspond to non-overlapping label spaces. For example, categories in segmentation datasets change vastly depending on the type of environment or application, yet share many valuable semantic relations. Existing approaches based on feature alignment or discrepancy minimization do not take such category shift into account. In this work, we present Cluster-to-Adapt (C2A), a computationally efficient clustering-based approach for domain adaptation across segmentation datasets with completely different, but possibly related categories. We show that such a clustering objective enforced in a transformed feature space serves to automatically select categories across source and target domains that can be aligned for improving the target performance, while preventing negative transfer for unrelated categories. We demonstrate the effectiveness of our approach through experiments on the challenging problem of outdoor to indoor adaptation for semantic segmentation in few-shot as well as zero-shot settings, with consistent improvements in performance over existing approaches and baselines in all cases.
Clinical and laboratory characteristics of symptomatic healthcare workers with suspected COVID-19: a prospective cohort study (2021)

A comprehensive clinical and microbiological assessments of COVID-19 in front-line healthcare workers (HCWs) is needed. Between April 10th and May 28th, 2020, 319 HCWs with acute illness were reviewed. In addition to SARS-CoV-2 RT-PCR screening, a multiplex molecular panel was used for testing other respiratory pathogens. For SARS-CoV-2 positive HCWs, the normalized viral load, viral culture, and virus neutralization assays were performed weekly. For SARS-CoV-2 negative HCWs, SARS-CoV-2 serological testing was performed one month after inclusion. Among the 319 HCWs included, 67 (21.0%) were tested positive for SARS-CoV-2; 65/67 (97.0%) developed mild form of COVID-19. Other respiratory pathogens were found in 6/66 (9.1%) SARS-CoV-2 positive and 47/241 (19.5%) SARS-Cov-2 negative HCWs (p = 0.07). The proportion of HCWs with a viral load > 5.0 log<sub>10</sub> cp/mL (Ct value < 25) was less than 15% at 8 days after symptom onset; 12% of HCWs were positive after 40 days (Ct > 37). More than 90% of cultivable virus had a viral load > 4.5 log<sub>10</sub> cp/mL (Ct < 26) and were collected within 10 days after symptom onset. Among negative HCWs, 6/190 (3.2%) seroconverted. Our data suggest that the determination of viral load can be used for appreciating the infectiousness of infected HCWs. These data could be helpful for facilitating their return to work.
Direct observation of aqueous secondary organic aerosol from biomass-burning emissions (2016)

The mechanisms leading to the formation of secondary organic aerosol (SOA) are an important subject of ongoing research for both air quality and climate. Recent laboratory experiments suggest that reactions taking place in the atmospheric liquid phase represent a potentially significant source of SOA mass. Here, we report direct ambient observations of SOA mass formation from processing of biomass-burning emissions in the aqueous phase. Aqueous SOA (aqSOA) formation is observed both in fog water and in wet aerosol. The aqSOA from biomass burning contributes to the "brown" carbon (BrC) budget and exhibits light absorption wavelength dependence close to the upper bound of the values observed in laboratory experiments for fresh and processed biomass-burning emissions. We estimate that the aqSOA from residential wood combustion can account for up to 0.1-0.5 Tg of organic aerosol (OA) per y in Europe, equivalent to 4-20% of the total OA emissions. Our findings highlight the importance of aqSOA from anthropogenic emissions on air quality and climate.
Transforming graph-based sentence representations to alleviate overfitting in relation extraction (2014)

Relation extraction (RE) aims at finding the way entities, such as person, location, organization, date, etc., depend upon each other in a text document. Ontology Population, Automatic Summarization, and Question Answering are fields in which relation extraction offers valuable solutions. A relation extraction method based on inductive logic programming that induces extraction rules suitable to identify semantic relations between entities was proposed by the authors in a previous work. This paper proposes a method to simplify graph-based representations of sentences that replaces dependency graphs of sentences by simpler ones, keeping the target entities in it. The goal is to speed up the learning phase in a RE framework, by applying several rules for graph simplification that constrain the hypothesis space for generating extraction rules. Moreover, the direct impact on the extraction performance results is also investigated. The proposed techniques outperformed some other state-of-the-art systems when assessed on two standard datasets for relation extraction in the biomedical domain.
Network Coding-Aware Queue Management for TCP Flows over Coded Wireless Networks (2010)

We are interested in unicast traffic over wireless networks that employ constructive inter-session network coding, including single-hop and multi-hop schemes. In this setting, TCP flows do not fully exploit the network coding opportunities due to their bursty behavior and due to the fact that TCP is agnostic to the underlying network coding. In order to improve the performance of TCP flows over coded wireless networks, we take the following steps. First, we formulate the problem as network utility maximization and we present a distributed solution. Second, mimicking the structure of the optimal solution, we propose a "network-coding aware" queue management scheme (NCAQM) at intermediate nodes; we make no changes to TCP or to the MAC protocol (802.11). We demonstrate, via simulation, that NCAQM significantly improves TCP performance compared to TCP over baseline schemes.
Cover Feature: Chromatography‐Free Multicomponent Synthesis of Thioureas Enabled by Aqueous Solution of Elemental Sulfur (ChemistryOpen 1/2021) (2021)

The Cover Feature shows the application of aqueous polysulfide solutions in the chromatography-free multicomponent synthesis of thioureas. We have used a large pool of bases to cleave the octasulfur ring generating water-soluble, zwitterionic polsulfide chains. Using these aqueous solutions as sulfurating agents, we were able to omit the otherwise mandatory chromatography to separate the organic products from the excess of sulfur. The methodology has been validated in a wide range of synthesis scenarios highlighting challenging biaryl derivatives and the marketed drug, thiocarlide. More information can be found in the Full Paper by András Gy. Németh et al.