jimnoneill/paper-to-field-training huggingface dataset:
Synthesis and Identification of New Chiral Compounds Containing Azomethine Ylide Core

Field: Chemistry (Physical Sciences)

Buçalışmada 14 adet kiral yapıda yeni dialkil(2-okso-2-{[(1S)-1-feniletil]amino}etil) ditiyoimidokarbonat ve(2-okso-2-{[(1R)-1-feniletil]amino}etil)ditiyoimidokarbonat bileşiği (4a-n)glisin tuzlarından (1) başlanılarak sentezlenmiştir. Bu bileşikler 1,3-dipolarsiklokatılma tepkimelerinde 1,3-dipol reaktifi olarak kullanılan azometin yilürçekirdeği içermektedir. Ayrıca sentezlenen azometin yilür bileşiklerisubstituent olarak kiral bir amit fonksiyonu da içermektedir. Bu bileşiklerinyapıları farklı spektroskopik yöntemler (IR, 1H NMR, 13CNMR ve COSY NMR) kullanılarak karakterize edilmiştir.
The Circadian System in Higher Plants

Field: Agricultural and Biological Sciences (Life Sciences)

The circadian clock regulates diverse aspects of plant growth and development and promotes plant fitness. Molecular identification of clock components, primarily in Arabidopsis, has led to recent rapid progress in our understanding of the clock mechanism in higher plants. Using mathematical modeling and experimental approaches, workers in the field have developed a model of the clock that incorporates both transcriptional and posttranscriptional regulation of clock genes. This cell-autonomous clock, or oscillator, generates rhythmic outputs that can be monitored at the cellular and whole-organism level. The clock not only confers daily rhythms in growth and metabolism, but also interacts with signaling pathways involved in plant responses to the environment. Future work will lead to a better understanding of how the clock and other signaling networks are integrated to provide plants with an adaptive advantage.
The Distribution and Formation of Permian-Triassic Red Beds

Field: Earth and Planetary Sciences (Physical Sciences)

Abstract Red beds, associated with desert, evaporite and fluviatile environments, have a widespread distribution in the Permian-Triassic of the Northern Hemisphere. This contrasts with the Gondwanaland countries where the major red beds are of Triassic age and lack extensive evaporites. The Permian includes glacial and coal-bearing facies in the southern continents. These differences are in accord with the paleomagnetic evidence which shows that during the Permo-Carboniferous, the southern parts of Africa and South America lay at a latitude near to the South Pole. A general northward drift to lower latitudes occurred during the Permian and Triassic, until North America — Eurasia and considerable parts of Gondwanaland lay within 30° N and S of the equator, respectively. Such latitudes readily explain the environmental significance of the various red bed facies. The occurrence of widespread continental red beds, often replacing marine sediments, and associated with late Paleozoic orogenies, supports the concept of large-scale continental emergence by Late Permian times, with concomitant withdrawal of shelf seas. This, and any fluctuations in salinity of sea water during the Permian evaporite maxima, was probably a contributory cause of the Late Permian biological revolution. The origin of the red colour of the red beds is considered to be due to in situ diagenetic processes, similar to those demonstrated in late Tertiary to Recent red desert sediments in Mexico.
StructSim: Querying Structural Node Similarity at Billion Scale

Field: Computer Science (Physical Sciences)

Structural node similarity is widely used in analyzing complex networks. As one of the structural node similarity metrics, role similarity has the good merit of indicating automorphism (isomorphism). Existing algorithms to compute role similarity (e.g., RoleSim and NED) suffer from severe performance bottlenecks, and thus cannot handle large real-world graphs. In this paper, we propose a new framework StructSim to compute nodes' role similarity. Under this framework, we prove that StructSim is guaranteed to be an admissible role similarity metric based on the maximum matching. While maximum matching is too costly to scale, we then devise the BinCount matching to speed up the computation. BinCount-based StructSim admits a precomputed index to query one single pair in O(k log D) time, where k is a small user-defined parameter and D is the maximum node degree. Extensive empirical studies show that StructSim is significantly faster than existing works for computing structural node similarities on the real-world graphs, with comparable effectiveness.
Modeling Storm Surges Using Discontinuous Galerkin Methods

Field: Mathematics (Physical Sciences)

Storm surges have a devastating impact on coastlines throughout the United States. In order to accurately understand the impacts of storm surges there needs to be an effective model. One of the governing systems of equations used to model storm surges' effects is the Shallow Water Equations (SWE). In this thesis, we solve the SWE numerically by means of a discontinuous Galerkin (DG) method. The DG method provides high-order accuracy and geometric flexibility on unstructured grids. To run the model, we used both implicit and explicit time integration for solving the SWE. Using explicit time integration as our fundamental truth, we found the error norm of the implicit method to be minimal. This study focuses on the impacts of a simulated storm surge in La Push, Washington, which had undergone a beach restoration project. The beach restoration involved altering the bathymetry along the shoreline to prevent overtopping waves from breaching the mainland. To validate the simulations, we ran three benchmark tests. Real bathymetry was used along with real storm and tidal data. We measured the momentum flux of a wave on the existing bathymetry and the new bathymetry to determine if the new bathymetry had less momentum flux. Our results showed there was less momentum flux with the new bathymetry, and therefore the new bathymetry was more resistant to storm surges. After running the model at a high resolution, we modified the grid resolution to vary throughout the domain with a focus on high resolution closer to the shoreline. In our simulation, we also learned of the effects spurious waves can have on the results. Due to boundary conditions, a spurious wave can reflect back into a model and impact the velocity and momentum flux.
DNA methylation in obesity and type 2 diabetes

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

To elucidate the mechanisms related to the development of type 2 diabetes (T2D) and other degenerative diseases at a molecular level, a better understanding of the changes in the chromatin structure and the corresponding functional changes in molecular pathways is still needed. For example, persons with low birth weight are at a high risk for development of T2D later in life, suggesting that the intrauterine environment contributes to the disease. One of the hypotheses is that epigenetic regulation, including changes in DNA methylation leading to modifications in chromatin structure, are behind metabolic alterations, e.g. leading to the phenomenon termed metabolic memory. Altered DNA methylation has been shown to affect healthy aging and also to promote age-related health problems. There is suggestive evidence that lifestyle changes including weight loss can have an impact on DNA methylation and consequently gene expression. In this review we provide an overview of human studies investigating DNA methylation in obesity and T2D and associated risk factors behind these diseases.
The effects of vocabulary pre-teaching and pre-questioning on intermediate Iranian EFL learnersâ€™ reading comprehension ability

Field: Social Sciences (Social Sciences)

Reading comprehension is a key issue in learning English as a foreign language, and it is critical that teachers utilize pre-reading strategies in reading classes in order to help students enhance their comprehension. The present study investigated the effectiveness of two pre-reading strategies of pre-questioning and vocabulary pre-teaching on EFL studentsâ€™ performance in reading comprehension. A group of 60 students participated in this study. An experimental design was used, with 20 students being assigned to the first experimental group that received one pre-reading strategy (vocabulary pre-teaching), while the second experimental group which also consisted 20 students received another pre-reading strategy (pre-questioning) and the remaining 20 students received the traditional method. Students in the groups were asked first to perform the pre-reading strategy, read a passage, and then answer comprehension questions. Results indicated that there were statistically significant differences between the groups. The experimental groups got better results than the control group. Comparison of the two experimental groups, moreover, showed that the vocabulary pre-teaching group outperformed the pre-questioning group. Key words: EFL teaching, Pre-reading strategies, Pre-questioning, Reading comprehension, Schema theory, Vocabulary pre-teaching
[NON-CLONAL MAST CELL ACTIVATION SYNDROME: DESCRIPTION OF SERIES OF PATIENTS, DIAGNOSTIC CRITERIA AND TREATMENT].

Field: Medicine (Health Sciences)

A non-clonal mast cell activation syndrome is a newly emerged diagnosis. It shares the clinical features of anaphylaxis and mastocytosis despite having distinct mast cell biology. In this,paper we describe a series of patients representing the spectrum of non-clonal mast cell activation syndrome (nc-MCAS). We highlight the clinical manifestations of nc-MCAS as well as the diagnostic criteria and treatment options.
Finite element modelling of soil nailing inclination effect on slope stability: Cibeureum slope case study

Field: Engineering (Physical Sciences)

On November 21, 2022, a 5.6 magnitude earthquake caused a landslide on one of the slopes in Cibeureum, Cianjur district. To repair the slope, reinforcement is necessary to achieve stability values that can withstand future earthquakes. One method for enhancing slope stability is soil nailing. Various soil nailing installation angles were analyzed to find the optimal design for the Cibeureum slope. Using the Plaxis 2D V20 program, the safety factor of the original slope without an earthquake was found to be 1.62. Increasing the installation angle of the soil nails from 10°, 15°, to 20° improved the safety factor, but the increase was not significant because the initial installation point was far from the slip line, requiring a nail length of 50 meters. The best configuration, yielding the highest safety value, was achieved with a modified slope angle of 19° and soil nails with a 50 m length installed at a 20° angle. This configuration produced a safety factor of 2.55 without an earthquake and 1.102 with an earthquake, as calculated using the Plaxis 2D V20 program.
First Description of Mycoplasma agalactiae Anatomical Localization in Naturally Infected Hard Ticks (Rhipicephalus bursa)

Field: Veterinary (Health Sciences)

Mycoplasma agalactiae (Ma) is considered the primary causative agent of contagious agalactia (CA) in sheep and goats, which causes severe losses to the small ruminant dairy industry. As early as 1816, it was thought that environmental factors played a role in pathogen maintenance in endemic areas. Specifically, recent studies hypothesized a vector role for arthropods in the epidemiology of disease. The aim of this study was to investigate the presence and anatomical localization of Ma in naturally infected Riphicephalus bursa ticks to better evaluate tick–pathogen interactions. Salivary glands and ovaries of confirmed Ma-positive R. bursa were analyzed to look for the Ma antigen using immunohistochemistry (IHC). IHC showed strong positivity to Ma in the cytoplasm of salivary cells as well as in cells from the ovary. Our work demonstrated for the first time the crossing of the tick midgut barrier by Ma and the subsequent infection of organs capable of spreading the infection, and this result represents an absolute novelty in disease-related knowledge. Our preliminary results provide conclusive evidence of the potential vector role represented by hard ticks in the epidemiology of CA. Further field and laboratory investigations are necessary to confirm the tick role in the transmission of clinical CA.
Entering the way of the great vehicle Dzogchen as the culmination of the Mahāyāna

Field: Arts and Humanities (Social Sciences)

"The first English translation of a classic treatise on how the Tibetan practice of Dzogchen, or Great Perfection, is in fact the culmination of the path of Mahayana Buddhism. Rongzom Chokyi Zangpo, also known as Rongzompa, is considered one of the three great pillars of the original tradition of Buddhism, the Nyingma, that arrived in Tibet in the eighth century and still thrives today. He was a pioneer at systematizing the philosophical underpinnings of the variety of views and practices of Buddhism in India and Tibet. Surprisingly, only one other work of his is in English and it is for a more academic audience than this. In this illuminating work, he clearly and powerfully presents the case that the highest form of practice in the Nyingma tradition, Dzogchen, is perfectly in accord with Mahayana Buddhism and refutes critics who tried to undermine this point"--
CHARACTERIZATION OF ANTIBODIES DIRECTED AGAINST THE IMMUNOGLOBULIN LIGHT KAPPA CHAIN VARIABLE CHAIN REGION (VK) OF HEPATITIS C VIRUS-RELATED TUPE II MIXED CRYOGLOBULINEMIA AND B-CELL PROLIFERATIONS

Field: Immunology and Microbiology (Life Sciences)

Autoimmune type-II cryoglobulinemia (II-MC) is sustained by hepatitis C virus (HCV) infection and B-cell (oligo)clones. This is the reason why the disease may be considered an "indolent B-cell lymphoma (NHL)." B clones show a restricted use of immunoglobulin variable genes (BCR), in particular in the use of the variable kappa (VK)3-20/15 light chain, and show a homology between their BCR functional regions and those of autoimmune rheumatoid factors. We underlined the BCR unique repertoire with frequent rheumatoid factor activity also observed in other autoimmune disorders associated with NHL. The immunoglobulin idiotype is a clonal B-cell marker and an ideal target for immunotherapy. Five monoclonal antibodies were produced in our laboratory toward the VK3-20 of a subject with HCV infection and a II-MC-associated NHL. Epitope determination was performed using the epitope excision approach. Monoclonal antibody reactivity was tested in vitro in ELISA, Western blot, and cytofluorimetry. Data confirmed that a panel of antibodies, reactive against shared idiotypes, can be produced from patients with HCV-associated B-cell lymphoproliferative diseases, thus obviating the need to produce an anti-idiotype antibody for each patient.
LHH1, a Novel Antimicrobial Peptide with Anti-Cancer Activity Identified from Lactobacillus casei HZ1

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Abstract

Antimicrobial peptides have been attracting increasing attention for their multiple beneficial effects. In present study, a novel AMP with a molecular weight of 1875.25 Da, was identified from the genome of Lactobacillus casei HZ1. The peptide, which was named as LHH1 was comprised of 16 amino acid residues, and its α-helix content was 95.34% when dissolved in 30 mM SDS. LHH1 exhibited a broad range of antimicrobial activities against gram-positive bacteria and fungus. It could effectively inhibit staphylococcus aureus with a minimum inhibitory concentration of 3.5 μM and showed a low hemolytic activity. The scanning electron microscope, confocal laser scanning microscope and flow cytometry results showed that LHH1 exerted its antibacterial activity by damaging the cell membrane of staphylococcus aureus. Meanwhile, LHH1 also exhibited anti-cancer activities against several cancer cells including MGC803, HCT116 and C666-1 cells, and one major action of its anti-cancer mechanism was breaking the cell membrane.
Pre‐clinical evaluation of the Hyaguard™ sub‐conjunctival insert in maintaining post‐trabeculectomy intra‐ocular pressure vs MMC and Prednisolone drops

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Aims/Purpose: Post‐trabeculectomy rabbit model efficacy and safety evaluation of HyaGuard™; a biodegradable sub‐conjunctival drug eluting platform, designed to replace Mitomycin C (MMC) and post‐operate steroid drops in glaucoma drainage surgeries. Methods: Pre‐clinical evaluation was conducted on normotensive New Zealand White rabbits (8‐12 weeks old, 50/50 male/female). A 4x4 mm trabeculectomy was performed on the left eye of each rabbit. All animals received Ofloxacin 3mg/ml (2 drops) 4 times daily for one week. Control and 1% w/w prednisolone HyaGuard groups did not receive MMC or prednisolone drops, whereas positive control animals were treated with 0.04% MMC for 4 minutes followed by prednisolone acetate 0.5% drops (2 drops) 4 times daily for two weeks. Intraocular pressure (IOP) was measured using TonoVet® pre‐operatively (week ‐1) and on days 3, 7, 14, and 28 post operation. Ophthalmic examinations were performed. Post study, eyes were histologically analyzed using H+E staining. Results: 1% prednisolone HyaGuard inserts demonstrated significantly better welfare and safety scores than standard of care. Histological analysis revealed no fibrotic encapsulation and intact conjunctivas. From an initial average IOP of 11.5 (± 1.0) mm Hg, the Day 28 ΔIOP (% of starting IOP) was ‐35.38 ±19.75% for MMC‐drops ( p < 0.01), ‐8.61 ±10.56% for blank HyaGuard (non‐significant), and ‐24.54 ±10.20% for 1% prednisolone HyaGuard ( p < 0.05). The 1% prednisolone HyaGuard group maintained a significantly greater reduction in IOP compared to the negative control ( p < 0.01) and was statistically equivalent to the positive control. Conclusions: HyaGuard demonstrated improved tolerability and safety following subconjunctival insertion in rabbits. The 1% prednisolone loaded HyaGuard effectively maintained significant decreases in post trabeculectomy IOP, without the need for MMC or repeat drop administration, suggesting its potential as a viable solution to the long running fibrotic failures associated with bleb forming drainage surgeries.
DTV-T2 coverage: comparison of measured and predicated signals

Field: Engineering (Physical Sciences)

Digital Video Broadcasting-Terrestrial Second Generation (DVB-T2) is currently the most up-to-date and advanced standard for Digital Television Broadcast. This standard was built on from its predecessor, the Digital Video Broadcasting-Terrestrial (DVB-T). Compared to DVB-T, the latest DVB-T2 standard offers several advantages in terms of spectrum efficiency, robustness, flexibility etc. Particularly in the case of Singapore, MediaCorp has been broadcasting its 7 free to air channels under the DVB-T2 format since 2013. However, although both the DVB-T and Analogue TV signals are also still being transmitted, it is expected that Singapore would fully switch over to DVB-T2 completely in the next few years. As such, the purpose of the Final Year Project was to measure the various parameters of the transmitted DVB-T/T2 signals such as Power, Carrier to Noise Ratio (C/N) etc. in different locations within Singapore. Apart from measuring, the results obtained were also analyzed to better understand the factors that can affect the TV signal reception. To attain these objectives, field meters such as the PROMAX TV Explorer HD+ and PROMAX HD Ranger+ were used along with antennas. Based on all the experiments that were conducted in the project, it can be concluded the TV signal reception is largely dependent on the obstructions around a test point for example. Obstacles such as trees and buildings can affect the Line of Sight from the transmitter to the receiver and can either block or reflect TV signals away. As such, the receiving antenna picks up many of these reflected signals which can either destructively degrade or constructively improve the signal power depending on their phase.
Improved maximum-likelihood estimation in a regression model with general parametrization

Field: Mathematics (Physical Sciences)

We analyse the finite-sample behaviour of two second-order bias-corrected alternatives to the maximum-likelihood estimator of the parameters in a multivariate normal regression model with general parametrization proposed by Patriota and Lemonte [A. G. Patriota and A. J. Lemonte, Bias correction in a multivariate regression model with genereal parameterization, Stat. Prob. Lett. 79 (2009), pp. 1655-1662]. The two finite-sample corrections we consider are the conventional second-order bias-corrected estimator and the bootstrap bias correction. We present the numerical results comparing the performance of these estimators. Our results reveal that analytical bias correction outperforms numerical bias corrections obtained from bootstrapping schemes.
Advances in the use of odour as forensic evidence through optimizing and standardizing instruments and canines

Field: Medicine (Health Sciences)

This paper explores the advances made in identifying trace amounts of volatile organic compounds (VOCs) that originate from forensic specimens, such as drugs, explosives, live human scent and the scent of death, as well as the probative value for detecting such odours. The ability to locate and identify the VOCs liberated from or left by forensic substances is of increasing importance to criminal investigations as it can indicate the presence of contraband and/or associate an individual to a particular location or object. Although instruments have improved significantly in recent decades—with sensitivities now rivalling that of biological detectors—it is widely recognized that canines are generally still more superior for the detection of odourants due to their speed, versatility, ruggedness and discriminating power. Through advancements in the detection of VOCs, as well as increased standardization efforts for instruments and canines, the reliability of odour as evidence has continuously improved and is likely to continue to do so. Moreover, several legal cases in which this novel form of evidence has been accepted into US courts of law are discussed. As the development and implementation of best practice guidelines for canines and instruments increase, their reliability in detecting VOCs of interest should continue to improve, expanding the use of odour as an acceptable form of forensic evidence.
E-2 Development of Islamic Counseling Protocol for Pakistani Muslim Adults to Manage their Mental Health Problems

Field: Psychology (Social Sciences)

Religion plays a fundamental role in our life. Therefore, a religious approach is known as a pivotal to be incorporated in counseling session with the clients. Researchers and religious scholars emphases that there is a crucial need to integrate the religious aspects during counseling process. This qualitative study was carried out to develop the Islamic Counseling Protocol (Counselor/Client Worksheet) for Pakistani Muslims adults in the light of Holy Quran, Al-Sunnah and the relevant literature available in the realm of Islamic Counseling. In this connection, firstly all the methods used in Islamic counseling available in literature review were identified. Secondly, the Quranic Versus were identified in relation to the treatment of mental health problems (stress, anxiety and depression). On the basis of selected versus and methods from the Holy Quran as well as from Al-Sunnah, the Islamic Counseling protocol (counselor client worksheet) was developed for Pakistani Muslim adults to manage their mental health problems (stress, anxiety and depression). The results of this qualitative research proposed 6-sessions of Islamic Counseling to manage the mental health problems of the individuals with stress, anxiety and depression.