jimnoneill/paper-to-field-training huggingface dataset:
Next-generation sequencing analysis of high-quality and high-quantity cell-free circulating DNA prepared from droplet volumes of patient plasma.

Field: Medicine (Health Sciences)

e22008 Background: It is in agreement and the growing belief that “liquid biopsy” can provide a global longitudinal picture of cancer progression beyond the heterogeneity presented in the primary tumor. Cell-free DNA (cfDNA) circulating in the bloodstream could become the unprecedented non-invasive, standard-of-care molecular marker for the treatment and management of cancer. However, cfDNA is highly fragmented and presented at very low concentrations; therefore, its isolation is challenging because of the requirement of large volume input, costs, and labor-intensity. A proprietary cfDNA enrichment process with novel characteristic of ultra-low input (as low as 20 uL of plasma) and high output ( > 300 ng/mL of cfDNA) has been developed and compared to the industry standard. Methods: The performance of our method was evaluated side-by-side with two leading extraction methods based on throughput, sample volume, yield, and cfDNA amplifiablity. The enriched products were further subjected to NGS on the Ion Torrent PGM to detect mutations. Results: Compared to the leading cfDNA extraction methods using different chemistries and workflows, our enrichment approach allows high-yield isolation of cfDNA directly from a small volume of unprocessed plasma, leading to a significant increase in isolation efficiency and > 20-fold recovery. The cfDNA prepared by our proprietary method displayed a high-degree genomic representation as demonstrated by SNP Cytochip array. Further NGS studies on cfDNA from 10 colorectal cancer plasma and 2 spiked samples demonstrated the superiority of our protocol in generating more usable, on-target, high-quality ≥ Q20 sequencing reads, and detecting more mutations over Qiagen kit. Conclusions: A seamless sample-preparation process is critical when analyzing low-quantity cfDNA in high-noise background. Our cfDNA enrichment process is the first non-invasive method that allows accurate NGS genomic analyses directly from droplet volumes of plasma. This protocol can be applied to a broad range of clinical genetic tests with the advantages of minimal sample volume, maximal yield, streamlined workflow with reduced costs and turnaround time.
Multi-Domain Dynamic Modelling of a Low-Cost Upper Limb Rehabilitation Robot

Field: Engineering (Physical Sciences)

Tracking patient progress through a course of robotic tele-rehabilitation requires constant position data logging and comparison, alongside periodic testing with no powered assistance. The test data must be compared with previous test attempts and an ideal baseline, for which a good understanding of the dynamics of the robot is required. The traditional dynamic modelling techniques for serial chain robotics, which involve forming and solving equations of motion, do not adequately describe the multi-domain phenomena that affect the movement of the rehabilitation robot. In this study, a multi-domain dynamic model for an upper limb rehabilitation robot is described. The model, built using a combination of MATLAB, SimScape, and SimScape Multibody, comprises the mechanical electro-mechanical and control domains. The performance of the model was validated against the performance of the robot when unloaded and when loaded with a human arm proxy. It is shown that this combination of software is appropriate for building a dynamic model of the robot and provides advantages over the traditional modelling approach. It is demonstrated that the responses of the model match the responses of the robot with acceptable accuracy, though the inability to model backlash was a limitation.
SPIDER: a balloon-borne CMB polarimeter for large angular scales

Field: Physics and Astronomy (Physical Sciences)

We describe SPIDER, a balloon-borne instrument to map the polarization of the millimeter-wave sky with degree angular resolution. Spider consists of six monochromatic refracting telescopes, each illuminating a focal plane of large-format antenna-coupled bolometer arrays. A total of 2,624 superconducting transition-edge sensors are distributed among three observing bands centered at 90, 150, and 280 GHz. A cold half-wave plate at the aperture of each telescope modulates the polarization of incoming light to control systematics. Spider's first flight will be a 20-30-day Antarctic balloon campaign in December 2011. This flight will map \sim8% of the sky to achieve unprecedented sensitivity to the polarization signature of the gravitational wave background predicted by inflationary cosmology. The Spider mission will also serve as a proving ground for these detector technologies in preparation for a future satellite mission.
Sexual maturation and metabolic profile among adolescents and children of the Health Worker Cohort Study in Mexico Madurez sexual y perfil metabólico de los adolescentes y niños del estudio de cohorte de trabajadores de la salud en México

Field: Medicine (Health Sciences)

OBJECTIVE:Our objective was to investigate the associations between level and timing of sexual development with metabolic profile in a cohort of Mexican adolescents in central Mexico. MATERIAL AND METHODS:Baseline data from children between the ages of 7 and 17 years (n= 582) who participated in the Health Worker Cohort Study, was used. The study participants included children of workers at the Mexican Institute of Social Security (IMSS) and the National Institute of Public Health, both located in Cuernavaca, in addition to children of workers at the Universidad Autónoma del Estado de México in Toluca who were enrolled between March 2004 and April 2006. Multiple linear regressions with robust estimates of variance, were used adjusting for specific covariates. RESULTS:Both pubertal boys and girls, compared to their pre-pubertal counterparts, had higher body mass index (girls: 4.59 kg/m², p<0.0001; boys: 1.12 kg/m², p= 0.05) and percent body fat (girls: 3.61, p<0.0001; boys: 1.48, p= 0.0001). A significant difference in level of insulin resistance (homeostasis model assessment, HOMA) was detectable among girls (0.92, p<0.0001). CONCLUSIONS:Timing and levels of sexual development were significantly associated with adverse differences in several critical anthropometric and metabolic parameters.
OBJETIVO:Investigar las asociaciones entre etapa y momento de inicio del desarrollo sexual y perfil metabólico en una cohorte de adolescentes mexicanos. MATERIAL Y MÉTODOS:Se usó la información basal de los jóvenes entre 7 y 17 años de edad (n= 582), que participaron en el Estudio de cohorte de trabajadores de la salud. Los participantes del estudio fueron los hijos e hijas de los trabajadores del Instituto Mexicano del Seguro Social (IMSS) y del Instituto Nacional de Salud Pública en Cuernavaca, Morelos, así como los hijos e hijas de los trabajadores de la Universidad Autónoma del Estado de México en Toluca. Se realizaron regresiones lineales múltiples con estimadores de varianza robustos, ajustando por covariables específicas. RESULTADOS:Se encontró un índice de masa corporal mayor en los niños y niñas en la etapa de pubertad, comparado con los de pre-pubertad (niñas: 4.59 kg/m², p<0.0001; niños: 1.12 kg/m², p= 0.05) y un mayor porcentaje de grasa corporal (niñas: 3.61, p<0.0001; niños: 1.48, p= 0.0001). Se encontró una diferencia significativa en el indicador de resistencia a la insulina (HOMA, por sus siglas en inglés) en las niñas (0.92, p<0.0001). CONCLUSIONES:La etapa y el momento de inicio del desarrollo sexual se asociaron significativamente con diferencias adversas en varios parámetros metabólicos y antropométricos críticos.
Patterns of hospital transfer for self-poisoned patients in rural Sri Lanka: implications for estimating the incidence of self-poisoning in the developing world

Field: Medicine (Health Sciences)

Fifty per cent of patients admitted to peripheral hospitals were discharged home, showing that CFRs based on secondary hospital data are inflated. However, while incidence of self-poisoning is similar to that in England, fatal self-poisoning is three times more common in Sri Lanka than fatal self-harm by all methods in England. Population based data are essential for making international comparisons of case fatality and incidence, and for assessing public health interventions.
Contextual Bandit Algorithms with Supervised Learning Guarantees

Field: Computer Science (Physical Sciences)

We address the problem of competing with any large set of N policies in the nonstochastic bandit setting, where the learner must repeatedly select among K actions but observes only the reward of the chosen action. We present a modification of the Exp4 algorithm of Auer et al. [2], called Exp4.P, which with high probability incurs regret at most O ( √ KT ln N). Such a bound does not hold for Exp4 due to the large variance of the importance-weighted estimates used in the algorithm. The new algorithm is tested empirically in a large-scale, real-world dataset. For the stochastic version of the problem, we can use Exp4.P as a subroutine to compete with a possibly infinite set of policies of VCdimension d while incurring regret at most O ( √ Td lnT) with high probability. These guarantees improve on those of all previous algorithms, whether in a stochastic or adversarial environment, and bring us closer to providing guarantees for this setting that are comparable to those in standard supervised learning.
The effects of low frequency ultrasound on the proliferation and apoptosis of smooth muscle cells in carotid atherosclerosis

Field: Medicine (Health Sciences)

Objective To investigate the effects of low frequency ultrasound (LFU) on the proliferation and apoptosis of smooth muscle cells (SMCs) in rabbits with carotid atherosclerosis(CA).Methods CA models were established in 30 New Zealand rabbits using a high fat diet and air-drying.They were randomly divided into a control group and four LFU groups:group A received 0.5 W/cm~2 LFU for 5 min/d,group B 0.5 W/cm~2 for 10 min/d, group C 1 W/cm~2,5 min/d,and group D 1 W/cm~2,10 min/d.The rabbits' carotid arteries were autopsied after 20 d of the LFU treatment.The expression of PCNA and TUNEL staining were used to explore the proliferation and apopto- sis of SMCs,and the proliferation rates (PRs) and apoptosis rates (ARs) were calculated.Results Compared with the control group,the PRs in groups B,C and D were significantly lower,while the ARs in groups B,C and D were significantly higher.There was no significant difference in ARs or PRs among groups B,C and D.Con- clusion LFU can induce SMC apoptosis and inhibit SMC proliferation in rabbits with CA.
Methylglyoxal‐induced apoptosis is dependent on the suppression of c‐FLIPL expression via down‐regulation of p65 in endothelial cells

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

Abstract Methylglyoxal (MGO) is a reactive dicarbonyl metabolite of glucose, and its plasma levels are elevated in patients with diabetes. Studies have shown that MGO combines with the amino and sulphhydryl groups of proteins to form stable advanced glycation end products (AGEs), which are associated with vascular endothelial cell (EC) injury and may contribute to the progression of atherosclerosis. In this study, MGO induced apoptosis in a dose‐dependent manner in HUVECs, which was attenuated by pre‐treatment with z‐VAD, a pan caspase inhibitor. Treatment with MGO increased ROS levels, followed by dose‐dependent down‐regulation of c‐FLIP L . In addition, pre‐treatment with the ROS scavenger NAC prevented the MGO‐induced down‐regulation of p65 and c‐FLIP L , and the forced expression of c‐FLIP L attenuated MGO‐mediated apoptosis. Furthermore, MGO‐induced apoptotic cell death in endothelium isolated from mouse aortas. Finally, MGO was found to induce apoptosis by down‐regulating p65 expression at both the transcriptional and posttranslational levels, and thus, to inhibit c‐FLIP L mRNA expression by suppressing NF‐κB transcriptional activity. Collectively, this study showed that MGO‐induced apoptosis is dependent on c‐FLIP L down‐regulation via ROS‐mediated down‐regulation of p65 expression in endothelial cells.
Antioxidant synergism and antagonism between tocotrienols, quercetin and rutin in model system

Field: Chemistry (Physical Sciences)

The aim of the study was to reveal antioxidant synergism or antagonism between quercetin, rutin and selected tocotrienols in linoleic acid emulsion. The oxidative stress was generated by 2,2′-azobis(2-amidinopropane) dihydrochloride (AAPH) or CuSO4; the increase of the concentration of peroxidation products was monitored using fluorescence probe 2,7-dichlorofluorescein (DCF). The antioxidant activity of tested substances depends on the form of the antioxidant (aglycone, glycoside), its concentration, localization in the emulsion, and the factors generating oxidative stress. The synergistic effect occurred when the effectiveness of individual antioxidant was relatively weak and mainly when the concentration of antioxidants was in the physiologically significant range of 1 μM. We suggest that tocotrienols were regenerated by flavonoids. The synergism benefitted from the proximity of the localization of interacting antioxidants (e.g. the presence of one of the antioxidants at the oil-water interface).
Minority Stress Impacts In-Group Attitudes and Reactions to Masculinity Threat of Gay Men

Field: Psychology (Social Sciences)

Gay men are known to experience higher levels of negative health outcomes (i.e., substance abuse disorder, depression) than the general population. These issues can be mitigated through a fostering a support system among a community of other gay men. One barrier to building this sense of solidarity is when there are gay men who discriminate against other gay men for being effeminate. Using a sample of gay men (n = 103), the current study used false feedback for an online personality test to assess role that threatened masculinity might play in this phenomenon. Addressing a gap in the research, it was determined that gay men do not, in general, react similarly to heterosexual men when masculinity is threatened. However, there were significant interactions between masculinity threat and heterosexist events, such that when masculinity was threatened and participants experienced frequent of heterosexist events, the overcompensation response to masculinity threat was seen. Participants who reported higher levels of minority stress (internalized homophobia, heterosexist events) reported higher negative attitudes towards other gay men. Overall, findings of the current study suggest that minority stress may interact with masculinity threat in gay men, in a way that is nuanced and unique from masculinity threat reactions documented in heterosexual men.
Income Diversification Strategies of Italian Peri-Urban Farms: A Structural Equation Modeling Approach

Field: Arts and Humanities (Social Sciences)

On-farm diversification in non-agricultural activities has been increasingly recognized as a rewarding farm strategy through which farmers produce on-farm non-agricultural goods and services. The main objective of this paper is to explore to what extent the condition of peri-urbanity affects farm income diversification in Italy by looking at the push and pull factors that allow peri-urban farmers to re-organize their business by developing diversification strategies that are tightly connected to the demand of goods and services coming from the urban society. A structural equation modeling (SEM) statistical technique has been applied to estimate direct and indirect causal relationships among the multiple variables involved. The SEM analytical approach allowed us to untie the complexity of the push and pull factors connections and to highlight the most significant ones. The strengths of the structural paths provide evidence on the key diversification strategies adopted by peri-urban farms.
[Construction of a divided maxillary bridge].

Field: Computer Science (Physical Sciences)

This paper introduces a high-security post-quantum stateless hash-based signature scheme that signs hundreds of messages per second on a modern 4-core 3.5GHz Intel CPU. Signatures are 41~KB, public keys are 1~KB, and private keys are 1~KB. The signature scheme is designed to provide long-term $2^{128}$ security even against attackers equipped with quantum computers. Unlike most hash-based designs, this signature scheme is stateless, allowing it to be a drop-in replacement for current signature schemes.\nKeywords: post-quantum cryptography, one-time signatures, few-time signatures, hypertrees, vectorized implementation
The Selection by Honey Comb Design and its Effect on Disk Area and Yield Under Three Plant Densities in Sunflower

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract The purpose of this study is to investigate the effect of honeycomb selection design on the production of high-yielding genotypes of sunflower. A field experiment was conducted in the Abu Sedira area of Saqlawiyah / Fallujah District / Anbar Governorate. Five genotypes were used, and selection was carried out using the honeycomb selection design for two seasons. Ten genotypes were obtained, five of which were the original and five were selected genotypes. These are the original genotypes: Aqmar, Haisin, Ishaqi, Sakha, and Flami, and the selected genotypes: Aqmar, Haisi, Ishaqi, Sakha, and Flami. The seeds were planted in three selection cycles in 2022 using honeycomb selection method at a distance of 1.3 m between the furrows and 1.5 m between plants. The selection was based on the largest disk area of the sunflower crop. The superior plants were produced, which were self-pollinated, and then their seeds were mixed and planted and left for random pollination in the third season. The seeds resulting from random pollination were planted in a comparison experiment to compare the original and selected genotypes at three plant densities of 88.88, 66.66, and 53.33 thousand plants ha -1 . The results showed that the Aqmar original genotype had the shortest days to flowering, at 66.78 days. The Ishaqi selected genotype had the longest days to flowering at 72.11 days. The Aqmar selected genotype also had the highest leaf area, at 0.7211 m 2 , compared to the original genotype, which had 0.5222 m 2 . The Ishaqi selected genotype had the highest disk area, at 421.9 cm 2 , while the original had 300.7 cm 2 . The Sakha selected genotype had the highest number of seeds per disk, at 1472.0 seeds, while the original had 1135.5 seeds. The Sakha selected genotype also had the highest plant yield, at 7.938 tons ha -1 . The low plant density (53.33 thousand plants ha -1 ) had the highest number of seeds per disk, at 1395.9 seeds, while the medium and high plant densities (66.66 and 88.88 thousand plants ha -1 ) had the lowest number of seeds per disk, at 1292.2 and 1152 seeds, respectively. The high plant density had the highest grain yield, at 7.355 tons ha -1 , compared to the low density, at 5.887 tons ha -1 . In the interaction between genotypes and plant densities, the Flami selected genotype had the highest disk area, at 476.1 cm 2 , at the low plant density of 53.33 thousand plants ha -1 , while the original had 375.7 cm 2 . The Sakha selected genotype had the highest yield trait at the high plant density, at 8.806 tons ha -1 . We recommend using the Sakha selected genotype with the medium and high plant densities of 66.66 and 88.88 thousand plants ha -1 .
Innovative methods to teach optics in the Grade 5 classroom

Field: Social Sciences (Social Sciences)

With the recent realignment of the Connecticut State Department of Education Core Science Curriculum Framework, light and vision were added to the science curriculum for 5th grade students and they will be tested on these concepts on the Connecticut Mastery Test (CMT) starting in 2008. In order to ready students for the test, our collaboration began with the development of a standards-based workshop to introduce optics concepts to fifth grade students in eastern Connecticut. After a successful initial workshop for students, it was apparent that more students would benefit from our lessons if their teachers were able to conduct the lessons in their own classrooms using authentic curriculum. We also found that the teachers were desperate for curriculum, knowledge and supplies to be able to teach the concepts. The result is a collection of lessons satisfying the needs of younger students and a professional development workshop for teachers in which hands-on lessons, scientific inquiry, and scientific literacy are combined to deepen the understanding and interest in the study of optics.
Potent and Selective RIPK1 Inhibitors Targeting Dual‐Pockets for the Treatment of Systemic Inflammatory Response Syndrome and Sepsis

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Abstract Sepsis, characterized with high risk of life‐threatening organ dysfunction, represents a major cause of health loss and the World Health Organization (WHO) labelled sepsis as the most urgent unmet medical need in 2017. The emerging biological understanding of the role of RIPK1 in sepsis has opened up an exciting opportunity to explore potent and selective RIPK1 inhibitors as an effective therapeutic strategy for SIRS and sepsis therapy. Herein, we have synthesized a class of highly potent dual‐mode RIPK1 inhibitors occupying both the allosteric and the ATP binding pockets, exemplified by compound 21 ( ZB‐R‐55 ) which is about 10‐fold more potent than GSK2982772 , and exhibits excellent kinase selectivity, good oral pharmacokinetics and good therapeutic effects in the LPS‐induced sepsis model, suggesting that compound ZB‐R‐55 is a highly promising preclinical candidate.
To Play or Not to Play: An Exploratory Content Analysis of Branded Entertainment in Facebook

Field: Business, Management and Accounting (Social Sciences)

Employing the conceptual framework of play themes, this study examined and reported the product categories that presented branded entertainment the most, the different types and features of branded entertainment, and how various play themes were incorporated in branded entertainment in the context of Facebook brand profile pages. The major findings were consistent with the conceptual framework and literature on branded entertainment. Some unexpected findings were also provided and discussed. The line between entertainment and marketing communication has become increasingly blended or even erased during recent years, particularly in the Internet context. Researchers and practitioners are highly interested in the marketing potential of branded entertainment since it may boost brand awareness and build strong consumer‐brand relationships. Little academic research to date has been conducted to systematically study branded entertainment on the Internet. This study is a nascent attempt to understand branded entertainment in user‐centered social networking websites (SNWs), since young users are shifting away from other online media to SNWs. Branded entertainment may help marketers gather segmented yet fun‐seeking SNW users and deliver nonintrusive marketing messages to them.
Multivariate Conditional Copula-GARCD-JSU Model and its Application

Field: Economics, Econometrics and Finance (Social Sciences)

Generalized autoregressive conditional density model provides a useful tool for simulating the probability density function of financial asset return. It is essential for describing the dynamic character of financial asset return comprehensively. Copula function can be used to combine some marginal distributions together. Based on Copula function, multivariate conditional Copula-GARCD-JSU model, a new model, is proposed in the paper. Fortunately, the famous “dimension disaster” in multivariate GARCD model can be overcome by the new model. Furthermore, the estimation and test method for the model are discussed in detail. In empirical analysis, the new model can not only be applied to describe the dynamic character of individual market, but also to simulate the dynamic relation between them.