jimnoneill/paper-to-field-training huggingface dataset:
Variable selection, response adaptive randomization, and covariate-adjusted response-adaptive randomization for personalized medicine

Field: Decision Sciences (Social Sciences)

As the increase of biomarker information, new methods are needed to seek the biomarkers which may be related with the disease outbreak. With the incorporation of the biomarker information, new clinical trial designs are demanded to detect important interactions among treatments and biomarkers, based on both efficiency and ethics. To find the genetic biomarkers related with targeted agents, it is necessary to rely on genetic association study. We proposed a two-steps-method by combining the principal component analysis and Tukey's 1-df method, to improve the problem of power loss in testing gene-gene and gene-environment interactions in association studies. We also apply the proposed methodology to a case-control study designed to investigate the association between Crohn's Disease (CD) and DNA variants in CD related genes. Both the simulated and real data examples demonstrated major power advantages for the proposed methodology over two alternative tests of association. In Response Adaptive Randomization (RAR) designs, patients are dynamically assigned to the treatment groups using a modified allocation probability based on the current observed data. We evaluated the bias of the treatment efficacy estimators in clinical trials with RAR designs. To gain a deeper understanding of the performance of RAR, we study the properties of the response rate estimators through both theoretical derivation and extensive simulation studies. Covariate-adjusted response-adaptive (CARA) designs are expected to become useful techniques for application in the field of personalized medicine. To introduce the mechanisms involved in CARA designs, we applied the logistic regression model to provide a clear exposition. We also conduct a simulation study to comprehend the operating characteristics of the proposed CARA designs for finite samples, including the measures of the degree of balance (in terms of allocation proportions), and ethics (in terms of treatment failure rate).
Oxidative Stress and Cortical Thickness in the Psychosis Spectrum: Investigating Glutathione Metabolism and Antioxidant Defenses in Youth

Field: Neuroscience (Life Sciences)

Introduction Oxidative stress, particularly through disruptions in glutathione metabolism and Total Antioxidant Capacity (TAC), has been implicated in cortical thinning and other brain structural changes seen in psychosis. These changes may be more pronounced in the early psychosis spectrum, but this relationship remains underexplored. Objectives This study investigated the relationships between key oxidative stress markers—reduced glutathione (GSH), oxidized glutathione (GSSG), the GSH/GSSG ratio, and TAC—and cortical thickness in the cingulate, insula, and fronto-temporal brain regions. Methods A total of 57 youths on the early psychosis spectrum and 44 healthy controls participated, with a mean age of 15.51 years. There were no significant differences in age or sex between the groups. Cortical thickness was measured using MRI, and blood samples were analyzed for oxidative stress markers. Partial correlations were performed, controlling for total intracranial volume, age, and sex, to examine the relationships between oxidative stress markers and cortical thickness. A permutation analysis was then conducted to assess group differences in these associations. Results In healthy individuals, a higher GSH/GSSG ratio was significantly associated with increased cortical thickness in the right insula (r = 0.50, p < 0.05). Conversely, in the early psychosis spectrum group, there was a consistent trend of negative correlations between TAC and cortical thickness, particularly in the left frontal cortex. Permutation analysis revealed significant group differences in the association between GSH and cortical thickness in both the left insula and left temporal regions (p < 0.05). Additionally, TAC showed significant differences in its relationship with cortical thickness in the left and right frontal regions (p = 0.01 and p < 0.05), indicating asymmetrical oxidative stress involvement across hemispheres in the early psychosis spectrum group compared to healthy controls. Conclusions These findings suggest that oxidative stress markers, particularly related to glutathione metabolism and TAC, are linked to regional cortical thickness variations. The results highlight distinct oxidative stress effects in the early psychosis spectrum compared to healthy individuals, emphasizing the potential role of oxidative stress markers as early indicators of neuroanatomical changes in psychosis. Disclosure of Interest R. Moreno-Comellas: None Declared, M. Ortuño: None Declared, I. Martínez: None Declared, F. Fesce: None Declared, E. de la Serna: None Declared, J. Castro-Fornieles: None Declared, I. Baeza: None Declared, G. Sugranyes Grant / Research support from: This study has been funded by the Spanish Ministry of Health, Instituto de Salud Carlos III «Health Research Fund»/ FEDER funds (PI2100330, FORT23/00002_SUGR_G6) and La Marató TV3 (grant number 202232-30-31).
Forming‐Free Grain Boundary Engineered Hafnium Oxide Resistive Random Access Memory Devices

Field: Materials Science (Physical Sciences)

Abstract A model device based on an epitaxial stack combination of titanium nitride (111) and monoclinic hafnia (11) is grown onto a c ‐cut Al 2 O 3 ‐substrate to target the role of grain boundaries in resistive switching. The texture transfer results in 120° in‐plane rotated m ‐HfO 2 grains, and thus, in a defined subset of allowed grain boundary orientations of high symmetry. These engineered grain boundaries thread the whole dielectric layer, thereby providing predefined breakdown paths for electroforming‐free resistive random access memory devices. Combining X‐ray diffraction and scanning transmission electron microscopy (STEM)–based localized automated crystal orientation mapping (ACOM), a nanoscale picture of crystal growth and grain boundary orientation is obtained. High‐resolution STEM reveals low‐energy grain boundaries with facing () and (21) surfaces. The uniform distribution of forming voltages below 2 V—within the operation regime—and the stable switching voltages indicates reduced intra‐ and device‐to‐device variation in grain boundary engineered hafnium‐oxide‐based random access memory devices.
Daxx ameliorates abdominal aortic aneurysm through inhibiting the TGF-β1-mediated PI3K/AKT/ID2 signaling pathway

Field: Medicine (Health Sciences)

Background Abdominal aortic aneurysm (AAA) is a potentially life-threatening vascular abnormality, that, if ruptured, is almost universally fatal without repair, and is associated with up to 50% mortality even if repaired in hospital. To date, there is no drug therapy that has clinically proven benefit to reduce or prevent expansion of AAA. The aim of this study was to investigate whether Daxx could affect AAA through inhibiting the PI3K/AKT/ID2 signaling pathway mediated by transforming growth factor β-1 (TGFβ1). Methods The AAA model was constructed by injecting angiotensin Ⅱ (Ang-Ⅱ) into rats, and the Daxx lentivirus vector was constructed. Hematoxylin and eosin (HE) staining was used to detect the wall thickness of the abdominal aorta in rats. The gene and protein expressions in abdominal aortic tissues were detected utilizing western blot, immunohistochemistry (IHC) and fluorescence quantitative real-time polymerase chain reaction (qRT-PCR). Finally, the concentration of TGF-β1 in abdominal aortic tissue was determined by ELISA. Results The abdominal aortic wall thickness was decreased in the Daxx expression group (by HE staining), and Daxx overexpression markedly reduced the protein expression levels of MMP2 and MMP9. Proteins related to the PI3K/AKT/ID2 signaling pathway were highly enhanced in the aneurysm wall of rats, but were reduced following Daxx addition. Moreover, Daxx reduced the damage to elastin (by IHC), and the expression levels of α-SMA and SM22α were up-regulated by Daxx (by qRT-PCR). The concentration of TGF-β1 was correlated with the activation of the PI3K/AKT/ID2 signaling pathway (by ELISA), whereas AKT overexpression weakened the inhibitory effect of Daxx. Conclusion Daxx ameliorated several mechanisms that contributed to expansion of AAA suppressing the tissue concentration of TGF-β1, thereby inhibiting the activation of the PI3K/AKT/ID2 signaling pathway. This evidence might form the basis to develop a therapeutic target for AAA.
To study the role of hematological biomarkers in type 2 diabetes patients with diabetic retinopathy

Field: Medicine (Health Sciences)

Abstract Background: Diabetic retinopathy (DR) is the most common and severe microvascular complication of diabetes mellitus (DM). It is the leading cause of irreversible blindness, and the prevalence is expected to double by 2030. Aim of this study was to compare the hematological biomarkers in diabetics with and without retinopathy. And also, as the grade of retinopathy increased. Methods: The study comprised three groups: DR ( n = 66), NDR ( n = 33), and controls ( n = 33). Detailed workup included HbA1c levels, platelet indices (mean platelet volume (MPV), platelet distribution width (PDW), platelet count, and plateletcrit. Results: The mean age was 54 years. The mean duration of DM was 10 and 4 years in the DR and NDR groups, respectively. MPV values were significantly higher in the DR group (10.77 ± 1.2) than NDR (9.2 ± 1.1) and least in controls (8.3 ± 0.89) ( P = 0.00). These values increased significantly with increasing severity of retinopathy ( P = 0.04). There was a 6.13 times increased risk of developing diabetic retinopathy with increased mean platelet volume (MPV). Mean PDW was significantly higher in the DR group (19.22 ± 2.5) than NDR (13.89 ± 2.9) and least in controls (11.3 ± 2.5) ( P = 0.00). These values increased significantly with increasing severity of retinopathy ( P = 0.00). Other markers were not significant. Conclusion: MPV and PDW are important biomarkers which can predict the development and severity of retinopathy. Therefore, it is suggested that platelet indices be routinely done in diabetic workup. Furthermore, these are conveniently obtained from automated cell counters.
Cerebral mechanisms of hypnotic hypoesthesia. An ERP investigation on the expectancy stage of perception

Field: Neuroscience (Life Sciences)

Abstract The present study aims at identifying reliable markers of neural preparatory processes during hypnosis. To this goal, we recorded the electroencephalographic activity of 23 volunteers regardless of their hypnotizability score. Somatosensory evoked potentials (SEPs) were elicited while participants received non‐painful electrical stimuli on the left median nerve in the conditions of relaxation and hypnosis with suggestions of reduced sensation. SEPs analysis was focused on the pre‐stimulus activity and revealed two main components: the prefrontal negativity (pN) and the somatosensory negativity (sN) over the frontal and parietal areas of the scalp, respectively. Results showed reduced amplitudes for both components under hypnosis, mostly for the pN, suggesting a change of top‐down control of parietal and prefrontal areas. Furthermore, the sLORETA source imaging showed a deactivation of the lateral and anterior portions of the prefrontal cortex (PFC) during the hypnotic state. The present study highlights the downregulation of the PFC as a core aspect of the adopted hypnotic task and confirms the ability of hypnosis to modulate the activity of frontal executive functions. Further, since the majority of participants fell into the medium range of hypnotizability, the present findings could reflect the hypnosis effects in most of the population.
Long-term employment outcomes among partners of patients with early-stage breast cancer.

Field: Medicine (Health Sciences)

12 Background: Undesired work loss comprises one of the many personal costs faced by cancer patients and their families. Multiple studies have described the long-term employment outcomes among patients with early-stage breast cancer, and show that a significant proportion of women face long-term job loss as a result of their cancer diagnosis and treatment. However, little is known about the employment outcomes of partners of breast cancer patients. Methods: Women with non-metastatic breast cancer identified by the Detroit and Los Angeles SEER registries between 6/05-2/07 were surveyed at 9 months (Time 1) and 4 years (Time 2) after diagnosis. Latina and black women were oversampled. Partners were surveyed at Time 2. We performed descriptive analyses of those partners who were not retired at the time they completed the survey. As part of a larger survey assessing the experiences of partners of breast cancer patients, partners were queried regarding the impact of the patient’s breast cancer diagnosis and treatment on their own employment and finances. Results: Of 774 eligible partners, 517 (67%) completed the survey. We included 280 non-retired partners in our analyses. 54% were white, 31% were Latino, and 10% were black. The majority of partners (86%) worked during the year following the patient’s diagnosis and 219 (90%) were working at the time of survey 4 years post-diagnosis. 50% of partners reported that work was a welcome source of support; 32% decreased their work hours as a result of the patient’s breast cancer. In order to maintain health insurance, 64% reported it was very/extremely important to keep their jobs and 51% reported it was very/extremely important to avoid changing jobs. 32% of partners reported their financial status was worse off because of the patient’s breast cancer; 20% were worse off regarding health insurance, and 19% were worse off regarding employment status. Conclusions: In contrast to breast cancer patients, most partners reported long-term job retention. Many partners kept working or avoided changing jobs in order to maintain health insurance. Nearly one-third of partners reported that their financial status was worse off because of the patient’s breast cancer diagnosis and treatment.
The Impact of Climate Change on Exploited Lobster Stocks

Field: Agricultural and Biological Sciences (Life Sciences)

Climate change is predicted to significantly affect the world's oceans, with increases in water temperature,changes in ocean currents, pH levels and winds. This chapter highlights the vulnerabilityof lobster stocks to climate change due to their long larval life. Western and southern rock lobstersin Australia are influenced by long-term increases in water temperatures which are projected tocontinue. These increases have influenced the size at maturity and size of migrating western rocklobsters. Climate change has been implicated in the abundance decline and increase in lobster diseasesin the southern part of the Homarus americanus stock and in the increase in catches in n01thernregions. Regime shift in the north Pacific has been implicated in changes in abundance of Japaneseand Hawaiian spiny lobsters. If the recmitment abundance is vulnerable then monitoring of prerecruitsbecomes very important and management strategies need to be sensitive to abundance trends.This chapter highlights the need to downscale climate change models to a spatial and temporal scalerelevant to lobster stocks and the uncertainties in the climate change projections and their effect onthe ecosystem.
Leukocyte Kinetics in Chronic Myeloid Leukemia: I. DNA Synthesis Time in Blood and Marrow Myelocytes

Field: Medicine (Health Sciences)

Abstract Using a double labeling technic the DNA synthesis time of CML blood myelocytes was found to be 14.2 ± 0.8 hours if all myelocytes were considered, and 13.6 ± 0.6 hours for large myelocytes only. The DNA synthesis time of CML marrow myelocytes did not differ significantly from that for blood myelocytes. These values are indistinguishable from previous estimates of DNA synthesis time in normal granulopoietic precursors.
On the Cardy-Verlinde Entropy Formula in Viscous Cosmology

Field: Physics and Astronomy (Physical Sciences)

The results of the paper of Verlinde [hep-th/0008140], discussing the holographic principle in a radiation dominated universe, are extended when allowing the cosmic fluid to possess a bulk viscosity. This corresponds to a non-conformally invariant theory. The generalization of the Cardy-Verlinde entropy formula to the case of a viscous universe seems from a formal point of view to be possible, although we question on physical grounds some elements in this kind of theory, especially the manner in which the Casimir energy is evaluated. Our discussion suggests that for non-conformally invariant theories the holographic definition of Casimir energy should be modified.
Analýza komplexity procesů souvisejících s auxinem a jejich regulace

Field: Agricultural and Biological Sciences (Life Sciences)

Phytohormone auxin plays an important role in various aspects of plant growth and development. The necessary concentration maxima at the region of its action are achieved by auxin metabolism, passive diffusion of auxin molecules across plasma membrane and by the carrier-mediated auxin transport, as well as by modulation of these processes. In our study we used a group of compounds structurally related to major endogenous auxin indole-3-acetic acid, as well as synthetic auxins 2,4-dichlorophenoxy acetic acid (2,4- D) and naphthalene-1-acetic acid (NAA). We aimed to characterize the auxin specificity of developmentally important processes such as carrier-mediated auxin transport, and 'genomic' (transcriptional) and 'non-genomic' (transcriptional) auxin signaling. In addition to the characterization of these compounds we also hoped to get an insight into the complex regulatory mechanism of auxin-related processes and to possibly find a particular compound with distinct behavior towards particular processes. By making use of such compounds and other molecular tools we aimed to analyze the mechanism of 'non-genomic' auxin signaling, to understand the mode of action of FM (Fei Mao) styryl dyes on the dynamics of membrane- localized auxin transporters, and to study the involvement of other phytohormones...
Characterisation of polyunsaturated fatty acid synthesis in peripheral blood mononuclear cells.

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

Conversion of the essential n-3 (18:3n-3) and n-6 (18:2n-6) fatty acids to longer chain polyunsaturated fatty acids (PUFA) involves sequential desaturation and elongation reactions. Previous studies have reported gender differences in n-3 PUFA synthesis, whereas the effect of age is less clear. n-3 PUFAs are reported to have important effects on immune cell function. A previous study reported long chain PUFA synthesis in mitogen stimulated but not quiescent peripheral blood mononuclear cells (PBMCs). However, the underlying mechanism is not known. \n \nPUFA synthesis was investigated in PBMCs incubated with [1-13C]18:3n-3 for 48 h. Activation with the T-lymphocyte mitogen concanavalin A (Con A) increased PUFA synthesis. 22:6n-3 synthesis was not detected. [1-13C] incorporation was greatest for 20:3n-3 suggesting initial chain elongation is an important fate for 18:3n-3. Con A increased expression of three key genes (FADS2, FADS1 and ELOVL5) involved in PUFA synthesis, suggesting upregulation of the pathway is controlled at the transcriptional level. ELOVL2 expression was negligible, possibly explaining the lack of 22:6n-3 synthesis. Con A increased methylation of 12 CpGs in the FADS2 promoter contradicting the general view that DNA methylation represses transcription. Subsequent 5’RACE analysis verified that activated PBMCs were not using an alternative promoter for FADS2 transcription. Contrary to expectation, 18:3n-3 conversion in activated PBMCs was not affected by gender or menopausal status and there was no clear age effect. \n \nPUFA synthesis was constitutive in the Jurkat T-lymphocyte leukaemic cell-line and was higher than in PBMCs. FADS2, FADS1 and ELOVL5 mRNA expression was also higher in Jurkat cells and was associated with 50% lower methylation of 17 CpGs in the FADS2 promoter, suggesting transcriptional dysregulation of PUFA synthesis in Jurkat cells involves altered DNA methylation. \n \nThese findings have provided novel insights into the regulation of PUFA biosynthesis in PBMCs and upregulation of the pathway in activated PBMCs suggests that newly synthesised PUFAs may be important for cell function.
Implicit Information Transfer via Streaker Bees in a Bio-Inspired Visual Feedback Swarm Framework

Field: Computer Science (Physical Sciences)

Experimentally-consistent engineering models of in-flight sensing and feedback mechanisms of insects in multi-agent flight do not always include a mechanism to direct the swarm. One biologically-motivated hypothesis for aerial swarm direction information transfer is the presence of high speed, informed bees termed ``streaker" bees during swarm flight, whose role has been recorded guiding other uninformed bees to new nesting sites. This paper implements a bio-inspired multi-agent visual feedback system based on an engineering model of optic flow response, and studies the response of a swarm to a minority of streaker agents on fixed trajectories. The performance of the multi-agent feedback system is evaluated in a multi-agent kinematic simulation. The agents are initialized to random initial configurations and the asymptotic swarm heading is found with and without streaker bees. The results indicate that the streaker agents can successfully change the trajectories of the swarm agents towards the streaker agents' trajectories, as quantified by average group orientation shown to change significantly in presence of the streaker agents. These results suggest that bio-inspired feedback models such as wide field integration can incorporate the biological effect of streaker bees in guiding the swarm towards a desired direction, and the position of the streaker bees plays a role in how much influence it has on the swarm agents and their cohesion.
Distribution and Volatilization of Organic Compounds Following Uptake by Hybrid Poplar Trees

Field: Environmental Science (Physical Sciences)

ABSTRACT Hybrid poplar trees were exposed to eleven organic compounds in hydroponic systems. The eleven contaminants were common pollutants with a wide range of physio-chemical properties such as the octanol-water partition coefficient, Henry's constant, vapor pressure, and molecular weight. Contaminants, 14C-labeled, were introduced into the root zone, and contaminant transport and fate were examined. Aqueous concentrations were monitored throughout each experiment as was vapor phase concentrations in the air stream passing over the leaves. At experiment conclusion, plant tissues were oxidized to determine 14C concentrations. The uptake, distribution, and volatilization of these contaminants varied greatly among the 11 contaminants in the study. Uptake and translocation of the contaminants ranged from < 0.3% (of the applied 14C-labeled compound) for 1,2,4-trichlorobenzene to 20% for benzene. Volatile compounds were volatilized from the leaves. Volatilization in the transpiration stream was related to the vapor pressure of the compound. The fate and transport mechanisms investigated in this study provide valuable insight into the potential fate of contaminants in full-scale phytoremediation. KEY WORDS: phytoremediationVOCspoplar