Miracle-dz/UniFAR-FTUs huggingface dataset:
Concentration of free radicals in pea seeds after pre-sowing treatment with magnetic field**

The aim of theresearch was the estimation of seed lot magnetic stimulation effect on free radicals concentration and dynamics of pea seeds germination. The first factor were two cultivars of pea: Rola (traditional form) and Piast (afila type), the second factor were the 3 exposure doses of magnetic field intensity: D0 - no stimulation (control), D1 - 10 750 Jm 3 s and D2 - 85 987 Jm 3 s. The stimulated seeds of both pea forms showed faster uptake of water and achieved larger mass during the seed imbibition in comparison to the seeds without stimulation. It was found that earlier and more steady emergence of these plants was a con- sequence of this process. Pea seedlings which were grown from stimulated seeds achieved in the following successive dates of measurement significantly larger hypocotyl and roots length in comparison to the seedlings without stimulation with magnetic field. A significant increase of free radicals concentration was ob- served in the seeds which were pre-sowing treated with magnetic field. There was no significant effect of the stimulation on the free radicals concentration in the organs of young pea plants grown from seeds of the varieties under examination. Free radicals num- bers in the leaves, stems and roots did not differ significantly from those which were found in the particular organs of plants which were grown from non-stimulated seeds. The laboratory tests did not show any larger number of free radicals in the seeds harvested from the plants which were grown from the stimulated seeds.
Yarn: Adding Meaning to Shared Personal Data through Structured Storytelling

People often do not receive the reactions they desire when they use social networking sites to share data collected through personal tracking tools like Fitbit, Strava, and Swarm. Although some people have found success sharing with close connections or in finding online communities, most audiences express limited interest and rarely respond. We report on findings from a human-centered design process undertaken to examine how tracking tools can better support people in telling their story using their data. 23 formative interviews contribute design goals for telling stories of accomplishment, including a need to include relevant data. We implement these goals in Yarn, a mobile app that offers structure for telling stories of accomplishment around training for running races and completing Do-It-Yourself projects. 21 participants used Yarn for 4 weeks across two studies. Although Yarn’s structure led some participants to include more data or explanation in the moments they created, many felt like the structure prevented them from telling their stories in the way they desired. In light of participant use, we discuss additional challenges to using personal data to inform and target an interested audience.
Serum Zonulin Measured by Commercial Kit Fails to Correlate With Physiologic Measures of Altered Gut Permeability in First Degree Relatives of Crohn's Disease Patients

Intestinal epithelial cell tight junctions (TJs) contribute to the integrity of the intestinal barrier allowing for control of the physical barrier between external antigens or bacterial products and the internal environment. Zonula occludens-1 (ZO-1) is a protein that modulates intestinal TJs, and serum levels of ZO-1 has been suggested as a biomarker of disrupted barrier function in humans. Previous studies suggested that increased intestinal permeability was associated with evidence of TJ abnormalities. However, there is limited information on the serological measurement of ZO-1 and its relation to other tests of barrier function in healthy subjects. We investigated the correlation of serum ZO-1, with physiologic measures of intestinal permeability (as the ratio of the fractional excretion of lactulose-mannitol or LMR) in a cohort of 39 healthy FDRs of Crohn's disease (CD) patients. No significant correlation was found between LMR and ZO-1 levels (r2 = 0.004, P < 0.71), or intestinal fatty acid binding proteins (I-FABP) (r2 = 0.004, P < 0.71). In conclusion, our data show that ZO-1 and I-FABP are not a marker of gut permeability as defined by LMR.
Clinical Characteristics of Severe COVID-19 Patients Admitted to an Intensive Care Unit in Lombardy During the Italian Pandemic

Italy was one of the worst affected European countries during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. More than 50% of Italian cases occurred in the northern region of Lombardy, where the saturation of health services between March and April 2020 forced hospitals to allocate patients according to available resources. Eighteen severe coronavirus disease 2019 (COVID-19) patients were admitted to our hospital needing intensive support. Given the disease fatality, we investigated the patients' characteristics to identify mortality predictors. We counted seven deaths from multiple organ failure, two from septic shock, and two from collapsed lungs. The maximum case fatality was observed in patients who contracted SARS-CoV-2 in hospitals. The fatal outcome was associated with the following baseline characteristics: polymorbidity (OR 2.519, p = 0.048), low body mass index (OR 2.288, p = 0.031), low hemoglobin (OR 3.012, p = 0.046), and antithrombin III (OR 1.172, p = 0.048), along with a worsening of PaO2/FiO2 ratio in the first 72 h after admission (OR 1.067, p = 0.031). The occurrence of co-infections during hospitalization was associated with a longer need for intensive care (B = 4.511, p = 0.001). More information is needed to inform intensive care for patients with severe COVID-19, but our findings would certainly contribute to shed some light on this unpredictable and multifaceted disease.
Impact of Distracting Emotional Stimuli on the Characteristics of Movement Performance: A Kinematic Study

It is well-documented that emotional stimuli impact both the cognitive and motor aspects of “goal-directed” behavior. However, how emotional distractors impact motor performance remains unclear. This study aimed to characterize how movement quality was impacted during emotional distractors. We used a modified oddball paradigm and documented the performance of pure movement. Participants were designated to draw a triangle or a polygon, while an emotional stimulus was presented. Speed was assessed using reaction time and movement time. The quality and precision of movement were assessed by calculating the accuracy and root-mean-square error (RMSE). Compared to drawings of triangles, polygons had higher accuracy under negative stimuli, but lower RMSE under positive stimuli. The results indicate that distracting emotional stimuli impact different aspects of movement quality, with movement complexity influencing accuracy under negative distractors and precision under positive distractors. This study provides further evidence that movement precision is an important feature of emotional embodiment that should be incorporated in future studies.
Colony Stimulating Factor 1 Receptor in Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is an aggressive heterogeneous blood cancer derived from hematopoietic stem cells. Tumor-stromal interactions in AML are of importance for disease development and therapy resistance, and bone marrow stroma seem like an attractive therapeutic target. Of particular interest is colony stimulating factor 1 receptor (CSF1R, M-CSFR, c-FMS, CD115) and its role in regulating plasticity of tumor-associated macrophages. We discuss first the potential of CSF1R-targeted therapy as an attractive concept with regards to the tumor microenvironment in the bone marrow niche. A second therapy approach, supported by preclinical research, also suggests that CSF1R-targeted therapy may increase the beneficial effect of conventional and novel therapeutics. Experimental evidence positioning inhibitors of CSF1R as treatment should, together with data from preclinical and early phase clinical trials, facilitate translation and clinical development of CSF1R-targeted therapy for AML.
Morphological and Genetic Recovery of Coral Polyps After Bail-Out

Contemporary advances in microfluidic and molecular techniques have enabled coral studies to shift from reef and colony scales to polyp- and molecular-level investigations. Polyp bail-out provides an alternative approach to acquire solitary polyps for studies at finer scales. Although induction of polyp bail-out has been reported in several studies, polyp health after bail-out has not been investigated. In this study, we monitored morphological and genetic changes in Pocillopora acuta polyps after bail-out induced by hyperosmosis. In isosmotic conditions, over 80% of bailed-out polyps survived, of which half regenerated normal polyp morphology within 5 days, including a polarized polyp body, extended tentacles, and a distinguishable oral disk. In contrast, the remaining polyps degenerated into tissue ball-like structures that resemble multicellular aggregates reported in earlier studies. In morphologically recovered polyps, transcriptomic analysis showed that ∼87% of genes altered during bail-out induction recovered from stress status, suggesting resumption of metabolism, cell division, and immunity, while in degenerated polyps, only ∼71% of genes recovered. Quantitative polymerase chain reaction data further demonstrated that genetic recovery of energy production, cell proliferation, and immune response was achieved in morphologically recovered polyps within 3 days after bail-out, but was not fully accomplished in degenerated polyps even after 5 days. Our findings indicate that solitary polyps generated by hyperosmosis-induced bail-out can recover rapidly from physiological stress under laboratory conditions, suggesting that bailed-out polyps could be used as new models for coral research.
A Retrospective Comparative Study in Patients With Cocaine Use Disorder Comorbid With Attention Deficit Hyperactivity Disorder Undergoing an rTMS Protocol Treatment

Background: Adult attention-deficit/hyperactivity disorder (ADHD) is associated with high comorbidity with other psychiatric diseases, including cocaine use disorder (CocUD). Given the common fronto-striatal dysfunction, ADHD patients often use cocaine as self-medication for ameliorating symptoms by increasing striatal dopamine release. Yet, comorbidity with ADHD is related to poor treatment outcomes. CocUD has been treated with transcranial magnetic stimulation (TMS), but no studies investigated the outcomes in patients comorbid with ADHD. Methods: Twenty-two ADHD/CocUD and 208 CocUD-only participants received a high-frequency (15 Hz) rTMS treatment stimulating the left-DLPFC. We investigated whether both groups of patients shared similar demographic and clinical characteristics at baseline. Then, we monitored the effect of treatment testing for potential differences between groups. Results: At baseline demographic, toxicology and clinical features were not different between the two groups except for global severity index (GSI from SCL-90): patients of ADHD/CocUD group reported higher general symptomatology compared to the CocUD-only group. Concerning the effect of treatment, both groups significantly improved over time regarding cocaine use, craving, and other negative affect symptoms. No differences were observed between groups. Conclusions: To our knowledge, this is the first study comparing the demographic characterization and rTMS clinical improvements of patients with a dual diagnosis of ADHD and CocUD against CocUD-only patients. Cocaine use and common self-reported withdrawal/abstinence symptoms appear to benefit from rTMS treatment with no differences between groups. Future studies are needed to further investigate these preliminary results.
The Combined Effects of Increased pCO2 and Warming on a Coastal Phytoplankton Assemblage: From Species Composition to Sinking Rate

In addition to ocean acidification, a significant recent warming trend in Chinese coastal waters has received much attention. However, studies of the combined effects of warming and acidification on natural coastal phytoplankton assemblages here are scarce. We conducted a continuous incubation experiment with a natural spring phytoplankton assemblage collected from the Bohai Sea near Tianjin. Experimental treatments used a full factorial combination of temperature (7 and 11°C) and pCO2 (400 and 800 ppm) treatments. Results suggest that changes in pCO2 and temperature had both individual and interactive effects on phytoplankton species composition and elemental stoichiometry. Warming mainly favored the accumulation of picoplankton and dinoflagellate biomass. Increased pCO2 significantly increased particulate organic carbon to particulate organic phosphorus (C:P) and particulate organic carbon to biogenic silica (C:BSi) ratios, and decreased total diatom abundance; in the meanwhile, higher pCO2 significantly increased the ratio of centric to pennate diatom abundance. Warming and increased pCO2 both greatly decreased the proportion of diatoms to dinoflagellates. The highest chlorophyll a biomass was observed in the high pCO2, high temperature phytoplankton assemblage, which also had the slowest sinking rate of all treatments. Overall, there were significant interactive effects of increased pCO2 and warming on dinoflagellate abundance, pennate diatom abundance, diatom vs. dinoflagellates ratio and the centric vs. pennate ratio. These findings suggest that future ocean acidification and warming trends may individually and cumulatively affect coastal biogeochemistry and carbon fluxes through shifts in phytoplankton species composition and sinking rates.
Cholinesterase is Associated With Prognosis and Response to Chemotherapy in Advanced Gastric Cancer

Background: Cholinesterase (CHE) is a routine serum biomarker in gastric cancer (GC). However, little research has been done on its clinical value in advanced GC. In addition, it is not clear whether it can be used as biomarker for the response and prognosis of advanced GC patients. Methods: Between Jan. 2013 and Dec. 2016, a total of 150 patients with advanced GC treated with first-line chemotherapy were admitted to Changzhou Tumor Hospital Affiliated to Soochow University. We retrospectively identified serum CHE level on the day before chemotherapy and at the end of chemotherapy and abstracted clinicopathologic features and treatment outcomes. Univariate and multivariate survival analyses were performed to assess the relationship between serum CHE levels and progression-free survival (PFS) and overall survival (OS). Results: A total of 150 advanced GC patients were included and divided into serum level ≥5,000 IU/L and serum level <5,000 IU/L. CHE level lower than 5,000 IU/L was associated with poorer PFS (HR, 1.60; 95% CI, 1.141–2.243; p = 0.006), poorer OS (HR, 1.76; 95% CI, 1.228–2.515; p = 0.002) and trend of poorer response (HR, 0.56; 95% CI, 0.272–1.129; p = 0.104). In univariate and multivariate logistic regression analysis, only liver metastasis and PS score were significantly associated with objective response (p < 0.05). The medium PFS was 8.0 months in patients with post-treatment CHE increased vs. 3.8 months in patients with CHE decreased after chemotherapy (HR, 1.82; 95% CI 1.28–2.57; p = 0.0002). The medium OS was 13.1 months in patients with increased post-treatment CHE vs. 8.1 months in patients with decreased post-treatment CHE (HR, 1.87; 95% CI 1.29–2.71; p = 0.0002). Conclusion: Advanced GC with CHE levels below 5,000 IU/L was significantly associated with poor PFS and OS. The results suggested that CHE analysis before chemotherapy was a promising prognostic marker for advanced GC.
Dinitroaniline Herbicide Resistance and Mechanisms in Weeds

Dinitroanilines are microtubule inhibitors, targeting tubulin proteins in plants and protists. Dinitroaniline herbicides, such as trifluralin, pendimethalin and oryzalin, have been used as pre-emergence herbicides for weed control for decades. With widespread resistance to post-emergence herbicides in weeds, the use of pre-emergence herbicides such as dinitroanilines has increased, in part, due to relatively slow evolution of resistance in weeds to these herbicides. Target-site resistance (TSR) to dinitroaniline herbicides due to point mutations in α-tubulin genes has been confirmed in a few weedy plant species (e.g., Eleusine indica, Setaria viridis, and recently in Lolium rigidum). Of particular interest is the resistance mutation Arg-243-Met identified from dinitroaniline-resistant L. rigidum that causes helical growth when plants are homozygous for the mutation. The recessive nature of the TSR, plus possible fitness cost for some resistance mutations, likely slows resistance evolution. Furthermore, non-target-site resistance (NTSR) to dinitroanilines has been rarely reported and only confirmed in Lolium rigidum due to enhanced herbicide metabolism (metabolic resistance). A cytochrome P450 gene (CYP81A10) has been recently identified in L. rigidum that confers resistance to trifluralin. Moreover, TSR and NTSR have been shown to co-exist in the same weedy species, population, and plant. The implication of knowledge and information on TSR and NTSR in management of dinitroaniline resistance is discussed.
ThermoScan: Semi-automatic Identification of Protein Stability Data From PubMed

During the last years, the increasing number of DNA sequencing and protein mutagenesis studies has generated a large amount of variation data published in the biomedical literature. The collection of such data has been essential for the development and assessment of tools predicting the impact of protein variants at functional and structural levels. Nevertheless, the collection of manually curated data from literature is a highly time consuming and costly process that requires domain experts. In particular, the development of methods for predicting the effect of amino acid variants on protein stability relies on the thermodynamic data extracted from literature. In the past, such data were deposited in the ProTherm database, which however is no longer maintained since 2013. For facilitating the collection of protein thermodynamic data from literature, we developed the semi-automatic tool ThermoScan. ThermoScan is a text mining approach for the identification of relevant thermodynamic data on protein stability from full-text articles. The method relies on a regular expression searching for groups of words, including the most common conceptual words appearing in experimental studies on protein stability, several thermodynamic variables, and their units of measure. ThermoScan analyzes full-text articles from the PubMed Central Open Access subset and calculates an empiric score that allows the identification of manuscripts reporting thermodynamic data on protein stability. The method was optimized on a set of publications included in the ProTherm database, and tested on a new curated set of articles, manually selected for presence of thermodynamic data. The results show that ThermoScan returns accurate predictions and outperforms recently developed text-mining algorithms based on the analysis of publication abstracts. Availability: The ThermoScan server is freely accessible online at https://folding.biofold. org/thermoscan. The ThermoScan python code and the Google Chrome extension for submitting visualized PMC web pages to the ThermoScan server are available at https://github.com/biofold/ThermoScan.
Detection of Parkinson's Disease Through Automated Pupil Tracking of the Post-illumination Pupillary Response

Parkinson's disease (PD) is one of the most common neurodegenerative disorders, but it is often diagnosed after the majority of dopaminergic cells are already damaged. It is critical to develop biomarkers to identify the disease as early as possible for early intervention. PD patients appear to have an altered pupillary response consistent with an abnormality in photoreceptive retinal ganglion cells. Tracking the pupil size manually is a tedious process and offline automated systems can be prone to errors that may require intervention; for this reason in this work we describe a system for pupil size estimation with a user interface to allow rapid adjustment of parameters and extraction of pupil parameters of interest for the present study. We implemented a user-friendly system designed for clinicians to automate the process of tracking the pupil diameter to measure the post-illumination pupillary response (PIPR), permit manual corrections when needed, and continue automation after correction. Tracking was automated using a Kalman filter estimating the pupil center and diameter over time. The resulting system was tested on a PD classification task in which PD subjects are known to have similar responses for two wavelengths of light. The pupillary response is measured in the contralateral eye to two different light stimuli (470 and 610 nm) for 19 PD and 10 control subjects. The measured Net PIPR indicating different responsiveness to the wavelengths was 0.13 mm for PD subjects and 0.61 mm for control subjects, demonstrating a highly significant difference (p < 0.001). Net PIPR has the potential to be a biomarker for PD, suggesting further study to determine clinical validity.
Modeling Microtubule Counterion Distributions and Conductivity Using the Poisson-Boltzmann Equation

Microtubules are highly negatively charged proteins which have been shown to behave as bio-nanowires capable of conducting ionic currents. The electrical characteristics of microtubules are highly complicated and have been the subject of previous work; however, the impact of the ionic concentration of the buffer solution on microtubule electrical properties has often been overlooked. In this work we use the non-linear Poisson Boltzmann equation, modified to account for a variable permittivity and a Stern Layer, to calculate counterion concentration profiles as a function of the ionic concentration of the buffer. We find that for low-concentration buffers ([KCl] from 10 μM to 10 mM) the counterion concentration is largely independent of the buffer's ionic concentration, but for physiological-concentration buffers ([KCl] from 100 to 500 mM) the counterion concentration varies dramatically with changes in the buffer's ionic concentration. We then calculate the conductivity of microtubule-counterion complexes, which are found to be more conductive than the buffer when the buffer's ionic concentrations is less than ≈100 mM and less conductive otherwise. These results demonstrate the importance of accounting for the ionic concentration of the buffer when analyzing microtubule electrical properties both under laboratory and physiological conditions. We conclude by calculating the basic electrical parameters of microtubules over a range of ionic buffer concentrations applicable to nanodevice and medical applications.