Miracle-dz/UniFAR-FTUs huggingface dataset:
Battery-free, skin-interfaced microfluidic/electronic systems for simultaneous electrochemical, colorimetric, and volumetric analysis of sweat

Battery-free, wireless microfluidic/electronic system for multiparameter sweat analysis. Wearable sweat sensors rely either on electronics for electrochemical detection or on colorimetry for visual readout. Non-ideal form factors represent disadvantages of the former, while semiquantitative operation and narrow scope of measurable biomarkers characterize the latter. Here, we introduce a battery-free, wireless electronic sensing platform inspired by biofuel cells that integrates chronometric microfluidic platforms with embedded colorimetric assays. The resulting sensors combine advantages of electronic and microfluidic functionality in a platform that is significantly lighter, cheaper, and smaller than alternatives. A demonstration device simultaneously monitors sweat rate/loss, pH, lactate, glucose, and chloride. Systematic studies of the electronics, microfluidics, and integration schemes establish the key design considerations and performance attributes. Two-day human trials that compare concentrations of glucose and lactate in sweat and blood suggest a potential basis for noninvasive, semi-quantitative tracking of physiological status.
A Novel Concept of Fundus-Ovary-Salpinx-Para-Aorta Implantation Promoting Unit during Human Embryo Implantation

Human embryo implantation is mainly regulated by the endocrine system. Since the ovary, fallopian tube, and fundus can directly communicate through the mesosalpinx and ovarian ligament, the local concentration of progesterone in the pathway of the developing embryo is considered to be higher than in systemic blood circulation. The immune system promotes embryo implantation by stimulating progesterone production of the ovary and by inducing endometrial differentiation. The recognition of the developing embryo in the fallopian tube by the immune system is achieved through the para-aortic lymph nodes. On the basis of the above evidence, the autologous immune cells activated in vitro were demonstrated to improve clinical pregnancy rates in patients with repeated implantation failures. In addition, the autonomic nerve system that innervates the fundus, the ovary, and the fallopian tube from the para-aortic region is proposed to regulate the environment of the pathway of the developing embryo. From these findings, we suppose that a unique unilateral functional unit to promote human embryo implantation exists in the pathway of the developing embryo including the para-aortic regions and propose naming this novel functional unit the Fundus-Ovary-Salpinx-Para-aorta Implantation Promoting unit (FOSPa-IP unit).
Bacteria: A novel source for potent mosquito feeding-deterrents

This study provides evidence that insect-killing bacteria produce fabclavines that can be used to deter mosquito feeding. Antibiotic and insecticidal bioactivities of the extracellular secondary metabolites produced by entomopathogenic bacteria belonging to genus Xenorhabdus have been identified; however, their novel applications such as mosquito feeding-deterrence have not been reported. Here, we show that a mixture of compounds isolated from Xenorhabdus budapestensis in vitro cultures exhibits potent feeding-deterrent activity against three deadly mosquito vectors: Aedes aegypti, Anopheles gambiae, and Culex pipiens. We demonstrate that the deterrent active fraction isolated from replicate bacterial cultures is highly enriched in two compounds consistent with the previously described fabclavines, strongly suggesting that these are the molecular species responsible for feeding-deterrence. The mosquito feeding-deterrent activity in the putative fabclavine-rich fraction is comparable to or better than that of N,N-diethyl-3-methylbenzamide (also known as DEET) or picaridin in side-by-side assays. These findings lay the groundwork for research into biologically derived, peptide-based, low–molecular weight compounds isolated from bacteria for exploitation as mosquito repellents and feeding-deterrents.
SAT: Free Software for the Semi-Automated Analysis of Rodent Brain Sections With 2,3,5-Triphenyltetrazolium Chloride Staining

Ischemic stroke places an increasing burden on individuals, families, and societies around the world. However, effective therapies or drugs for ischemic stroke are lacking. Therefore, animal models mimicking ischemic stroke in humans are of great value for preclinical experiments. middle cerebral artery occlusion (MCAO) in mice or rats and subsequent 2,3,5-triphenyltetrazolium chloride (TTC) staining of brain sections are common methods in the study of experimental animal ischemic stroke. In this study, we present and assess the utility of the semi-automated analysis of the TTC staining (SAT) software program, a novel, small, user-friendly, and free software program, in the quantification of the infarct size in rodent brain sections, with TTC staining, by analyzing images captured by cell phones or scan systems. We performed MCAO and TTC staining in adult mice. We then utilized the SAT software and Image J to analyze the infarct size in the brain sections with TTC staining and compared the findings of the two analysis methods. We found that the data on infarct size from SAT and from Image J were comparable, suggesting that the SAT software could be an alternative option to Image J in the evaluation of ischemic stroke.
Shared Gene Expression Between Multiple Sclerosis and Ischemic Stroke

Patients with multiple sclerosis (MS) appear to have an increased risk of ischemic stroke (IS). Although MS and IS have very different phenotypes, gene-based and pathway-based analyses of large-scale genome-wide association studies (GWAS) have increasingly enhanced our understanding of these two diseases. Whether there are common molecular mechanisms connecting MS and IS is still unclear. Here, we describe the outcome of gene-based test and pathway-based analysis of GWAS datasets that explored potential gene expression links between MS and IS. After identifying significant gene sets individually of MS and IS, we performed pathway-based analysis in four biological pathway databases (KEGG, PANTHER, REACTOME, and WikiPathways) and GO categories. We discovered that there were 9 shared pathways between MS and IS in KEGG, 2 in PANTHER, 14 in REACTOME, 1 in WikiPathways, and 194 in GO annotations (p < 0.05). These results provide an improved understanding about possible shared mechanisms and treatments strategies for MS and IS. They also provide some basis for further studies of how these two diseases are linked at the molecular level.
Measures and Approaches in Trait-Based Phytoplankton Community Ecology – From Freshwater to Marine Ecosystems

Trait-based approaches to investigate (short- and long-term) phytoplankton dynamics and community assembly have become increasingly popular in freshwater and marine science. Although the nature of the pelagic habitat and the main phytoplankton taxa and ecology are relatively similar in both marine and freshwater systems, the lines of research have evolved, at least in part, separately. We compare and contrast the approaches adopted in marine and freshwater ecosystems with respect to phytoplankton functional traits. We note differences in study goals relating to functional trait use that assess community assembly and those that relate to ecosystem processes and biogeochemical cycling that affect the type of characteristics assigned as traits to phytoplankton taxa. Specific phytoplankton traits relevant for ecological function are examined in relation to herbivory, amplitude of environmental change and spatial and temporal scales of study. Major differences are identified, including the shorter time scale for regular environmental change in freshwater ecosystems compared to that in the open oceans as well as the type of sampling done by researchers based on site-accessibility. Overall, we encourage researcher to better motivate, why they apply trait-based analyses to their studies and to make use of process-driven approaches, which are more common in marine studies. We further propose fully comparative trait studies conducted along the habitat gradient spanning freshwater to brackish to marine systems or along geographic gradients. Such studies will benefit from the combined strength of both fields.
Automated Detection of High-Frequency Oscillations in Epilepsy Based on a Convolutional Neural Network

Epilepsy is one of the most common chronic neurological diseases. High-frequency oscillations (HFOs) have emerged as promising biomarkers for the epileptogenic zone. However, visual marking of HFOs is a time-consuming and laborious process. Several automated techniques have been proposed to detect HFOs, yet these are still far from being suitable for application in a clinical setting. Here, ripples and fast ripples from intracranial electroencephalograms were detected in six patients with intractable epilepsy using a convolutional neural network (CNN) method. This approach proved more accurate than using four other HFO detectors integrated in RIPPLELAB, providing a higher sensitivity (77.04% for ripples and 83.23% for fast ripples) and specificity (72.27% for ripples and 79.36% for fast ripples) for HFO detection. Furthermore, for one patient, the Cohen's kappa coefficients comparing automated detection and visual analysis results were 0.541 for ripples and 0.777 for fast ripples. Hence, our automated detector was capable of reliable estimates of ripples and fast ripples with higher sensitivity and specificity than four other HFO detectors. Our detector may be used to assist clinicians in locating epileptogenic zone in the future.
Ecological Niche Modeling of Three Species of Stenella Dolphins in the Caribbean Basin, With Application to the Seaflower Biosphere Reserve

Dolphins of the genus Stenella occur in pelagic waters of both tropical and warm-temperate oceans. Three species, the Atlantic spotted dolphin (Stenella frontalis), the pantropical spotted dolphin (S. attenuata), and the spinner dolphin (S. longirostris) are abundant worldwide, but in the Caribbean Basin they have been poorly studied and information on their distribution patterns is scarce. Specifically, in Colombia’s remote Seaflower Biosphere Reserve (SFBR) S. attenuata has been reported occasionally, but S. frontalis and S. longirostris have never been recorded before. To address this information gap, an ecological niche modeling approach was used to determine the potential distribution patterns of these three dolphin species in the region. Records of these species for the Caribbean Basin were compiled, including both published and unpublished data. Environmental information, including bathymetry, bathymetric slope, distance to shore, sea surface temperature, sea surface salinity, and chlorophyll-a concentration was gathered from public databases (MARSPEC and Bio-ORACLE) in raster format. The maximum entropy algorithm (Maxent) for modeling species’ geographic distributions with presence-only data was used. After filtering the data, 210 records of S. attenuata, 204 of S. frontalis, and 80 of S. longirostris were used to run models. The best configuration for each model was chosen based on the ΔAICc criterion. For all three species, the final ecological niche models returned AUC test values higher than 0.8, indicating satisfactory model performance. The resulting potential distribution maps suggested that areas closest to continental shorelines of the Caribbean Basin and surrounding islands had the highest environmental suitability for all species (>70%). All models reported high environmental suitability for S. attenuata and S. longirostris in the SFBR, mainly in the southernmost part surrounding San Andres and Providence Archipelago. Assessment of niche overlap from the predictions of species distributions using the similarity statistic and pairwise map overlap indicated that S. frontalis and S. longirostris had niches slightly more similar in comparison to S. attenuata. As this was a first effort to fill a gap in our understanding of the distribution of species in the genus Stenella in the Caribbean Basin, further studies are necessary using both niche modeling and biological/ecological approaches.
Plant Genome Engineering for Targeted Improvement of Crop Traits

To improve food security, plant biology research aims to improve crop yield and tolerance to biotic and abiotic stress, as well as increasing the nutrient contents of food. Conventional breeding systems have allowed breeders to produce improved varieties of many crops; for example, hybrid grain crops show dramatic improvements in yield. However, many challenges remain and emerging technologies have the potential to address many of these challenges. For example, site-specific nucleases such as TALENs and CRISPR/Cas systems, which enable high-efficiency genome engineering across eukaryotic species, have revolutionized biological research and its applications in crop plants. These nucleases have been used in diverse plant species to generate a wide variety of site-specific genome modifications through strategies that include targeted mutagenesis and editing for various agricultural biotechnology applications. Moreover, CRISPR/Cas genome-wide screens make it possible to discover novel traits, expand the range of traits, and accelerate trait development in target crops that are key for food security. Here, we discuss the development and use of various site-specific nuclease systems for different plant genome-engineering applications. We highlight the existing opportunities to harness these technologies for targeted improvement of traits to enhance crop productivity and resilience to climate change. These cutting-edge genome-editing technologies are thus poised to reshape the future of agriculture and food security.
EBV Viral Loads in Diagnosis, Monitoring, and Response Assessment

The quantification of circulating Epstein Barr virus (EBV) DNA loads has played an important role in the diagnosis and management of EBV-associated lymphoid malignancies. Viral load measurement is particularly useful for monitoring EBV-DNA in hematopoietic stem cell transplant patients, and for assessing the prognosis or response to therapy of EBV-associated intractable lymphomas like extranodal NK/T-cell lymphoma, nasal type. Cell-free EBV-DNA in plasma can be used as a biomarker for estimating the severity or prognosis of these lymphomas. In addition to plasma, whole blood has been used for the management of transplant patients. Although measuring EBV-DNA has been useful, there is a lack of standardization and the optimal specimens for measuring viral loads are unknown. This can be attributed to the different forms of EBV-DNA that exist in peripheral blood and the different pathologies that result from diverse EBV disease states. As a result, guidelines for EBV diagnosis or the initiation of treatment are unclear. However, the newly established World Health Organization standard for EBV quantification will encourage collaborative studies across institutions and countries to establish proper guidelines for EBV diagnosis and the initiation of treatment.
Anodal tDCS and High-Frequency tRNS Targeting the Occipitotemporal Cortex Do Not Always Enhance Face Perception

There has been increasing interest in the utility of transcranial electrical stimulation as a tool to enhance cognitive abilities. In the domain of face perception, enhancements have been reported for both transcranial direct current stimulation (tDCS) and high-frequency transcranial random noise stimulation (tRNS) targeting the occipitotemporal cortex. In a series of two experiments, we attempted to replicate these findings for face identity perception, and extend on previous studies, to determine if similar enhancements are also observed for object and facial expression perception. In Experiment 1, using a single blind, between-subjects design in healthy volunteers (N = 53), we examined whether anodal tDCS over the occipitotemporal cortex enhanced performance on tasks involving perception of face identity, facial expression, and object stimuli, when compared to sham stimulation. We failed to replicate previous findings of enhanced performance on face and object perception, nor extend findings to facial expression perception. In Experiment 2, using a single blind, between-subjects design (N = 39), we examined the effect of high-frequency tRNS over the occipitotemporal cortex using the same three tasks employed in Experiment 1. We failed to replicate previous findings of enhanced face perception following high-frequency tRNS over the occipitotemporal cortex, relative to sham stimulation (although we used different stimulation parameters to that employed in a previous study). We also found no evidence of enhanced facial expression and object perception following high-frequency tRNS. The findings align with a growing body of studies that have failed to replicate previously reported enhancements following administration of tDCS and hint for different efficacy of, on first sight, related stimulation protocols. Future studies should explore the foundation of these differential effects in greater detail.
A Preliminary Study Investigating Maternal Neurocognitive Mechanisms Underlying a Child-Supportive Parenting Intervention

Although interventions that promote child-supportive parenting for children have been shown to positively impact caregiving behaviors as well as child behavioral and neurobiological functioning, less is known about which aspects of maternal brain functioning are affected by such interventions. In the present study, we conducted a preliminary evaluation of the impact of the Filming Interactions to Nurture Development (FIND) video coaching program on mothers with at least one child age four or younger. We employed a waitlist control design with pre-post data. Compared to mothers in the control condition (n = 16), mothers who received FIND (n = 16) showed changes in neural measures of inhibitory control and behavioral measures of parenting self-evaluation during a series of functional neuroimaging tasks. Specifically, we found a group by time interaction in clusters in the left inferior frontal gyrus (IFG) and insula for the Correct Stop > Correct Go contrast of the stop signal task (SST), where FIND increased brain activity associated with inhibitory control compared to mothers in the control condition; and FIND increased mothers’ endorsement of child-supportive parenting traits in the parenting self-evaluation task (PSET). Exploratory moderators, study limitations, and the implications of these findings for strength-based parenting programs are discussed.
The Association of Depressive Symptoms With Brain Volume Is Stronger Among Diabetic Elderly Carriers of the Haptoglobin 1-1 Genotype Compared to Non-carriers

Aim: Depression is highly prevalent in type 2 diabetes and is associated with lower adherence to medical treatments, worse glycemic control, and increased risk for diabetes-related complications. The mechanisms underlying depression in type 2 diabetes are unclear. The haptoglobin (Hp) genotype is associated with type 2 diabetes related complications including increased risk for cerebrovascular pathology and worse cognitive performance. Its relationship with depression is unknown. We investigated the role of Hp genotype on the association of depression with brain and white matter hyperintensities (WMH) volumes. Methods: Depressive symptoms (measured with the 15-item Geriatric Depression Scale), brain MRI, and Hp genotypes, were examined in elderly subjects with type 2 diabetes [29 (13.8%) Hp 1–1 carriers and 181 (86.2%) non-carriers]. The interaction of Hp genotype with number of depressive symptoms on regional brain measures was assessed using regression analyses. Results: The significant interactions were such that in Hp 1–1 carriers but not in non-carriers, number of depressive symptoms was associated with overall frontal cortex (p = 0.01) and WMH (p = 0.04) volumes but not with middle temporal gyrus volume (p = 0.43). Conclusions: These results suggest that subjects with type 2 diabetes carrying the Hp 1–1 genotype may have higher susceptibility to depression in the context of white matter damage and frontal lobe atrophy. The mechanisms underlying depression in diabetes may differ by Hp genotype.
The Role of P53 Exonuclease in Accuracy of DNA Synthesis and Sensitivity to Nucleoside Analogs in Various Compartments of Cells

Genomic DNA is susceptible to a variety of mutagenic processes. The maintenance of the stability of genetic material, which is an important and essential feature of every living or‐ ganism, depends on an accurate DNA replication [1]. Organisms across all kingdoms have developed diverse and highly efficient repair mechanisms to safeguard the genome from deleterious consequences of various kinds of stresses that might tend to destabilize the in‐ tegrity of the genome. DNA is constantly being damaged. A low fidelity of DNA synthesis in various compartments of the cells by main replicative DNA polymerases leads to genom‐ ic instability (mutator phenotype) [2]. The errors produced during DNA synthesis could re‐ sult from three fidelity determining processes: a)nucleotide misinsertion into the nascent DNA, b)lack of exonucleolytic proofreading activity, i.e the mechanism to identify and ex‐ cise incorrect nucleotide incorporated during DNA synthesis, and c)extension of mismatch‐ ed 3’-termini of DNA [3]. Failure to repair DNA can lead to mutations, genomic instability, chromosomal abnormalities, progression of cancer and premature aging.
Using a Treebank to study Weak and Strong Object Re exives in Dutch LASSY case study

In this case study, we explain how to use the lassy treebank for studying the distribution of weak and strong object re exives in Dutch. The results of this work have been published elsewhere as Bouma and Spenader (2009). Here we concentrate on the technical aspects of gathering the data, and some of the statistical manipulation we did on the basis of this. The linguistic motivation for carrying out this research is a conjecture by Haspelmath, which says that the probability of using a strong re exive increases if the governing verb is a verb that in general has a strong tendency to be used non-re exively. To study this hypothesis, we need counts for the number of times a verb is used re exively and nonre exively, and, for the re exive uses, counts for the number of times a weak and a strong re exive pronoun is used. As will become clear below, various subtleties play a role in deciding what counts as a relevant case of non-re exive and re exive use, and in deciding how to distinguish verbs (i.e. on the basis of form or meaning). We start with an overview of the research question in Bouma and Spenader (2009). Next, we explain how the relevant data collection was carried out, on the basis the LASSY Large Corpus, a large newspaper corpus that was automatically annotated (by Alpino) with syntactic dependency trees. The data was analyzed using the statistics package R. We also document this part of the research. Finally, we give the results of Bouma and Spenader (2009).