Miracle-dz/UniFAR-FTUs huggingface dataset:
Prey capture in zebrafish larvae serves as a model to study cognitive functions

Prey capture in zebrafish larvae is an innate behavior which can be observed as early as 4~days postfertilization, the day when they start to swim. This simple behavior apparently involves several neural processes including visual perception, recognition, decision-making, and motor control, and, therefore, serves as a good model system to study cognitive functions underlying natural behaviors in vertebrates. Recent progresses in imaging techniques provided us with a unique opportunity to image neuronal activity in the brain of an intact fish in real-time while the fish perceives a natural prey, paramecium. By expanding this approach, it would be possible to image entire brain areas at a single-cell resolution in real-time during prey capture, and identify neuronal circuits important for cognitive functions. Further, activation or inhibition of those neuronal circuits with recently developed optogenetic tools or neurotoxins should shed light on their roles. Thus, we will be able to explore the prey capture in zebrafish larvae more thoroughly at cellular levels, which should establish a basis of understanding of the cognitive function in vertebrates.
Protective Effect of 2,4′,5′-Trihydroxyl-5,2′-dibromo diphenylmethanone, a New Halophenol, against Hydrogen Peroxide-Induced EA.hy926 Cells Injury

Vascular endothelial cells produce reactive oxygen species (ROS) during the process of energy metabolism in aerobic respiration. A growing body of evidence indicates that excessive ROS is implicated in the pathogenesis of cardiovascular diseases including atherosclerosis. The newly synthesized halophenol, 2,4′,5′-trihydroxyl-5,2′-dibromo diphenylmethanone (TDD), exhibits antioxidative and cytoprotective activities in vitro. In this study, the protective effect of TDD against hydrogen peroxide (H2O2)-induced oxidative injury of EA.hy926 cells was investigated. Cell viability was measured by 3-(4,5-dimethylthiazol-2-yl)-2,5-dephenyltetrazolium bromide (MTT) assay, while the effect of TDD on the transcription profile of EA.hy926 cells subjected to H2O2-induced oxidative injury was evaluated by microarray analysis. Several signaling pathways, including apoptosis, were significantly associated with TDD. Flow cytometric analysis was used to evaluate anti-apoptotic effect of TDD. Subsequently, RT-PCR and Western blot were used to detect the expressions of the apoptosis-associated protein, Bcl-2 and Bax. Meanwhile the expression of cleaved caspase-3, an executioner of apoptosis, was also detected by Western blot. The results showed that pretreatment of EA.hy926 cells with TDD prevented the decrease of cell viability induced by H2O2, and attenuated H2O2-induced elevation of Bax and cleaved caspase-3 while increased Bcl-2 expressions. In summary, TDD inhibited H2O2-induced oxidative injury of EA.hy926 cells through negative regulation of apoptosis. These findings suggest that TDD is a potential candidate for therapeutic intervention in oxidative stress-associated cardiovascular diseases.
Water Quality Analysis of the San Pedro River and Proposal of a Water Treatment Design for its Use as a Water Source for a Communitarian Irrigation Project

The majority of developing countries are currently facing a lack of renewable fresh water resources, especially in rural communities, threatening agricultural productivity. These communities’ agriculture currently depends solely on precipitation, resulting in low crop productivity and erosion of the land. The objective of this study was to analyze the San Pedro River as a water source for a communitarian irrigation project, based on water quality analysis and water demand estimation for irrigation purposes. The analysis determined that the San Pedro River could not be used as irrigation water without prior treatment, since parameters such as potassium, fecal coliforms and total suspended solids exceeded the national standards for irrigation water, presenting concentrations of 12 mg L-1, 8000 UFC 100 mL-1 and 353 mg L-1, respectively. The biological analysis revealed ABI index values between 3 and 14, determining that the river is highly contaminated. In order to treat and reduce the concentration of these parameters between 75 and 90% a horizontal sub superficial flow wetland treatment was proposed. The irrigation water demand for the 226 ha of the agricultural land of the Lumbisi Community was estimated to be of 0.05 m3 s-1 based on crop evapotranspiration and it was used as the design flow rate for the system. The proposed wetland design presents a retention time of 2.2 days and a superficial area of 9495 m2. The estimation of effluent pollutant concentration shows that the proposed treatment would allow the San Pedro River´s water to meet national standards for irrigation water except for potassium.
Laparoscopic versus open transhiatal esophagectomy for distal and junction cancer.

BACKGROUND the only curative treatment for esophageal cancer is surgical resection. This treatment is associated with a high morbidity rate and long in-hospital recovery period. Both transthoracic and transhiatal esophagectomies are performed worldwide. The transhiatal approach may reduce the respiratory infection rate in compromised patients with distal esophageal and gastro-esophageal (GE) cancers. Minimally invasive esophagectomy could further improve post-operative outcome. Two cohorts of laparoscopic and open transhiatal esophagectomy for cancer were compared for short- and long-term outcome. METHODS from January 2001 through December 2004, 50 patients who underwent laparoscopic transhiatal esophagectomy were compared to a historical group of 50 patients who had undergone open transhiatal esophagectomy between January 1998 and December 2000. Post-operative management was identical in both groups. RESULTS no significant differences were seen between the two groups with regard to baseline characteristics and oncological parameters including resection margin (R0 82 vs. 74%, p = 0.334) and 5-year survival. Operation time did not differ significantly between the groups. (300 vs. 280 min, p = 0.110). Median hospital stay and intensive care unit stay were significantly shorter in the laparoscopic group (13 vs. 16 days, p = 0.001 and 1 vs. 3 days, p = 0.000 respectively). CONCLUSION minimally invasive transhiatal esophagectomy is feasible and has the same oncological outcome as open transhiatal esophagectomy. Faster recovery without a significant longer operation time could be the major benefit of the laparoscopic transhiatal approach. To our knowledge, this is the largest comparative study in literature comparing laparoscopic transhiatal with open transhiatal esophagectomy for cancers of distal and GE junction. Randomized trials are needed to further clarify the role of laparoscopic transhiatal approach for esophageal cancer.
Physical Activity and the Strength of the Lumbar Spine

The cadaveric lumbar spines of nine young men killed in road accidents were subjected to a range of mechanical tests, and the results compared with the men's occupational and recreational histories. It was found that the compressive strength of the spines tended to increase with the level of physical activity in life, but the increase was significant only in the eight spines aged 18 or over. Compressive failure usually occurred in the vertebral body, but in three cases, the disc prolapsed into the vertebral canal; these discs came from three of the four most physically active individuals. It is concluded that physical activity strengthens both the vertebrae and the discs. A high level of activity can cause vertebral strength to exceed that of the discs.
Eif-2a Protects Brainstem Motoneurons in a Murine Model of Sleep Apnea

Obstructive sleep apnea is associated with neural injury and dysfunction. Hypoxia/reoxygenation exposures, modeling sleep apnea, injure select populations of neurons, including hypoglossal motoneurons. The mechanisms underlying this motoneuron injury are not understood. We hypothesize that endoplasmic reticulum injury contributes to motoneuron demise. Hypoxia/reoxygenation exposures across 8 weeks in adult mice upregulated the unfolded protein response as evidenced by increased phosphorylation of PERK [PKR-like endoplasmic reticulum (ER) kinase] in facial and hypoglossal motoneurons and persistent upregulation of CCAAT/enhancer-binding protein-homologous protein (CHOP)/growth arrest and DNA damage-inducible protein (GADD153) with nuclear translocation. Long-term hypoxia/reoxygenation also resulted in cleavage and nuclear translocation of caspase-7 and caspase-3 in hypoglossal and facial motoneurons. In contrast, occulomotor and trigeminal motoneurons showed persistent phosphorylation of eIF-2a across hypoxia/reoxygenation, without activations of CHOP/GADD153 or either caspase. Ultrastructural analysis of rough ER in hypoglossal motoneurons revealed hypoxia/reoxygenation-induced luminal swelling and ribosomal detachment. Protection of eIF-2α phosphorylation with systemically administered salubrinal throughout hypoxia/reoxygenation exposure prevented CHOP/GADD153 activation in susceptible motoneurons. Collectively, this work provides evidence that long-term exposure to hypoxia/reoxygenation events, modeling sleep apnea, results in significant endoplasmic reticulum injury in select upper airway motoneurons. Augmentation of eIF-2a phosphorylation minimizes motoneuronal injury in this model. It is anticipated that obstructive sleep apnea results in endoplasmic reticulum injury involving motoneurons, whereas a critical balance of phosphorylated eIF-2a should minimize motoneuronal injury in obstructive sleep apnea.
Differentiating multiple system atrophy from Parkinson’s disease: contribution of striatal and midbrain MRI volumetry and multi-tracer PET imaging

Objectives: The differential diagnosis between typical idiopathic Parkinson’s disease (PD) and the striatonigral variant of multiple system atrophy (MSA-P) is often difficult because of the presence of signs and symptoms common to both forms of parkinsonism, particularly at symptom onset. This study investigated striatal and midbrain findings in MSA-P and PD patients in comparison with normal controls with the use of positron emission tomography (PET) and three dimensional magnetic resonance imaging (3D MRI) based volumetry to increase the differential diagnostic accuracy between both disease entities. Methods: Nine patients with MSA-P, 24 patients with PD, and seven healthy controls were studied by MRI and PET with 6-[18F]-fluoro-L-dopa (FDOPA), [18F]fluoro-deoxyglucose (FDG), and 11-C-Raclopride (RACLO). Striatal and extrastriatal volumes of interest (VOI) were calculated on the basis of the individual MRI data. The PET data were transferred to the VOI datasets and subsequently analysed. Results: MSA-P differed significantly from PD patients in terms of decreased putaminal volume, glucose metabolism, and postsynaptic D2 receptor density. The striatal FDOPA uptake was equally impaired in both conditions. Neither MRI volumetry nor PET imaging of the midbrain region further contributed to the differential diagnosis between PD and MSA-P. Conclusions: The extent and spatial distribution of functional and morphological changes in the striatum permit the differentiation of MSA-P from PD. Both, multi-tracer PET and 3D MRI based volumetry, may be considered equivalent in the assessment of different striatal abnormality in both disease entities. In contrast, MRI and PET imaging of the midbrain does not provide a further gain in diagnostic accuracy.
Emergence and Spread of Community-Associated Methicillin-Resistant Staphylococcus aureus in Rural Wisconsin, 1989 to 1999

ABSTRACT We investigated the emergence and spread of community-associated strains of methicillin-resistant Staphylococcus aureus (CA-MRSA) in central and northern Wisconsin by determining the temporal and clonal relationships and geographic expansion among 581 of 956 clinical isolates of MRSA collected between 1989 and 1999. Based on EcoRI plasmid profiles (PP), two types, PP-11 and PP-13, were highly stable over time and were consistently associated with multidrug-sensitive strains recovered from outpatients treated at Native American community clinics. Pulsed-field gel electrophoresis (PFGE) yielded six major clonal groups (MCGs) and 19 minor clonal groups. The six MCGs represented 82% of the isolates. All strains with either PP-11 or -13 were present in MCG-2. Eighty-nine percent of the isolates in MCG-2 originated from Native American clinics, and 90% belonged to two PFGE types (19 and 20), the types associated with an outbreak of MRSA in a Native American community in 1992. MCG-2 isolates were multidrug sensitive, harbored type IVa staphylococcal cassette chromosome mec, and were very closely related by PFGE to the Midwestern CA-MRSA strain MW2. MCG-2 strains were mostly obtained from skin infections and affected patients with a mean age of 24 (±18.0) years. MCG-2 strains spread to four additional Native American communities and 20 other communities. Our findings suggest that CA-MRSA in Wisconsin likely originated in Native American communities in the early 1990s and since has become widespread throughout the state. Two early CA-MRSA strains (WI-33 and WI-34) in Wisconsin represent progenitors of the MW2 strain, based on their almost indistinguishable genotypic characteristics.
Lipid-Altering Therapy and Atrial Fibrillation

Atrial fibrillation (AF) is a common cardiac arrhythmia with significant morbidity and public health cost. Because of limitations of efficacy and safety of conventional antiarrhythmic agents, alternative therapies for AF are needed. The potential antiarrhythmic properties of lipid-altering therapy, including the 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitors and fish oils, are increasingly recognized, particularly in light of their potential anti-inflammatory properties. This review examines the known effects of lipid-altering therapy on atrial arrhythmias in both experimental and clinical settings. Inflammatory states, such as postcardiac surgery and AF of recent onset, show promise as targets. In contrast, lipid-lowering therapy is less likely to affect longstanding persistent AF. Current recommendations for the use of lipid-altering therapy for prevention and treatment of AF are summarized.
Failed Stabilization for Long-Term Potentiation in the Auditory Cortex of Fmr1 Knockout Mice

Fragile X syndrome is a developmental disorder that affects sensory systems. A null mutation of the Fragile X Mental Retardation protein 1 (Fmr1) gene in mice has varied effects on developmental plasticity in different sensory systems, including normal barrel cortical plasticity, altered ocular dominance plasticity and grossly impaired auditory frequency map plasticity. The mutation also has different effects on long-term synaptic plasticity in somatosensory and visual cortical neurons, providing insights on how it may differentially affect the sensory systems. Here we present evidence that long-term potentiation (LTP) is impaired in the developing auditory cortex of the Fmr1 knockout (KO) mice. This impairment of synaptic plasticity is consistent with impaired frequency map plasticity in the Fmr1 KO mouse. Together, these results suggest a potential role of LTP in sensory map plasticity during early sensory development.
Cycle Lengths and Correlation Properties of Finite Precision Chaotic Maps

This paper investigates cycle and transient lengths of spatially discretized chaotic maps with respect to different initial condition values. By investigating cycle lengths and their correlation properties using fixed point arithmetic, it is observed that for different initial condition values only a limited number of cycles occur for each resolution and rounding type. Additionally, it is seen that cycles with the same length are actually identical due to intersections between pseudo trajectories. The drawbacks of this situation are demonstrated for chaos based cryptosystems that use initial conditions as key. It is shown that highly correlated outputs for different initial conditions cause serious security vulnerabilities, although the statistical tests indicate otherwise. Finally, correlations in the perturbed systems are discussed.
On the Number of Samples Needed to Learn the Correct Structure of a Bayesian Network

Bayesian Networks (BNs) are useful tools giving a natural and compact representation of joint probability distributions. In many applications one needs to learn a Bayesian Network (BN) from data. In this context, it is important to understand the number of samples needed in order to guarantee a successful learning. Previous work have studied BNs sample complexity, yet it mainly focused on the requirement that the learned distribution will be close to the original distribution which generated the data. In this work, we study a different aspect of the learning, namely the number of samples needed in order to learn the correct structure of the network. We give both asymptotic results, valid in the large sample limit, and experimental results, demonstrating the learning behavior for feasible sample sizes. We show that structure learning is a more difficult task, compared to approximating the correct distribution, in the sense that it requires a much larger number of samples, regardless of the computational power available for the learner.
From Odor Molecules to Plume Tracking: An Interdisciplinary, Multilevel Approach to Olfaction in Stomatopods1

Abstract Like many marine crustaceans, mantis shrimp rely on their sense of smell to find food, mates, and habitat. In order for olfaction to function, odorant molecules in the surrounding fluid must gain access to the animal's chemosensors. Thus fluid motion is important for olfaction, both in terms of the large scale fluid movements (currents, waves, etc.) that advect the odorants to the vicinity of the sensors, and the small-scale viscosity dominated flows that determine odorant access to the surface of the sensor. In order to understand how stomatopods interpret their chemical environment, I investigated how stomatopod chemosensory morphology and the movement of the structures bearing the chemosensors affect fluid access to the sensor surface in Gonodactylaceus mutatus. Preliminary results from new directions are presented, including mathematical modeling of molecular flux at the sensor surface, field studies of the effects of ambient flow on odor sampling behavior, and flume experiments testing the ability of stomatopods to trace odor plumes. Finally, I show how the use of multiple techniques from several disciplines leads to new ideas about the functional morphology of stomatopod antennules.
The DOCA-Salt Hypertensive Rat as a Model of Cardiovascular Oxidative and Inflammatory Stress

Oxidative stress and inflammation are two sides of the same coin that are intricately combined to elicit a chronic pathophysiological stress state, especially as seen in cardiovascular remodelling. In this review, we argue that administration of deoxycorticosterone acetate (DOCA) and sodium chloride to uninephrectomised rats, defined as DOCA-salt hypertensive rats, provides a reliable animal model of oxidative and inflammatory stress in the cardiovascular system. The supporting evidence includes pathophysiological and biochemical changes together with pharmacological responses to synthetic and natural compounds that lower the concentrations of reactive free radical species and that curtail inflammatory responses in the cardiovascular system.
Collection of cell-free DNA for genomic analysis of solid tumors in a clinical laboratory setting

The breadth of diagnostic procedures that utilize cell free DNA (cfDNA) from human plasma has increased dramatically in recent years. Here, we confirm that tumor-derived cfDNA fragments are similar in size distribution to cfDNA derived from normal tissues. Therefore, collection procedures optimized with healthy donor specimens are likely to be applicable to the diagnosis and monitoring of many different cancer types. We verify that the distribution and DNA sequences of fragmentation sites in cfDNA from both normal-germline and tumor-derived cfDNA are non-random. A broad survey of cfDNA from healthy donors suggests that average individuals possess ~6 ng of cfDNA per mL of plasma. Importantly, the cfDNA present in plasma samples that were initially collected as whole blood in K2-EDTA tubes and subsequently processed by centrifugation is stable for several days at ambient temperatures. This observation has the potential to significantly reduce the cost and logistical complexity of shipping clinical samples from the site of collection to centers proficient in diagnostic analysis. Finally, plasma samples collected with high-volume plasma collection devices possess abundant quantities of cfDNA. Since the quantity of analyzed cfDNA is directly proportional to sensitivity of diagnostic assays, this method of plasma collection, where available, could enable highly sensitive post-treatment disease monitoring and early detection of cancer in at-risk individuals.
Assessment of natural variation in the first pore domain of the tomato HKT1;2 transporter and characterization of mutated versions of SlHKT1;2 expressed in Xenopus laevis oocytes and via complementation of the salt sensitive athkt1;1 mutant

Single Nucleotide Polymorphisms (SNPs) within the coding sequence of HKT transporters are important for the functioning of these transporters in several plant species. To unravel the functioning of HKT transporters analysis of natural variation and multiple site-directed mutations studies are crucial. Also the in vivo functioning of HKT proteins, via complementation studies performed with athkt1;1 plants, could provide essential information about these transporters. In this work, we analyzed the natural variation present in the first pore domain of the HKT1;2 coding sequence of 93 different tomato accessions, which revealed that this region was conserved among all accessions analyzed. Analysis of mutations introduced in the first pore domain of the SlHKT1;2 gene showed, when heterologous expressed in Xenopus laevis oocytes, that the replacement of S70 by a G allowed SlHKT2;1 to transport K+, but also caused a large reduction in both Na+ and K+ mediated currents. The study of the transport characteristics of SlHKT1;2 revealed that Na+-transport by the tomato SlHKT1;2 protein was inhibited by the presence of K+ at the outside of the membrane. GUS expression under the AtHKT1;1 promoter gave blue staining in the vascular system of transgenic Arabidopsis. athkt1;1 mutant plants transformed with AtHKT1;1, SlHKT1;2, AtHKT1;1S68G, and SlHKT1;2S70G indicated that both AtHKT1;1 and SlHKT1;2 were able to restore the accumulation of K+ in the shoot, although the low accumulation of Na+ as shown by WT plants was only partially restored. The inhibition of Na+ transport by K+, shown by the SlHKT1;2 transporter in oocytes (and not by AtHKT1;1), was not reflected in Na+ accumulation in the plants transformed with SlHKT1;2. Both AtHKT1;1-S68G and SlHKT1;2-S70G were not able to restore the phenotype of athkt1;1 mutant plants.
Supporting map-based wayfinding with tactile cues

Paper maps are a proven means for navigating in unfamiliar environments, however, they do not prevent people from getting lost or taking unwanted detours. A well-known issue is interpreting the map's geocentric content, which is known to become prone to errors when the map is not aligned to the environment. In this paper we report our investigation of providing a cue about the destination's location from an egocentric perspective in order to improve the interpretation of the map. We used a vibrotactile belt to continuously indicate a destination's direction relative to the user's orientation. In an outdoor field study we compared the performance of map-based navigation with and without the added tactile cue. We found evidence that people take shorter routes, consult the map less often, and were less often disoriented with the tactile cue. Furthermore, females found the tactile cue more useful and used it more often.