Miracle-dz/UniFAR-FTUs huggingface dataset:
Organelle transport in melanophores analyzed by white light image correlation spectroscopy

Intracellular transport of organelles, vesicles and proteins is crucial in all eukaryotic cells, and is accomplished by motor proteins that move along cytoskeletal filaments. A widely used model of intracellular transport is Xenopus laevis melanophores. These cells help the frog to change color by redistributing melanin‐containing organelles in the cytoplasm. The high contrast of the pigment organelles permits changes in distribution to be observed by ordinary light microscopy; other intracellular transport systems often require fluorescence labeling. Here we have developed white light Image Correlation Spectroscopy (ICS) to monitor aggregation and dispersion of pigment. Hitherto in ICS, images of fluorescent particles from Confocal Laser Scanning Microscopy (CLSM) have been used to calculate autocorrelation functions from which the density can be obtained. In the present study we show that ICS can be modified to enable analysis of light‐microscopy images; it can be used to monitor pigment aggregation and dispersion, and distinguish between different stimuli. This new approach makes ICS applicable not only to fluorescent but also to black‐and‐white images from light or electron microscopy, and is thus very versatile in different studies of movement of particles on the membrane or in the cytoplasm of cells without potentially harmful fluorescence labeling and activation.
Recruitment of MBD1 to target genes requires sequence-specific interaction of the MBD domain with methylated DNA

MBD1, a member of the methyl-CpG-binding domain family of proteins, has been reported to repress transcription of methylated and unmethylated promoters. As some MBD1 isoforms contain two DNA-binding domains—an MBD, which recognizes methylated DNA; and a CXXC3 zinc finger, which binds unmethylated CpG—it is unclear whether these two domains function independently of each other or if they cooperate in facilitating recruitment of MBD1 to particular genomic loci. In this report we investigate DNA-binding specificity of MBD and CXXC3 domains in vitro and in vivo. We find that the methyl-CpG-binding domain of MBD1 binds more efficiently to methylated DNA within a specific sequence context. We identify genes that are targeted by MBD1 in human cells and demonstrate that a functional MBD domain is necessary and sufficient for recruitment of MBD1 to specific sites at these loci, while DNA binding by the CXXC3 motif is largely dispensable. In summary, the binding preferences of MBD1, although dependent upon the presence of methylated DNA, are clearly distinct from those of other methyl-CpG-binding proteins, MBD2 and MeCP2.
Virtual reality posttraumatic stress disorder (PTSD) exposure therapy results with active duty OIF/OEF service members

Abstract Posttraumatic stress disorder (PTSD) is reported to be caused by exposure to traumatic events including (but not limited to) military combat, violent personal assault, being kidnapped or taken hostage and terrorist attacks. Initial data suggest that at least 1 out of 6 Iraq War veterans are exhibiting symptoms of depression, anxiety and PTSD. Virtual reality (VR) delivered exposure therapy for PTSD has been used with reports of positive outcomes. The aim of the current paper, is to present the rationale and brief description of a Virtual Iraq/Afghanistan PTSD VR therapy application and present initial findings from its use with PTSD patients. Thus far, Virtual Iraq/Afghanistan consists of a series of customizable virtual scenarios designed to represent relevant Middle Eastern VR contexts for exposure therapy, including a city and desert road convoy environment. User-centered design feedback, needed to iteratively evolve the system, was gathered from returning Iraq War veterans in the USA and from a system deployed in Iraq and tested by an Army Combat Stress Control Team. Results from an open clinical trial at San Diego Naval Medical Center of the first 20 treatment completers indicate that 16 no longer met PTSD screening criteria at post-treatment, with only one not maintaining treatment gains at 3 month follow-up.
Epistemic needs and learned helplessness

This study assesses the impact of non‐specific epistemic needs—the need for structure and the fear of invalidity—on expectancy of control and performance following unsolvable problems. Subjects answered a questionnaire tapping their non‐specific epistemic needs and were exposed to either no feedback or failure in unsolvable problems. Then their expectancies of control and performance were assessed. The results showed that a high need for structure was associated with a transfer of the expectancy of uncontrollability and worse performance following failure. The results are discussed in terms of Kruglanski's lay epistemic theory.
Interphase cytogenetics of melanocytic neoplasms: numerical aberrations of chromosomes can be detected in interphase nuclei using centromeric DNA probes

This study shows that fluorescence in situ hybridization (FISH) to thin sections cut from paraffin‐embedded material can lie used to distinguish between groups of melanocytic neoplasms and thus may be useful as an investigational and diagnostic tool. FISH with a probe for a repealed, alpha satellite sequence specific to chromosome 17 was used to investigate the chromosomal composition of dysplastic (or Clark's nevus) and Spitz's nevi and malignant melanomas. Hybridization was to thin (∼6 μm) sections cut from paraffin blocks. The number of signals per nucleus in normal diploid cells is expected to be less than 2 since the sections are thinner than one nuclear diameter. Keratinocytes and lymphocytes m these same sections showed 1–2 signals per nucleus with a mean of 1.2. Dysplastic nevi showed 1–4 hybridization signals per nucleus with a mean of 1.5. Spitz's nevi showed 1–2 signals per nucleus with a mean of 1.3. Melanomas showed 1–6 signals per nucleus with a mean of 2.1. We were thus able to use FISH to demonstrate differences in chromosome numbers between groups of benign and malignant melanocytic neoplasms. Technical improvements in the near future can be expected lo result in more precise estimates of chromosomal number.
Cardiovascular Risk Factors Associated With Blood Metabolite Concentrations and Their Alterations During a 4-Year Period in a Population-Based Cohort

Background—The effects of lifestyle risk factors considered collectively on the human metabolism are to date unknown. We aim to investigate the association of these risk factors with metabolites and their changes during 4 years. Methods and Results—One hundred and sixty-three metabolites were measured in serum samples with the AbsoluteIDQ kit p150 (Biocrates) following a targeted metabolomics approach, in a population-based cohort of 1030 individuals, aged 45 to 83 years at baseline. We evaluated associations between metabolite concentrations (28 acylcarnitines, 14 amino acids, 9 lysophosphocholines, 72 phosphocholines, 10 sphingomyelins and sum of hexoses) and 5 lifestyle risk factors (body mass index [BMI], alcohol consumption, smoking, diet, and exercise). Multilevel or simple linear regression modeling adjusted for relevant covariates was used for the evaluation of cross-sectional or longitudinal associations, respectively; multiple testing correction was based on false discovery rate. BMI, alcohol consumption, and smoking were associated with lipid metabolism (reduced lyso- and acyl-alkyl-phosphatidylcholines and increased diacylphosphatidylcholines concentrations). Smoking showed positive associations with acylcarnitines, and BMI correlated inversely with nonessential amino acids. Fewer metabolites showed relative changes that were associated with baseline risk factors: increases in 5 different acyl-alkyl phosphatidylcholines were associated with lower alcohol consumption and BMI and with a healthier diet. Increased levels of tyrosine were associated with BMI. Sex-specific effects of smoking and BMI were found specifically related to acylcarnitine metabolism: in women higher BMI and in men more pack-years were associated with increases in acylcarnitines. Conclusions—This study showed sex-specific effects of lifestyle risks factors on human metabolism and highlighted their long-term metabolic consequences.
Assessment of Muscle Contractile Properties at Acute Moderate Altitude Through Tensiomyography.

Under hypoxia, alterations in muscle contractile properties and faster fatigue development have been reported. This study investigated the efficacy of tensiomyography (TMG) in assessing muscle contractile function at acute moderate altitude. Biceps femoris (BF) and vastus lateralis (VL) muscles of 18 athletes (age 20.1 ± 6.1 years; body mass 65.4 ± 13.9 kg; height 174.6 ± 9.5 cm) were assessed at sea level and moderate altitude using electrically evoked contractions on two consecutive days. Maximum radial displacement (Dm), time of contraction (Tc), reaction time (Td), sustained contraction time (Ts), and relaxation time (Tr) were recorded at 40, 60, 80, and 100 mA. At altitude, VL showed lower Dm values at 40 mA (p = 0.008; ES = -0.237). Biceps femoris showed Dm decrements in all electrical stimulations (p < 0.001, ES > 0.61). In VL, Tc was longer at altitude at 40 (p = 0.031, ES = 0.56), and 100 mA (p = 0.03, ES = 0.51). Regarding Td, VL showed significant increases in all electrical intensities under hypoxia (p ≤ 0.03, ES ≥ 0.33). TMG appears effective at detecting slight changes in the muscle contractile properties at moderate altitude. Further research involving TMG along with other muscle function assessment methods is needed to provide additional insight into peripheral neuromuscular alterations at moderate altitude.
Prospective evaluation of analgesic use and risk of renal cell cancer.

BACKGROUND Epidemiologic data suggest that analgesic use increases the risk of renal cell cancer (RCC), but few prospective studies have been published. We investigated the association between analgesic use and RCC in 2 large prospective studies. METHODS We examined the relationship between analgesic use and RCC risk in the Nurses' Health Study and the Health Professionals Follow-up Study. Use of aspirin, other nonsteroidal anti-inflammatory drugs (NSAIDs), and acetaminophen was ascertained in 1990 in the Nurses' Health Study and in 1986 in the Health Professionals Follow-up Study, and every 2 years thereafter. We evaluated baseline and duration of use of analgesics. RESULTS During follow-up of 16 years among 77,525 women and 20 years among 49,403 men, we documented 333 RCC cases. Aspirin and acetaminophen use were not associated with RCC risk. However, regular use of nonaspirin NSAIDs was associated with an increased RCC risk; the pooled multivariate relative risk was 1.51 (95% confidence interval, 1.12-2.04) at baseline. The absolute risk differences for users vs nonusers of nonaspirin NSAIDs were 9.15 per 100 000 person-years in women and 10.92 per 100,000 person-years in men. There was a dose-response relationship between duration of nonaspirin NSAID use and RCC risk; compared with nonregular use, the pooled multivariate relative risks were 0.81 (95% confidence interval, 0.59-1.11) for use less than 4 years, 1.36 (0.98-1.89) for 4 to less than 10 years, and 2.92 (1.71-5.01) for use for 10 or more years (P < .001 for trend). CONCLUSION Our prospective data suggest that longer duration of use of nonaspirin NSAIDs may increase the risk of RCC.
Poxvirus-Induced Immunostimulating Effects on Porcine Leukocytes

ABSTRACT The prophylactic application of inactivated parapox ovis viruses (Baypamun; Bayer AG, Leverkusen, Germany) has been shown to reduce efficiently the outbreak of stress-mediated diseases in different species. However, little is known about the basic mechanism behind this observed stimulatory property. We therefore tested eight inactivated poxvirus strains belonging to three different genera (Orthopoxvirus, Avipoxvirus, andParapoxvirus) for their capacity to activate cells of the porcine innate and specific immune systems in vitro. The results indicated that poxviruses failed to induce increased phagocytosis, oxidative burst, or natural killer cell activity in swine. In contrast, enhanced release of interleukin-2, alpha interferon, and gamma interferon, as well as strong proliferation, could be measured. Flow cytometric analyses and cell sorting experiments identified T-helper cells as the main target responding to inactivated poxviruses: the activated cells had a CD4high CD25+ major histocompatibility complex type II-positive phenotype and were the major source of secreted cytokines. Together, the results demonstrated that all tested poxviruses possessed immunostimulating capacity. These in vitro poxvirus-induced effects may be responsible at least in part for the in vivo immunostimulating capacity of inactivated poxviruses.
Acute Cognitively Engaging Exergame-Based Physical Activity Enhances Executive Functions in Adolescents

The study aimed to elucidate the influence of cognitive engagement comprised in an acute bout of exergame-based physical activity on executive functions (inhibition, cognitive flexibility) in adolescents. Therefore, the level of cognitive engagement and the intensity of physical activity were systematically varied across three experimental conditions. Sixty-five healthy male adolescents (13–16 years) were randomly assigned to one of three conditions: (a) physical activity with high levels of cognitive engagement during active video gaming, (b) physical activity with low levels of cognitive engagement during active video gaming, (c) sedentary with low levels of cognitive engagement during passive video watching. Manipulation checks, including subjective and objective operationalizations of cognitive engagement, were applied. Executive functions were assessed before and after each condition using the D-KEFS design fluency test. Results showed that cognitive engagement, operationalized by subjects’ ratings and heart rate variability, differed between conditions. The physical activity condition with a high level of cognitive engagement resulted in significantly better performance in cognitive flexibility compared to conditions with low levels of cognitive engagement. Regarding benefits for executive functions in male adolescents, the results indicate that acute physical activity with high cognitive engagement could be more efficient than physical activity of the same intensity with low cognitive engagement. Even though further evidence is needed, these results extend previous research and suggest a methodological approach for measuring cognitive engagement.
Ieee Transactions on Visualization and Computer Graphics Combining Hierarchy and Energy for Drawing Directed Graphs

— We present an algorithm for drawing directed graphs, which is based on rapidly solving a unique one-dimensional optimization problem for each of the axes. The algorithm results in a clear description of the hierarchy structure of the graph. Nodes are not restricted to lie on fixed horizontal layers, resulting in layouts that convey the symmetries of the graph very naturally. The algorithm can be applied without change to cyclic or acyclic digraphs, and even to graphs containing both directed and undirected edges. We also derive a hierarchy index from the input digraph, which quantitatively measures its amount of hierarchy.
Resistance effects on hydraulic instability

<Q* *•* tm c^e. •y „u„UUUv, ^-^ have ^n ^e concerning the flow of water down an inclined open channel. Hydrauiicians have evolved empirical laws in confusing multiplicity to de^ciibe a uniform flow a<s a function of the slope and the resistance caused by friction with the channel walls and by turbulence. Each of the laws has its own best rarge of applicability, but most aw of the same basic type, vu. the effective resistance is considered in the momentum equation as an opposing body force of form —Xu*/y", u being the velocity, y the "hydraulic radius" and X a coefficient describing the channel roughness, which in this notation is independent of u and y. The exponents m, n > 0 have specific values characteristic of the different formulas. For a wide rectangular channel, y will be also the depth of the water. A uniform (turbulent) flow with a free surface, being subject to some such resistance law, sometimes reaches a condition of instability, then changes into a complicated progressing wave pattern called "roll v.avcs" which are periodic in distance, with the profile moving downstream faster than the water particles. Mathematical analyses have been made of certain aspects of the final roll wave motion by Thomas [1] and one of the present authors [21. Results giving necessary criteria have been obtained by conridering the correct elope o£ the roll wave profile or by satisfying the energy inequality at the moving discontinuities (bores). Our present purpose, however, is rather to investigate the instability of the original uniform flow in its dependence ttpon the specific resistance function assumed, following the method of Jeffreys [3] who first did thus in 1925 for the Chezy formula (n » 2, m — 1 in our present notation). The criterion obtained by Jeffreys for instability is identical with the condition later obtained for roll wave formation in [1] and [2]. Each of the papers [1], [2] and {? } used the Chezy resistance fuuetiuu. In 1940 Keulegan and Patterson [4] derived a stability criterion for the Manning formula, based upon an expression for wave celerity due to Boussincsq. Another type of stability argument was later used by Vedernikov [51, using certain approximations of Saint Venant. His method is rather complicated, but the results are applicable for a general resistance term. More recently Craya [6] has refined this approach by considering the growth of an infinitesimal shock ("elementary wave") with results applying also in the case of a general resistance. From the qualitative standpoint, Cornish [7], with appendix by Harold Jeffreys, has presented some interesting remarks on the formation of roll waves with respect to the resistive action of the stream bed.
Associations between Oxidized LDL to LDL Ratio, HDL and Vascular Calcification in the Feet of Hemodialysis Patients

Cardiovascular mortality is associated with vascular calcification (VC) in hemodialysis (HD) patients. The present study was designed to find factors related with medial artery calcification on the plain radiography of feet by comparing C-reactive protein (CRP), plasminogen activator inhibitor type 1 (PAI-1) and lipid profile including oxidized low density lipoprotein (ox-LDL) and to elucidate associations among these factors in HD patients. Forty-eight HD patients were recruited for this study. VC in the feet was detected in 18 patients (37.5%) among total patients and 12 patients (85.7%) among diabetic patients. Diabetes, cardiovascular disease (CVD), pulse pressure, ox-LDL/LDL were higher and high density lipoprotein (HDL) was lower in patients with VC than in patients without VC. Negative associations were found between HDL and CRP, PAI-1. PAI-1 had positive association with ox-LDL/LDL. History of CVD was the only determinant of vascular calcification on the plain radiography of feet. Ox-LDL/LDL, HDL, CRP, and PAI-1 were closely related with one another in HD patients. History of CVD is the most important factor associated with the presence of VC and low HDL and relatively high oxidized LDL/LDL ratio may affect VC formation on the plain radiography in the feet of HD patients.
Utilizing tactile feedback for biomimetic grasping control in upper limb prostheses

A biomimetic system for enhancing the control and reliability of grasping with prosthetic hands was designed and experimentally evaluated. Barometric pressure sensors as well as a force-sensitive resistor (FSR) were placed on a prosthetic hand to provide valuable tactile feedback. Contact and slip detection grip control algorithms were developed to interpret force signals for enhancing stable grasping. Recent advances in radio-frequency identification (RFID) technology enable the amputee to select between grip control strategies based on the desired object to be grasped. Experimental results indicate that the control algorithms are capable of utilizing real-time force responses to detect object contact as well as slip. By allowing the user to act as a high-level controller with RFID technology, a multi-faceted low-level controller that responds to tactile feedback can be developed for enhancing grasping functionality in prosthetic hands.
Outcome after Desensitization in HLA or ABO-Incompatible Kidney Transplant Recipients: A Single Center Experience

Background The shortage of deceased donors led to an increase of living donor kidney (LDK) transplantations performed in the presence of donor-specific antibodies (DSA) or ABO incompatibility (ABOi) using various desensitization protocols. Methods We herein analyzed 26 ABOi and 8 Luminex positive DSA patients who were successfully desensitized by anti-CD20, antigen-specific immunoadsorption and/or plasmapheresis to receive an LDK transplant. Twenty LDK recipients with non-donor-specific HLA-antibodies (low risk) and 32 without anti-HLA antibodies (no risk) served as control groups. Results 1-year graft survival rate and renal function was similar in all 4 groups (creatinine: 1.63 ± 0.5 vs 1.78 ± 0.6 vs 1.64 ± 0.5 vs 1.6 ± 0.3 mg/dl in ABOi, DSA, low risk and no risk group). The incidence of acute T-cell mediated rejections did not differ between the 4 groups (15% vs 12, 5% vs 15% vs 22% in ABOi, DSA, low risk and no risk), while antibody-mediated rejections were only found in the DSA (25%) and ABOi (7.5%) groups. Incidence of BK nephropathy (BKVN) was significantly more frequent after desensitization as compared to controls (5/34 vs 0/52, p = 0.03). Conclusion We demonstrate favorable short-term allograft outcome in LDK transplant recipients after desensitization. However, the desensitization was associated with an increased risk of BKVN.
Cplus 2 ASP : Computing Action Language C + in Answer Set Programming

We present Version 2 of system Cplus2ASP, which implements the definite fragment of action language C+. Its input language is fully compatible with the language of the Causal Calculator Version 2, but the new system is significantly faster thanks to modern answer set solving techniques. The translation implemented in the system is a composition of several recent theoretical results. The system orchestrates a tool chain, consisting of f2lp, clingo, iclingo, and as2transition. Under the incremental execution mode, the system translates a C+ description into the input language of iclingo, exploiting its incremental grounding mechanism. The correctness of this execution is justified by the module theorem extended to programs with nested expressions. In addition, the input language of the system has many useful features, such as external atoms by means of Lua calls and the user interactive mode. The system supports extensible multi-modal translations for other action languages, such as B and BC, as well.