Miracle-dz/UniFAR-FTUs huggingface dataset:
Translocation of Biomolecules Through Solid-State Nanopores: Theory Meets Experiments

The interest in polynucleotide translocation through nanopores has moved from purely biological to the need of real- izing nanobiotechnological applications related to personalized genome sequencing. Polynucleotide translocation is a process in which biomolecules, like DNA or RNA, are electrophoreti- cally driven through a narrow pore and their passage can be monitored by the change in the ionic current through the pore. Such a translocation process, which will be described here offers a very promising technology aiming at ultra-fast low-cost sequencing of DNA, though its realization is still confronted with challenges and drawbacks. In this review, we present the main aspects involved in the polynucleotide translocation through solid-state nanopores by discussing the most relevant experi- mental, theoretical, and computational approaches and the way these can supplement each other. The discussion will expose the goals that have been reached so far, the open questions, and contains an outlook to the future of nanopore sequencing. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 985-1011, 2011
Surface Soil Moisture Retrieval Using the L-Band Synthetic Aperture Radar Onboard the Soil Moisture Active–Passive Satellite and Evaluation at Core Validation Sites

This paper evaluates the retrieval of soil moisture in the top 5-cm layer at 3-km spatial resolution using L-band dual-copolarized Soil Moisture Active-Passive (SMAP) synthetic aperture radar (SAR) data that mapped the globe every three days from mid-April to early July, 2015. Surface soil moisture retrievals using radar observations have been challenging in the past due to complicating factors of surface roughness and vegetation scattering. Here, physically based forward models of radar scattering for individual vegetation types are inverted using a time-series approach to retrieve soil moisture while correcting for the effects of static roughness and dynamic vegetation. Compared with the past studies in homogeneous field scales, this paper performs a stringent test with the satellite data in the presence of terrain slope, subpixel heterogeneity, and vegetation growth. The retrieval process also addresses any deficiencies in the forward model by removing any time-averaged bias between model and observations and by adjusting the strength of vegetation contributions. The retrievals are assessed at 14 core validation sites representing a wide range of global soil and vegetation conditions over grass, pasture, shrub, woody savanna, corn, wheat, and soybean fields. The predictions of the forward models used agree with SMAP measurements to within 0.5 dB unbiased-root-mean-square error (ubRMSE) and −0.05 dB (bias) for both copolarizations. Soil moisture retrievals have an accuracy of 0.052 m3/m3 ubRMSE, −0.015 m3/m3 bias, and a correlation of 0.50, compared to in situ measurements, thus meeting the accuracy target of 0.06 m3/m3 ubRMSE. The successful retrieval demonstrates the feasibility of a physically based time series retrieval with L-band SAR data for characterizing soil moisture over diverse conditions of soil moisture, surface roughness, and vegetation.
Evidence that both cyclosporin and azathioprine prevent warm ischemia reperfusion injury to the rat liver

The present work was undertaken to study whether the immunosuppressive agents cyclosporin (CyA) and azathioprine (AZA) ameliorate hepatic injury after warm ischemia. A temporary, normothermic liver ischemia was induced in female Sprague-Dawley rats. The rats were treated with CyA (10 mg/kg per day p.o.), AZA (8 mg/kg per day p.o.), or vehicles for 4 days before surgery. Seven-day survival rates after 60 min of ischemia improved significantly with CyA (76.2%, P<0.005) and AZA (78.6%, P<0.001) treatment, compared with 43.0% for the control group. The highest levels of serum aminotransferases in the treatment groups tended to be lower than those in the control group. The peak values for the percentage of liver necrosis, an indicator of the extent of hepatic necrosis, in the animals treated with CyA (26.1%±7.2%, mean±SEM) and AZA (32.1%±5.7%) were significantly lower than in the control group (47.4%±3.7%). Lipid peroxidative damage after reperfusion, assessed as the hepatic malondialdehyde (MDA) concentration, was significantly suppressed by pretreatment with CyA and AZA. Histological findings coincided with other parameters. This study demonstrates that both AZA and CyA have beneficial effects on normothermic liver ischemia in rats. It is suggested that the diminished lipid peroxidative damage with these agents might be one of the mechanisms responsible for this.
Room temperature operational single electron transistor fabricated by focused ion beam deposition

We present the fabrication and room temperature operation of single electron transistors using 8nm tungsten islands deposited by focused ion beam deposition technique. The tunnel junctions are fabricated using oxidation of tungsten in peracetic acid. Clear Coulomb oscillations, showing charging and discharging of the nanoislands, are seen at room temperature. The device consists of an array of tunnel junctions; the tunnel resistance of individual tunnel junction of the device is calculated to be as high as 25. 13GΩ. The effective capacitance of the array of tunnel junctions was found to be 0.499aF, giving a charging energy of 160.6meV.
Impact Of Nursing Rehabilitation Program On Outcome Of Patients Undergoing Arthroscopy For Anterior Cruciate Ligament Injury

An estimated 200,000 ACLrelated injuries occur annually in the United States . The aims of this study : are three folds; to assess knowledge and practice of patients, to evaluate the effect of applying a rehabilitation program on patients knowledge and practice, to assess the effect of the rehabilitation program on reducing patients complications. Patient and Methods: Quasi experimental research design was utilized in this study . This study was conducted in arthroscopy and sports injuries unit at Asyut University Hospital. A convenient sample of 60 patients was included in this study. Tools utilized for data collection were:( I) Patient's health needs assessment sheet. (I I)Modified Cincinnati Rating System Questionnaire. (III) Assessment of patient's knowledge, practices . ( V) represents the rehabilitation program . Results: high a statistical significant difference between the study and the control group regarding their knowledge and practice , Cincinnati Rating System , mid thigh circumference with P value (0.001) Conclusion: providing written rehabilitation program was much more effective on patients outcome than those patients in the control group who received residents’ oral instructions. Recommandation: A specialized nurse rehabilitator is to be full time attending the outpatient arthroscopy clinic.
Prognostic significance of neutrophil to lymphocyte ratio in ovarian cancer: evidence from 4,910 patients

Increasing evidence indicates that elevated neutrophil to lymphocyte ratio (NLR) are related with poor prognosis in various types of tumors. However, the prognostic role of NLR in patients with ovarian cancer (OC) remains controversial. Thus, the current meta-analysis aimed to investigate the prognostic role of NLR in patients with OC. A total of 16 studies with 4,910 patients were included. By pooling hazard ratios (HRs) with 95% confidence intervals (CIs) and odds ratios (ORs) with 95% CIs from each study. The results demonstrated that elevated pretreatment NLR was significantly related to poor OS (HR: 1.50, 95% CI: 1.27-1.77) and PFS (HR: 1.53, 95% CI: 1.28-1.84) in patients with OC. Subgroup analyses was divided by ethnicity, sample size, histologic types, cut-off value of NLR, analysis method and NOS score, but the results did not showed any significant change the main results. This meta-analysis revealed that elevated pretreatment NLR might be a predicative factor of poor prognosis in OC patients.
Consumption of omega-3 fatty acids and fish and risk of age-related hearing loss.

BACKGROUND Identification of modifiable risk factors that could prevent or slow the development of age-related hearing loss (presbycusis) would be valuable. Dietary polyunsaturated fatty acid (PUFA) intake may be related to age-related hearing loss. OBJECTIVE We aimed to determine the association between dietary intakes of omega-3 (n-3) PUFAs and fish and the risk of presbycusis. DESIGN The Blue Mountains Hearing Study is a population-based survey of age-related hearing loss (1997-1999 to 2002-2004). We collected dietary data by using a semiquantitative food-frequency questionnaire and calculated PUFA and fish intakes. In 2956 participants (aged > or =50 y), we measured presbycusis, which we defined as the pure-tone average of frequencies 0.5, 1.0, 2.0, and 4.0 kHz >25 decibels of hearing loss. RESULTS There was an inverse association between total n-3 PUFA intake and prevalent hearing loss [odds ratio (OR) per SD increase in energy-adjusted n-3 PUFAs: 0.89; 95% CI: 0.81, 0.99]. There was an inverse association between long-chain n-3 PUFAs and incident hearing loss (OR per SD increase in long-chain n-3 PUFAs: 0.76; 95% CI: 0.60, 0.97). Participants who had > or =2 servings of fish/wk compared with participants who had <1 serving of fish/wk had a significantly reduced risk (42%) of developing presbycusis at follow-up (multivariate-adjusted OR: 0.58; 95% CI: 0.35, 0.95). There was an association between consumption of > or =1 to <2 servings/wk of fish and a reduced risk of a progression of hearing loss (OR: 0.53; 95% CI: 0.32, 0.88). CONCLUSIONS There was an inverse association between higher intakes of long-chain n-3 PUFAs and regular weekly consumption of fish and hearing loss. Dietary intervention with n-3 PUFAs could prevent or delay the development of age-related hearing loss.
The Network of Antigen-Antibody Reactions in Adult Women with Breast Cancer or Benign Breast Pathology or without Breast Pathology

The Immunoglobulin G (IgG) antibody response to different protein antigens of the mammary ductal carcinoma by adult women affected by Breast Cancer (BC) distinguishes at least 103 proteins that differ in their molecular weights (MW). The IgG producing cell clones (nodes) coexist with each other in each individual organism and share energy resources among themselves, as well as factors that control the level of expression and Specificity of their IgG antibodies. So, it can be proposed that among them there is a Network of interconnections (links) unveiled by the antigens, which specifically react with the IgG antibodies produced by the clones. This Network possibly regulates IgG antibodies' activity and effectiveness. We describe the Network of nodes and links that exists between the different antigens and their respective IgG producing cell clones against the extracted protein antigens from the cells of the T47D Cell-Line, in 50 women with BC, 50 women with Benign Breast Pathology (BBP) and 50 women without breast pathology (H). We have found that women with BBP have the highest number of Links, followed by the H group and, lastly, the women with BC, a finding which suggests that cancer interferes with the Connectivity between the IgG producing cell clones and blocks the expression of 322 links in women with BBP and 32 links in women with H. It is also plausible that the largest number of links in the women with BBP indicates the Network’s state of arousal that provides protection against BC. On the other hand, there were many missing links in the BC group of women; the clone which lost more links in the BC group was the hub 24, which point to some of the antigens of T47D as potentially useful as vaccines, as the immune system of women with BBP is well aware of them.
Adolescent Gender Differences in Cognitive Control Performance and Functional Connectivity Between Default Mode and Fronto-Parietal Networks Within a Self-Referential Context

Ineffective reduction of functional connectivity between the default mode network (DMN) and frontoparietal network (FPN) during cognitive control can interfere with performance in healthy individuals—a phenomenon present in psychiatric disorders, such as depression. Here, this mechanism is studied in healthy adolescents by examining gender differences in task-regressed functional connectivity using functional magnetic resonance imaging (MRI) and a novel task designed to place the DMN—supporting self-referential processing (SRP)—and FPN—supporting cognitive control—into conflict. Compared to boys, girls showed stronger functional connectivity between DMN and FPN during cognitive control in an SRP context (n = 40; boys = 20), a context that also elicited more errors of omission in girls. The gender difference in errors of omission was mediated by higher self-reported co-rumination—the extensive and repetitive discussion of problems and focus on negative feelings with a same-gender peer—by girls, compared to boys. These findings indicate that placing internal and external attentional demands in conflict lead to persistent functional connectivity between FPN and DMN in girls, but not boys; however, deficits in performance during this context were explained by co-rumination, such that youth with higher co-rumination displayed the largest performance deficits. Previous research shows that co-rumination predicts depressive symptoms during adolescence; thus, gender differences in the mechanisms involved with transitioning from internal to external processing may be relevant for understanding heightened vulnerability for depression in adolescent girls.
Quantitative Profiling of Colorectal Cancer-Associated Bacteria Reveals Associations between Fusobacterium spp., Enterotoxigenic Bacteroides fragilis (ETBF) and Clinicopathological Features of Colorectal Cancer

Various studies have presented clinical or in vitro evidence linking bacteria to colorectal cancer, but these bacteria have not previously been concurrently quantified by qPCR in a single cohort. We quantify these bacteria (Fusobacterium spp., Streptococcus gallolyticus, Enterococcus faecalis, Enterotoxigenic Bacteroides fragilis (ETBF), Enteropathogenic Escherichia coli (EPEC), and afaC- or pks-positive E. coli) in paired tumour and normal tissue samples from 55 colorectal cancer patients. We further investigate the relationship between a) the presence and b) the level of colonisation of each bacterial species with site and stage of disease, age, gender, ethnicity and MSI-status. With the exception of S. gallolyticus, we detected all bacteria profiled here in both tumour and normal samples at varying frequencies. ETBF (FDR = 0.001 and 0.002 for normal and tumour samples) and afaC-positive E. coli (FDR = 0.03, normal samples) were significantly enriched in the colon compared to the rectum. ETBF (FDR = 0.04 and 0.002 for normal and tumour samples, respectively) and Fusobacterium spp. (FDR = 0.03 tumour samples) levels were significantly higher in late stage (III/IV) colorectal cancers. Fusobacterium was by far the most common bacteria detected, occurring in 82% and 81% of paired tumour and normal samples. Fusobacterium was also the only bacterium that was significantly higher in tumour compared to normal samples (p = 6e-5). We also identified significant associations between high-level colonisation by Fusobacterium and MSI-H (FDR = 0.05), age (FDR = 0.03) or pks-positive E. coli (FDR = 0.01). Furthermore, we exclusively identified atypical EPEC in our cohort, which has not been previously reported in association with colorectal cancer. By quantifying colorectal cancer-associated bacteria across a single cohort, we uncovered inter- and intra-individual patterns of colonization not previously recognized, as well as important associations with clinicopathological features, especially in the case of Fusobacterium and ETBF.
Network Dynamics Underlying Speed-Accuracy Trade-Offs in Response to Errors

The ability to dynamically and rapidly adjust task performance based on its outcome is fundamental to adaptive, flexible behavior. Over trials of a task, responses speed up until an error is committed and after the error responses slow down. These dynamic adjustments serve to optimize performance and are well-described by the speed-accuracy trade-off (SATO) function. We hypothesized that SATOs based on outcomes reflect reciprocal changes in the allocation of attention between the internal milieu and the task-at-hand, as indexed by reciprocal changes in activity between the default and dorsal attention brain networks. We tested this hypothesis using functional MRI to examine the pattern of network activation over a series of trials surrounding and including an error. We further hypothesized that these reciprocal changes in network activity are coordinated by the posterior cingulate cortex (PCC) and would rely on the structural integrity of its white matter connections. Using diffusion tensor imaging, we examined whether fractional anisotropy of the posterior cingulum bundle correlated with the magnitude of reciprocal changes in network activation around errors. As expected, reaction time (RT) in trials surrounding errors was consistent with predictions from the SATO function. Activation in the default network was: (i) inversely correlated with RT, (ii) greater on trials before than after an error and (iii) maximal at the error. In contrast, activation in the right intraparietal sulcus of the dorsal attention network was (i) positively correlated with RT and showed the opposite pattern: (ii) less activation before than after an error and (iii) the least activation on the error. Greater integrity of the posterior cingulum bundle was associated with greater reciprocity in network activation around errors. These findings suggest that dynamic changes in attention to the internal versus external milieu in response to errors underlie SATOs in RT and are mediated by the PCC.
Effects of Environment on Vessel Characters in Cactus Wood

Vessel size classes within several cactus species were studied to determine if theoretically advantageous patterns of vessel widths are produced in plants cultivated in dry conditions. Clones of five cacti (Cleistocactus, Harrisia, Pereskia, Rhipsalis, Selenicereus) were given either mesic or xeric watering regimens for more than 2 yr, and then were studied with light microscopy. Plants cultivated in drought conditions all produced a modified wood that had characters suited for surviving water deficits. All plants cultivated in xeric conditions produced wood with narrower vessels in both roots and shoots. Relative abundances of narrow and wide vessels varied with cultivation conditions: xeric‐cultivated plants had greater percentages of narrow vessels (rather than being normally distributed, vessel widths were positively skewed), whereas mesic‐cultivated plants had comparatively lower percentages of narrow vessels (negatively skewed, or at least less positively skewed). If wide vessels cavitate before narrow ones during water stress, then xeric‐cultivated plants produced wood that had so many narrow vessels that even if a plant were to lose half its conducting capacity from cavitation of some of its widest vessels, it would still have a large fraction of its vessels water filled and functional. In contrast, mesic‐cultivated plants would have smaller fractions of their vessels functional at the point when half their wood’s conducting capacity had been lost. Three of the species studied are capable of producing dimorphic wood: they produce one type of wood while young and a second type when older. Xeric cultivation inhibited or retarded the transition to the second wood type.
The effect of a solid boundary on the dynamics of a small group of ultrasound driven microbubbles

The dynamical behaviour of a small cluster of microbubbles s ubjected to ultrasound near a solid boundary is investigated. An equation for radial oscillation for bubbles nea r a plane rigid wall is derived using method of images and solved numerically for a given set of ultrasound parameters . In this paper, it is assumed that all bubbles in the system have the same equilibrium radius and are equidistant from on e another and from the solid boundary. With the current mathematical model, it is demonstrated that the presence of a s lid wall has a significant effect on the bifurcation struc ture and the route to chaos of the bubble system. As separatio n distance between microbubbles and solid boundary is decreased, the bubble system is more likely to exhibit chaos and chaotic behaviour occurs at lower pressure amplitude. Furthermore, the maximum amplitude of the bubble oscillati ons near solid wall is shown to be related to the number of dominant frequencies in the response of the bubble system. S maller oscillation amplitude is associated bubble respons e with smaller number of frequencies while chaotic bubble osc illations will lead to larger oscillation amplitude.
Investigation of PV Power Plant Structures Based on Monte Carlo Reliability and Economic Analysis

With the increasing deployment of photovoltaic (PV) sources in the power grid and their contribution to power generation, it is imperative to obtain accurate models for the reliability and stability of these plants. In this paper, a novel method is proposed for reliability assessment for the different structures involved in the implementation of PV plants, in which the failure rate of system components is calculated using the FIDES Guide standard, taking into account environmental conditions such as radiation curves, temperature, and humidity. Failure rates of the insulated gate bipolar transistor and converter capacitor were found to be greater than other components. After precise calculation of failure and repair rates, the probability of functioning in three states of full generation, partial failure, and down was obtained through Monte Carlo simulations. Considering the effect of the system's structure on its stability, the reliability of the system can be increased by adding inverter paths to its structure. Several such structures are proposed, and the most economical design is identified by analyzing load duration curves to obtain the energy loss in each configuration. The proposed algorithm was implemented in Isfahan University's 20 kW PV power plant. Simulations demonstrate the efficiency of the proposed algorithm in design and evaluation of economic system structures.
A Machine Learning Approach to Automated Gait Analysis for the Noldus Catwalk System

Objective: Gait analysis of animal disease models can provide valuable insights into in vivo compound effects and thus help in preclinical drug development. The purpose of this paper is to establish a computational gait analysis approach for the Noldus Catwalk system, in which footprints are automatically captured and stored. Methods: We present a - to our knowledge - first machine learning based approach for the Catwalk system, which comprises a step decomposition, definition and extraction of meaningful features, multivariate step sequence alignment, feature selection, and training of different classifiers (gradient boosting machine, random forest, and elastic net). Results: Using animal-wise leave-one-out cross validation we demonstrate that with our method we can reliable separate movement patterns of a putative Parkinson's disease animal model and several control groups. Furthermore, we show that we can predict the time point after and the type of different brain lesions and can even forecast the brain region, where the intervention was applied. We provide an in-depth analysis of the features involved into our classifiers via statistical techniques for model interpretation. Conclusion: A machine learning method for automated analysis of data from the Noldus Catwalk system was established. Significance: Our works shows the ability of machine learning to discriminate pharmacologically relevant animal groups based on their walking behavior in a multivariate manner. Further interesting aspects of the approach include the ability to learn from past experiments, improve with more data arriving and to make predictions for single animals in future studies.