Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of Hepatitis C Virus Sequence Complexity by Electrophoretic Mobilities of Both Single-and Double-Stranded DNAs

ABSTRACT To assess genetic variation in hepatitis C virus (HCV) sequences accurately, we optimized a method for identifying distinct viral clones without determining the nucleotide sequence of each clone. Twelve serum samples were obtained from seven individuals soon after they acquired HCV during a prospective study, and a 452-bp fragment from the E2 region was amplified by reverse transcriptase PCR and cloned. Thirty-three cloned cDNAs representing each specimen were assessed by a method that combined heteroduplex analysis (HDA) and a single-stranded conformational polymorphism (SSCP) method to determine the number of clonotypes (electrophoretically indistinguishable cloned cDNAs) as a measure of genetic complexity (this combined method is referred to herein as the HDA+SSCP method). We calculated Shannon entropy, incorporating the number and distribution of clonotypes into a single quantifier of complexity. These measures were evaluated for their correlation with nucleotide sequence diversity. Blinded analysis revealed that the sensitivity (ability to detect variants) and specificity (avoidance of false detection) of the HDA+SSCP method were very high. The genetic distance (mean ± standard deviation) between indistinguishable cloned cDNAs (intraclonotype diversity) was 0.6% ± 0.9%, and 98.7% of cDNAs differed by <2%, while the mean distance between cloned cDNAs with different patterns was 4.0% ± 3.2%. The sensitivity of the HDA+SSCP method compared favorably with either HDA or the SSCP method alone, which resulted in intraclonotype diversities of 1.6% ± 1.8% and 3.5% ± 3.4%, respectively. The number of clonotypes correlated strongly with genetic diversity (R2, 0.93), but this correlation fell off sharply when fewer clones were assessed. This HDA+SSCP method accurately reflected nucleotide sequence diversity among a large number of viral cDNA clones, which should enhance analyses to determine the effects of viral diversity on HCV-associated disease. If sequence diversity becomes recognized as an important parameter for staging or monitoring of HCV infection, this method should be practical enough for use in laboratories that perform nucleic acid testing.
The effect of water immersion during exercise on cerebral blood flow.

INTRODUCTION Regular exercise induces recurrent increases in cerebrovascular perfusion. In peripheral arteries, such episodic increases in perfusion are responsible for improvement in arterial function and health. We examined the hypothesis that exercise during immersion augments cerebral blood flow velocity compared with intensity-matched land-based exercise. METHODS Fifteen normotensive participants were recruited (26 ± 4 yr, 24.3 ± 1.9 kg·m). We continuously assessed mean arterial blood pressure, HR, stroke volume, oxygen consumption, and blood flow velocities through the middle and posterior cerebral arteries before, during, and after 20-min bouts of water- and land-based stepping exercise of matched intensity. The order in which the exercise conditions were performed was randomized between subjects. Water-based exercise was performed in 30°C water to the level of the right atrium. RESULTS The water- and land-based exercise bouts were closely matched for oxygen consumption (13.3 mL·kg·min (95% confidence interval (CI), 12.2-14.6) vs 13.5 mL·kg·min (95% CI, 12.1-14.8), P = 0.89) and HR (95 bpm (95% CI, 90-101) vs 96 bpm (95% CI, 91-102), P = 0.65). Compared with land-based exercise, water-based exercise induced an increase in middle cerebral artery blood flow velocity (74 cm·s (95% CI, 66-81) vs 67 cm·s (95% CI, 60-74) P < 0.001), posterior cerebral artery blood flow velocity (47 cm·s (95% CI, 40-53) vs 43 cm·s (95% CI, 37-49), P < 0.001), mean arterial blood pressure (106 mm Hg (95% CI, 100-111) vs 101 mm Hg (95% CI, 95-106), P < 0.001), and partial pressure of expired CO2 (P ≤ 0.001). CONCLUSIONS Our findings suggest that water-based exercise augments cerebral blood flow, relative to land-based exercise of similar intensity, in healthy humans.
Field-omics—understanding large-scale molecular data from field crops

The recent advances in gene expression analysis as well as protein and metabolite quantification enable genome-scale capturing of complex biological processes at the molecular level in crop field trials. This opens up new possibilities for understanding the molecular and environmental complexity of field-based systems and thus shedding light on the black box between genotype and environment, which in agriculture always is influenced by a multi-stress environment and includes management interventions. Nevertheless, combining different types of data obtained from the field and making biological sense out of large datasets remain challenging. Here we highlight the need to create a cross-disciplinary platform for innovative experimental design, sampling and subsequent analysis of large-scale molecular data obtained in field trials. For these reasons we put forward the term field-omics: “Field-omics strives to couple information from genomes, transcriptomes, proteomes, metabolomes and metagenomes to the long-established practice in crop science of conducting field trials as well as to adapt current strategies for recording and analysing field data to facilitate integration with ‘-omics’ data. ”
Rac1 Is a Novel Regulator of Contraction-Stimulated Glucose Uptake in Skeletal Muscle

In skeletal muscle, the actin cytoskeleton-regulating GTPase, Rac1, is necessary for insulin-dependent GLUT4 translocation. Muscle contraction increases glucose transport and represents an alternative signaling pathway to insulin. Whether Rac1 is activated by muscle contraction and regulates contraction-induced glucose uptake is unknown. Therefore, we studied the effects of in vivo exercise and ex vivo muscle contractions on Rac1 signaling and its regulatory role in glucose uptake in mice and humans. Muscle Rac1-GTP binding was increased after exercise in mice (∼60–100%) and humans (∼40%), and this activation was AMP-activated protein kinase independent. Rac1 inhibition reduced contraction-stimulated glucose uptake in mouse muscle by 55% in soleus and by 20–58% in extensor digitorum longus (EDL; P < 0.01). In agreement, the contraction-stimulated increment in glucose uptake was decreased by 27% (P = 0.1) and 40% (P < 0.05) in soleus and EDL muscles, respectively, of muscle-specific inducible Rac1 knockout mice. Furthermore, depolymerization of the actin cytoskeleton decreased contraction-stimulated glucose uptake by 100% and 62% (P < 0.01) in soleus and EDL muscles, respectively. These are the first data to show that Rac1 is activated during muscle contraction in murine and human skeletal muscle and suggest that Rac1 and possibly the actin cytoskeleton are novel regulators of contraction-stimulated glucose uptake.
A Lumped Thermal Model Including Thermal Coupling and Thermal Boundary Conditions for High-Power IGBT Modules

Detailed thermal dynamics of high-power IGBT modules are important information for the reliability analysis and thermal design of power electronic systems. However, the existing thermal models have their limits to correctly predict these complicated thermal behavior in the IGBTs: The typically used thermal model based on one-dimensional RC lumps have limits to provide temperature distributions inside the device; moreover, some variable factors in the real-field applications like the cooling and heating conditions of the converter cannot be adapted. On the other hand, the more advanced three-dimensional (3-D) thermal models based on finite-element method (FEM) need massive computations, which make the long-term thermal dynamics difficult to calculate. In this paper, a new lumped 3-D thermal model is proposed, which can be easily characterized from FEM simulations and can acquire the critical thermal distribution under long-term studies. Meanwhile, the boundary conditions for the thermal analysis are modeled and included, which can be adapted to different real-field applications of power electronic converters. Finally, the accuracy of the proposed thermal model is verified by FEM simulations and experimental results show a good agreement.
Influence of Motor Imagery of Isometric Opponens Pollicis Activity on the Excitability of Spinal Motor Neurons: A Comparison Using Different Muscle Contraction Strengths

[Purpose] This study aimed to determine the differences in the excitability of spinal motor neurons during motor imagery of a muscle contraction at different contraction strengths. [Methods] We recorded the F-wave in 15 healthy subjects. First, in a trial at rest, the muscle was relaxed during F-wave recording. Next, during motor imagery, subjects were instructed to imagine maximum voluntary contractions of 10%, 30%, and 50% while holding the sensor of a pinch meter, and F-waves were recorded for each contraction. F-waves were recorded immediately and at 5, 10, and 15 min after motor imagery. [Results] Both persistence and F/M amplitude ratios during motor imagery under maximum voluntary contractions of 10%, 30%, and 50% were significantly higher than that at rest. In addition, persistence, F/M amplitude ratio, and latency were similar during motor imagery under the three muscle contraction strengths. [Conclusion] Motor imagery under maximum voluntary contractions of 10%, 30%, and 50% can increase the excitability of spinal motor neurons. The results indicated that differences in muscle contraction strengths during motor imagery are not involved in changes in the excitability of spinal motor neurons.
Detection of Methicillin-Resistant Coagulase-Negative Staphylococci and Surveillance of Antibacterial Resistance in a Multi-Center Study from Iran

Background: Coagulase-negative staphylococci (CNS) are a common cause of nosocomial infections. In recent years, an increase in the incidence of methicillin-resistant coagulase-negative staphylococci (MRCNS) has led to the severity of the disease. Objectives: The aim of this study was to isolate and identify MRCNS strains by oxacillin disk agar diffusion, oxacillin agar screening, and polymerase chain reaction (PCR) and to evaluate their antibacterial resistance patterns. Patients and Methods: Totally, 122 CNS isolates were collected from the clinical specimens of four hospitals in Iran. Susceptibility testing was performed by disk agar diffusion against 15 antimicrobial agents. Then, disk agar diffusion, agar screening, and PCR were applied to determine susceptibility to oxacillin. Results: Out of the 122 isolates, 92 isolates were found to be MRCNS by PCR. The sensitivities and specificities of disk agar diffusion and agar screening were 89.2% and 69% and 93.8% and 96.3%, respectively. Also, 93 CNS isolates were resistant to Methicillin according to disk agar diffusion. Discussion: Our results indicated that agar screening was superior to oxacillin disk agar diffusion. A comparison between the antibiotic sensitivity patterns of the MRCNS and the Methicillin-Susceptible Coagulase-Negative Staphylococci (MSCNS) showed that the MRCNS were predominantly multiple-drug resistant isolates as the simultaneous resistance rate to 4 or more antibiotics in the MRCNS and MSCNS was 93% and 56%, respectively.
Periodontal plastic surgery: Made easy with acellular dermal matrix

Esthetics has become an important part in periodontal plastic surgery, and soft-tissue architecture plays an important role in achieving it. Among the various techniques, the use of autogenous connective tissue graft has been proved to be an effective and a successful approach in treating gingival recession. Recently, acellular dermal matrix (ADM) allograft has been used as a substitute for palatal connective tissue and it has shown to be a successful alternative for root coverage. This case report is an effort to evaluate the clinical effectiveness of ADM in coverage of denuded root with 6-month follow-up.
Trauma and psychological distress observed in journalists: a comparison of Israeli journalists and their Western counterparts.

BACKGROUND There is limited evidence on how reporting war influences journalists' psychological wellbeing. A significant minority of journalists may develop symptoms of emotional distress; however it is unclear whether the type and amount of distress differs between those journalists who report from potentially dangerous areas within their own country compared to those who do so from war zones in other countries. METHOD We compared indices of psychological health in 38 Israeli journalists with 38 Western journalists whose careers have been defined by work in war zones. RESULTS While both groups reported high levels of exposure to traumatic events, there were no significant differences in frequency or type of exposure between the groups. Western journalists reported more frequent posttraumatic stress disorder (PTSD), intrusion-type symptoms and drank more alcohol while Israeli journalists reported higher levels of depression, anxiety and somatic distress. CONCLUSION This pattern of results suggests that social circumstances and environmental factors may influence how different groups of individuals respond to traumatic events.
Facial Action and Emotional Language: ERP Evidence that Blocking Facial Feedback Selectively Impairs Sentence Comprehension

There is a lively and theoretically important debate about whether, how, and when embodiment contributes to language comprehension. This study addressed these questions by testing how interference with facial action impacts the brain's real-time response to emotional language. Participants read sentences about positive and negative events (e.g., “She reached inside the pocket of her coat from last winter and found some (cash/bugs) inside it. ”) while ERPs were recorded. Facial action was manipulated within participants by asking participants to hold chopsticks in their mouths using a position that allowed or blocked smiling, as confirmed by EMG. Blocking smiling did not influence ERPs to the valenced words (e.g., cash, bugs) but did influence ERPs to final words of sentences describing positive events. Results show that affectively positive sentences can evoke smiles and that such facial action can facilitate the semantic processing indexed by the N400 component. Overall, this study offers causal evidence that embodiment impacts some aspects of high-level comprehension, presumably involving the construction of the situation model.
Comments on "Evaluation of interactions of electric fields due to electrostatic discharge with human Tissue"

Attention is drawn to recent paper by Rogers et al. (Aug., 2004) in which ultra-wideband pulses are applied to an isolated muscle as part of deriving a strength-duration curve for threshold stimulation. The paper extends the strength-duration threshold curve for unipolar pulses down to a pulse duration of about 1 ns, on the order of 1000 times shorter than previously studied. Results of the work justify use of traditional mathematical models of the strength-duration curve for nanosecond pulses, as done recently for the electric field resulting from electrostatic discharge through the body (Dawson, et al., 2004).
JNK inhibitor SP600125 protects against lipopolysaccharide-induced acute lung injury via upregulation of claudin-4

Although in vitro studies have previously demonstrated that mitogen-activated protein kinases are important for the activation of transcription factors and the regulation of proinflammatory mediators, the function of c-Jun NH2-terminal kinase (JNK) in acute lung injury (ALI) remains to be fully elucidated. The present study aimed to investigate the effect of the JNK selective inhibitor SP600125 on lipopolysaccharide (LPS)-induced ALI. Pulmonary edema, the expression of inflammatory cytokines and pathological alterations were found to be significantly attenuated in LPS-induced ALI following treatment with SP600125 in vivo. In vitro, it was demonstrated that SP600125 administration significantly improved A549 cell viability in a dose-dependent manner using the Cell Counting kit-8 and the 5-ethynyl-2′-deoxyuridine incorporation assay. Furthermore, flow cytometric analysis demonstrated that the apoptotic rate was significantly reduced in a concentration-dependent manner following SP600125 injection. At the molecular level, SP600125 treatment dose-dependently inhibited JNK activation and upregulated claudin-4 expression in vivo and in vitro. In combination, the results from the present study indicated that the JNK inhibitor SP600125 protected against LPS-induced ALI in vivo and in vitro, possibly by upregulating the expression of claudin-4.
Computational analysis of the effect of physical activity on the changes in femoral bone density in prepubertal children

Human bone health, and osteoporosis in particular, are a highly topical research. A causal and positive effect of physical activity on bone mineral density is supported by a bunch of clinical-based research studies. Moreover, actual research suggests long-term benefits of childhood physical activity to the prevention of osteoporosis in adulthood. Complementary to the clinical-based study is the computational analysis, based on a bone remodeling model. Although many different remodeling models are developed by several research groups, very little research is done in the application of computational remodeling in children. The current study is performed in this gap and consists of two major parts. First, a model is developed to represent the femoral bone of a prepubertal child. A finite element with assigned material properties based on Computed Tomography scans is created and verified. The musculoskeletal loads are obtained from experimental kinematic data by the faculty of movement. Gait, stance, run and countermovement jump as performed by prepubertal children are represented by superposition of crucial timeframes in the activity cycle. The effect of physical activity on bone mineral density in prepubertal children is investigated with the Lisbon bone remodeling model. An optimal value of model parameters k and m is investigated, which take into account the inter-subject variability. A value of k = 0.0025 and m = 4 are considered as best to represent the prepubertal population. In the second part of the research, the effect of additional physical activity on bone mineral density is investigated. It is concluded that results of the computational model are in agreement with clinical results. Spending more time in physical activity, high-intensive activity in particular, the bone mineral density increases. It is stated that an initial increase in activity time leads to a greater increase in bone mass compared to a further increase in activity time. Further, the results suggest that physical activity decreases the risk for typical (osteoporotic) femoral fractures, as suggested by former research. In the region of the femoral neck, this happens by the periosteal apposition of bone: a relative increase in density of the outer shell. In the trochanteric region, the fracture risk is decreased by an increased bone mineral density.
Insights into the gyrification of developing ferret brain by magnetic resonance imaging

The developmental mechanisms underlying the formation of human cortical convolutions (gyri and sulci) remain largely unknown. Genetic causes of lissencephaly (literally ‘smooth brain’) would imply that disorders in neuronal migration cause the loss of cortical convolutions. However, prior studies have suggested that loss of sulci and gyri can also arise from impaired proliferation, disrupted lamination and loss of intracortical connections. To gain further insight into the mechanisms underlying the formation of cortical convolutions, we examined the progressive brain development of the gyrencephalic ferret. In this study, we used magnetic resonance imaging to follow the temporal and spatial pattern of neuronal migration, proliferation and differentiation in relation to the onset and development of cortical convolutions. In this manner, we demonstrate that the onset of gyrification begins largely after completion of neuronal proliferation and migration. Gyrification occurs in a lateral to medial gradient, during the period of most rapid cerebral cortical growth. Cortical folding is also largely complete prior to myelination of the underlying cortical axons. These observations are consistent with gyrification arising secondary to cortical processes involving neuronal differentiation.
Psychological Barriers in Gold Prices?

This paper examines for the first time the existence of psychological barriers in a variety of daily and intra-day gold price series. This paper uses a number of statistical procedures and presents evidence of psychological barriers in gold prices. We document that prices in round numbers act as barriers with important effects on the conditional mean and variance of the gold price series around psychological barriers.
Holocene subsurface temperature variability in the eastern Antarctic continental margin

We reconstructed subsurface (∼45–200 m water depth) temperature variability in the eastern Antarctic continental margin during the late Holocene, using an archaeal lipid‐based temperature proxy (TEX86L). Our results reveal that subsurface temperature changes were probably positively coupled to the variability of warmer, nutrient‐rich Modified Circumpolar Deep Water (MCDW, deep water of the Antarctic circumpolar current) intrusion onto the continental shelf. The TEX86Lrecord, in combination with previously published climatic records, indicates that this coupling was probably related to the thermohaline circulation, seasonal variability in sea ice extent, sea temperature, and wind associated with high frequency climate dynamics at low‐latitudes such as internal El Niño Southern Oscillation (ENSO). This in turn suggests a linkage between centennial ENSO‐like variability at low‐latitudes and intrusion variability of MCDW into the eastern Antarctic continental shelf, which might have further impact on ice sheet evolution.
Attention to Arrows: Pointing to a New Direction

It was long believed that central arrows needed to be spatially predictive to produce a shift in spatial attention. Recent evidence indicates, however, that central spatially nonpredictive directional cues, like arrows, will trigger reflexive shifts in attention. We asked what this recent discovery means for past studies that used predictive directional cues such as arrows. Our findings indicate that predictive arrows produce attention effects that greatly exceed the individual or summed effects of reflexive orienting to nonpredictive arrows and volitional orienting to predictive numbers. This suggests that the especially large effect produced by predictive arrows reflects an interaction between reflexive and volitional orienting. Given the broad application of the predictive arrow cueing paradigm in both past and current research, the present data shed new light on a wide range of investigations, from psychophysical studies of basic attention to behavioural and neuroimaging studies of cognition and social development.