Miracle-dz/UniFAR-FTUs huggingface dataset:
The Cardioprotective Effect of Brief Acidic Reperfusion after Ischemia in Perfused Rat Hearts is not Mimicked by Inhibition of the Na+/H+ Exchanger NHE1

Background: Ischemic postconditioning (PostC), i.e. brief ischemia-reperfusion cycles before full reperfusion, is protective against cardiac ischemia/reperfusion (I/R) injury. Inhibition of the Na+/H+ exchanger NHE1 and delayed intracellular pH-normalization have been proposed to underlie protection by PostC. Methods and Results: We used Langendorff perfused rat hearts exposed to 35 min global ischemia to show that 15 min acidic (pH 6.5) treatment at onset of reperfusion decreased infarct size and functional deterioration at least to the same extent as PostC. In contrast, NHE1 inhibition by EIPA was detrimental. To evaluate HL-1 atrial cardiomyocytes as a cellular model for PostC, we exposed the cells to simulated ischemia/reperfusion (I/R) mimicking that in perfused hearts. Necrosis and apoptosis induced by I/R were unaffected by 15 min of pH 6.0 at onset of reperfusion. I/R increased the activity of c-Jun N-terminal Kinase 1/2 (JNK1/2) and Akt, but not of p38 MAPK, with no further effect of acidic reperfusion or EIPA. Conclusion: In rat hearts, 15 min acidic reperfusion improves myocardial performance at least as much as does PostC, whereas NHE1 inhibition is detrimental. In contrast, in HL-1 cardiomyocytes, acidic reperfusion or NHE1 inhibition affect neither survival nor JNK1/2-, Akt-, and p38 MAPK activity after I/R, pointing to different mechanisms of damage and protection in these systems.
Neuroimaging and emerging psychotic disorders: The Melbourne ultra-high risk studies

Although the underlying neurobiology of emerging psychotic disorders is not well understood, evidence from structural imaging and other studies support the notion that schizophrenia arises as a consequence of both an ‘early neurodevelopmental’ disturbance, as well as ‘late neurodevelopmental’ changes occurring during the initial stages of a psychotic illness, including around the time of transition to illness. In line with this, our longitudinal MRI findings in individuals at ultra-high risk for developing a psychotic illness show that there are excessive neuroanatomical changes in those who convert to psychosis. These aberrant changes are observed most prominently in medial temporal and prefrontal lobe regions. In a further series of longitudinal studies in first-episode psychosis, we have identified changes in prefrontal regions that indicate an accelerated loss of grey matter in patients compared to healthy control subjects. We suggest that the available evidence is consistent with the presence of subtle regionally and temporally specific neurobiological changes through the course of psychosis (Pantelis et al., 53), including: (1) evidence for early (pre- and peri-natal) neurodevelopmental anomalies, (2) evidence for progressive grey matter loss involving medial temporal and orbital prefrontal regions around the time of transition to illness, and (3) evidence of late (post-pubertal) neurodevelopmental changes soon after the onset of psychosis, involving an acceleration of normal brain maturational processes, associated with significant loss of grey matter in dorsal prefrontal regions. The pathological processes underlying such changes remain unclear and may reflect anomalies in genetic and/or other endogenous mechanisms responsible for brain maturation, the adverse effects of intense or prolonged stress, or other environmental factors. These findings suggest that early markers of impending illness may prove difficult to define, and that brain changes in psychosis may better be conceptualized as anomalous trajectories of brain development. Further, active changes during transition to illness may present the potential to intervene and ameliorate these changes with potential benefit clinically.
Magnetic design and experimental evaluation of Integrated Magnetic Components used in Interleaved Multi-phase DC/DC converter with Phase Drive Control

Interleaved Multi-phase DC/DC Converters (IMDDC) with Integrated Magnetic Components (IMC) are well-known as one of the converter topologies that can achieve high-power-density. However, as one of the drawbacks of IMDDCs, the power conversion efficiency when all phases are driven may decrease between light and middle loads. The main causes of the efficiency reduction are non-load losses caused by parasitic capacitances in power devices and magnetic components. These losses especially increase under higher switching frequency and hard switching condition. To deal with this problem, IMDDCs with Phase Drive Control (PDC) has already been proposed as an attractive control scheme which can improve power conversion efficiency in all load ranges, by changing the number of drive phases. However, employing PDC in IMDDCs with IMC comes with two main drawbacks: 1) Magnetic saturation may occur due to the biased magnetization while driving a single-phase. 2) The circulating current flow in the anti-parallel diode of off-switch reduces the power conversion efficiency. Therefore, to overcome these problems, this paper proposes a novel design method of IMCs used in IMDDCs with PDC. The effectiveness of the proposed design method is discussed from theoretical and experimental viewpoints.
A 0.4 V low power baseband processor for UHF passive RFID tags

In this paper, a RFID baseband processor designed according to the EPC C1G2 protocol is presented. By adjusting the processor's activities according to the RF modulated envelop — the received signal strength, and by distributing data processing in different period, a low voltage, energy-aware design is achieved. Special care was taken in backend design to extend the clock frequency range and the supply range, so the robustness of the processor is ensured. The processor was fabricated in standard 180nm CMOS technology. It consumes less than 180 nW at 0.4V supply.
Body Mass Index and Percentage of Body Fat as Indicators for Obesity in an Adolescent Athletic Population

Background: Body mass index (BMI) is widely accepted in determining obesity. Skinfold thickness measurements have been commonly used to determine percentage of body fat. Hypothesis: The authors hypothesize that because BMI does not measure fat directly but relies on body weight alone, a large percentage of athletic adolescents will be misclassified as obese by BMI. Design: Cross-sectional study. Methods: To compare BMI and skinfold measurements as indicators for obesity in the adolescent athletic population, anthropometric data (height, weight, percentage body fat, age, and sex) were recorded from 33 896 student athletes (average age, 15 years; range, 11-19 years) during preparticipation physical examinations from 1985 to 2003. BMI was calculated from height and weight. Percentage of body fat was determined by measuring skinfold thickness. Results: According to their BMI percentile, 13.31% of adolescent athletes were obese. Using the skinfold method, only 5.95% were obese. Of those classified as obese by the BMI, 62% were considered false positives by the skinfold method. In contrast, there was a 99% probability that the nonobese by BMI would not be obese by the skinfold method (negative predictive value = 0.99). Conclusions: BMI is a measurement of relative body weight, not body composition. Because lean mass weighs far more than fat, many adolescent athletes are incorrectly classified as obese based on BMI. Skinfold testing provides a more accurate body assessment than BMI in adolescent athletes. Clinical Relevance: Correct body composition data can help to provide better diet and activity guidelines and prevent the psychological problems associated with being labeled as obese.
Robust automatic speech recognition and modeling of auditory discrimination experiments with auditory spectro-temporal features

Automatic speech recognition (ASR) systems still do not perform as well as human listeners under realistic conditions. The unmatched ability of humans to understand speech in most difficult acoustic conditions originates from the superior properties of their auditory system. The aim of this thesis is to improve the recognition performance of ASR systems in difficult acoustic conditions by carefully integrating auditory signal processing strategies. To this end, the physiologically inspired extraction of spectro-temporal modulation patterns was successfully integrated into the front-end of a standard ASR system. Further, the joint spectro-temporal processing could be separated into independent temporal and spectral processes. To investigate the reason for the remaining "man-machine-gap" in recognition performance, a range of critical auditory discrimination tasks were performed using ASR systems. The comparison with empirical data showed that the separate spectro-temporal modulation front-end provides a suitable auditory model and revealed the importance of across-frequency processing in speech recognition.
Glass and Jamming Transitions: From Exact Results to Finite-Dimensional Descriptions

Despite decades of work, gaining a first-principle understanding of amorphous materials remains an extremely challenging problem. However, recent theoretical breakthroughs have led to the formulation of an exact solution in the mean-field limit of infinite spatial dimension, and numerical simulations have remarkably confirmed the dimensional robustness of some of the predictions. This review describes these latest advances. More specifically, we consider the dynamical and thermodynamic descriptions of hard spheres around the dynamical, Gardner and jamming transitions. Comparing mean-field predictions with the finite-dimensional simulations, we identify robust aspects of the description and uncover its more sensitive features. We conclude with a brief overview of ongoing research.
The coordination numbers of Na and K atoms in low albite and microcline as determined from a procrystal electron-density distribution

Abstract Procrystal models for the electron-density distributions of low albite and microcline were constructed by placing spherically averaged Clementi-Roetti atomic wave functions at experimentally observed atomic positions. The topography of the model electron-density distribution was analyzed to locate (3, -1) critical points between the Na or K positions and the positions of the surrounding framework O atoms. Because the number of (3,-1) critical points associated with a given atom corresponds with its coordination number, the analysis indicated that Na is fivefold and K is sevenfold coordinated. In particular, the results indicate that the Oco atom in low albite is not coordinated with Na, whereas in microcline it is coordinated with K. This suggests that in low albite the Oco atom is underbonded and thus a possible hydrophilic site, whereas in microcline the bonding requirements of Oco are satisfied. Details of the local bonding explain the effects of pressure, H, and H20 on ordering of Al and Si, as well as compressibility systematics.
Phosphatidylinositol‐4,5‐bisphosphate (PIP2) regulation of strong inward rectifier Kir2.1 channels: multilevel positive cooperativity

Inwardly rectifying potassium (Kir) channels are gated by the interaction of their cytoplasmic regions with membrane‐bound phosphatidylinositol‐4,5‐bisphosphate (PIP2). In the present study, we examined how PIP2 interaction regulates channel availability and channel openings to various subconductance levels (sublevels) as well as the fully open state in the strong inward rectifier Kir2.1 channel. Various Kir2.1 channel constructs were expressed in Xenopus oocytes and single channel or macroscopic currents were recorded from inside‐out patches. The wild‐type (WT) channel rarely visited the subconductance levels under control conditions. However, upon reducing Kir2.1 channel interaction with PIP2 by a variety of interventions, including PIP2 antibodies, screening PIP2 with neomycin, or mutating PIP2 binding sites (e.g. K188Q), visitation to the sublevels was markedly increased before channels were converted to an unavailable mode in which they did not open. No channel activity was detected in channels with the double mutation K188A/R189A, a mutant which exhibits extremely weak interaction with PIP2. By linking subunits together in tandem dimers or tetramers containing mixtures of WT and K188A/R189A subunits, we demonstrate that one functional PIP2‐interacting WT subunit is sufficient to convert channels from the unavailable to the available mode with a high open probability dominated by the fully open state, with similar kinetics as tetrameric WT channels. Occasional openings to sublevels become progressively less frequent as the number of WT subunits increases. Quantitative analysis reveals that the interaction of PIP2 with WT subunits exerts strong positive cooperativity in both converting the channels from the unavailable to the available mode, and in promoting the fully open state over sublevels. We conclude that the interaction of PIP2 with only one Kir2.1 subunit is sufficient for the channel to become available and to open to its full conductance state. Interaction with additional subunits exerts positive cooperativity at multiple levels to further enhance channel availability and promote the fully open state.
Angiosarcoma developing in a breast after conservation treatment for breast cancer.

CASE REPORT In February 1997, this 80-year-old woman had conservation treatment for a moderately well-differentiated infiltrating ductal carcinoma in the left breast. This primary tumor in the upper outer quadrant of the left breast was 1.8 cm in largest dimension. The surgical margins after excision were tumor free, although there was a noncomedo ductal carcinoma in situ component within 0.1 mm of one margin. An axillary dissection was not done. The breast was irradiated through opposed tangential fields to a calculated dose of 5,040 cGy at the 90% isodose line using 6-MV photons. A boost of 1,600 cGy was delivered to the 90% isodose line using a 10-MeV electron beam. The left supraclavicular fossa and axilla were irradiated with photons to a dose of 5,040 cGy calculated at a depth of 3.0 cm from the anterior surface. The overall treatment time was 49 days. The patient tolerated the treatment without difficulty with only a mild, diffuse skin erythema. She was started and continued on tamoxifen 20 mg daily. Since treatment, the left breast was visibly and palpably normal until August 2001 when a purplish-red discoloration with serpiginous margins measuring 8.0 cm in greatest dimension was noted surrounding the nipple. There were no signs of inflammation. The breast was palpably normal. On October 31, 2001, a biopsy of the skin was interpreted as low grade angiosarcoma. On a mammogram dated November 29, 2001, the findings were “benign” without change from previous mammograms. No metastases were visible on a computed tomography examination of the chest. There has been no edema of the left upper limb. On February 19, 2002, a left mastectomy was done. Gross pathologic analysis of the mastectomy specimen revealed violaceous discoloration of the skin around the nipple. There was no ulceration or dominant mass. Microscopic pathologic analysis revealed a proliferation of mature and slightly immature vascular channels lined by endothelial cells in the papillary dermis (Fig. 1A) and reticular dermis (Fig. 1B). The vascular channels were angulated, were not confined to lobules, and infiltrated the adjacent dermal layers. In some areas, the vascular proliferation consisted of “back-toback” vascular structures with diminutive lumina. The vascular proliferation was most dense directly under the epidermis and became sparser with increasing depth from the skin surface. The vascular proliferation was confined to the dermis and did not penetrate the underlying subcutaneous tissue or the underlying breast. Immunocytochemical analysis with antibodies to CD31 and factor VIII-related antigen (Von Willebrand factor) revealed that the endothelial cells lining the proliferating vascular channels exhibited intense immunoreactivity for both endothelial antigens (Fig. 1C). All of these features supported a diagnosis of low grade angiosarcoma of the skin of the breast.
Conservation of Mammals in Eastern North American Wildlife Reserves: How Small Is Too Small?

Abstract: A common objective of methods of systematic reserve selection has been to maximize conservation benefits—frequently current species richness—while reducing the costs of acquiring and maintaining reserves. But the probability that a reserve will lose species in the future is frequently not known because the minimum area requirements for most species have not been estimated empirically. For reserves within the Alleghenian‐Illinoian mammal province of eastern North America, we empirically estimated the minimum area requirement of terrestrial mammals such that reserves should not lose species because of insularization. We compared this estimate to the actual size of 2355 reserves and reserve assemblages within the mammal province. The estimated minimum area requirement was 5037 km2 (95% CI: 2700–13,296 km2). Fourteen reserves and reserve assemblages were> 2700 km2, 9 were> 5037 km2, and 3 were> 13,296 km2. These 14 reserves accounted for 73% of the total area of reserves and 10% of the total area of the mammal province. Few reserves appear large enough to avoid loss of some mammal species without the additional cost of active management of habitat or populations. Immigration corridors and buffer zones that combine small reserves into assemblages totaling at least 2700 km2 may be the most efficient means of conserving mammals in these reserves.
Transition from Simple Rotating Chemical Spirals to Meandering and Traveling Spirals.

Experiments on the Belousov-Zhabotinksy reaction unfold the bifurcation from simple (temporally periodic) rotating spirals to meandering (quasiperiodic) spirals in the neighborhood of a codimension-2 point. There are two types of meandering spirals, inward-petal (epicycloid) spirals and outward-petal (hypocycloid) spirals. These two types of meandering regimes are separated in the phase diagram by a line of traveling spirals that terminates at the codimension-2 point. The observations are in good accord with theory. {copyright} {ital 1996 The American Physical Society. }
Optimum design of manipulators under dynamic isotropy conditions

The optimum design of manipulator architectures under dynamic isotropy conditions is addressed. The goal of the design is to choose the kinematic and inertial parameters of manipulators such that their generalized inertia matrices can attain values as close to isotropy as possible. Two design examples are given. One pertains to a three-degree-of-freedom serial manipulator, and the other to a platform parallel manipulator. <<ETX>>
RNA-Seq differential expression analysis: An extended review and a software tool

The correct identification of differentially expressed genes (DEGs) between specific conditions is a key in the understanding phenotypic variation. High-throughput transcriptome sequencing (RNA-Seq) has become the main option for these studies. Thus, the number of methods and softwares for differential expression analysis from RNA-Seq data also increased rapidly. However, there is no consensus about the most appropriate pipeline or protocol for identifying differentially expressed genes from RNA-Seq data. This work presents an extended review on the topic that includes the evaluation of six methods of mapping reads, including pseudo-alignment and quasi-mapping and nine methods of differential expression analysis from RNA-Seq data. The adopted methods were evaluated based on real RNA-Seq data, using qRT-PCR data as reference (gold-standard). As part of the results, we developed a software that performs all the analysis presented in this work, which is freely available at https://github.com/costasilvati/consexpression. The results indicated that mapping methods have minimal impact on the final DEGs analysis, considering that adopted data have an annotated reference genome. Regarding the adopted experimental model, the DEGs identification methods that have more consistent results were the limma+voom, NOIseq and DESeq2. Additionally, the consensus among five DEGs identification methods guarantees a list of DEGs with great accuracy, indicating that the combination of different methods can produce more suitable results. The consensus option is also included for use in the available software.
The evolutionary genetics of egg size plasticity in a butterfly

The evolution of phenotypic plasticity requires that it is adaptive, genetically determined, and exhibits sufficient genetic variation. For the tropical butterfly Bicyclus anynana there is evidence that temperature‐mediated plasticity in egg size is an adaptation to predictable seasonal change. Here we set out to investigate heritability in egg size and genetic variation in the plastic response to temperature in this species, using a half‐sib breeding design. Egg size of individual females was first measured at a high temperature 4 days after eclosion. Females were then transferred to a low temperature and egg size was measured after acclimation periods of 6 and 12 days respectively. Overall, additive genetic variance explained only 3–11% of the total phenotypic variance, whereas maternal effects were more pronounced. Genotype–environment interactions and cross‐environmental correlations of less than unity suggest that there is potential for short‐term evolutionary change. Our findings strengthen the support for the adaptive nature of temperature‐mediated plasticity in egg size.
[Effect of Aloe coarse polysaccharide on cytokine secretion of keratinocytes in vitro].

OBJECTIVE To study the effects of Aloe coarse polysaccharide on the levels of growth factors (EGF, TGF-alpha, TGF-beta1) and interleukins (IL-1beta, IL-6, IL-8) and tumor necrosis factor (TNF) in cultured keratinocytes. METHOD The cultured keratinocytes were treated with Aloe coarse polysaccharide at concentrations of 75, 150, 300, 600, 1 200 mg x L(-1) land the equal volume of media as control group. The levels of EGF, TGF-alpha, TGF-beta1, IL-1beta, IL-6, IL-8 and TNF in the supernatants of cultured keratinocytes were assayed by enzyme-linked immunosorbent assay (ELISA) and radioimmunoassay (RIA). RESULT Compared with the control group, the levels of EGF, TGF-alpha, IL-1beta, IL-6 and IL-8 were significantly increased by treatment with Aloe coarse polysaccharide (P < 0.05, P < 0.01) and in a dose dependent manner, and the levels of TGF-beta1 and TNF were also increased but no statistical significance. CONCLUSION Aloe coarse polysaccharide may promote keratinocytes to secrete EGF, TGF-alpha, IL-1beta, IL-6 and IL-8.