Miracle-dz/UniFAR-FTUs huggingface dataset:
Shape changes and motion of a vesicle in a fluid using a lattice Boltzmann model

To study erythrocyte deformation and movement in fluid flows, the membrane bending rigidity and elastic modulus are incorporated with a lattice Boltzmann simulation. The stable static biconcave shape is found to resist pathological membrane changes, and the erythrocyte exhibits tank tread-like motion with a highly flattened shape in a shear flow. With intrinsically parallel dynamics, this lattice Boltzmann method may apply to both single and multi-vesicle suspension and complex open membranes in various fluid flows for a wide range of Reynolds numbers.
Asymmetry in sympathetic and vagal activities during sleep-wake transitions.

STUDY OBJECTIVES To explore the role of autonomic nervous system in initiation of sleep-wake transitions. DESIGN Changes in cardiovascular variability during sleep-wake transitions of adult male Wistar-Kyoto rats on their normal daytime sleep were analyzed. INTERVENTIONS A 6-h daytime sleep-wakefulness recording session was performed. MEASUREMENTS AND RESULTS Electroencephalogram and electromyogram (EMG) signals were subjected to continuous power spectral analysis, from which mean power frequency of the electroencephalogram (MPF) and power of the EMG were quantified. Active waking (AW), quiet sleep (QS), and paradoxical sleep (PS) were defined every 8 s according to corresponding MPF and EMG power. Continuous power spectral analysis of R-R intervals was performed to quantify its high-frequency power (HF, 0.6-2.4 Hz), low-frequency power (0.06-0.6 Hz) to HF ratio (LF/HF). MPF exhibited two phases of change during AW-QS and QS-AW transitions: a slowly changing first phase followed by a rapidly changing second phase. HF increased linearly with the decrease of MPF during the first phase of AW-QS transition whereas LF/HF increased linearly with the increase of MPF during the first phase of QS-AW transition. However, the LF/HF was not correlated with the HF. The MPF and HF exhibited only a rapidly changing phase during QS-PS transition. The LF/HF declined transiently during the QS-PS transition, followed by a sustained increase in PS. CONCLUSIONS The parasympathetic activity before falling asleep and the sympathetic activity before waking up change coincidentally with EEG frequency, and may respectively contain the messages of sleeping and waking drives.
Semantic Segmentation with Reverse Attention

Recent development in fully convolutional neural network enables efficient end-to-end learning of semantic segmentation. Traditionally, the convolutional classifiers are taught to learn the representative semantic features of labeled semantic objects. In this work, we propose a reverse attention network (RAN) architecture that trains the network to capture the opposite concept (i.e., what are not associated with a target class) as well. The RAN is a three-branch network that performs the direct, reverse and reverse-attention learning processes simultaneously. Extensive experiments are conducted to show the effectiveness of the RAN in semantic segmentation. Being built upon the DeepLabv2-LargeFOV, the RAN achieves the state-of-the-art mIoU score (48.1%) for the challenging PASCAL-Context dataset. Significant performance improvements are also observed for the PASCAL-VOC, Person-Part, NYUDv2 and ADE20K datasets.
Defect-induced Raman spectra in doped CeO2.

Polarized Raman-scattering spectra are obtained from oriented single crystals of yttria-doped ${\mathrm{CeO}}_{2}$. The temperature and dopant dependencies of Raman spectra strongly suggest that many structures in the Raman spectra of yttria-doped ${\mathrm{CeO}}_{2}$ are induced by the defect space including an ${\mathrm{O}}^{2\mathrm{\ensuremath{-}}}$ vacancy. The contribution to the frequency distributions of Raman-active modes from the whole Brillouin zone are estimated from the imaginary part of the simple projection of the phonon displacement-displacement Green's functions of undoped ${\mathrm{CeO}}_{2}$ crystals onto several defect spaces. The observed spectra are well explained by the linear combination of the calculated frequency distributions from the defect space consisting of the four metal ions and from that consisting of the six next-nearest-neighbor ${\mathrm{O}}^{2\mathrm{\ensuremath{-}}}$ ions surrounding an ${\mathrm{O}}^{2\mathrm{\ensuremath{-}}}$ vacancy. Brillouin-scattering spectra of ${\mathrm{CeO}}_{2}$ are also measured in order to calculate the phonon-dispersion curves of ${\mathrm{CeO}}_{2}$. The dependencies of type and concentration of defect space on dopant concentration in doped ${\mathrm{CeO}}_{2}$ are also discussed.
Acute Kidney Injury: New Definitions and Beyond

Acute kidney injury (AKI) previously known as acute renal failure is a common clinical syndrome, with multiple etiologies and a complex array of clinical and biochemical changes. AKI affecting all age groups with increasing incidence in hospitalized patients and associated with significant morbidity and mortality. It is until 2004, when the Acute Dialysis Quality Initiative (ADQI) group proposed RIFLE (risk, injury, and failure, loss of function and end-stage renal failure) as consensus criteria for AKI definition and staging. Subsequent refinements and modifications had been proposed to increase specificity and sensitivity of diagnosis and prognosis, including pRIFLE (for children), AKIN and KDIGO. This review focuses on the recent advances in AKI definitions and classifications and highlights area of limitations and controversies.
Improving Accuracy for 3D RFID Localization

Radio Frequency Identification (RFID) becomes a prevalent labeling and localizing technique in the recent years. Deploying indoor RFID localization systems facilitates many applications. Previous approaches, however, are most based on 2D design and cannot provide 3D location information. The lack of one-dimensional information may lead 2D-based systems to inaccurate localization. In this paper, we develop an indoor 3D RFID localization system based on active tag array. In particular, we employ the geometric mean to filter the explicit 3D location information with high accuracy. The experimental results show that our system is efficient in tracking objects and improving the localization accuracy.
Submicroscopic structure of canine articular cartilage

Canine articular cartilage was studied in male dogs at age 1, 4, 5 and 8 years. Samples collected from four hip joints and two humeral joints in each age category were processed by standard methods to be examined by scanning and transmission electron microscopy. The cartilage of both joints was similar in structure. In the superficial cartilage layer of one-year-old animals, individual spindle-shaped chondrocytes in the extracellular matrix were, together with associated collagen fibrils, located parallel to the surface. When viewed by scanning electron microscopy, they were distinctly prominent above the surrounding surface. Changes in the thickness and arrangement of both the chondrosynovial membrane and intercellular matrix were apparent in the 4-, 5and 8-yearold animals, indicating the onset or progression of an osteoarthritic process. The middle cartilage layer in young animals showed elliptical chondrocytes occurring in pairs. The voluminous cytoplasm contained a great amount of granular endoplasmic reticulum, a large Golgi complex and numerous transport vesicles. The pericellular matrix, up to 1 μm thick, was composed of aperiodic fibrils. In the old animals the pericellular matrix was absent and was replaced by thick collagen fibrils with a marked periodicity. The deep cartilage layer in young dogs included groups of three to four chondrocytes situated in a common territory. The cytoplasm contained distinct bundles of intermediary filaments. The pericellular matrix occasionally formed septa between adjoining cells. The intracellular matrix included bundles of collagen fibrils arranged in a ma�ed structure. In the old animals aggregation of chondrocytes into groups almost disappeared. The cytoplasm showed only short cisternae of granular endoplasmic reticulum, small numbers of mitochondria and transport vesicles, frequent lipid droplets and small glycogen deposits. The intercellular matrix consisted of only short collagen fibrils with no distinct periodicity.
Effect of age on survival of critically ill patients with cancer*

Objectives:To estimate the effects of age on 6-month survival of critically ill patients with cancer. Design:Prospective cohort study analyzed using Cox proportional hazard models. Setting:Ten-bed oncologic medical-surgical intensive care unit. Patients:Eight hundred sixty-two patients with cancer, excluding bone marrow transplant patients. Interventions:None. Measurements and Main Results:The mean age was 57.8 ± 16.2 yrs. The hospital and 6-month mortality rates were 48% and 58%, respectively. Age was independently associated with increased mortality (hazard ratio, 1.015; 95% confidence interval, 1.009–1.021). Martingale residual analysis, however, suggested an inflection point in the effect of age, with an upward trend for patients aged >60 yrs. Therefore, patients were stratified in two groups: young (≤60 yrs, n = 431, 50%) and elderly (>60 yrs, n = 431, 50%). In young patients, uncontrolled cancer, mechanical ventilation, and number of organ failures were associated with poor outcome, whereas surgery before intensive care unit admission was protective. The variables associated with increased mortality for elderly patients were performance status 3–4, uncontrolled cancer, number of organ failures, and the presence of a severe comorbidity. In this group, age was associated with a lower survival rate. In general, the effect of covariates on the outcome was higher in the elderly group. Conclusions:Aging was associated with increased mortality, especially for patients >60 yrs. The severity of organ failures and the presence of uncontrolled cancer were the main predictive factors, but there were important differences among the outcome predictors for young and elderly patients. Our results suggest that selected older patients with cancer can benefit from intensive care.
Biological activity, membrane‐targeting modification, and crystallization of soluble human decay accelerating factor expressed in E. coli

Decay‐accelerating factor (DAF, CD55) is a glycophosphatidyl inositol‐anchored glycoprotein that regulates the activity of C3 and C5 convertases. In addition to understanding the mechanism of complement inhibition by DAF through structural studies, there is also an interest in the possible therapeutic potential of the molecule. In this report we describe the cloning, expression in Escherichia coli, isolation and membrane‐targeting modification of the four short consensus repeat domains of soluble human DAF with an additional C‐terminal cysteine residue to permit site‐specific modification. The purified refolded recombinant protein was active against both classical and alternative pathway assays of complement activation and had similar biological activity to soluble human DAF expressed in Pichia pastoris. Modification with a membrane‐localizing peptide restored cell binding and gave a large increase in antihemolytic potency. These data suggested that the recombinant DAF was correctly folded and suitable for structural studies as well as being the basis for a DAF‐derived therapeutic. Crystals of the E. coli‐derived protein were obtained and diffracted to 2.2 Å, thus permitting the first detailed X‐ray crystallography studies on a functionally active human complement regulator protein with direct therapeutic potential.
Neurofeedback in Psychological Practice.

Advances in technology occasionally allow for innovations in the practice of psychology. Neurofeedback is one such modality; in it, individuals learn to change patterns of brain waves through operant conditioning. Research shows that a number of neurological and psychological disorders can be characterized by distinctive EEG patterns and that neurofeedback may help clients to change those patterns. The evidence regarding neurofeedback’s efficacy for attention-deficit/hyperactivity disorder (ADHD), depression, and other disorders is reviewed. Using control group designs, four different research teams have found neurofeedback to be effective for ADHD participants; research on outcomes for other disorders is at a much more preliminary stage. Practicing psychologists are encouraged to explore the potential of this alternative and distinctly psychological modality. Neurofeedback, also known as EEG biofeedback or EEG operant conditioning, is an emerging modality with the potential of becoming an important part of effective psychological practice. Neurofeedback is a process whereby individuals learn to selfregulate their brain waves. Preliminary findings indicate that teaching individuals to alter electrocortical activity may have beneficial effects for attention-deficit/hyperactivity disorder (ADHD). Other research is ongoing to determine the effectiveness of neurofeedback for other disorders as well, including depression and schizophrenia. Its promise notwithstanding, neurofeedback has been virtually ignored by the mainstream investigators and clinicians. Even accounting for the absence of conclusive empirical efficacy, a process that combines two pillars of psychology— operant conditioning and brain function— deserves greater attention from the psychological community. With this article we hope to call attention to this modality by presenting some of the history and research pertaining to brain wave self-regulation.
Aspiration in bilateral stroke patients

Seventy patients with bilateral strokes underwent neurologic and videofluoroscopic barium swallowing examinations; 34 (48.6%) aspirated. Patients with aspiration were more likely to have posterior circulation strokes, abnormal cough, abnormal gag, and dysphonia. However, patients likely to aspirate can be identified best by the presence of an abnormal voluntary cough, an abnormal gag reflex, or both. The prediction of patients at risk for aspiration was not improved by additional clinical information (ie, presence of dysphonia or bilateral neurologic signs).
Anadromy, potamodromy and residency in brown trout Salmo trutta: the role of genes and the environment

Abstract Brown trout Salmo trutta is endemic to Europe, western Asia and north‐western Africa; it is a prominent member of freshwater and coastal marine fish faunas. The species shows two resident (river‐resident, lake‐resident) and three main facultative migratory life histories (downstream–upstream within a river system, fluvial–adfluvial potamodromous; to and from a lake, lacustrine–adfluvial (inlet) or allacustrine (outlet) potamodromous; to and from the sea, anadromous). River‐residency v. migration is a balance between enhanced feeding and thus growth advantages of migration to a particular habitat v. the costs of potentially greater mortality and energy expenditure. Fluvial–adfluvial migration usually has less feeding improvement, but less mortality risk, than lacustrine–adfluvial or allacustrine and anadromous, but the latter vary among catchments as to which is favoured. Indirect evidence suggests that around 50% of the variability in S. trutta migration v. residency, among individuals within a population, is due to genetic variance. This dichotomous decision can best be explained by the threshold‐trait model of quantitative genetics. Thus, an individual's physiological condition (e.g., energy status) as regulated by environmental factors, genes and non‐genetic parental effects, acts as the cue. The magnitude of this cue relative to a genetically predetermined individual threshold, governs whether it will migrate or sexually mature as a river‐resident. This decision threshold occurs early in life and, if the choice is to migrate, a second threshold probably follows determining the age and timing of migration. Migration destination (mainstem river, lake, or sea) also appears to be genetically programmed. Decisions to migrate and ultimate destination result in a number of subsequent consequential changes such as parr–smolt transformation, sexual maturity and return migration. Strong associations with one or a few genes have been found for most aspects of the migratory syndrome and indirect evidence supports genetic involvement in all parts. Thus, migratory and resident life histories potentially evolve as a result of natural and anthropogenic environmental changes, which alter relative survival and reproduction. Knowledge of genetic determinants of the various components of migration in S. trutta lags substantially behind that of Oncorhynchus mykiss and other salmonines. Identification of genetic markers linked to migration components and especially to the migration–residency decision, is a prerequisite for facilitating detailed empirical studies. In order to predict effectively, through modelling, the effects of environmental changes, quantification of the relative fitness of different migratory traits and of their heritabilities, across a range of environmental conditions, is also urgently required in the face of the increasing pace of such changes.
Comparison of enteral nutrition and drug treatment in active Crohn's disease: results of the European Cooperative Crohn's Disease Study IV.

This study compares the effect of drug treatment for Crohn's disease with that of enteral nutrition alone as a therapeutic modality for this disease. Patients were randomly divided into two groups: One group (n = 52) was treated with 6-methylprednisolone (48 mg/day, subsequently tapered) and sulfasalazine (3 g/day). The second group (n = 55) was treated with enteral nutrition consisting of an oligopeptide diet. The two groups were matched for severity of illness and demographic characteristics. Remission was defined as a decrease in Crohn's Disease Activity Index by 40% (or at least 100 points). Significantly more (p < .01, χ 2) patients in the drug treatment group (41 of 52) achieved remission, compared with the dietary treatment group (29 of 55). The median time to remission for the drug treatment group was 8.2 days compared with 30.7 days for the dietary treatment group (p < .01; Mantel Cox). Further data analysis was carried out to determine whether certain subgroups within the dietary group might hav.
Diagnostic efficacy of two rapid tests for detection of respiratory syncytial virus antigen

With the availability of ribavirin therapy for serious respiratory syncytial virus (RSV) infections, rapid diagnostic tests for the detection of RSV antigen are increasingly important. Efficacies of a commercially available enzyme immunoassay (EIA) (Abbott Laboratories, North Chicago, Ill.) and a fluorescent-antibody assay (FA) were evaluated in a study involving 135 specimens from children with respiratory symptoms. A nasal wash specimen was cultured immediately on RSV-sensitive A549 cells; the nasal wash was also used for EIA. FA was performed on a nasopharyngeal swab specimen with bovine anti-RSV and anti-bovine immunoglobulin G antisera (Burroughs Wellcome Co., Research Triangle Park, N.C.). A total of 39 specimens (28%) were tissue culture positive, including 35 EIA-positive and 37 FA-positive samples (sensitivities, 90 and 95%, respectively). All 96 tissue culture-negative specimens were EIA negative (specificity, 100%); 94 of these 96 specimens were FA negative (specificity, 98%). Positive and negative predictive values for the tests were as follows: 100 and 96% for EIA, respectively, and 95 and 98% for FA, respectively. Other viruses, including influenza A virus, adenovirus, enterovirus, and herpes simplex virus, were isolated in nine cases. One adenovirus-positive specimen had a false-positive RSV FA result; all nine specimens were RSV EIA negative. Both tests performed well in our study and provide cost-effective alternatives to tissue culture. The RSV EIA, in particular, uses standard serologic techniques and equipment and does not require expertise in virology. More widespread availability of rapid diagnostic tests for RSV will hopefully result in early and appropriate use of antiviral therapy in patients at risk for serious RSV infections.
Transcription profile of Helicobacter pylori in the human stomach reflects its physiology in vivo.

BACKGROUND Little is known about levels of expression of Helicobacter pylori genes in the human host. We therefore developed a quantitative real-time reverse-transcriptase polymerase chain reaction (qRT-PCR) assay to measure transcript profiles of H. pylori in the human stomach. METHODS In vivo expression of 16 genes on the cag pathogenicity island and of 18 putative virulence genes was quantitated by isolation of total RNA directly from infected human gastric mucosa. The results were compared with in vitro expression determined from H. pylori cells grown in culture. RESULTS The highest levels of expression were found for cag1 and cag25 and for genes, such as urease and catalase, that may be important for bacterial homeostasis in the relatively hostile environment of the gastric mucosa. Transcript abundance, relative to 16S rRNA, was lower in vivo than in vitro, which suggests that H. pylori cells are in stationary phase in the gastric environment. This was particularly apparent for cagA. Since CagA is arguably of unique importance, in terms of interaction with the host, tight control of its in vivo expression might be particularly important. CONCLUSIONS qRT-PCR is a powerful tool to measure gene expression in human or animal tissue that contains minute amounts of microbial mRNA, and the results reflect on the physiology of the pathogen in its natural host.
Autocrine Regulation of Eotaxin in Normal Human Bronchial Epithelial Cells

Normal human bronchial epithelial cells (NHBECs) spontaneously synthesize and store chemokines including eotaxin, RANTES, or MCP-3. We also observed the constitutive expression of mRNA specific for CC chemokine receptor-3 (CCR3) in these cells. The stimulation of these cells by eotaxin (1–100 ng/ml) dose-dependently increased eotaxin production. In addition, RANTES or eotaxin-2 but not MCP-3 at the higher concentrations (100 ng/ml), also induced slight eotaxin production. Eotaxin elicited the expression of eotaxin mRNA at 6 h after stimulation. Antibody against eotaxin or CCR3, and actinomycin D inhibited these effects of eotaxin. These antibodies also significantly inhibited the ability of eotaxin to produce further eotaxin. These findings strongly suggest that eotaxin which originates from inflammatory cells or cells resident in the airway of bronchial asthmatics can induce further production of eotaxin and participate in expansion of allergic inflammation.