Miracle-dz/UniFAR-FTUs huggingface dataset:
Deletion of creB in Aspergillus oryzae Increases Secreted Hydrolytic Enzyme Activity

ABSTRACT Aspergillus oryzae has been used in the food and beverage industry for centuries, and industrial strains have been produced by multiple rounds of selection. Targeted gene deletion technology is particularly useful for strain improvement in such strains, particularly when they do not have a well-characterized meiotic cycle. Phenotypes of an Aspergillus nidulans strain null for the CreB deubiquitinating enzyme include effects on growth and repression, including increased activity levels of various enzymes. We show that Aspergillus oryzae contains a functional homologue of the CreB deubiquitinating enzyme and that a null strain shows increased activity levels of industrially important secreted enzymes, including cellulases, xylanases, amylases, and proteases, as well as alleviated inhibition of spore germination on glucose medium. Reverse transcription-quantitative PCR (RT-qPCR) analysis showed that the increased levels of enzyme activity in both Aspergillus nidulans and Aspergillus oryzae are mirrored at the transcript level, indicating transcriptional regulation. We report that Aspergillus oryzae DAR3699, originally isolated from soy fermentation, has a similar phenotype to that of a creB deletion mutant of the RIB40 strain, and it contains a mutation in the creB gene. Collectively, the results for Aspergillus oryzae, Aspergillus nidulans, Trichoderma reesei, and Penicillium decumbens show that deletion of creB may be broadly useful in diverse fungi for increasing production of a variety of enzymes.
Defining a roadmap towards comparative research in online activity recognition on mobile phones

Many context-aware applications based on activity recognition are currently using mobile phones. Most of this work is done in an offline way. However, there is a shift towards an online approach in recent studies, where activity recognition systems are implemented on mobile phones. Unfortunately, most of these studies lack proper reproducibility, resource consumption analysis, validation, position-independence, and personalization. Moreover, they are hard to compare in various aspects due to different experimental setups. In this paper, we present a short overview of the current research on online activity recognition using mobile phones, and highlight their limitations. We discuss these studies in terms of various aspects, such as their experimental setups, position-independence, resource consumption analysis, performance evaluation, and validation. Based on this analysis, we define a roadmap towards a better comparative research on online activity recognition using mobile phones.
Frontiers in Cellular Neuroscience Cellular Neuroscience

In vision and olfaction, two senses involving GPCRs as main detectors, RGS9-1 and RGS2 respectively have been reported to attenuate light or odorant responses (Sinnarajah et al., 2001; Nishiguchi et al., 2004) while Ric-8B a putative GEF for Gαolf that is abundant in olfactory sensory neurons amplifi es odorant receptor signaling (Von Dannecker et al., 2005, 2006). Ric-8B has one other known mammalian homologue, Ric-8A, which was shown to enhance Gαq-mediated ERK activation by GPCRs (Nishimura et al., 2006) as well as interact and display GEF activity for Gαi1, Gαq and Gαo but not Gαs in vitro (Tall et al., 2003). The GEF activity of Ric-8A on the Gαι subunit has been extensively studied in receptor-independent G-protein-mediated events regulating microtubules pulling forces during cell division (Tall and Gilman, 2005). In this system the action of Ric-8A is similar to that of a GPCR while the GDI activity of GPR/GoLoco motif-containing proteins resemble that of Gβγ subunits (Thomas et al., 2008). In gustation, RGS21 has been reported to be expressed specifically in taste cells and to play a role in gustducin signaling (von Buchholtz et al., 2004); however, no reports of GEFs further controlling this system have been made. To study whether GEFs are involved in the transduction of the signal downstream of the taste GPCRs we investigated the expression of Ric-8A and Ric-8B in mouse taste cells and their interaction with G-protein subunits found in taste buds.
Exhaled air temperature in children with bronchopulmonary dysplasia

Because they have similar functional and clinical profiles, bronchopulmonary dysplasia (BPD) survivors are often treated as asthmatic patients. In truth, very little is known about the possible biochemical and inflammatory mechanisms playing a part in BPD survivors' lungs. The aim of this study was to measure exhaled breath temperature in BPD survivors by comparison with asthmatic cases and healthy controls.
The Computational Hardness of Estimating Edit Distance [Extended Abstract]

We prove the first non-trivial communication complexity lower bound for the problem of estimating the edit distance (aka Levenshtein distance) between two strings. A major feature of our result is that it provides the first setting in which the complexity of computing the edit distance is provably larger than that of Hamming distance. Our lower bound exhibits a trade-off between approximation and communication, asserting, for example, thai protocols with O(1) bits of communication can only obtain approximation a ges Omega(log d/log log d), where d is the length of the input strings. This case of O(1) communication is of particular importance, since it captures constant-size sketches as well as embaddings into spaces like L1 and squared-L2. two prevailing algorithmic approaches for dealing with edit distance. Furthermore, the bound holds not only for strings over alphabet Sigma= {0, 1}, but also for strings that are permu-tations (called the Ulam metric). Besides being applicable to a much richer class of algorithms than all previous results, our bounds are near-tight in at. least one case, namely of embedding permutations into L1. The proof uses a new technique, that relies on Fourier analysis in a rather elementary way.
Commentaries on Viewpoint: Is the resting bradycardia in athletes the result of remodeling of the sinoatrial node rather than high vagal tone?

TO THE EDITOR: Resting bradycardia is an unquestionable marker of exercise training adaptation (1) and has been consistently documented in different species (2, 4). The question is whether this cardiac adaptation is due to increased vagal tone, sympathetic tone reduction, or decrease in intrinsic heart rate. In our investigations, exercise training reduces vagal and sympathetic tonus in a similar matter (5), which implies that no change in resting heart rate should be expected. However, we found a reduced resting heart rate, as extensively demonstrated by other investigators. These findings strongly suggest that the bradycardia provoked by exercise training is not simply a result of changes in the vagal and sympathetic balance. In fact, further investigation with double blockade with methylatropine and propranolol showed that intrinsic heart rate was significantly reduced in exercise-training animals compared with untrained animals. Our studies provide no evidence for increased vagal function after exercise training. On the contrary, exercise training virtually decreases vagal function. Baroreflex bradycardia provoked by vasoconstrictor drug, bradycardic responses caused by electrical stimulation of the vagal nerve, and responses to methacholine injection are all depressed after exercise training. These findings lead us to strongly agree with Boyett and collaborators (3) that “resting bradycardia cannot be explained by high vagal tone. ” The resting bradycardia is a consequence of pacemaker cell alterations and intrinsic heart rate reduction.
Free vibration analysis of a functionally graded material beam: evaluation of the Haar wavelet method

The current study focuses on the evaluation of the Haar wavelet method, i.e. its comparison with widely used strong formulation based methods (FDM-finite difference method and DQM-differential quadrature method). A solid element 3D finite element model is developed and the numerical results obtained by using simplified approaches are confirmed.
Variations in colonoscopy practice in Europe: A multicentre descriptive study (EPAGE)

Objective. The volume of colonoscopies performed is increasing and differences in colonoscopy practice over time and between centres have been reported. Examination of current practice is important for benchmarking quality. The objective of this study was to examine variations in colonoscopy practice in endoscopy centres internationally. Material and methods. This observational study prospectively included consecutive patients referred for colonoscopy from 21 centres in 11 countries. Patient, procedure and centre characteristics were collected through questionnaires. Descriptive statistics were performed and the variation between centres while controlling for case-mix was examined. Results. A total of 6004 patients were included in the study. Most colonoscopies (93%; range between centres 70–100%) were performed for diagnostic purposes. The proportion of main indications for colonoscopy showed wide variations between centres, the two most common indications, surveillance and haematochezia, ranging between 7–24% and 5–38%, respectively. High-quality cleansing occurred in 74% (range 51–94%) of patients, and 30% (range 0–100%) of patients received deep sedation. Three-quarters (range 0–100%) of the patients were monitored during colonoscopy, and one-quarter (range 14–35%) underwent polypectomy. Colonoscopy was complete in 89% (range 69–98%) of patients and the median total duration was 20 min (range of centre medians 15–30 min). The variation between centres was not reduced when case-mix was controlled for. Conclusions. This study documented wide variations in colonoscopy practice between centres. Controlling for case-mix did not remove these variations, indicating that centre and procedure characteristics play a role. Centres generally were within the existing guidelines, although there is still some work to be done to ensure that all centres attain the goal of providing high-quality colonoscopy.
Soluble P-Selectin and the Risk of Future Cardiovascular Events

Background —P-selectin, a cell-surface adhesion molecule involved in leukocyte rolling and attachment, has been hypothesized to play a role in the initiation of atherosclerosis. However, little clinical data are available evaluating the role of soluble P-selectin in determining vascular risk. Methods and Results —In a large-scale prospective study of apparently healthy women, we measured baseline plasma concentration of soluble P-selectin among 115 participants who subsequently developed cardiovascular events and among 230 age- and smoking-matched participants who remained free of disease during 3.5 years of follow-up. Overall, mean levels of soluble P-selectin were significantly higher at baseline among women who subsequently experienced cardiovascular events compared with those who did not (83.2 versus 69.3 ng/mL;P =0.003). The risk of future cardiovascular events increased with increasing quartiles of soluble P-selectin (P =0.02), such that women in the highest quartile at study entry had an age- and smoking-matched relative risk 2.2 times higher than those in the lowest quartile (95% confidence interval, 1.2 to 4.2;P =0.01). This effect was independent of traditional risk factors. For each quartile increase in soluble P-selectin, the risk of future cardiovascular events increased 28% (P =0.03) after additional adjustment for obesity, hypertension, hyperlipidemia, diabetes, and exercise frequency. The highest risks were observed among women with the very highest levels of P-selectin (>137.3 ng/mL, the 95th percentile cut point of the control distribution). Conclusions —Soluble P-selectin levels are elevated among apparently healthy women at risk for future vascular events.
Expression of Immunoregulatory Cytokines by Recombinant Coxsackievirus B3 Variants Confers Protection against Virus-Caused Myocarditis

ABSTRACT Clinical and laboratory investigations have demonstrated the involvement of viruses and bacteria as potential causative agents in cardiovascular disease and have specifically found coxsackievirus B3 (CVB3) to be a leading cause. Experimental data indicate that cytokines are involved in controlling CVB3 replication. Therefore, recombinant CVB3 (CVB3rec) variants expressing the T-helper-1 (TH1)-specific gamma interferon (IFN-γ) or the TH2-specific interleukin-10 (IL-10) as well as the control virus CVB3(muIL-10), which produce only biologically inactive IL-10, were established. Coding regions of murine cytokines were cloned into the 5′ end of the CVB3 wild type (CVB3wt) open reading frame and were supplied with an artificial viral 3Cpro-specific Q-G cleavage site. Correct processing releases active cytokines, and the concentration of IFN-γ and IL-10 was analyzed by enzyme-linked immunosorbent assay and bioassays. In mice, CVB3wt was detectable in pancreas and heart tissue, causing massive destruction of the exocrine pancreas as well as myocardial inflammation and heart cell lysis. Most of the CVB3wt-infected mice revealed virus-associated symptoms, and some died within 28 days postinfection. In contrast, CVB3rec variants were present only in the pancreas of infected mice, causing local inflammation with subsequent healing. Four weeks after the first infection, surviving mice were challenged with the lethal CVB3H3 variant, causing casualties in the CVB3wt- and CVB3(muIL-10)-infected groups, whereas almost none of the CVB3(IFN-γ)- and CVB3(IL-10)-infected mice died and no pathological disorders were detectable. This study demonstrates that expression of immunoregulatory cytokines during CVB3 replication simultaneously protects mice against a lethal disease and prevents virus-caused tissue destruction.
Network measures predict neuropsychological outcome after brain injury

Significance Thought depends on the brain, and cognitive neuroscience has shown that different sets of brain regions (systems) support different cognitive abilities. We hypothesized that complex cognition might be especially supported by hub brain locations that participate in many such systems. We studied neurological patients with focal brain lesions, and found that damage to hub locations produced much greater cognitive impairment than damage to other locations. This work may improve the understanding of outcomes of brain injuries (from, e.g., stroke, resection, or trauma) and help inform prognosis and rehabilitation efforts. Hubs are network components that hold positions of high importance for network function. Previous research has identified hubs in human brain networks derived from neuroimaging data; however, there is little consensus on the localization of such hubs. Moreover, direct evidence regarding the role of various proposed hubs in network function (e.g., cognition) is scarce. Regions of the default mode network (DMN) have been frequently identified as “cortical hubs” of brain networks. On theoretical grounds, we have argued against some of the methods used to identify these hubs and have advocated alternative approaches that identify different regions of cortex as hubs. Our framework predicts that our proposed hub locations may play influential roles in multiple aspects of cognition, and, in contrast, that hubs identified via other methods (including salient regions in the DMN) might not exert such broad influence. Here we used a neuropsychological approach to directly test these predictions by studying long-term cognitive and behavioral outcomes in 30 patients, 19 with focal lesions to six “target” hubs identified by our approaches (high system density and participation coefficient) and 11 with focal lesions to two “control” hubs (high degree centrality). In support of our predictions, we found that damage to target locations produced severe and widespread cognitive deficits, whereas damage to control locations produced more circumscribed deficits. These findings support our interpretation of how neuroimaging-derived network measures relate to cognition and augment classic neuroanatomically based predictions about cognitive and behavioral outcomes after focal brain injury.
Antisense expression of PKCalpha improved sensitivity of SGC7901/VCR cells to doxorubicin.

AIM To explore whether antisense blocking of protein kinase C alpha (PKCalpha) would reverse multi-drug resistance (MDR) in the vincristine (VCR)-resistant human gastric cancer cell line SGC7901/VCR. METHODS SGC7901/VCR cells expressing antisense PKCalpha, SGC7901/VCR/aPKC, were established by transfection with a recombinant plasmid reversely inserted with PKCalpha cDNA. Empty vector (PCI-neo)-transfected cell clones, SGC7901/VCR/neo, served as the control. Western blot method was used to detect PKCalpha content in SGC7901, SGC7901/VCR, SGC7901/VCR/neo and SGC7901/VCR/aPKC cells, using PKCalpha-specific antibody. The sensitivity of SGC7901, SGC7901/VCR, SGC7901/VCR/neo and SGC7901/VCR/aPKC cells to doxorubicin (DOX) in vitro was determined by MTT assay. The uptake of DOX in these cells was detected with fluorescence spectrophotometer. RESULTS Western blot analysis showed that the PKCalpha protein level was about 8.7-fold higher in SGC7901/VCR cells than that in SGC7901 cells, whereas the protein expression of PKCalpha was reduced by 78% in SGC7901/VCR/aPKC cells when compared with the SGC7901/VCR cells. SGC7901/VCR/aPKC cells had a 4.2-fold increase in DOX cytotoxicity, accompanied by a 1.7-fold increase of DOX accumulation in comparison with SGC7901/VCR cells. CONCLUSION PKCalpha positively regulates MDR in SGC7901 cells, and inhibition of PKCalpha can partially attenuate MDR in human gastric cancer cells.
Estimating uncertainty in respondent-driven sampling using a tree bootstrap method

Significance Some hidden or hard-to-reach populations of interest to researchers are difficult to study with standard statistical methods because there is not a reliable list of members from which samples can be drawn. Respondent-driven sampling (RDS) is a common way to reach members of these populations by allowing a small number of respondents to recruit further respondents in the target population from their personal contacts. However, estimates derived from RDS are known to have a high degree of uncertainty, for which current methods do not fully account. We present a method that overcomes this problem and allows for better statistical inference from RDS data. Respondent-driven sampling (RDS) is a network-based form of chain-referral sampling used to estimate attributes of populations that are difficult to access using standard survey tools. Although it has grown quickly in popularity since its introduction, the statistical properties of RDS estimates remain elusive. In particular, the sampling variability of these estimates has been shown to be much higher than previously acknowledged, and even methods designed to account for RDS result in misleadingly narrow confidence intervals. In this paper, we introduce a tree bootstrap method for estimating uncertainty in RDS estimates based on resampling recruitment trees. We use simulations from known social networks to show that the tree bootstrap method not only outperforms existing methods but also captures the high variability of RDS, even in extreme cases with high design effects. We also apply the method to data from injecting drug users in Ukraine. Unlike other methods, the tree bootstrap depends only on the structure of the sampled recruitment trees, not on the attributes being measured on the respondents, so correlations between attributes can be estimated as well as variability. Our results suggest that it is possible to accurately assess the high level of uncertainty inherent in RDS.
Developmentally Regulated Extinction of Ly-49 Receptor Expression Permits Maturation and Selection of NK1.1+ T Cells

Clonally distributed inhibitory receptors negatively regulate natural killer (NK) cell function via specific interactions with allelic forms of major histocompatibility complex (MHC) class I molecules. In the mouse, the Ly-49 family of inhibitory receptors is found not only on NK cells but also on a minor (NK1.1+) T cell subset. Using Ly-49 transgenic mice, we show here that the development of NK1.1+ T cells, in contrast to NK or conventional T cells, is impaired when their Ly-49 receptors engage self-MHC class I molecules. Impaired NK1.1+ T cell development in transgenic mice is associated with a failure to select the appropriate CD1-reactive T cell receptor repertoire. In normal mice, NK1.1+ T cell maturation is accompanied by extinction of Ly-49 receptor expression. Collectively, our data imply that developmentally regulated extinction of inhibitory MHC-specific receptors is required for normal NK1.1+ T cell maturation and selection.
Tibial Condylar Fractures

IT is generally accepted that fractures into joints must, if possible, be afforded perfect reduction, and that when accurate reduction has not been achieved, some considerable stiffness and degenerative arthritis may confidently be expected. This was once commonly illustrated by the malunited fracture-dislocation of the ankle, and incongruities of the scaphoid, olecranon and acetabulum provoke early wear of their respective joints. An exception to this general rule is the tibial condylar fracture, which may be treated by skeletal traction and early movement with justifiable optimism. The lateral tibial condyle is fractured when a valgus force acts on a knee through which weight is being taken, causing the corresponding femoral condyle to be driven downwards into the tibia. This combination of valgus and compression seems to occur in middle-aged people who fall short distances. The term "bumper fracture" or "fender fracture", introduced by Cotton and Berg in 1929, misstates the cause more often than not, and but for its useful brevity could well be discarded. Both the radiographic appearances and the mechanics of the fracture have in the past suggested problems in treatment which have divided surgeons into two distinct schools, namely, those who recommend open reduction and internal fixation, and those who are content to rely on closed methods. Three types of lateral condylar fracture are customarily recognised, according to the classification of Palmer (1951). (1) A vertical fracture splits off a wedge of lateral condyle, which may be little displaced, or displaced downwards and outwards. This type is most amenable to simple closed reduction, and also provides the simplest condylar fracture for internal fixation. (2) There is a variable degree of compression of the lateral tibial plateau; a radiographic
Generic Exploration and K-armed Voting Bandits

We study a stochastic online learning scheme with partial feedback where the utility of decisions is only observable through an estimation of the environment parameters. We propose a generic pure-exploration algorithm, able to cope with various utility functions from multi-armed bandits settings to dueling bandits. The primary application of this setting is to offer a natural generalization of dueling bandits for situations where the environment parameters reflect the idiosyncratic preferences of a mixed crowd.
Basal ganglia functional parcellation into specific and overlapping territories with resting state F-MRI

The basal ganglia (BG) are divided into functional territories being connected to specific cortical areas. Some regions are also connected to more than one cortical area constituting overlapping territories, which may correspond to regions of lower neuronal selectivity. Changes in the spatial extent of overlapping regions could thus indicate reduced selectivity of neuronal representation as reported in BG disorders such as Parkinson’s disease (PD). We propose an innovative method to parcellate the BG non-invasively into specific and overlapping functional territories using resting state fMRI data. Parcellation was coherent into groups of subjects. PD was associated with significant differences in the extent of overlap predominating in the motor circuit in line with the expected reduction in neuronal selectivity in the BG of PD patients.