Miracle-dz/UniFAR-FTUs huggingface dataset:
Functions and regulation of the Nox family in the filamentous fungus Podospora anserina: a new role in cellulose degradation

NADPH oxidases are enzymes that produce reactive oxygen species. Studies in mammals, plants and fungi have shown that they play important roles in differentiation, defence, host/pathogen interaction and mutualistic symbiosis. In this paper, we have identified a Podospora anserina mutant strain impaired for processes controlled by PaNox1 and PaNox2, the two Nox isoforms characterized in this model ascomycete. We show that the gene mutated is PaNoxR, the homologue of the gene encoding the regulatory subunit p67phox, conserved in mammals and fungi, and that PaNoxR regulates both PaNox1 and PaNox2. Genome sequence analysis of P. anserina reveals that this fungus posses a third Nox isoform, PaNox3, related to human Nox5/Duox and plant Rboh. We have generated a knock‐out mutant of PaNox3 and report that PaNox3 plays a minor role in P. anserina, if any. We show that PaNox1 and PaNox2 play antagonist roles in cellulose degradation. Finally, we report for the first time that a saprobic fungus, P. anserina, develops special cell structures dedicated to breach and to exploit a solid cellulosic substrate, cellophane. Importantly, as for similar structures present in some plant pathogens, their proper differentiation requires PaNox1, PaNox2, PaNoxR and the tetraspanin PaPls1.
Scaling of photosynthesis and constitutive and induced volatile emissions with severity of leaf infection by rust fungus (Melampsora larici-populina) in Populus balsamifera var. suaveolens.

Fungal infections result in decreases in photosynthesis, induction of stress and signaling volatile emissions and reductions in constitutive volatile emissions, but the way different physiological processes scale with the severity of infection is poorly known. We studied the effects of infection by the obligate biotrophic fungal pathogen Melampsora larici-populina Kleb. , the causal agent of poplar leaf rust disease, on photosynthetic characteristics, and constitutive isoprene and induced volatile emissions in leaves of Populus balsamifera var. suaveolens (Fisch.) Loudon. exhibiting different degrees of damage. The degree of fungal damage, quantified by the total area of chlorotic and necrotic leaf areas, varied between 0 (noninfected control) and ∼60%. The rates of all physiological processes scaled quantitatively with the degree of visual damage, but the scaling with damage severity was weaker for photosynthetic characteristics than for constitutive and induced volatile release. Over the whole range of damage severity, the net assimilation rate per area (AA) decreased 1.5-fold, dry mass per unit area 2.4-fold and constitutive isoprene emissions 5-fold, while stomatal conductance increased 1.9-fold and dark respiration rate 1.6-fold. The emissions of key stress and signaling volatiles (methanol, green leaf volatiles, monoterpenes, sesquiterpenes and methyl salicylate) were in most cases nondetectable in noninfested leaves, and increased strongly with increasing the spread of infection. The moderate reduction in AA resulted from the loss of photosynthetically active biomass, but the reduction in constitutive isoprene emissions and the increase in induced volatile emissions primarily reflected changes in the activities of corresponding biochemical pathways. Although all physiological alterations in fungal-infected leaves occurred in a stress severity-dependent manner, modifications in primary and secondary metabolic pathways scaled differently due to contrasting operational mechanisms.
Regulatory Skill as a Resilience Factor for Adults With a History of Foster Care: A Pilot Study

Individuals with a history of foster care (FC) are at elevated risk for emotion regulation-related mental illness. The purpose of the current study was to characterize regulatory function in a group of adults with a history of FC (N = 26) relative to those without a history of FC (N = 27) and how regulatory function moderates adverse caregiving-related outcomes (daily cortisol production and trait anxiety). Self-report items (anxiety, emotion regulation strategies, inhibitory control, caregiving history) were collected along with more objective measures (computerized task and salivary cortisol). Inhibitory control was assessed via self-report and a computerized task (emotional face go/nogo). Results showed that for adults with a history of FC, higher levels of inhibitory control were associated with higher accuracy on the emotional face go/nogo task and greater reported use of the emotion regulation strategy cognitive reappraisal. Greater use of cognitive reappraisal in turn was associated with healthier stress-related outcomes (decreased trait anxiety and steeper sloped cortisol production throughout the day). Dose-response associations were observed between self-reported regulatory skills and FC experiences (i.e., number of placements and age when exited foster care). These findings suggest that adverse caregiving can have long-term influences on mental health that extend into adulthood; however, individual differences in regulatory skills moderate these outcomes and may be an important target for intervention following caregiving adversity. © 2014 The Authors. Developmental Psychobiology published by Wiley Periodicals, Inc. Dev Psychobiol 57: 1–16, 2015.
A hybrid PLSA approach for warmer cold start in folksonomy recommendation

We investigate the problem of item recommendation during the first months of the collaborative tagging community Ci­ teULike. CiteULike is a so-called folksonomy where users have the possibility to organize publications through anno­ tations tags. Making reliable recommendations during the initial phase of a folksonomy is a difficult task, since infor­ mation about user preferences is meager. In order to im­ prove recommendation results during this cold start period, we present a probabilistic approach to item recommenda­ tion. Our model extends previously proposed models such as probabilistic latent semantic analysis (PLSA) by merging both user-item as well as item-tag observations into a unified representation. We find that bringing tags into play reduces the risk of overfitting and increases overall recommendation quality. Experiments show that our approach outperforms other types of recommenders.
Multiuser capacity in block fading with no channel state information

Consider M independent users, each user having his own transmit antenna, that transmits simultaneously to one receiver antenna through a Rayleigh block-fading channel having a coherence interval of T symbols, with no channel state information available to either the transmitters or to the receiver. The total transmitted power is independent of the number of users. For a given coherence time T, we wish to identify the best multi-access strategy that maximizes the total throughput, where all users are subjected to the same average power constraint. If perfect channel state information were available to the receiver, it is known that the total capacity increases monotonically with the number of users. If the channel state information is available to both the receiver and all transmitters, the throughput maximizing strategy implies that only a single user that enjoys the best channel condition transmits. In the absence of any channel state information one is forced to a radically different conclusion. In particular we show that if the propagation coefficients take on new independent values for every symbol (e.g., T=1) then the total capacity for any M>1 users is equal to the capacity for M=1 user, in which case TDMA is an optimal scheme for handling multiple users. This result follows directly from a previous treatment of the single-user multiple antenna block fading channel. Again, motivated by the single-user results, one is lead to the following conjecture for the multiple user case: for any T>1 the maximum total capacity can be achieved by no more than M=T users. The conjecture is supported by establishing the asymptotic result that, for a constant M/T for large T, the total capacity is maximized when M/T/spl rarr/0, which yields a total capacity per symbol of log(1+/spl rho/), where /spl rho/ is the expected SNR at the receiver.
Multi-Disciplinary Vascular Access Care and Access Outcomes in People Starting Hemodialysis Therapy.

BACKGROUND AND OBJECTIVES Fistulas, the preferred form of hemodialysis access, are difficult to establish and maintain. We examined the effect of a multidisciplinary vascular access team, including nurses, surgeons, and radiologists, on the probability of using a fistula catheter-free, and rates of access-related procedures in incident patients receiving hemodialysis. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We examined vascular access outcomes in the first year of hemodialysis treatment before (2004-2005, preteam period) and after the implementation of an access team (2006-2008, early-team period; 2009-2011, late-team period) in the Calgary Health Region, Canada. We used logistic regression to study the probability of fistula creation and the probability of catheter-free fistula use, and negative binomial regression to study access-related procedure rates. RESULTS We included 609 adults (mean age, 65 [±15] years; 61% men; 54% with diabetes). By the end of the first year of hemodialysis, 102 participants received a fistula in the preteam period (70%), 196 (78%) in the early-team period (odds ratios versus preteam, 1.47; 95% confidence interval, 0.92 to 2.35), and 139 (66%) in the late-team period (0.85; 0.54 to 1.35). Access team implementation did not affect the probability of catheter-free use of the fistula (odds ratio, 0.87; 95% confidence interval, 0.52 to 1.43, for the early; and 0.89; 0.52 to 1.53, for the late team versus preteam period). Participants underwent an average of 4-5 total access-related procedures during the first year of hemodialysis, with higher rates in women and in people with comorbidities. Catheter-related procedure rates were similar before and after team implementation; relative to the preteam period, fistula-related procedure rates were 40% (20%-60%) and 30% (10%-50%) higher in the early-team and late-team periods, respectively. CONCLUSION Introduction of a multidisciplinary access team did not increase the probability of catheter-free fistula use, but resulted in higher rates of fistula-related procedures.
Schools as sanctuaries: A systematic review of contextual factors which contribute to student retention in alternative education

Early school leaving is an international concern. Previous research indicates that the school context contributes to early school leaving. This systematic review is aimed to gather marginalised young peoples’ perceptions concerning contextual factors that contributed to and interfered with their decisions to stay in alternative education. Twenty-three databases and reference lists of reviews were searched, eliciting 1586 studies, which were then screened. Data from 24 mixed-methods studies that met the inclusion criteria were extracted and synthesised. Findings suggested that alternative schools which provided a sanctuary for students increased student engagement. Schools were sanctuaries when they offered physical, emotional and psychological safe spaces; fostered a sense of community; enabled students to affirm their racial/ethnic pride and employed flexible behavioural supports. Implications for practice and research are discussed.
Social Factors but Not Stress-Coping Styles Predict Relapse in Detoxified Alcoholics

Alcohol-dependent patients face a substantial risk of relapse after detoxification. Though psychosocial stress and coping strategies are regarded as major contributing factors in returning to drinking, the direct effects of coping styles on relapse are not clear. In this treatment outcome study, a mixed gender sample of 130 detoxified and well-characterized alcohol-dependent patients (37 women) was followed up over a period of 12 months after 6 weeks of inpatient treatment. Patients had completed a comprehensive baseline assessment, including a stress coping questionnaire (SVF120). We hypothesized that these individual stress coping styles would contribute to treatment outcome. A logistic regression analysis was used to evaluate the impact of stress coping styles, as well as the effect of pretreatment drinking and social characteristics on relapse. Approximately half the patients (49%) relapsed within 1 year after treatment. In contrast to our hypothesis, stress coping styles did not predict relapse. However, significant predictors of relapse were social factors related to living situation (living alone), marital status (being separated from the spouse) and pretreatment frequency of alcohol intake. These findings suggest that a partnership is more relevant for the risk of relapse than stress coping styles.
Increased markers of oxidative stress in plasma of patients with chronic pancreatitis.

OBJECTIVES Chronic pancreatitis (CP) is a heterogeneous disease defined as chronic inflammatory changes of the pancreatic tissue caused by variety of aetiologies. Oxidative stress accompanying the inflammatory processes has been suggested as an important factor contributing to CP development. The aim of this study was to determine levels of lipid peroxidation products malondialdehyde (MDA) and 4-hydroxynonenal (4-HNE), together with nitrites and the total antioxidant capacity in the plasma of patients with CP and control subjects. DESIGN One hundred and five patients with chronic pancreatitis and twenty seven healthy controls were included into this study. Levels of MDA and 4-HNE were analyzed using high-performance liquid chromatography. The total antioxidant capacity of plasma against peroxyl radicals was evaluated using chemiluminescent determination. Nitrites were determined using Griess reaction. Biochemical and haematological parameters were measured by standard methods. RESULTS The plasma levels of both MDA and 4-HNE, together with the plasma levels of nitrites, were significantly higher in CP patients, compared to healthy controls. The total antioxidant capacity did not differ significantly. Biochemical parameters were in the normal range. The MDA and 4-HNE levels correlated positively with the levels of high-density lipoprotein cholesterol. Nitrite levels correlated positively with C-reactive protein, total white blood cells, and triglycerides. CONCLUSION The significantly increased plasma levels of MDA, 4-HNE, and nitrites indicate that oxidative stress is present in patients with CP and that it may play a role in initiation and maintenance of inflammation within the pancreatic tissue in CP patients.
BENEFICIAL EFFECTS OF FENOLDOPAM TREATMENT ON RENAL FUNCTION IN STREPTOZOTOCIN-INDUCED DIABETIC RATS

We have studied the effect of chronic treatment with dopamine D1 receptor agonist fenoldopam (1 mg/kg, i.p. daily for 6 weeks) on renal function and metabolic parameters in streptozotocin (STZ)-diabetic rats. Diabetes was induced by a single tail vein injection of STZ (45 mg/kg). STZ produced severe hyperglycemia, hypoinsulinemia, hypercholesterolemia, hypertriglyceridemia, hypertension and bradycardia. Fenoldopam treatment significantly reduced fasting but not fed blood glucose levels and lowered the blood pressure in diabetic animals. Significant change was not observed in insulin, cholesterol, triglyceride levels. Diabetic animals showed increase in AUCglucose and decrease in AUCinsulin during oral glucose tolerance test. Fenoldopam treatment did not significantly change these values in diabetic animals. STZ produced increase in serum urea, creatinine and blood urea nitrogen. Diuresis and urinary sodium retention was observed in diabetic animals. Renal hypertrophy was observed as seen from increased kidney weight/body weight ratio and increased total RNA content as well as decreased total DNA content. Fenoldopam treatment significantly lowered serum urea, creatinine and blood urea nitrogen. Urinary sodium retention was significantly reduced and renal hypertrophy was prevented with fenoldopam treatment as seen from the improved kidney weight/body weight ratio. Fenoldopam treatment significantly prevented reduction in total DNA content and increase in total RNA content further substantiating reduced renal hypertrophy. Our data suggest that STZ induced diabetes is associated with renal dysfunctions and fenoldopam treatment could be beneficial in a condition where diabetes mellitus co-exists with hypertension and compromised renal function.
Parental investment strategies in two species of nuthatch vary with stage-specific predation risk and reproductive effort

Life-history theory predicts that differences in reproductive effort and residual reproductive value among species should result in differences in the level of risk that parents are willing to tolerate to themselves versus their offspring. Specifically, highly fecund and shorter-lived species are expected to place greater value in current offspring than themselves, whereas less fecund and longer-lived species are expected to place greater value in their own survival and future breeding opportunities. Here, we test the prediction that parental investment decisions are correlated with life histories by comparing risk-taking behaviour in two species of nuthatch that differ in reproductive effort: the white-breasted nuthatch, Sitta carolinensis (more fecund, lower survival) and the red-breasted nuthatch, S. canadensis (less fecund, higher survival). We experimentally manipulated stage-specific predation risk by presenting models of an adult predator (hawk) and an egg predator (wren) and measured the willingness of males to feed incubating females on the nest. We found that both species of nuthatch responded to predators by increasing the length of time between visits and aborting more visits to the nest. However, as predicted by their life histories, S. carolinensis displayed a significantly stronger response to the egg predator, whereas S. canadensis responded more strongly to the adult predator. Thus, species can differ in their willingness to tolerate risk to themselves and their young, and such differences appear to be related to differences in investment in current reproduction and the probability of future survival. Copyright 2000 The Association for the Study of Animal Behaviour.
Comparison of Laparoscopy and Laparotomy in Surgical Staging of Apparent Early Ovarian Cancer

Abstract The aim of this study was to compare the safety and morbidity of laparoscopic versus laparotomic comprehensive staging of apparent early stage ovarian cancer. In this retrospective study, the outcomes of patients with apparent stage I ovarian cancer who underwent laparoscopic or laparotomic comprehensive surgical staging from January 2002 to January 2014 were evaluated. The long-term survival of patients with early ovarian cancer was compared. Forty-two patients were treated by laparoscopy, and 50 were treated by laparotomy. The median operative time was 200 minutes in the laparoscopy group and 240 minutes in the laparotomy group (P >0.05). The median length of hospital stay was 3 days in the laparoscopy group and 7 days in the laparotomy group (P <0.05). Following laparoscopic and laparotomic staging, the cancer was upstaged for 9 (21.4%) and 10 (20.0%) women, respectively. The median follow-up time was 82 months in the laparoscopic and laparotomic groups, respectively. Excluding the upstaged patients, no recurrence was observed in the present study, and the overall survival and 5-year survival rates were 100% in both the laparoscopy and laparotomy groups. Laparoscopic and laparotomic comprehensive staging of early ovarian cancer were similar in terms of staging adequacy, accuracy and survival rate. Laparoscopic staging was associated with a significantly reduced hospital stay. Prospective randomized trials are required to evaluate the overall oncologic outcomes.
A glimpsing model of speech perception

Do listeners utilise glimpses of a clean speech target in noisy backgrounds? This paper presents a model of speech perception motivated by the glimpses notion. Using a corpus of VCV sequences, listeners' identification performance is measured in a number of noise conditions chosen to vary both in global SNR and in the number and distribution of glimpses they afford. Subjects’ performance is compared to that of a computational model which employs missing data techniques to handle glimpses. A close match to subjects’ performance can be obtained by assuming that listeners require available glimpses to occupy a certain minimum extent in time and frequency.
Playing with fermion couplings in Higgsless models

We discuss the fermion couplings in a four dimensional SU(2) linear moose model by allowing for direct couplings between the left-handed fermions on the boundary and the gauge fields in the internal sites. This is realized by means of a product of nonlinear {sigma}-model scalar fields which, in the continuum limit, is equivalent to a Wilson line. The effect of these new nonlocal couplings is a contribution to the {epsilon}{sub 3} parameter which can be of opposite sign with respect to the one coming from the gauge fields along the string. Therefore, with some fine-tuning, it is possible to satisfy the constraints from the electroweak data.
Hydrothermal method for preparing calcium phosphate monoliths

A new hydrothermal route for preparing biphasic calcium phosphate monoliths is proposed. Firstly, a slurry of b-tricalcium phosphate/ortho-phosphoric acid (b-TCP/H3PO4) is cast into the desired final shape and size to obtain a block composed of dicalcium phosphate dihydrate (DCPD) and b-TCP. This block is then treated in 1.0 M Na2HPO4 at 60 °C in order to hydrolyze the DCPD into Ca10-x(HPO4)x(PO4) 6-x(OH)2-x (CDHA) and Ca8H2(PO4)6 . 5H2O (OCP). The result is a monolithic piece which preserves the initial shape and size, but which is composed instead of CDHA, OCP, and b-TCP. During the initial stage, when the pH is slightly alkaline, the product of DCPD hydrolysis is CDHA. However, when a neutral or slightly acidic pH is reached OCP is formed. Test samples processed by this method showed complete conversion of DCPD into CDHA and OCP after 112 h of hydrolysis, and with a compressive strength of 16.2 MPa, similar to cancellous bone.
High-speed flow visualization in a pump-turbine under off-design operating conditions

The flow hydrodynamics in a low specific speed radial pump-turbine reduced scale model is experimentally investigated under off-design operating conditions in generating mode. Wall pressure measurements, in the stator, synchronized with high-speed flow visualizations in the vaneless space between the impeller and the guide vanes using air bubbles injection are performed. When starting from the best efficiency point and increasing the runner speed, a significant increase of the pressure fluctuations is observed mainly in channels between wicket gates. The spectral analysis shows a rise of one stall cell, rotating with about 70% of the impeller frequency, at runaway, which further increases as the zero discharge condition is approached. Then a specific image processing technique is detailed and applied to create a synthetic instantaneous view of the flow pattern on the entire guide vanes circumference for an operating point in turbine-brake mode, where backflow and vortices accompany the stall passage.
Expanded View Figures

▸ Figure EV1. Protein copy number and RNA levels (TPM) for all quantified genes. The absolute copy numbers of proteins (blue) and the level of RNA (purple) measured as TPM are shown for all 55 genes across nine cell lines and 11 tissues. All values can be found in Table EV3 and Table EV6.