Miracle-dz/UniFAR-FTUs huggingface dataset:
Prion formation by a yeast GLFG nucleoporin

The self-assembly of proteins into higher order structures is both central to normal biology and a dominant force in disease. Certain glutamine/asparagine (Q/N)-rich proteins in the budding yeast Saccharomyces cerevisiae assemble into self-replicating amyloid-like protein polymers, or prions, that act as genetic elements in an entirely protein-based system of inheritance. The nuclear pore complex (NPC) contains multiple Q/N-rich proteins whose self-assembly has also been proposed to underlie structural and functional properties of the NPC. Here we show that an essential sequence feature of these proteins—repeating GLFG motifs—strongly promotes their self-assembly into amyloids with characteristics of prions. Furthermore, we demonstrate that Nup100 can form bona fide prions, thus establishing a previously undiscovered ability of yeast GLFG nucleoporins to adopt this conformational state in vivo.
Induction of Resistance by Silicon in Wheat Plants to Alate and Apterous Morphs of Sitobion avenae (Hemiptera: Aphididae)

ABSTRACT Despite the knowledge about the effects of silicon augmenting antibiosis and nonpreference of plants by apterous aphids, few studies exist on such effects with alate aphids. This study evaluated the effects of silicon fertilization on the biology of alate and apterous morphs of Sitobion avenae (F.) (Hemiptera: Aphididae), and the effect on nonpreference by S. avenae alates for wheat plants with or without silicon fertilization. A method for rearing aphids on detached leaves was evaluated comparing the biology of apterous aphids reared on wheat leaf sections and on whole plants with and without silicon fertilization. Because the use of detached leaves was a reliable method, the effect of silicon fertilization on the biology of apterous and alate S. avenae was assessed using wheat leaf sections. Biological data of aphids were used to calculate a fertility life table. Finally, the effect of silicon fertilization on the nonpreference of alate aphids was carried out for both vegetative and reproductive phases of wheat. Thirty alate aphids were released in the center of a cage, and the number of aphids per whole plant with or without silicon fertilization was observed. Silicon fertilization induced antibiosis resistance in wheat plants to apterous morphs as shown by reduced fecundity, reproductive period, longevity, intrinsic rate of increase, and net reproductive rate; however, alates were unaffected. Plants that received silicon fertilization had fewer alate aphids in both the vegetative and reproductive phases. Thus, silicon fertilization can reduce colonization by alates, enhancing nonpreference resistance, and population growth of apterous S. avenae in wheat plants.
Crowdsourcing with All-Pay Auctions: A Field Experiment on Taskcn

To explore the effects of different incentives on crowdsourcing participation and submission quality, we conduct a randomized field experiment on Taskcn, a large Chinese crowdsourcing site using mechanisms with features of an all-pay auction. In our study, we systematically vary the size of the reward as well as the presence of a soft reserve, or early high-quality submission. We find that a higher reward induces significantly more submissions and submissions of higher quality. In comparison, we find that high-quality users are significantly less likely to enter tasks where a high-quality solution has already been submitted, resulting in lower overall quality in subsequent submissions in such soft reserve treatments. Data, as supplemental material, are available at http://dx.doi. org/10.1287/mnsc.2013. 1845 . This paper was accepted by Uri Gneezy, behavioral economics.
Stability of the Dispersed Band in a Shallow Layer Settler

The present study is aimed at shallow-layer settler s, involving data collecting about the thickness of the dispersion band at different points along it s length and its use in simulation work. At steady state, after step inputs in the agitation po wer, the length of the dispersed band varied in time, and didn’t return to its initial condition. A lthough clean, pure fluids were used, crud formation was observed and acquired relevance espec ially for long period experiments. This behavior brought out the fact that crud formed during the experimentation disturbed the st abili y of the dispersed band. Crud analysis, performed by fluorescence microscopy, su ggested the presence of bacteria. Thus, in order to make the ex p rimental data reliable and reproducible, the effects of the formation and accumulation of crud at the water-organic interface must be taken into consideration, controlled and minimized by usi ng appropriate biocides.
Molecular Epidemiology of Mycobacterium avium subsp.paratuberculosis: IS900 Restriction Fragment Length Polymorphism and IS1311 Polymorphism Analyses of Isolates from Animals and a Human in Australia

ABSTRACT The distribution and prevalence of strains of Mycobacterium avium subsp. paratuberculosis were determined among sheep, cattle, and other species with Johne's disease in Australia. A total of 328 isolates were evaluated from numerous farms in New South Wales, Victoria, Tasmania, and South Australia, Australia. Restriction fragment length polymorphism (RFLP) analysis of genomic DNA usingBstEII and an IS900 probe and IS1311 polymorphism analysis using PCR and restriction endonuclease analysis (PCR-REA) was used to classify isolates as cattle (C) or sheep (S) strains. IS1311 PCR-REA provided similar information to IS900 RFLP analysis but was more useful than RFLP analysis where DNA was degraded or scarce. Twelve IS900 RFLP types were found. Johne's disease in sheep was always due to S strains, while cattle were infected only with C strains. RFLP type S1 was the dominant strain in sheep in New South Wales (97% of isolates) and was the only strain found in sheep from Victoria. Seven RFLP types were present in cattle. RFLP types C3 and C1 were most common (collectively, 85% of isolates), but C1 was not found in New South Wales and C3 was present in dairy cattle but not in beef cattle in Victoria. These differences may be explained by restricted livestock trading patterns between different segments of the cattle industry. Up to five RFLP types were present in some geographic regions in Victoria, while up to three RFLP types were found among cattle on some farms. Individual cattle usually were infected with only one RFLP type, but one animal was infected with both C5 and CU4. Two isolates from goats were C type as were three from alpacas, one from a rhinoceros, and two from a human with Crohn's disease. The prevalences of specific RFLP types in Australia differ from those reported in Europe and elsewhere. Given the existence of geographical and farm enterprise differences in IS900 RFLP type, this technique may be applied selectively to trace the spread of Johne's disease, at least in the cattle industries. As these observations reflect past exposure of livestock to M. avium subsp.paratuberculosis, the monitoring of strains present in animals in Australia is continuing.
Melarsoprol Sensitivity Profile of Trypanosoma brucei gambiense Isolates from Cured and Relapsed Sleeping Sickness Patients from the Democratic Republic of the Congo

Background Sleeping sickness caused by Trypanosoma brucei (T.b.) gambiense constitutes a serious health problem in sub-Sahara Africa. In some foci, alarmingly high relapse rates were observed in patients treated with melarsoprol, which used to be the first line treatment for patients in the neurological disease stage. Particularly problematic was the situation in Mbuji-Mayi, East Kasai Province in the Democratic Republic of the Congo with a 57% relapse rate compared to a 5% relapse rate in Masi-Manimba, Bandundu Province. The present study aimed at investigating the mechanisms underlying the high relapse rate in Mbuji-Mayi using an extended collection of recently isolated T.b. gambiense strains from Mbuji-Mayi and from Masi-Manimba. Methodology/Principal Findings Forty five T.b. gambiense strains were used. Forty one were isolated from patients that were cured or relapsed after melarsoprol treatment in Mbuji-Mayi. In vivo drug sensitivity tests provide evidence of reduced melarsoprol sensitivity in these strains. This reduced melarsoprol sensitivity was not attributable to mutations in TbAT1. However, in all these strains, irrespective of the patient treatment outcome, the two aquaglyceroporin (AQP) 2 and 3 genes are replaced by chimeric AQP2/3 genes that may be associated with resistance to pentamidine and melarsoprol. The 4 T.b. gambiense strains isolated in Masi-Manimba contain both wild-type AQP2 and a different chimeric AQP2/3. These findings suggest that the reduced in vivo melarsoprol sensitivity of the Mbuji-Mayi strains and the high relapse rates in that sleeping sickness focus are caused by mutations in the AQP2/AQP3 locus and not by mutations in TbAT1. Conclusions/Significance We conclude that mutations in the TbAQP2/3 locus of the local T.b. gambiense strains may explain the high melarsoprol relapse rates in the Mbuji-Mayi focus but other factors must also be involved in the treatment outcome of individual patients.
A New App for At-Home Cognitive Training: Description and Pilot Testing on Patients with Multiple Sclerosis

Background Cognitive impairment is common in people with neurological diseases and severely affects their social and professional life. It has been shown that intensive and personalized cognitive rehabilitation (CR), based on working memory exercises, leads to improved cognitive status of healthy and cognitive-impaired subjects. New technologies would help to promote accessible, at-home, and self-managed CR interventions. Objective The aim of this paper is to describe the design of Cognitive Training Kit (COGNI-TRAcK), an app for mobile devices, to self-administer an at-home, intensive, and personalized CR intervention based on working memory exercises, and test its disposability-to-use (usability, motivation to use, compliance to treatment) on cognitive-impaired patients with multiple sclerosis (MS). Methods COGNI-TRAcK includes user-friendly interfaces for personal data input and management and for CR intervention configurations. Inner routines automatically implement adaptive working load algorithms and allow data processing and analysis. A dedicated team developed COGNI-TRAcK with C# programming language, by using the platform Xamarin Studio 4.0. 10 for Android (API level 15 and following). Three exercises based on working memory are now available. To assess the disposability-to-use of the system, patients with MS were selected as likely users due to the young age of disease onset. Cognitive-impaired patients with MS (N=16) with a mean age of 49.06 years (SD 9.10) and a mean score of 3.75 (SD 1.92) on the Expanded Disability Status Scale (EDSS) were submitted to an 8-week at-home intervention administered by the app. The intervention consisted of 5 daily scheduled 30-minute sessions per week. Disposability-to-use of COGNI-TRAcK was investigated by means of a questionnaire administered to patients at the end of the training. Results The adherence to the treatment was 84% (33.4/40). Of the patients with MS, 94% (15/16) understood the instructions given, 100% (16/16) felt independent to use COGNI-TRAcK at home, 75% (12/16) found the exercises interesting, and 81% (13/16) found the exercises useful and were motivated to use the app again. Moreover, during the exercises, patients with MS were highly motivated to perform well (mean score 3.19/4, SE 0.16), experienced rather low levels of stress (mean score 2.19/4, SE 0.26), were not bored (mean score 1.81/4, SE 0.30), and felt amusement (mean score 2.25/4, SE 0.23). Conclusions As COGNI-TRAcK is highly usable, motivating, and well-accepted by patients with MS, its effectiveness can now be investigated. To improve COGNI-TRAcK, new releases should contain more working memory exercises, have enhanced perceived amusement, and promote Internet communication procedures for data transfer and fostering remote control of the intervention.
Transplantation Report. 2: Pre-emptive renal transplantation in adults aged over 15 years. The EDTA-ERA Registry. European Dialysis and Transplant Association-European Renal Association.

Between 1985 to 1992, 2545 renal transplantation (RTx) were performed as pre-emptive grafts in adults. This procedure represented 7.2% of first RTx for patients starting first renal replacement therapy (RRT) during this period, 6.1% of RTx performed in 1992 and 5.6% of all RTx ever performed and reported to the EDTA Registry. The procedure is more frequent in cases of live donor grafts, representing one third of pre-emptive RTx. Both 5 year patient and graft survivals are unaffected by dialysis duration prior to the first RTx: none in pre-emptive, < 1 years, 1-5 years or > 5 years. In our personal view, this procedure should be developed.
Colloid Normalizes Resuscitation Ratio in Pediatric Burns

Fluid resuscitation of burned children is challenging because of their small size and intolerance to over- or underresuscitation. Our American Burn Association-verified regional burn center has used colloid “rescue” as part of our pediatric resuscitation protocol. With Institutional Review Board approval, the authors reviewed children with ≥15% TBSA burns admitted from January 1, 2004, to May 1, 2009. Resuscitation was based on the Parkland formula, which was adjusted to maintain urine output. Patients requiring progressive increases in crystalloid were placed on a colloid protocol. Results were expressed as an hourly resuscitation ratio (I/O ratio) of fluid infusion (ml/kg/%TBSA/hr) to urine output (ml/kg/hr). We reviewed 53 patients; 29 completed resuscitation using crystalloid alone (lactated Ringer's solution [LR]), and 24 received colloid supplementation albumin (ALB). Groups were comparable in age, gender, weight, and time from injury to admission. ALB patients had more inhalation injuries and larger total and full-thickness burns. LR patients maintained a median I/O of 0.17 (range, 0.08–0.31), whereas ALB patients demonstrated escalating ratios until the institution of albumin produced a precipitous return of I/O comparable with that of the LR group. Hospital stay was lower for LR patients than ALB patients (0.59 vs 1.06 days/%TBSA, P = .033). Twelve patients required extremity or torso escharotomy, but this did not differ between groups. There were no decompressive laparotomies. The median resuscitation volume for ALB group was greater than LR group (9.7 vs 6.2 ml/kg/%TBSA, P = .004). Measuring hourly I/O is a helpful means of evaluating fluid demands during burn shock resuscitation. The addition of colloid restores normal I/O in pediatric patients.
Listeria monocytogenes Surface Proteins: from Genome Predictions to Function

SUMMARY The genome of the human food-borne pathogen Listeria monocytogenes is predicted to encode a high number of surface proteins. This abundance likely reflects the ability of this bacterium to survive in diverse environments, including soil, food, and the human host. This review focuses on the various mechanisms by which listerial proteins are attached at the bacterial surface and their many functions, including peptidoglycan metabolism, protein processing, adhesion to host cells, and invasion of host tissues. Extensive in silico analysis of the domains or motifs present in these mosaic proteins reveals that diverse structural features allow the surface proteome to interact with diverse bacterial or host components. This diversity offers new clues about the molecular bases of Listeria pathogenesis.
Should organs from hepatitis C virus‐infected donors be used for transplantation in the era of DAAs?

Hepatitis C virus (HCV) infection has been demonstrated to deleteriously impact both patient and graft survival following nonhepatic organ transplantation [1,2]. Interferon (IFN)-based therapies prior to nonhepatic transplant in HCV-infected patients improved their survival; however, tolerability and low cure rates practically limited those therapies [3]. In addition, due to the risk of allograft rejection, IFN-based therapy following nonhepatic solid organ transplant is not generally recommended. The recent appreciation of IFN-free therapy with direct-acting antiviral agents (DAAs) dramatically changes the landscape of HCV infection treatment. Compared to IFN-based regimens, DAAs have less incidence and severity of adverse effects, shorter durations of therapy, and higher cure rates. The advent of safe and highly effective DAA had significant implications for the HCV transplant field and improved the management of both patients on the waiting list and those with HCV graft reinfection after liver transplantation (LT) [4]. Of the IFN-free DAA combinations studied to date in the post-LT population, all have an excellent safety and tolerability profile and hence a significantly lower discontinuation rate when compared to IFN-based regimens [5], although some DAAs would have a limited use due to the frequent drug–drug interactions with various immunosuppressants and the many other drugs LT recipients are frequently prescribed. Those principles of DAA therapy in LT are currently extrapolated to nonhepatic solid organ transplant recipients.
Under Consideration for Publication in Theory and Practice of Logic Programming a Denotational Semantics for Equilibrium Logic *

In this paper we provide an alternative semantics for Equilibrium Logic and its monotonic basis, the logic of Here-and-There (also known as Gödel's G3 logic) that relies on the idea of denotation of a formula, that is, a function that collects the set of models of that formula. Using the three-valued logic G3 as a starting point and an ordering relation (for which equilibrium/stable models are minimal elements) we provide several elementary operations for sets of interpretations. By analysing structural properties of the denotation of formulas, we show some expressiveness results for G3 such as, for instance, that conjunction is not expressible in terms of the other connectives. Moreover, the denotational semantics allows us to capture the set of equilibrium models of a formula with a simple and compact set expression. We also use this semantics to provide several formal definitions for entailment relations that are usual in the literature, and further introduce a new one called strong entailment. We say that α strongly entails β when the equilibrium models of α ∧ γ are also equilibrium models of β ∧ γ for any context γ. We also provide a characterisation of strong entailment in terms of the denotational semantics, and give an example of a sufficient condition that can be applied in some cases.
The Role of Oxidative Stress and Lipid Peroxidation in Ventricular Remodeling Induced by Tobacco Smoke Exposure after Myocardial Infarction

OBJECTIVE: To evaluate the roles of oxidative stress and lipid peroxidation in the ventricular remodeling that is induced by tobacco smoke exposure after myocardial infarction. METHODS: After induced myocardial infarction, rats were allocated into two groups: C (control, n=25) and ETS (exposed to tobacco smoke, n=24). After 6 months, survivors were submitted to echocardiogram and biochemical analyses. RESULTS: Rats in the ETS group showed higher diastolic (C = 1.52 ± 0.4 mm2, ETS = 1.95 ± 0.4 mm2; p=0.032) and systolic (C = 1.03 ± 0.3, ETS = 1.36 ± 0.4 mm2/g; p=0.049) ventricular areas, adjusted for body weight. The fractional area change was smaller in the ETS group (C = 30.3 ± 10.1 %, ETS = 19.2 ± 11.1 %; p=0.024) and E/A ratios were higher in ETS animals (C = 2.3 ± 2.2, ETS = 5.1 ± 2.5; p=0.037). ETS was also associated with a higher water percentage in the lung (C = 4.8 (4.3–4.8), ETS = 5.5 (5.3–5.6); p=0.013) as well as higher cardiac levels of reduced glutathione (C = 20.7 ± 7.6 nmol/mg of protein, ETS = 40.7 ± 12.7 nmol/mg of protein; p=0.037) and oxidized glutathione (C = 0.3 ± 0.1 nmol/g of protein, ETS = 0.9 ± 0.3 nmol/g of protein; p=0.008). No differences were observed in lipid hydroperoxide levels (C = 0.4 ± 0.2 nmol/mg of tissue, ETS = 0.1 ± 0.1 nmol/mg of tissue; p=0.08). CONCLUSION: In animals exposed to tobacco smoke, oxidative stress is associated with the intensification of ventricular remodeling after myocardial infarction.
Effect of Exercise on Markers of Inflammation in Breast Cancer Survivors: The Yale Exercise and Survivorship Study

Physical activity is associated with improved breast cancer survival, but the underlying mechanisms, possibly including modification of the inflammatory state, are not well understood. We analyzed changes in interleukin (IL)-6, C-reactive protein (CRP), and TNF-α in a randomized controlled trial of exercise in postmenopausal breast cancer survivors. Seventy-five women, recruited through the Yale-New Haven Hospital Tumor Registry, were randomized to either a six-month aerobic exercise intervention or usual care. Correlations were calculated between baseline cytokines, adiposity, and physical activity measures. Generalized linear models were used to assess the effect of exercise on IL-6, CRP, and TNF-α. At baseline, IL-6 and CRP were positively correlated with body fat and body mass index (BMI) and were inversely correlated with daily pedometer steps (P < 0.001). We found no significant effect of exercise on changes in inflammatory marker concentrations between women randomized to exercise versus usual care, though secondary analyses revealed a significant reduction in IL-6 among exercisers who reached 80% of the intervention goal compared with those who did not. Future studies should examine the effect of different types and doses of exercise and weight loss on inflammatory markers in large-scale trials of women diagnosed with breast cancer. Cancer Prev Res; 6(2); 109–18. ©2012 AACR.
Knowledge, attitude, and practices toward ayurvedic medicine use among allopathic resident doctors: A cross-sectional study at a tertiary care hospital in India

Context: Ayurveda is most commonly practiced form of complementary and alternative medicine (CAM) in India. There are very few studies showing the knowledge, attitude, and practices (KAP) of allopathic doctors about Ayurvedic drugs and its use. Aims: The study was initiated to assess KAP toward Ayurvedic medicine use among allopathic resident doctors. Settings and Design: Cross-sectional and prospective study. Materials and Methods: After obtaining permission from the Institutional Ethics Committee, allopathic resident doctors from clinical departments were approached personally. They were given pre-formed validated questionnaire to assess KAP toward Ayurvedic medicine use. Statistical Analysis Used: Descriptive statistics. Results: Allopathic residents had little knowledge about basic concepts of Ayurveda, that is, ‘panchakarma’ and ‘tridosha’. Majority residents (99%) had no opportunity to learn basics of Ayurveda, but 67% residents prescribed Ayurvedic medicines to patients. However, many residents (76%) mentioned that cross practice should not be allowed due to lack of knowledge. One resident knew that cross-practice was not allowed by law. The commonly prescribed proprietary Ayurvedic medicines were Liv-52 (39%), Shatavari (13%), Cystone (12%) and common ailments for which these medicines prescribed were liver disorders (34%), arthritis (18%), cough and cold (13%), kidney stones (11%), and piles (10%). Nearly 76% residents felt incorporation of Ayurveda with modern medicine would attract more patients and at the same time most residents (92%) agreed that Ayurvedic medicines need scientific testing before use. Though 50% of the residents agreed for voluntary training in Ayurveda, 80% denied compulsory training. Nearly 63% residents recommended Ayurveda among all CAMs. Most of residents heard of Ayurveda from their colleagues. Conclusions: This study reveals that allopathic resident doctors had little knowledge about Ayurveda and Ayurvedic medicine use but engaged in prescription of Ayurvedic medicines. So some interventions should be taken to increase the knowledge and awareness of allopathic resident doctors about Ayurvedic medicine use.