Miracle-dz/UniFAR-FTUs huggingface dataset:
Early evolution of HLA-associated escape mutations in variable Gag proteins predicts CD4+ decline in HIV-1 subtype C infected women.

Objective—HIV-1 escape from cytotoxic T-lymphocytes (CTL) results in the accumulation of HLA-associated mutations in the viral genome. To understand the contribution of early escape to disease progression, this study investigated the evolution and pathogenic implications of CTL escape in a cohort followed from infection for five years. Methods—Viral loads and CD4+ counts were monitored in 78 subtype C infected individuals from onset of infection until CD4+ decline to <350 cells/μl or five years post-infection. The gag gene was sequenced and HLA-associated changes between enrolment and 12 months postinfection were mapped. Results—HLA-associated escape mutations were identified in 48 (62%) of the participants and were associated with CD4+ decline to <350 copies/ml (p=0.05). Escape mutations in variable Gag proteins (p17 and p7p6) had a greater impact on disease progression than escape in more conserved regions (p24) (p=0.03). The association between HLA-associated escape mutations and CD4+ decline was independent of protective HLA allele (B*57, B*58:01, B*81) expression. Conclusion—The high frequency of escape contributed to rapid disease progression in this cohort. While HLA-adaption in both conserved and variable Gag domains in the first year of infection was detrimental to long term clinical outcome, escape in variable domains had greater impact. Corresponding Author: Carolyn Williamson, PhD, Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa, Tel: +27-21-406 6683, carolyn.williamson@uct.ac. za. Conflicts of interest: The authors declare no conflicts of interest. HHS Public Access Author manuscript AIDS. Author manuscript; available in PMC 2018 January 14. Published in final edited form as: AIDS. 2017 January 14; 31(2): 191–197. doi:10.1097/QAD.0000000000001298. A uhor M anscript
Improve the Micro-hardness of Single Point Incremental Forming Product Using Magnetic Abrasive Finishing

In this paper the Magnetic Abrasive Finishing (MAF) was utilized after Single Point Incremental Forming (SPIF) process as a combined finishing process. Firstly, the Single Point Incremental forming was form the truncated cone made from low carbon steel (1008-AISI) based on Z-level tool path then the magnetic abrasive finishing process was applied on the surface of the formed product. Box-Behnken design of experiment in Minitab 17 software was used in this study. The influences of different parameters (feed rate, machining step size, coil current and spindle speed) on change in Micro-Vickers hardness were studied. The maximum and minimum change in Micro-Vickers hardness that achieved from all the experiments were (40.4 and 1.1) respectively. The contribution percent of (feed rate, machining step size, coil current and spindle speed) were (7.1, 18.068, 17.376 and 37.894) % respectively. After MAF process all the micro surface cracks that generated on the workpiece surface was completely removed from the surface.
Novel microsatellite markers for the endangered neotropical fish Brycon orbignyanus and cross-amplification in related species

Abstract Brycon orbignyanus is a neotropical fish found in several South American countries. This species has high ecological importance and is included in the list of fish threatened with extinction. In this study, we report the development and characterisation of 12 microsatellite primers of B. orbignyanus for future genetic studies. Screening of the 12 markers in a sample of 35 individuals identified seven polymorphic loci and 22 alleles, with one to three alleles per locus. The polymorphic information content ranged from 0.054 to 0.542, with four loci showing significant deviation from Hardy–Weinberg equilibrium. Two loci possessed null alleles. Cross-species amplification tests in two closely related species showed that 11 loci are transferrable to Brycon gouldingi (B. gouldingi) and nine are transferrable to B. falcatus. The microsatellite primers designed may be used for genetic variability and population structure studies in wild populations, fish farms and restocking programmes of B. orbignyanus and the two related species.
Otitis externa in the dog and the eat

Η έξω ωτίτιδα eίναι η συχνότeρη παθολογική κατάσταση του έξω ακουστικού πόρου στα μικρά ζώα μe συχνότητα που eίναι μeγαλύτeρη στο σκύλο απ' ότι στη γάτα. Η πολυπαραγωντική της αιτιολογία πeριλαμβάνeι τους προδιαθeσικούς παράγοντeς, τα προκαλούντα αίτια καθώς και τους παράγοντeς eκeίνους που eυθύνονται για τις συχνές υποτροπές. Στα σπουδαιότeρα προκαλούντα αίτια πeριλαμβάνονται η ατοπία, η τροφική αλλeργία, η ωτοδηκτική ψώρα, τα ξένα σώματα, οι eνδοκρινοπάθeιeς και οι διαταραχές της κeρατινοποίησης. Τα βακτηρίδια και οι ζύμeς, που σαπροφυτούν στον eξωακουστικό πόρο, συχνά eπιπλέκουν τις αρχικές αλλοιώσeις, οδηγώντας έτσι στην eγκατάσταση κυψeλιδοπαραγωγικής ή πυώδους έξω ωτίτιδας. Η μέση ωτίτιδα και οι υπeρπλαστικές αλλοιώσeις του έξω ακουστικού πόρου eίναι υπeύθυνeς για τη διαιώνιση της νόσου. Η διάγνωση γίνeται eύκολα μe την καλή διeρeύνηση του ιστορικού, τον καθαρισμό του έξω ακουστικού πόρου και την ωτοσκόπηση, την κυτταρολογική και παρασιτολογική eξέταση των eξιδρωμάτων, την καλλιέργeια για βακτηρίδια και το αντιβιόγραμμα και την ακτινολογική eξέταση (τιτάνωση του χόνδρου, μέση ωτίτιδα). Η διαγνωστική διeρeύνηση και η θeραπeυτική αντιμeτώπιση της υποκeίμeνης δeρματοπάθeιας κρίνονται απαραίτητeς. Η θeραπeία της έξω ωτίτιδας eξαρτάται από την ταυτοποίηση και τον έλeγχο των προδιαθeσικών παραγόντων και των αιτιών, eφόσον βέβαια αυτό eίναι δυνατό. Η συντηρητική θeραπeία συνίσταται στον καθαρισμό ή και στη συστηματική χορήγηση διαφόρων φαρμακeυτικών ουσιών (ακαρeοκτόνα, αντιμυκητικά, αντιβιοτικά, γλυκοκορτικοeιδή). Οι διορθωτικές χeιρουργικές eπeμβάσeις θα πρέπeι να γίνονται στα πeριστατικά eκeίνα που δeν ανταποκρίνονται στη συντηρητική αγωγή.
Development aid and international migration to Italy: Does aid reduce irregular flows?

In recent years, donors have claimed to tackle the root causes of migration from low-income countries using aid. While others have studied the eﬀects of aid on regular migration, we test whether aid deters irregular migration to Italy using two innovative dependent variables: asylum applications and apprehensions at border. For asylum applications, the largest signiﬁcant eﬀect size implies we should expect one extra application for an additional $180,000 in bilateral aid. For border crossings, the only signiﬁcant eﬀect implies the marginal cost in bilateral aid is $1.8 million per deterred migrant. The conclusion that eﬀect sizes are small is robust to diﬀerent types of aid, measures of migration and various controls. We ﬁnd robust evidence that irregular migration ﬂows are signiﬁcantly aﬀected by conﬂict, poverty, and the pre-existing stocks from that country. Comparing our results to the existing aid-migration literature, we ﬁnd similar eﬀect sizes. The cost per deterred (regular) migrant is in the range $2-7 million. Statistically signiﬁcant estimates for the eﬀect of aid on regular migration are only found for sub-samples or speciﬁc speciﬁcations. In short, aid does not deter regular or irregular migration, so should be used for other purposes
Penguatan Kapasitas Kelembagaan dalam Pembangunan Kelurahan Berkelanjutan Berbasis Agrowisata di Kumpulrejo, Kota Salatiga

Kumpulrejo Village becomes the priority of Salatiga City in the sustainable village development based on the local potential of agrotourism. Kumpulrejo holds potential in livestock farming, nearly 80% of the population are dairy farmers. Suboptimal institutional capacity of the Livestock Farmer Groups in managing potentials results in problems regarding sustainable village development program in Kumpulrejo. The community’s social capital is expected to significantly affect the Livestock Farmer Groups’s institutional capacity strengthening. The present study aims to find out the affect of social capital on the institutional capacity strengthening with regard to argoturism-based sustainable village development in Kumpulrejo. The method that used was quantitative-descriptive, data obtained from questionnaires, observation, and interview. The sampling technique used by simple random sampling, to the 60 respondents. The study showed that social capital which consist of a trust, social network, and norms significantly affect to the institutional capacity strengthening by 57,9%. Partially, a trust did not hold significantly affect, while social network and norms significantly affect the institutional capacity strengthening of livestock farmer groups in Kumpulrejo Village.
Reconstitution of Helical Soluble α-Synuclein through Transient Interaction with Lipid Interfaces

α-synuclein (αSyn) is one of the key players in the pathogenesis of Parkinson’s disease (PD) and other synucleinopathies. Its misfolding and subsequent aggregation into intracellular inclusions are the pathological hallmark of these diseases and may also play a central role in the molecular cascade leading to neurodegeneration. In this work, we report the existence of a novel soluble α-helical conformer of αSyn, an archetypal “intrinsically disordered protein” (IDP), obtained through transient interaction with lipid interfaces. We describe how the stability of this conformer is highly dependent on the continuous, dynamic oligomerization of the folded species. The conformational space of αSyn appears to be highly context-dependent, and lipid bilayers might play crucial roles as molecular chaperones for cytosolic species in a cellular environment, as they do in the case of this previously unreported structure. Significance Statement Both genetic and histopathologic evidence tie α-synuclein (αSyn) to the pathogenesis of Parkinson’s disease (PD), a widespread neurodegenerative disorder. Lipids play a central role in the dynamics of αSyn in physiology and disease. αSyn undergoes a coil-to-helix transition when binding to lipid vesicles and it is involved in the regulation of synaptic vesicle trafficking. Furthermore, recently discovered α-helical, aggregation-resistant “multimers” of αSyn could constitute a protective conformational pathway. We report the existence of a folded, lipid-unbound αSyn conformer that forms upon transient interaction with lipids and is stabilized by dynamic homooligomerization, suggesting that synaptic activity could modulate resistance towards aggregation. Our results are therefore important both for the molecular pathology of PD and the structural biology of intrinsically disordered proteins.
Where and When Soil Amendment is Most Effective as a Low Impact Development Practice in Residential Areas

Improving the infiltration capacity of urban soil is critical for effective stormwater management, but existing guidance on soil amendment in residential areas typically calls for tilling and amending soil throughout the entire yard, an approach that is most feasible during development or redevelopment. To develop guidance on less‐extensive soil amendment interventions which a homeowner could implement postconstruction, we designed a modeling study to compare four scenarios targeting soil amendment in a single‐family yard (1) at disconnected impervious features, (2) at locations with large upslope drainage areas, (3) at locations with a high topographic wetness index (TWI), and (4) randomly (control). We find that soil amendment may be ineffective at reducing runoff from residential areas with high near‐surface infiltration rates (e.g., Ksat > 1 × 10−2 m/hr), but can reduce runoff by 46%–73% (up to 15% of precipitation) on yards with lower near‐surface infiltration rates. We find that targeting amendment at interfacial hotspots near disconnected impervious surfaces can reduce runoff by over 10× more than amending a random equivalent area and by at least 2× more than targeting amendment by drainage area or TWI. We suggest including this intervention in the suite of low impact development practices promoted to residential property owners since it effectively and efficiently reduces runoff and may appeal to homeowners who are wary of maintenance needs of other practices.
Biofilm Production by Organisms Causing Ventilator Associated Pneumonia

Ventilator associated pneumonia (VAP) has been defined as pneumonia that occurs 48 hours after patients have received mechanical ventilation. Early onset VAP occurs within 4 days of mechanical ventilation and late onset VAP occurs after 4 days (American Thoracic Society, 2005). It is the second most common nosocomial infection and the most common infection in ventilated patients. The prevalence varies between 9 to 27 % with the maximum risk in the first five days after mechanical ventilation (Chastre and Fagon, 2002; International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 02 (2018) Journal homepage: http://www.ijcmas. com
Campus dining goes mobile: Intentions of college students to adopt a mobile food-ordering app

ABSTRACT Mobile food-ordering apps are here to stay in the foodservice industry and their popularity is only expected to grow in the coming years. Given this knowledge some college campus dining operations have started to develop their own mobile food-ordering applications. Thus, the current study sought to assess how various aspects of the Unified Theory of Acceptance and Use of Technology and its extensions influence students’ adoption intentions. The study also assessed the moderating effects of productivity orientation and fear of missing out (FoMO) two behavioral constructs that can have an influence on college students’ overall behaviors. Theoretical and practical implications are discussed.
Stereotypes in the face of reality: Intergroup contact inconsistent with group stereotypes changes attitudes more than stereotype-consistent contact

In a longitudinal two-wave study we examined the effects of positive and negative intergroup contact on outgroup attitudes in participants who perceived positive, negative, or ambivalent group stereotypes. We focused on stereotype-consistent contact, occurring when the valence of participants’ contact matches the valence of the perceived group stereotype (e.g., negative–negative), and on stereotype-inconsistent contact, occurring when the valence of contact contradicts the valence of the group stereotype (e.g., positive–negative). In relations of the Czech majority (N = 890) with two distinctly stereotyped minorities, the Roma and the Vietnamese, stereotype-inconsistent contact predicted changes in attitudes better than stereotype-consistent contact. In the case of negatively stereotyped groups, positive intergroup contact is a viable way to improve attitudes. For positively stereotyped groups, negative contact can worsen attitudes, while positive contact does not have any attitude-improving effect. Interventions aimed at improving outgroup attitudes need to be applied with caution, considering the valence of group stereotypes.
Analysis of floral nectar characteristics of Korean and Chinese hawthorns (Crataegus pinnatifida Bunge)

Crataegus pinnatifida Bunge is a deciduous tree belonging to the Rosaceae and native to Korea, China and Japan. In a previous study, Chinese C. pinnatifida showed the possibility to become a major honey plant species. In this research, we investigated nectar characteristics of Korean and Chinese hawthorns with regard to: secreted nectar volume; sugar concentration of nectar; and its amino acid content, in order to increase knowledge about the honey potential of this subspecies. On average, Korean C. pinnatifida secreted 1.43 μl nectar per flower and its sugar concentration was 27.2%. However, nectar volume of Chinese C. pinnatifida varieties (Geumsung, Daegeumsung, Change and Maban) ranged from 3.65 to 5.39 μl with 11.3–12.6% sugar concentration of nectar. Nectar sugar content was evaluated at 69.2 μg and 50.6–79.0 μg per flower for Korean and Chinese varieties, respectively, which was not significantly different. The minimum estimate of honey that can be harvested from a flower of Korean and Chinese hawthorns was 81.4 μg per flower and 59.5–92.9 μg per flower. The amino acid complement of the nectar of both species were also determined. Asparagine, glutamine, glutamic acid, proline and serine comprised more than 65% of total amino acid content in both flowers of Korean and Chinese C. pinnatifida. Korean and Chinese hawthorns showed different patterns in nectar volume, sugar concentration of nectar and the amount of free sugar and amino acid content. Collectively, our findings showed similar patterns in sugar composition and nectar sugar content which could be influenced by breeding and selection of this honey tree.
Tolerance of fen mosses to submergence, and the influence on moss community composition and ecosystem resilience

Co-ordinating Editor: Hans Henrik Bruun Abstract Question: Flood disturbance in peatlands can create temporary or permanently submerged areas where tolerant species may persist and replace intolerant species over time. Fen moss species and communities occur along a hummock–hollow gradient in natural ecosystems, but their resistance and resilience to different durations of submergence has yet to be tested. We asked what are the shortand longterm effects of submergence duration on four common boreal fen moss species and the implications for ecosystem resilience? Location: Rich fen near Fort McMurray, Alberta, Canada. Methods: To examine the effect of submergence duration on fen moss species and communities, we harvested and submerged monoculture plugs dominated by Hamatocaulis vernicosus, Sphagnum warnstorfii, Tomentypnum nitens and Aulacomnium palustre in the field under rich fen water for 1–8 weeks. After submergence, we planted the plugs in bare peat at the same site to evaluate the shortand longterm responses of each species and changes in moss community composition over time. Results: We found that moss species response to duration of submergence is not strictly related to their occurrence along a hummock–hollow gradient and that tolerant species maintain or restore moss cover. H. vernicosus was most tolerant to submergence of all durations, whereas S. warnstorfii was nearly eliminated by submergence. Over the long term, more tolerant species replaced less tolerant species, increasing diversity and moss community resilience. Overall, moss communities without S. warnstorfii were resilient to 4 weeks of submergence because T. nitens and H. vernicosus maintained dominance or established where the cover of less resilient species was limited. Conclusions: We show that moss species varied in their responses to submergence duration, resulting in shifts in community composition and longterm effects on community resilience with longer durations of submergence. This provides insight into how moss communities provide stability to peatlands in response to disturbance through shifts in community composition that support tolerant dominant species.
Effect of Impulse Polarity on a New Grounding Device with Spike Rods (GDSR)

The characterizations of grounding systems subjected to high impulse conditions are known to be dependent on the polarity, current to peak time and discharge time, as well as the electrical properties of the soil, and the grounding electrodes themselves. It is therefore important to investigate the behavior of grounding systems under high impulse conditions under negative impulse polarity, and compare it with positive impulse polarity results. Experimental test results for the same grounding systems installed with various earth electrodes at several sites under positive impulse polarity have previously been presented. In comparison, this paper presents the results of negative impulse polarity injected on the same grounding systems. It is found that a significant difference between positive and negative impulse polarities is observed for the grounding systems installed at high soil resistivity.
Seed dispersal via a new watercourse in a reconnected floodplain: differences in species groups and seasonality

Reconnection of floodplains to rivers to enhance fluvial dynamics is a favored method of floodplain restoration in Europe. It is believed that the restoration of hydrological conditions of the floodplain facilitates natural dispersal of target species, and hence the reestablishment, of typical plant communities. The aim of our study was to investigate whether floodplain target species could reach restoration sites via hydrochorous dispersal. We analyzed seed inflow from the river and seed dispersal in different sectors of a new watercourse in the Danube floodplain. Seeds were captured using 27 seed traps during three sampling periods of 3 weeks each from summer 2011 to spring 2012. After germination seedlings were identified, we detected a total of almost 39,000 seeds of 176 species, including 80 target species of riparian habitats. We found significant differences between seasons (most seeds in autumn/winter) and between stream sectors. Fewer seeds came in from the Danube (2,800 seeds) than were transported within the floodplain. Several new floodplain target species were detected, which had not been found in the aboveground vegetation or soil seed bank before the start of the restoration. Seeds of nonnative species did not disperse further than approximately 1 km. Our results indicated that hydrochorous seed dispersal from upstream habitats along the new watercourse was important for the establishment of target species and hence for the success of floodplain restoration. Technical water diversion weirs must be traversable for seeds, and small donor sectors upstream might enhance the reestablishment of target vegetation along new sectors downstream.
Solar Wind Turbulence from 1 to 45 au. IV. Turbulent Transport and Heating of the Solar Wind Using Voyager Observations

We adopt the theory for turbulent transport of energy by solar wind fluctuations and apply that theory to observations by the Voyager 1 and 2 spacecraft to obtain rates of thermal proton heating that are controlled by two sources: the large-scale fluctuations in the solar wind that arise from solar sources and the excitation of waves by newborn interstellar ions. In the process, we compute magnetic spectra for 839 data intervals spanning the range from 1 to 35 au when thermal ion data is available and use those spectra to obtain independent estimates for the energy cascade rates at intermediate scales that we assume equals the rate of thermal proton heating by the turbulence. We compare three analyses that describe different aspects of the solar wind heating problem: the rate of energy cascade through the intermediate scales of the magnetic spectrum, the rate at which energy is supplied to that cascade from the large-scale fluctuations as described by magnetohydrodynamic transport theory, and the rate at which energy is injected into the spectrum via wave excitation by newborn interstellar ions. The first two expressions are found to be in good agreement while the latter source dynamics become important beyond 10 au.
Diallel analysis in cotton (Gossypium hirsutum L.) for water stress tolerance

Information about combining ability is important in determining breeding strategies. The objective of this study was to estimate the general (GCA) and specific (SCA) combining abilities among twenty cotton hybrid combinations submitted to water stress, based on agronomic traits. The trails were carried out in semiarid environment (Barbalha, CE), during two years, in dry season under irrigation, and submitted to 23 days of water suppression. Wide variability was verified among parents and their hybrids, with additive effects to seed yield, lint percentage, blooming and boll weight. Dominance effect was found only to plant height. The combinations BRS 286 x CNPA 5M, BRS RUBI x CNPA 5M, FM 966 x CNPA 5M and BRS 286 x BRS Seridó showed the best SCAs and averages for the majority of the traits. In addition, at least one of their parents had high CGA. These combinations must be advanced in cotton breeding program.