Miracle-dz/UniFAR-FTUs huggingface dataset:
The Importance of Physical Habitat Assessment for Evaluating River Health

1. Physical habitat is the living space of instream biota; it is a spatially and temporally dynamic entity determined by the interaction of the structural features of the channel and the hydrological regime. 2. This paper reviews the need for physical habitat assessment and the range of physical habitat assessment methods that have been developed in recent years. These methods are needed for assessing improvements made by fishery enhancement and river restoration procedures, and as an intrinsic element of setting environmental flows using instream flow methods. Consequently, the assessment methods must be able to evaluate physical habitat over a range of scales varying from broad river segment scale (up to hundreds of kilometres) down to the microhabitat level (a few centimetres). 3. Rapid assessment methods involve reconnaissance level surveys (such as the habitat mapping approach) identifying, mapping and measuring key habitat features over long stretches of river in a relatively short space of time. More complex appraisals, such as the Physical Habitat Simulation System (PHABSIM), require more detailed information on microhabitat variations with flow. 4. Key research issues relating to physical habitat evaluation lie in deciding which levels of detail are appropriate for worthwhile yet cost-effective assessment, and in determining those features that are biologically important and hence can be considered habitat features rather than simple geomorphic features. 5. The development of new technologies particularly relating to survey methods should help improve the speed and level of detail attainable by physical habitat assessments. These methods will provide the necessary information required for the development of the two-and three-dimensional physical and hydraulic habitat models. 6. A better understanding of the ways in which the spatial and temporal dynamics of physical habitat determine stream health, and how these elements can be incorporated into assessment methods, remains a key research goal.
An Efficient Protocol for Isolation of Functional RNA from Peel Tissue of Different Banana (Musa spp.) Cultivars for Gene Expression Studies on Anthracnose Development

Extraction of good quality RNA in larger quantities is a prerequisite for gene expression studies. Existing protocols for RNA extraction from banana pulp tissues were not successful on peel tissues of banana (Musa spp) as they contain higher concentrations of polyphenols, polysaccharides and latex. This study developed a new protocol by modifying the existing protocols. The modifications included combining of pre-warmed Tris-Borate extraction buffer, incorporation of CTAB in the extraction buffer, incubation in extraction buffer at 65 o C for one hour, and a three-day long extraction procedure with phenol, phenol:chloroform (1:1) and chloroform:isoamyl alcohol (24:1) together with centrifugation steps at high speeds (i.e. 12,000 –14,000 rpm). Spectrophotometric analysis of the extracted RNA, denaturing agarose gel electrophoresis, cDNA library construction, sequence information of cDNA inserts and RT-PCR confirmed the quality of RNA extracted by the method developed in the present study for gene expression work. Furthermore, it is shown that the developed method is useful to extract good quality RNA from peel tissues of a range of dessert- and cooking-type banana cultivars. Tropical Agricultural Research Vol. 26 (2): 329 – 342 (2015)
From gametogenesis to spawning: How climate-driven warming affects teleost reproductive biology.

Ambient temperature modulates reproductive processes, especially in poikilotherms such as teleosts. Consequently, global warming is expected to impact the reproductive function of fish, which has implications for wild population dynamics, fisheries, and aquaculture. In this extensive review spanning tropical and cold-water environments, we examine the impact of higher-than-optimal temperatures on teleost reproductive development and physiology across reproductive stages, species, generations, and sexes. In doing so, we demonstrate that warmer-than-optimal temperatures can affect every stage of reproductive development from puberty through to the act of spawning, and these responses are mediated by age at spawning and are associated with changes in physiology at multiple levels of the brain-pituitary-gonad axis. Response to temperature is often species-specific, and changes with environmental history/transgenerational conditioning, and the amplitude, timing, and duration of thermal exposure within a generation. Thermally-driven changes to physiology, gamete development and maturation typically culminate in poor sperm and oocyte quality, and/or advancement/delay/inhibition of ovulation/spermiation and spawning. Although the field of teleost reproduction and temperature is advanced in many respects, we identify areas where research is lacking, especially for males and egg quality from "omics" perspectives. Climate-driven warming will continue to disturb teleost reproductive performance and therefore guide future research, especially in the emerging areas of transgenerational acclimation and epigenetic studies, which will help to understand and project climate change impacts on wild populations and could also have implications for aquaculture. This article is protected by copyright. All rights reserved.
Fear of Heterosexism Among Sexuality and Gender Diverse Staff and Students

Fear of heterosexism—as distinct from actual experiences of heterosexism—plays a significant role in staff and students lives on campus. Ambient workplace heterosexism provides a context for staff and students about what to expect from their peers and colleagues, and shapes the daily activities of those who perceive heterosexism as a regulating force. In this article, we consider the psychometrics of the Fear of Heterosexism Scale (FoHS), which was integrated into a campus climate survey of Western Sydney University staff and students (N = 3,106; n = 412). This scale was considered in relation to a range of associated factors, including perceived safety on campus, bystander efficacy, responsibility to intervene, and awareness of lesbian, gay, bisexual, transgender, intersex, queer/questioning, asexual, and many other terms such as nonbinary and pansexual (LGBTIQA+) issues. In turn, the results of the FoHS are considered across a range of demographic factors such as gender, sexuality, role, dis/ability, and membership of campus-based support organizations. Supporting the findings from the initial operationalization of the FoHS by Fox and Asquith in 2018, this research identifies the consequences of fear of heterosexism on daily activities and engagement with study/work. Understanding the factors associated with fear of heterosexism is critical in creating more inclusive and respectful university environments.
Fishery and biology of Sepia pharaonis Ehrenberg, 1831 off Mumbai, northwest coast of India

Fishery of Sepia pharaonis by trawlers at New Ferry Wharf (NFW) during 2000 - 2011 in Mumbai waters is described. The landings ranged from 438 t (2004) to 1,763 t (2005) and the catch rate ranged from 0.17 kg/hr (2003) to 1.04 kg/hr (2005). The relationship between dorsal mantle length (DML) and total body weight (TBW) for males, TBW = 0.0008414 * DML 2.57989 and for females, TBW = 0.0009723 * DML 2.55201. Fish formed the major food item in both the sexes (87.1% in males and 86% in females) followed by prawns. Females were dominant in the catch with a sex-ratio of 1:1.24. Maximum numbers of males were mature (43.6%) while maximum numbers of females (37.2%) were spawning. The size at 50% maturity for females was estimated as 153 mm. The major peak spawning season for the species is during February to May.
A flexible hierarchical framework for improving inference in area-referenced environmental health studies

Study designs where data have been aggregated by geographical areas are popular in environmental epidemiology. These studies are commonly based on administrative databases and, providing a complete spatial coverage, are particularly appealing to make inference on the entire population. However, the resulting estimates are often biased and difficult to interpret due to unmeasured confounders, which typically are not available from routinely collected data. We propose a framework to improve inference drawn from such studies exploiting information derived from individual‐level survey data. The latter are summarized in an area‐level scalar score by mimicking at ecological level the well‐known propensity score methodology. The literature on propensity score for confounding adjustment is mainly based on individual‐level studies and assumes a binary exposure variable. Here, we generalize its use to cope with area‐referenced studies characterized by a continuous exposure. Our approach is based upon Bayesian hierarchical structures specified into a two‐stage design: (i) geolocated individual‐level data from survey samples are up‐scaled at ecological level, then the latter are used to estimate a generalized ecological propensity score (EPS) in the in‐sample areas; (ii) the generalized EPS is imputed in the out‐of‐sample areas under different assumptions about the missingness mechanisms, then it is included into the ecological regression, linking the exposure of interest to the health outcome. This delivers area‐level risk estimates, which allow a fuller adjustment for confounding than traditional areal studies. The methodology is illustrated by using simulations and a case study investigating the risk of lung cancer mortality associated with nitrogen dioxide in England (UK).
Measles, mumps, rubella, and varicella-zoster virus serology and infections in solid organ transplant recipients during the first year post-transplantation.

BACKGROUND Mumps, measles, rubella, and varicella-zoster viruses (MMRV) may cause severe infections in seronegative adult solid organ transplant (SOT) recipients but can be prevented by vaccination. We aimed to determine MMRV serostatus in adult SOT recipients before and one-year post-transplantation as well as evidence of MMRV infections in a large, prospective cohort of SOT recipients. METHODS A prospective study of 1182 adult SOT recipients included in the Management of Posttransplant Infections in Collaborating Hospitals (MATCH) cohort from 2011 to 2017 with a one-year follow-up. Systematic monitoring of MMRV serology was performed prior to transplantation and one-year post-transplantation. PCR was used to confirm viral replication in SOT-recipients presenting with clinical evidence of infection. RESULTS Among 1182 adult SOT recipients, 28 (2.4%), 77 (6.5%), 65 (5.5%), and 22 (1.9%) were seronegative for measles, mumps, rubella, and VZV, respectively, and 165 (14%) were seronegative for at least one of the MMRV viruses. One-year post-transplantation, 29/823 (3.5%) of seropositive SOT recipients had seroreverted, and 63/111 (57%) of seronegative SOT recipients seroconverted for at least one MMRV virus. No evidence of MMR infections was found, but 8 (0.7%) SOT recipients developed symptoms and had a positive VZV PCR. CONCLUSIONS A large proportion of SOT recipients were seronegative for at least one of the MMRV viruses. MMRV infections in SOT recipients may disseminate and become fatal, and although only few cases of VZV infection were detected, results from this study suggest increase attention towards vaccination of patients waiting for SOT.
Relationship Between Progression‐Free Survival, Objective Response Rate, and Overall Survival in Clinical Trials of PD‐1/PD‐L1 Immune Checkpoint Blockade: A Meta‐Analysis

PD‐1/PD‐L1 immune checkpoint blockade (ICB) has improved overall survival (OS) in solid tumor trials; however, parallel improvements in Response Evaluation Criteria in Solid Tumors (RECIST)‐based surrogate end points, progression‐free survival (PFS), and objective response rate (ORR), are not always observed. Here, we assess the surrogacy of PFS/ORR for OS with ICB therapy across advanced/metastatic tumors. In a trial‐level analysis (N = 40 randomized trials), PFS, ORR, and OS treatment effects were correlated (Spearman's rho). In a patient‐level analysis, data were extracted from available trials of durvalumab; the correlation of PFS and OS was evaluated (Bayesian normal‐induced‐copula‐estimation model) and the ordinal association between objective response and OS hazard ratio (HR) were assessed with concordance index measures. High correlation was observed between PFS HR and OS HR in intention‐to‐treat (ITT; rho = 0.76) and PD‐L1‐enriched populations (0.74); modest (or limited) benefit in PFS was associated with meaningful improvement in OS. Moderate correlations were observed between ΔORR and OS HR: ITT, −0.63; PD‐L1‐enriched, −0.53. At the patient level, a positive association was observed between PFS and OS in non‐small cell lung cancer (Kendall’s Tau = 0.793; 95% confidence interval, 0.789–0.797), head and neck squamous cell carcinoma (0.794; 0.789–0.798), and bladder cancer (0.872; 0.869–0.875). Objective responders had significantly better OS (concordance index > 0.9) than nonresponders across these tumor types. Modest (or limited) improvement in RECIST‐based end points did not rule out meaningful OS benefit, indicating they are imperfect surrogates and do not fully capture ICB clinical benefit. Therefore, caution is advised when basing early discontinuation of novel ICB agents on these end points.
Nitrogen dynamics in grassland streams along a gradient of agricultural development

We examined nitrogen (N) uptake in seven grassland streams lying in catchments along a gradient (0–84%) of agricultural land use in New Zealand using a stable isotope (15N) addition of NH4+ to quantify whole‐stream uptake rates and uptake by specific compartments within the streams. Whole‐stream uptake of NH4+ ranged from 1.2 mmol N m−2 min−1 to 7.9 mmol N m−2 min−1 and showed no evidence of strong saturation of uptake with increasing NH4+ availability along the land use gradient. The relatively simple pattern of increasing N uptake along the gradient occurred despite substantial shifts in uptake among community members. Uptake of NH4+ by epilithic biofilms followed a subsidy‐stress relationship, with highest uptake rates at intermediate levels of pastoral development and lowest uptake rates at high pastoral development. At high (>60%) pastoral development, reduced uptake by epilithon was compensated for by enhanced uptake by macrophytes. Compensatory uptake can play an important role in streams when community composition is reorganized by human activity.
Effect of foliar-applied potassium silicate on coffee leaf infection by Hemileia vastatrix

Coffee leaf rust, caused by Hemileia vastatrix, is the most devastating disease of coffee. Since limited information is available in the literature on silicon (Si) affecting plant diseases in coffee, this study was designed to investigate foliar application of potassium silicate (PS), a source of soluble (Si), on infection process of coffee leaf rust at the microscopic level. The foliar Si concentration for plants sprayed with water and PS has no significant difference (0.24 and 0.30 dag kg−1, respectively). X-ray microanalysis indicated that the deposition of Si on the leaves of the plants that were sprayed with PS was greater in comparison to the leaf samples from the plants sprayed with water. Rust severity on leaves of plants sprayed with water or sprayed with PS reached 44% and 32%, respectively, at 36 days after inoculation (dai). Plates of polymerised PS were observed on the leaf surfaces of the plants sprayed with the product, in contrast to its absence on the leaf surfaces of plants sprayed with water. At 36 dai, a greater number of uredia were observed on the leaf surfaces of plants sprayed with water in comparison to the leaf surfaces of plants sprayed with PS. On fractured leaf tissues that were sprayed with PS, less fungal colonisation was observed in comparison to the leaves of plants sprayed with water. In conclusion, the results of this study suggest that the effect of foliar-applied Si on the control of the coffee leaf rust development may be attributed to the physical role of the polymerised PS, its osmotic effect against urediniospores germination, or both.
An Endeavour for Autonomy

In discussion of troubled adolescent girls, their mental health often is in focus and a discourse constructing girls as vulnerable victims therefore dominates Swedish social services and secure care. This article is an investigation of how the girls themselves are navigating the discursive terrain where understandings of troubled adolescent girls in secure care are regulated. The results show that even though the girls’ stories show considerable similarities with what is previously known about troubled adolescent girls, their understandings of their lived experiences differ. The girls resist the dominating discourses that view them as victims by emphasizing their autonomy and own responsibility. However, in trying to distance themselves from devaluing interpretations, they take an attitude that ultimately obstructs their possibilities of getting help, since it inevitably puts them in opposition to the care system.
A Survey on Caprine Nematodiasis in Ladakh

The present study was conducted for the time period of one year on goats of Ladakh (JK Trichuris ovis, Haemonchus contortus, Dictyocaulus filaria and Chabertia ovina. It was also observed that among these T. ovis (48.03%) was most dominant followed by H. contortus (41.02%), D. filaria (37.05%) and C. ovina (22.35%) respectively. A significant difference was observed in prevalence of nematode parasites with respect to season, wherein higher prevalence (50.00%) was observed during the rainy season as compared to the dry season 35.93%. Similarly an association was observed between sex and age of the host with prevalence of nematode infections. It was also observed that females were more infected (46.15%) as compared to males (40.57%). Likewise young animals were more infected (45.83%) than the adult ones (41.21%). Similarly an association was observed between prevalence and agro-ecology of the study area where in higher values (45.45%) were recorded for comparatively lowland (Kargil) areas as compared to highland (Leh) areas (40.08%). The study also shown slight relationship between body condition and prevalence wherein the intensity of infection was higher (47.22%) in weak animals as compare to healthy ones (40.62%). Hence, it was concluded that season, sex, age, agro-ecology and body condition are some of the important risk factors associated with nematode parasitism in this area.
The discounting-by-interruptions hypothesis: model and experiment

Experimental animals often prefer small but immediate rewards even when larger-delayed rewards provide a higher rate of intake. This impulsivity has important implications for models of foraging and cooperation. Behavioral ecologists have hypothesized that animals discount delayed rewards because delay imposes a collection risk. According to this long-standing hypothesis, delay reduces value because an interruption that occurs while an animal is waiting may prevent it from collecting the delayed reward. Although there have been many experimental demonstrations of animal preferences for immediacy, none have included any interruptions. This paper develops a simple model of discounting by interruptions and then tests this model experimentally. The model considers the effects of interruption rate and duration on choice behavior. The experiment tests the effects of interruptions on the choice behavior of captive blue jays (Cyanocitta cristata) using a factorial design that manipulates the rate and duration of interruptions. The results do not support the discounting-by-interruptions hypothesis. This represents one of several lines of evidence suggesting that investigators should seek alternative explanations of the animal impulsivity. Copyright 2008, Oxford University Press.
Shifts in community leaf functional traits are related to litter decomposition along a secondary forest succession series in subtropical China

Aims We investigated shifts in community-weighted mean traits (CWM) of 14 leaf functional traits along a secondary successional series in an evergreen broadleaf forest in subtropical southeast China. Most of the investigated traits have been reported to affect litter decomposition in previous studies. We asked whether changes in CWMs along secondary succession followed similar patterns for all investigated traits and whether the shifts in CWM indicated a change in resource use strategy along the successional gradient. Using community decomposition rates (k-rates) estimated from annual litter production and standing litter biomass, we asked whether the dynamics of litter decomposition were related to changes in leaf functional traits along the successional series. Methods Twenty-seven plots were examined for shifts in leaf CWM traits as well as in k-rates along a series of secondary forest succession covered in the framework of the BEF-China project. We investigated whether the changes in CWMs followed similar patterns for all traits with ongoing succession. Three alternative linear models were used to reveal the general patterns of shifts in CWM trait values. Moreover, multiple regression analysis was applied to investigate whether there were causal relationships between the changes in leaf functional traits and the dynamics of litter decomposition along secondary succession. We furthermore assessed which traits had the highest impact on community litter decomposition. Important Findings Shifts in CWM values generally followed logarithmic patterns for all investigated traits, whereas community k -rates remained stable along the successional gradient. In summary, the shifts in CWM values indicate a change in community resource use strategy from high nutrient acquisition to nutrient retention with ongoing succession. Stands with higher CWM values of traits related to nutrient acquisition had also higher CWM values of traits related to chemical resistance, whereas stands with higher CWM values of traits related to nutrient retention exhibited higher CWM values in leaf physical defense. Moreover, high values in CWM values related to nutritional quality (such as high leaf phosphorus concentrations) were found to promote community k-rates, whereas high values in physical or chemical defense traits (such as high contents in polyphenols or high leaf toughness) decreased litter decomposition rates. In consequence, litter decomposition, which was simultaneously affected by these characteristics, did not change significantly along succession. Our findings show that leaf decomposition within the investigated communities is dependent on the interplay of several traits and is a result from interactions of traits that affect decomposition in opposing directions.
Compositional and physical properties of yogurts manufactured from milk and whey cheese concentrated by ultrafiltration

Summary Yogurts made with 80% milk retentate (MR) [Volume Reduction Factor (VRF) = 1.5] and 20% cheese whey retentate (WR; VRF = 8.0) (yogurt 1) and yogurts made with 100% MR through ultrafiltration have been evaluated as to flow, texture profile analysis (TPA) and syneresis index. As with MR and WR, their physico-chemical composition was also determined. The yogurt to which WR had been added showed; less apparent viscosity and greater tixotrophya; less firmness and adhesiveness and greater cohesiveness; higher syneresis index, less protein and mineral content, and greater lipid content in comparison with the yogurt made only with MR.