Miracle-dz/UniFAR-FTUs huggingface dataset:
Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB)

Abstract Fungi have crucial roles in ecosystems, and are important associates for many organisms. They are adapted to a wide variety of habitats, however their global distribution and diversity remains poorly documented. The exponential growth of DNA barcode information retrieved from the environment is assisting considerably the traditional ways for unraveling fungal diversity and detection. The raw DNA data in association to environmental descriptors of metabarcoding studies are made available in public sequence read archives. While this is potentially a valuable source of information for the investigation of Fungi across diverse environmental conditions, the annotation used to describe environment is heterogenous. Moreover, a uniform processing pipeline still needs to be applied to the available raw DNA data. Hence, a comprehensive framework to analyses these data in a large context is still lacking. We introduce the MycoDiversity DataBase, a database which includes public fungal metabarcoding data of environmental samples for the study of biodiversity patterns of Fungi. The framework we propose will contribute to our understanding of fungal biodiversity and aims to become a valuable source for large-scale analyses of patterns in space and time, in addition to assisting evolutionary and ecological research on Fungi.
Disparities in Burnout and Satisfaction With Work–Life Integration in U.S. Physicians by Gender and Practice Setting

Purpose To explore the interaction between practice setting (academic practice [AP], private practice [PP]) and gender in relation to physician burnout and satisfaction with work–life integration (WLI). Method In 2017, the authors administered a cross-sectional survey of U.S. physicians and characterized rates of burnout and satisfaction with WLI using previously validated and/or standardized tools. They conducted multivariable logistic regression to determine the interaction between the included variables. Results Of the 3,603 participants in the final analysis, female physicians reported a higher prevalence of burnout than male physicians in both AP (50.7% vs 38.2%, P < .0001) and PP (48.1% vs 40.7%, P = .001). However, the multivariable analysis found no statistically significant gender-based differences in burnout (odds ratio [OR] 0.94, 95% confidence interval [CI] 0.76–1.17, P = .60). Women and men in AP were less likely to report burnout than men in PP (OR 0.70, 95% CI 0.52–0.94, P = .01 and OR 0.69, 95% CI 0.53–0.90, P < .01, respectively); women in PP did not report different burnout rates from men in PP (OR 0.89, 95% CI 0.68–1.16, P = .38). Women in both AP and PP were less likely to be satisfied with WLI than men in PP (OR 0.62, 95% CI 0.47–0.83, P < .01 and OR 0.75, 95% CI 0.58–0.97, P = .03, respectively); men in AP did not report different satisfaction with WLI than men in PP (OR 1.05, 95% CI 0.82–1.33, P = .71). Conclusions Gender differences in rates of burnout are related to practice setting and other differences in physicians’ personal and professional lives. These results highlight the complex relationships among gender, practice setting, and other personal and professional factors in their influence on burnout and satisfaction with WLI.
Dimensions of group home culture as predictors of quality of life outcomes

Abstract Background Research has shown that there is variability in quality of life (QOL) outcomes for people with intellectual disabilities who live in group homes. The aim was to examine dimensions of group home culture as predictors of QOL outcomes. Method The Group Home Culture Scale (GHCS) was used to measure staff perceptions of culture in 23 group homes. QOL data were available from 98 people with intellectual disabilities. Multilevel modelling was used to examine the associations between the GHCS subscales and four QOL‐dependent variables. Results Of the GHCS subscales, Effective Team Leadership and Alignment of Staff with Organizational Values significantly predicted residents’ engagement in activities. Supporting Well‐Being significantly predicted residents’ community involvement. None of the GHCS subscales significantly predicted domestic participation and choice making. Conclusions The findings suggest that strategies to improve Effective Team Leadership and Supporting Well‐Being dimensions of culture may contribute to enhancing certain QOL outcomes.
Lake Erie: Effects of exploitation, environmental changes and new species on the fishery resources

In no other lake as large as Lake Erie (surface area, 25,690 km2) have such extensive changes taken place in the drainage basin, the lake environment, and the fish populations over the last 100 years. Deforestation and prairie burning led to erosion and siltation of valuable spawning grounds. Marsh spawning areas were drained. Lake-to-river spawning migrations were blocked by mill dams. Accelerated cultural nutrient loading increased total dissolved solids by nearly 50% (1920–70). Average summer water temperatures increased 1.1 C. Phytoplankton and zooplankton abundance increased severalfold. Severe oxygen depletion developed in the bottom waters of all three basins of the lake. Lake sturgeon were fished out as nuisance fish in the late 1800s. The commercial fisheries for lake trout, lake whitefish, and lake herring collapsed by 1940 and those for blue pike and walleye by 1960. Yellow perch production became unstable in the 1960s. The effects of exploitation, environmental changes, and new species on thes.
Intestinal P‐gp and Putative Hepatic OATP1B Induction: International Transporter Consortium Perspective on Drug Development Implications

There is an increasing interest in transporter induction (i.e., decreased systemic drug exposure due to increased efflux‐limited absorption or transporter‐mediated clearance) as a mechanism of drug–drug interactions (DDIs), although evidence of clinical relevance is still evolving. Intestinal P‐glycoprotein (P‐gp) and hepatic organic anion transporting polypeptides 1B (OATP1B) can be important determinants of drug absorption and disposition, as well as targets for DDIs. Current data indicate that intestinal P‐gp protein levels can be induced up to threefold to fourfold in humans primarily with pregnane X receptor (PXR) activators, and that this induction can decrease the systemic exposure of drugs with P‐gp efflux‐limited absorption (e.g., ≤ 67% decrease in the exposure of total dabigatran following rifampin multiple oral dosing). Evaluation of the clinical relevance of P‐gp induction as a DDI mechanism must consider the induction potential of the perpetrator drug for P‐gp and attenuation of exposure of the victim drug in the context of its therapeutic window. Practical drug development recommendations are provided herein. Reports are contradictory on OATP1B induction by PXR activators in human hepatocytes and liver biopsies. Some clinical investigations demonstrated that rifampin pretreatment decreased exposure of OATP1B substrates, while other studies found no differences, and the potential involvement of other mechanisms in these observed DDIs cannot be definitively ruled out. Thus, further studies are needed to understand hepatic OATP1B induction and potential involvement of other mechanisms contributing to reduced exposure of OATP1B substrates. This review critically summarizes the state‐of‐the‐art on intestinal P‐gp and hepatic OATP1B induction, and highlights implications for drug development.
HYBRIDIZATION OF TAMARIX RAMOSISSIMA AND T. CHINENSIS (SALTCEDARS) WITH T. APHYLLA (ATHEL) (TAMARICACEAE) IN THE SOUTHWESTERN USA DETERMINED FROM DNA SEQUENCE DATA

ABSTRACT Morphological intermediates between Tamarix ramosissima or T. chinensis (saltcedars) and T. aphylla (athel) were found recently in three locations in the southwestern USA, and were assumed to be hybrids or a previously unreported species. We sequenced chloroplast and nuclear DNA from putative parental and hybrid morphotypes and hybrid status of morphological intermediates was supported. Chloroplast data suggest that the seed source for these hybrids is T. aphylla. Invasive T. aphylla genotypes found in Australia match those found in the USA. Seed was collected from one of the hybrids, and a low percentage of it was viable. This hybrid combination has not been previously reported in the USA or the native ranges of the species. Although populations of this novel Tamarix hybrid appear to be uncommon at present, both parental species are considered invasive (saltcedars in North America; athel in Australia), and it is possible that more aggressive hybrid genotypes could be produced. Therefore, natural resource managers concerned with the potential spread of non-native species should be aware of the existence of these plants and monitor their future spread.
“Hitting as Light as Feathers”: Religious Leaders’ Voices on Domestic Violence

Abstract Domestic violence (DV) is described as a major public health issue that negatively affects women’s physical, mental, reproductive, and sexual health. In Lebanon, there are 18 religious sects that are allowed by the Lebanese constitution to manage their own affairs, judge, legislate, and issue rulings. These laws discriminate against married women and favor men over women. The purpose of this research is to explore the views and attitudes of religious leaders on DV, and their experiences of dealing with DV in Lebanon. This study involved in-depth interviews with 13 male religious leaders from various religious denominations. Each religious leader participated in an in-depth interview to assess understanding and perceptions about DV, and how DV cases are usually dealt with. All of the participants stated that they were involved in the affairs of their communities by counseling on familial and marital problems. Thus, several themes emerged throughout this study which are related to types and prevalence of DV, causes of DV, responding to DV through counseling and taking legal measures, religious leaders’ opinions on the DV law, and the support they need from the community and stakeholders to encourage the implementation of the law against DV. The results demonstrated that religious leaders are one of the many stakeholders concerned with addressing community-level issues because religion is a prominent part of people’s lives in Lebanon. Therefore, religious leaders could have a pivotal role in raising awareness about and responding to DV. Providing them with proper information and referral options in the communities they serve would improve society’s response to DV. Finally, their request for building their skills in DV counseling in the form of trainings or workshops indicates a need that can be met by local community organizations.
Synergism between albumin, bicarbonate and cAMP upregulation for cholesterol efflux from ram sperm.

Compared to other mammalian species, ram spermatozoa are difficult to capacitate in vitro. Dibutyryl cAMP (db-cAMP) and the phosphodiesterase (PDE) inhibitors, caffeine and theophylline (cAMP up-regulators), must be added to traditional capacitation media (containing bicarbonate, calcium and bovine serum albumin; BSA), to elicit a capacitation response. In this exploratory study, we assessed whether bicarbonate was still required for ram spermatozoa if cAMP is upregulated by the addition of db-cAMP and PDE inhibitors, and what role BSA plays in cholesterol efflux under these conditions. In this study, the validated BODIPY-cholesterol assay was used for the first time in ram spermatozoa to quantify cholesterol efflux by tracking the loss of BODIPY-cholesterol from the sperm plasma membrane using flow cytometry. The results show that under cAMP upregulated conditions, an increase in membrane fluidity and tyrosine phosphorylation of sperm proteins remain as bicarbonate-dependent processes. In fact, the supplementation of bicarbonate under these conditions was necessary to further enhance cAMP production in ram spermatozoa, which correlated with the presence of these capacitation-related processes. When BSA was supplemented with cAMP up-regulators (as well as bicarbonate), there was a loss of approximately 20-23% of BODIPY-cholesterol (79.5±30.5% to 76.9±12.3% remaining from 10 min), indicating that BSA is essential for mediating cholesterol efflux in ram spermatozoa as measured by the BODIPY-cholesterol assay. The current study identifies the functional relationship between bicarbonate, BSA and cAMP up-regulators that is required to support capacitation-related processes in ram spermatozoa, specifically cholesterol efflux.
Inhibition of the NAD salvage pathway in schistosomes impairs metabolism, reproduction, and parasite survival

NAD, a key co-enzyme required for cell metabolism, is synthesized via two pathways in most organisms. Since schistosomes apparently lack enzymes required for de novo NAD biosynthesis, we evaluated whether these parasites, which infect >200 million people worldwide, maintain NAD homeostasis via the NAD salvage biosynthetic pathway. We found that intracellular NAD levels decline in schistosomes treated with drugs that block production of nicotinamide or nicotinamide mononucleotide–known NAD precursors in the non-deamidating salvage pathway. Moreover, in vitro inhibition of the NAD salvage pathway in schistosomes impaired egg production, disrupted the outer membranes of both immature and mature parasites and caused loss of mobility and death. Inhibiting the NAD salvage pathway in schistosome-infected mice significantly decreased NAD levels in adult parasites, which correlated with reduced egg production, fewer liver granulomas and parasite death. Thus, schistosomes, unlike their mammalian hosts, appear limited to one metabolic pathway to maintain NAD-dependent metabolic processes.
Abundance and distribution of cavity trees in an old-growth subtropical montane evergreen broad-leaved forest

We examined the relationship between the density of cavity trees and forest structure characteristics and explored the occurrence of cavity trees among different tree species and diameter breast height (DBH) size in a subtropical evergreen broad-leaved forest in the Ailao Mountains in southwestern China. Cavity trees accounted for 7.9% of living trees and 16.3% of dead trees. Average density of living cavity trees (86.3 trees·ha–1) was 6.9 times that of dead cavity trees. Density of living cavity trees was positively correlated with the density of living trees. Cavity trees showed a skewed distribution among DBH classes that peaked at DBHs of 20–40 cm. Moreover, the probability that a living tree was cavity-bearing was logistically related to DBH. Overall, the likelihood of trees being cavity-bearing differed significantly among species. The proportions of cavity trees among the 23 species having more than 63 trees were positively related to the average DBH and to the largest DBH recorded for each species.
The Prevalence and Stability of Sleep-Wake Disturbance and Fatigue throughout the First Year after Mild Traumatic Brain Injury

In this prospective, longitudinal study, we aimed to determine the prevalence and stability of sleep-wake disturbance (SWD) and fatigue in a large representative sample of patients (Trondheim mild traumatic brain injury [mTBI] follow-up study). We included 378 patients with mTBI (age 16–60), 82 matched trauma controls with orthopedic injuries, and 83 matched community controls. Increased sleep need, poor sleep quality, excessive daytime sleepiness, and fatigue were assessed at 2 weeks, 3 months, and 12 months after injury. Mixed logistic regression models were used to evaluate clinically relevant group differences longitudinally. Prevalence of increased sleep need, poor sleep quality, and fatigue was significantly higher in patients with mTBI than in both trauma controls and community controls at all time points. More patients with mTBI reported problems with excessive daytime sleepiness compared to trauma controls, but not community controls, at all time points. Patients with complicated mTBI (intracranial findings on computed tomography or magnetic resonance imaging) had more fatigue problems compared to those with uncomplicated mTBI, at all three time points. In patients with mTBI who experienced SWDs and fatigue 2 weeks after injury, around half still had problems at 3 months and approximately one third at 12 months. Interestingly, we observed limited overlap between the different symptom measures; a large number of patients reported one specific problem with SWD or fatigue rather than several problems. In conclusion, our results provide strong evidence that mTBI contributes significantly to the development and maintenance of SWDs and fatigue.
Family Functioning, Perceived Social Support, and Adaptation to a Stoma: A Descriptive, Cross-sectional Survey.

The creation of a stoma is a life-saving surgical procedure that requires major adjustments. PURPOSE The aim of this study was to examine the relationships among family functioning, perceived social support, and adaptation to living with a stoma. METHOD A descriptive, cross-sectional survey was conducted between October 2013 and June 2015 among consecutive patients who visited the stomatherapy unit of a university hospital in Ankara, Turkey, for regular follow-up visits. Eligibility criteria stipulated participants must be at least 18 years of age, literate, live with family, have their stoma for at least 2 months, and be willing to participate. Instruments included a demographic and stoma-related information form, the Multidimensional Scale of Perceived Social Support (MSPSS; subscale range 4-28, total score range 12-84; higher scores indicate better perceived support), the McMaster Family Assessment Scale (FAS; range 1.32-3.15; higher scores indicate deteriorating family function), and the Ostomy Adjustment Inventory Scale-23 (OAI-23; range 19-85; higher scores indicate increasing adaptation). Data were entered into statistical software for analysis that included descriptive statistics and Mann-Whitney U and Spearman correlation tests. RESULTS Among the 75 participants (mean age 55.4 ± 12.96 years; average stoma duration 3.77 ± 4.97 years), 41 (54.7%) were male, 59 (78.7%) were married, and mean duration of living with a stoma was 3.77 ± 4.97 years. The average MSPSS score was 61.0 5 ± 15.00, the average FAS score was 1.98 ± 0.38, and the average OAI-23 score was 49.39 ± 14.62, all within the "moderate" range for their measures. Stoma complications, time since surgery, stoma self-care, marital status, whether the surgery was planned or an emergency, and employment status significantly affected MSPSS, FAS, and OAI-23 scores. As the FAS scores increased, the MSPSS (r = -.399; P = .001), and OAI-23 (r = -.300; P = .009) scores decreased. CONCLUSION The results suggest wound, ostomy, continence nurses should assess and encourage familial and social support. Prospective studies examining the effect of familial and social support on stoma adjustment are warranted.
Estimation of self-sustained activity produced by persistent inward currents using firing rate profiles of multiple motor units in humans.

Persistent inward calcium and sodium currents (IP) activated during motoneuron recruitment help synaptic inputs maintain self-sustained firing until de-recruitment. Here, we estimate the contribution of the IP to self-sustained firing in human motoneurons of varying recruitment threshold by measuring the difference in synaptic input needed to maintain minimal firing once the IP is fully activated compared with the larger synaptic input required to initiate firing prior to full IP activation. Synaptic input to ≈20 dorsiflexor motoneurons simultaneously recorded during ramp contractions was estimated from firing profiles of motor units decomposed from high-density surface-EMG. To avoid errors introduced when using high-threshold units firing in their nonlinear range, we developed methods where the lowest-threshold units firing linearly with force were used to construct a composite (control) firing rate profile to estimate synaptic input to the higher-threshold (test) units. The difference in the composite firing rate (synaptic input) at the time of test unit recruitment and de-recruitment (ΔF=Frecruit-Fde-recruit) was used to measure IP amplitude that sustained firing. Test units with recruitment thresholds 1-30% of maximum had similar ΔFs, which likely included both slow and fast motor units activated by small and large motoneurons, respectively. This suggests that the portion of the IP that sustains firing is similar across a wide range of motoneuron sizes. Higher-threshold units had more prolonged accelerations in firing rate at the onset of recruitment compared to lower-threshold units, likely reflecting IP activation closer to firing onset in the higher-threshold units, but well before firing onset in the lower-threshold units.
Effects of combining manual lymphatic drainage and Kinesiotaping on pain, edema, and range of motion in patients with total knee replacement: a randomized clinical trial

Total knee replacement (TKR) is continuously increasing with significantly faster recovery times. Soft tissue pain and edema of operated limbs play an important role in early functional recovery. The present study aims to evaluate the effectiveness of the combination of Kinesiotaping and Lymphatic drainage for the containment of pain and edema as well as the improvement of the range of motion of the knee as integration with standard postoperative rehabilitation. Ninety-nine TKR patients were included in the randomized clinical trial and divided into three groups: Kinesiotaping and Lymphatic drainage Group, Lymphatic drainage Group, and Kinesiotaping Group. The assessment was carried out on days 2-4-6 postoperation. All the patients had also standard reeducation sessions. It was observed that both Kinesiotaping and Lymphatic drainage was useful in reducing pain and edema. A significantly higher improvement was observed in the group in which Lymphatic drainage was associated with Kinesiotaping with respect to the individual treatments, for pain and leg circumference over and under the knee, and at the ankle. Range of motion of the knee did not show any difference since the flexion degree was similar in all the three groups. No difference was found between Kinesiotaping and Lymphatic drainage. In conclusion, the treatment with a combination Kinesiotaping and Lymphatic drainage provided better results on pain and edema observed as early as the first days after the intervention, thus may be considered a valid support for standard rehabilitation and pharmacological intervention.
Cobalt Uptake and Resistance to Trace Metals in Comamonas testosteroni Isolated From a Heavy-Metal Contaminated Site in the Zambian Copperbelt

A biogeochemical study of a polluted wetland site in Kitwe, Zambia shows high concentration of trace metals (e.g., > 25 and ≈ 2 fold higher than the Eco-toxic threshold values of copper and cobalt, respectively) with many sequestered with the sediment organic phase. Depth profiles in surface sediments suggest trace metal cycling between porewater and solid phases, including that of cobalt. This study documents a bacterium displaying resistance to, and accumulation of cobalt, and that cobalt has a positive effect on growth. The isolate was enriched from the microbial community and identified using 16S rRNA gene sequence analysis as a strain of Comamonas testosteroni (designated C. testosteroni TDKW). Improved growth of C. testosteroni TDKW was seen with the addition of up to 200 μM cobalt (optimal growth ca. 100 μM), while concentrations above 4 mM completely inhibited growth. C. testosteroni TDKW also exhibited resistance to high concentrations of iron and manganese, but showed limited resistance to copper or nickel. Further analysis revealed cellular cobalt accumulation and the presence of heavy-metal resistance genes, tentatively suggesting that this organism could contribute to in situ biological cycling of cobalt in mineral contaminated aquatic systems.