Miracle-dz/UniFAR-FTUs huggingface dataset:
Global patterns of kelp forest change over the past half-century

Significance Kelp forests support diverse and productive ecological communities throughout temperate and arctic regions worldwide, providing numerous ecosystem services to humans. Literature suggests that kelp forests are increasingly threatened by a variety of human impacts, including climate change, overfishing, and direct harvest. We provide the first globally comprehensive analysis of kelp forest change over the past 50 y, identifying a high degree of variation in the magnitude and direction of change across the geographic range of kelps. These results suggest region-specific responses to global change, with local drivers playing an important role in driving patterns of kelp abundance. Increased monitoring aimed at understanding regional kelp forest dynamics is likely to prove most effective for the adaptive management of these important ecosystems. Kelp forests (Order Laminariales) form key biogenic habitats in coastal regions of temperate and Arctic seas worldwide, providing ecosystem services valued in the range of billions of dollars annually. Although local evidence suggests that kelp forests are increasingly threatened by a variety of stressors, no comprehensive global analysis of change in kelp abundances currently exists. Here, we build and analyze a global database of kelp time series spanning the past half-century to assess regional and global trends in kelp abundances. We detected a high degree of geographic variation in trends, with regional variability in the direction and magnitude of change far exceeding a small global average decline (instantaneous rate of change = −0.018 y−1). Our analysis identified declines in 38% of ecoregions for which there are data (−0.015 to −0.18 y−1), increases in 27% of ecoregions (0.015 to 0.11 y−1), and no detectable change in 35% of ecoregions. These spatially variable trajectories reflected regional differences in the drivers of change, uncertainty in some regions owing to poor spatial and temporal data coverage, and the dynamic nature of kelp populations. We conclude that although global drivers could be affecting kelp forests at multiple scales, local stressors and regional variation in the effects of these drivers dominate kelp dynamics, in contrast to many other marine and terrestrial foundation species.
High dietary vitamin D prevents hypocalcemia and osteomalacia in CYP27B1 knockout mice

25‐hydroxyvitamin D (25OH D) 1α‐hydroxylase (CYP27B1) knockout (KO) mice are growth retarded, hypocalcemic, and have osteomalacia. This can be prevented by 1,25 dihydroxyvitamin D (1,25 D) injections or by feeding a 2% calcium (Ca), 20% lactose rescue diet. We tested whether high dietary vitamin D3 (VD) could exert biological effects in the absence of CYP27B1 in vivo. Male weanling KO and wild‐type (WT) mice were randomized to the rescue diet or AIN93G diets (0.5% Ca, 0.4% phosphorus) with 1,000 (1K, the rodent requirement), 10,000 (10K) or 20,000 (20K) IU VD/kg diet. Growth and food intake were monitored until 12 weeks of age, at which time blood and tissues were taken. Serum 25OH D was >500 nM (10 fold elevated) in mice fed the 10K and 20K IU VD diets. Serum 1,25 D was at the limit of detection in KO mice and did not increase when 25OH D was elevated by diet. While KO mice on the 1,000 IU diet displayed impaired growth and hypocalcemia, both the 10K and 20K IU VD diets were as effective as the rescue diet in promoting growth and normalizing serum Ca. In KO mice, high dietary VD also restored calbindin D9K gene expression in intestine and kidney and normalized bone parameters as assessed by microCT scanning. These data demonstrate that high serum 25OH D can regulate calcium and bone metabolism independent of its conversion to 1,25 D.
Diversification of Secondary Metabolite Biosynthetic Gene Clusters Coincides with Lineage Divergence in Streptomyces

We have identified Streptomyces sister-taxa which share a recent common ancestor and nearly identical small subunit (SSU) rRNA gene sequences, but inhabit distinct geographic ranges demarcated by latitude and have sufficient genomic divergence to represent distinct species. Here, we explore the evolutionary dynamics of secondary metabolite biosynthetic gene clusters (SMGCs) following lineage divergence of these sister-taxa. These sister-taxa strains contained 310 distinct SMGCs belonging to 22 different gene cluster classes. While there was broad conservation of these 22 gene cluster classes among the genomes analyzed, each individual genome harbored a different number of gene clusters within each class. A total of nine SMGCs were conserved across nearly all strains, but the majority (57%) of SMGCs were strain-specific. We show that while each individual genome has a unique combination of SMGCs, this diversity displays lineage-level modularity. Overall, the northern-derived (NDR) clade had more SMGCs than the southern-derived (SDR) clade (40.7 ± 3.9 and 33.8 ± 3.9, mean and S.D., respectively). This difference in SMGC content corresponded with differences in the number of predicted open reading frames (ORFs) per genome (7775 ± 196 and 7093 ± 205, mean and S.D., respectively) such that the ratio of SMGC:ORF did not differ between sister-taxa genomes. We show that changes in SMGC diversity between the sister-taxa were driven primarily by gene acquisition and deletion events, and these changes were associated with an overall change in genome size which accompanied lineage divergence.
Serum 25-hydroxyvitamin D concentrations and related dietary factors in peri- and postmenopausal Japanese women.

BACKGROUND Few studies of vitamin D nutrition in Asian populations have been conducted. OBJECTIVE The objective was to assess 25-hydroxyvitamin D [25(OH)D] concentrations in healthy elderly Japanese women during the winter and to determine whether 25(OH)D concentrations are associated with lifestyle. DESIGN We investigated 151 women aged 66.5 +/- 6.7 y (f1.gif" BORDER="0"> +/- SD) living in a rural community in February 1999. Serum 25(OH)D and intact parathyroid hormone were measured by using HPLC and an immunoradiometric assay, respectively. Information on lifestyle factors, including sunshine exposure and the consumption of vitamin D-rich foods, was also obtained through an interview. RESULTS The mean (+/-SD) 25(OH)D concentration was 59.9 +/- 17.0 nmol/L. Vitamin D insufficiencies (<30 nmol/L) were found in 4.6% of the women, a value lower than that found in white populations. No correlation was found between age and 25(OH)D concentrations (r = 0.004, P = 0.957). The 25(OH)D concentration of subjects who consumed fish frequently (>/=4 times/wk) was 10.1 nmol/L higher (P < 0.001) than that of subjects with a moderate consumption of fish (1-3 times/wk). Additionally, those who did not consume eggs had significantly lower 25(OH)D concentrations than did those who consumed eggs >/=1 time/wk (P < 0.05). CONCLUSIONS : The nutritional status of vitamin D in Japanese populations seems to be better than that in most Western populations. Frequent fish consumption is believed to help maintain adequate concentrations of serum 25(OH)D in elderly Japanese women during the winter.
Global risk model for vector-borne transmission of Zika virus reveals the role of El Niño 2015

Significance This study quantifies the impact of climate variability on Zika virus (ZIKV) transmission by two mosquito vectors with distinct characteristics: Aedes aegypti and Aedes albopictus. Observed climate data were used to dynamically drive a two vectors–one host R0 epidemiological model. Our modeling results indicate that temperature conditions related to the 2015 El Niño climate phenomenon were exceptionally conducive for mosquito-borne transmission of ZIKV over South America. The virus is believed to have entered the continent earlier in 2013. This finding implicates that such a large ZIKV outbreak occurred not solely because of the introduction of ZIKV in a naive population, but because the climatic conditions were optimal for mosquito-borne transmission of ZIKV over South America in 2015. Zika, a mosquito-borne viral disease that emerged in South America in 2015, was declared a Public Health Emergency of International Concern by the WHO in February of 2016. We developed a climate-driven R0 mathematical model for the transmission risk of Zika virus (ZIKV) that explicitly includes two key mosquito vector species: Aedes aegypti and Aedes albopictus. The model was parameterized and calibrated using the most up to date information from the available literature. It was then driven by observed gridded temperature and rainfall datasets for the period 1950–2015. We find that the transmission risk in South America in 2015 was the highest since 1950. This maximum is related to favoring temperature conditions that caused the simulated biting rates to be largest and mosquito mortality rates and extrinsic incubation periods to be smallest in 2015. This event followed the suspected introduction of ZIKV in Brazil in 2013. The ZIKV outbreak in Latin America has very likely been fueled by the 2015–2016 El Niño climate phenomenon affecting the region. The highest transmission risk globally is in South America and tropical countries where Ae. aegypti is abundant. Transmission risk is strongly seasonal in temperate regions where Ae. albopictus is present, with significant risk of ZIKV transmission in the southeastern states of the United States, in southern China, and to a lesser extent, over southern Europe during the boreal summer season.
Diffusible cytokinin repression establishes symmetry and passage cells in the endodermis

Summary The root endodermis surrounds the central vasculature as a protective sheath, analogous to an animal polarised epithelium, and restricts diffusion by its ring-shaped Casparian strips (CS)1. Following a lag phase, individual endodermal cells suberise in an apparently random fashion, leading to a “patchy” suberisation that eventually gives rise to a zone of continuous deposition2. Casparian strips and suberin lamellae affect paracellular and transcellular transport, respectively. Interestingly, most angiosperms maintain some isolated cells in an unsuberised state3. These so-called “passage cells” are speculated to allow uptake across an otherwise impermeable endodermal barrier. Here, we demonstrate that these passage cells are late emanations of a meristematic patterning process that reads-out the underlying non-radial symmetry of the vasculature. This process is mediated by non-cell autonomous cytokinin repression in the root meristem, leading to distinct phloem and xylem pole-associated endodermal cells. The latter can resist ABA-dependent suberisation and give rise to passage cell formation. Our data further demonstrate that during meristematic patterning, xylem pole-associated endodermal cells can dynamically adapt passage cell numbers in response to nutrient status and that passage cells express transporters and locally impact their expression in adjacent cortical cells.
Radiosensitization by the ATR Inhibitor AZD6738 through Generation of Acentric Micronuclei

AZD6738 is an orally active ATR inhibitor (ATRi) currently in phase I clinical trials. We found in vitro growth inhibitory activity of this ATRi in a panel of human cancer cell lines. We demonstrated radiosensitization by AZD6738 to single radiation fractions in multiple cancer cell lines independent of both p53 and BRCA2 status by the clonogenic assay. Radiosensitization by AZD6738 to clinically relevant doses of fractionated radiation was demonstrated in vitro using a 3D tumor spheroid model and, in vivo, AZD6738 radiosensitized by abrogating the radiation-induced G2 cell-cycle checkpoint and inhibiting homologous recombination. Mitosis with damaged DNA resulted in mitotic catastrophe as measured by micronucleus formation by live-cell fluorescent-ubiquitination cell-cycle imaging of cell-cycle progression and nuclear morphology. Induction of micronuclei was significantly more prominent for AZD6738 compared with inhibition of the downstream kinase CHK1 alone at isoeffective doses. Micronuclei were characterized as acentric chromosomal fragments, which displayed characteristics of increased DNA damage and cell-cycle dyssynchrony when compared with the primary nucleus. Mol Cancer Ther; 16(1); 25–34. ©2016 AACR.
Targeting the diuretic hormone receptor to control the cotton leafworm, Spodoptera littoralis

Abstract The cotton leafworm, Spodoptera littoralis Boisduval (Lepidoptera: Noctuidae), is one of the most devastating pests of crops worldwide. Several types of treatments have been used against this pest, but many of them failed because of the rapid development of genetic resistance in the different insect populations. G protein coupled receptors have vital functions in most organisms, including insects; thus, they are appealing targets for species-specific pest control strategies. Among the insect G protein coupled receptors, the diuretic hormone receptors have several key roles in development and metabolism, but their importance in vivo and their potential role as targets of novel pest control strategies are largely unexplored. With the goal of using DHR genes as targets to control S. littoralis, we cloned a corticotropin-releasing factor-like binding receptor in this species and expressed the corresponding dsRNA in tobacco plants to knock down the receptor activity in vivo through RNA interference. We also expressed the receptor in mammalian cells to study its signaling pathways. The results indicate that this diuretic hormone receptor gene has vital roles in S. littoralis and represents an excellent molecular target to protect agriculturallyimportant plants from this pest.
Ichthyosis fetalis in Polled Hereford and Shorthorn calves

Inherited forms of ichthyosis, or generalized scaling of the skin, have been reported in many animal species, including cattle, and are characterized by an autosomal recessive mode of inheritance. We investigated 2 calves affected with ichthyosis fetalis, a Polled Hereford and a Shorthorn. Both cases had hard white plaques on the skin consistent with excessive keratinization. This was confirmed by histopathology, which showed severe diffuse epidermal and follicular orthokeratotic hyperkeratosis. The known mutation (H1935R) in gene ABCA12, responsible for ichthyosis fetalis in Chianina cattle, was shown to be absent in both affected calves and their obligate heterozygous parents. These molecular findings indicate that allelic heterogeneity exists for this condition in cattle.
Dissection of neuronal gap junction circuits that regulate social behavior in Caenorhabditis elegans

Significance Electrical coupling through gap junctions is an important form of neuronal communication, but methods to interrogate electrical coupling are limited. We identified the UNC-9 gap junction protein (innexin) as an essential component of a circuit that regulates social aggregation and related behaviors in Caenorhabditis elegans. By transgenic expression of dominant-negative UNC-1 stomatin and rescue with gain-of-function UNC-9::GFP, we selectively interrogated and restored gap junction coupling between neurons, allowing fine dissection of the neuronal circuit for social behavior. A hub-and-spoke circuit of neurons connected by gap junctions controls aggregation behavior and related behavioral responses to oxygen, pheromones, and food in Caenorhabditis elegans. The molecular composition of the gap junctions connecting RMG hub neurons with sensory spoke neurons is unknown. We show here that the innexin gene unc-9 is required in RMG hub neurons to drive aggregation and related behaviors, indicating that UNC-9–containing gap junctions mediate RMG signaling. To dissect the circuit in detail, we developed methods to inhibit unc-9–based gap junctions with dominant-negative unc-1 transgenes. unc-1(dn) alters a stomatin-like protein that regulates unc-9 electrical signaling; its disruptive effects can be rescued by a constitutively active UNC-9::GFP protein, demonstrating specificity. Expression of unc-1(dn) in RMG hub neurons, ADL or ASK pheromone-sensing neurons, or URX oxygen-sensing neurons disrupts specific elements of aggregation-related behaviors. In ADL, unc-1(dn) has effects opposite to those of tetanus toxin light chain, separating the roles of ADL electrical and chemical synapses. These results reveal roles of gap junctions in a complex behavior at cellular resolution and provide a tool for similar exploration of other gap junction circuits.
Ornithine restores ureagenesis capacity and mitigates hyperammonemia in Otcspf‐ash mice

We have previously shown that Otcspf‐ash mice, a model of ornithine transcarbamylase deficiency, were able to sustain ureagenesis at the same rate as control mice, despite vestigial enzyme activity, when a complete mixture of amino acids was provided. To study the effect of ornithine supplementation (Orn; 316 μmol kg−1 h−1) on urea and glutamine kinetics in conscious Otcspf‐ash mice under a glycine‐alanine load (86 mg N kg−1 h−1), a multiple isotope infusion protocol was conducted. 13C18O urea, 15N (amido) glutamine, 2H5 glutamine and 2H5 phenylalanine were infused for 4 h. Orn restored ureagenesis (3.18 vs 4.56 mmol kg−1 h−1, P < 0.001), reduced plasma ammonia concentration (1125 vs 193 μM, P < 0.001) and prevented acute hepatic enlargement (P < 0.006) in Otcspf‐ash mice. Orn also increased (96 vs 120 μmol kg−1 h−1, P < 0.001) the transfer of 15N from glutamine to urea, to values observed in the control mice (123 μmol kg−1 h−1). Amido N glutamine flux increased (2.23 vs 3.65 mmol kg−1 h−1; P < 0.001) in Otcspf‐ash mice, but Orn had no effect (P < 0.23). The flux of glutamine carbon skeleton was affected by both genotype (P < 0.0001) and by Orn (P 0. 024). Phenylalanine flux was increased (P < 0.003) by Orn supplementation and there was a trend (P < 0.06) to further increase in supplemented Otcspf‐ash mice. In conclusion, Orn restored ureagenesis, mitigated hyperammonemia, prevented liver enlargement and normalized the transfer of 15N from glutamine to urea. These data strongly suggest that Orn has the potential for the biochemical correction of OTCD in Otcspf‐ash mice.
New horizons: the management of hypertension in people with dementia.

The optimal management of hypertension in people with dementia is uncertain. This review explores if people with dementia experience greater adverse effects from antihypertensive medications, if cognitive function is protected or worsened by controlling blood pressure (BP) and if there are subgroups of people with dementia for whom antihypertensive therapy is more likely to be harmful. Robust evidence is scant, trials of antihypertensive medications have generally excluded those with dementia. Observational data show changes in risk association over the life course, with high BP being a risk factor for cognitive decline in mid-life, while low BP is predictive in later life. It is therefore possible that excessive BP lowering in older people with dementia might harm cognition. From the existing literature, there is no direct evidence of benefit or harm from treating hypertension in people with dementia. So what practical steps can the clinician take? Assess capacity, establish patient preferences when making treatment decisions, use ambulatory monitoring to thoroughly assess BP, individualise and consider deprescribing where side effects (e.g. hypotension) outweigh the benefits. Future research might include pragmatic randomised trials of targeted deprescribing, which include patient-centred outcome measures to help support decision-making and studies to address mechanistic uncertainties.
Reporting and Handling of Indeterminate Bone Scan Results in the Staging of Prostate Cancer: A Systematic Review

Bone scintigraphy is key in imaging skeletal metastases in newly diagnosed prostate cancer. Unfortunately, a notable proportion of scans are not readily classified as positive or negative but deemed indeterminate. The extent of reporting of indeterminate bone scans and how such scans are handled in clinical trials are not known. A systematic review was conducted using electronic databases up to October 2016. The main outcome of interest was the reporting of indeterminate bone scans, analyses of how such scans were managed, and exploratory analyses of the association of study characteristics and the reporting of indeterminate bone scan results. Seventy-four eligible clinical trials were identified. The trials were mostly retrospective (85%), observational (95%), large trials (median 195 patients) from five continents published over four decades. The majority of studies had university affiliation (72%), and an author with imaging background (685). Forty-five studies (61%) reported an indeterminate option for the bone scan and 23 studies reported the proportion of indeterminate scans (median 11.4%). Most trials (44/45, 98%) reported how to handle indeterminate scans. Most trials (n = 39) used add-on supplementary imaging, follow-up bone scans, or both. Exploratory analyses showed a significant association of reporting of indeterminate results and number of patients in the study (p = 0.024) but failed to reach statistical significance with other variables tested. Indeterminate bone scan for staging of prostate cancer was insufficiently reported in clinical trials. In the case of indeterminate scans, most studies provided adequate measures to obtain the final status of the patients.
Validity and reliability of GPS and LPS for measuring distances covered and sprint mechanical properties in team sports

This study aimed to investigate the validity and reliability of global (GPS) and local (LPS) positioning systems for measuring distances covered and sprint mechanical properties in team sports. Here, we evaluated two recently released 18 Hz GPS and 20 Hz LPS technologies together with one established 10 Hz GPS technology. Six male athletes (age: 27±2 years; VO2max: 48.8±4.7 ml/min/kg) performed outdoors on 10 trials of a team sport-specific circuit that was equipped with double-light timing gates. The circuit included various walking, jogging, and sprinting sections that were performed either in straight-lines or with changes of direction. During the circuit, athletes wore two devices of each positioning system. From the reported and filtered velocity data, the distances covered and sprint mechanical properties (i.e., the theoretical maximal horizontal velocity, force, and power output) were computed. The sprint mechanical properties were modeled via an inverse dynamic approach applied to the center of mass. The validity was determined by comparing the measured and criterion data via the typical error of estimate (TEE), whereas the reliability was examined by comparing the two devices of each technology (i.e., the between-device reliability) via the coefficient of variation (CV). Outliers due to measurement errors were statistically identified and excluded from validity and reliability analyses. The 18 Hz GPS showed better validity and reliability for determining the distances covered (TEE: 1.6–8.0%; CV: 1.1–5.1%) and sprint mechanical properties (TEE: 4.5–14.3%; CV: 3.1–7.5%) than the 10 Hz GPS (TEE: 3.0–12.9%; CV: 2.5–13.0% and TEE: 4.1–23.1%; CV: 3.3–20.0%). However, the 20 Hz LPS demonstrated superior validity and reliability overall (TEE: 1.0–6.0%; CV: 0.7–5.0% and TEE: 2.1–9.2%; CV: 1.6–7.3%). For the 10 Hz GPS, 18 Hz GPS, and 20 Hz LPS, the relative loss of data sets due to measurement errors was 10.0%, 20.0%, and 15.8%, respectively. This study shows that 18 Hz GPS has enhanced validity and reliability for determining movement patterns in team sports compared to 10 Hz GPS, whereas 20 Hz LPS had superior validity and reliability overall. However, compared to 10 Hz GPS, 18 Hz GPS and 20 Hz LPS technologies had more outliers due to measurement errors, which limits their practical applications at this time.