Miracle-dz/UniFAR-FTUs huggingface dataset:
Laboratory maintenance does not alter ecological and physiological patterns among species: a Drosophila case study

Large comparative studies in animal ecology, physiology and evolution often use animals reared in the laboratory for many generations; however, the relevance of these studies hinges on the assumption that laboratory populations are still representative for their wild living conspecifics. In this study, we investigate whether laboratory‐maintained and freshly collected animal populations are fundamentally different and whether data from laboratory‐maintained animals are valid to use in large comparative investigations of ecological and physiological patterns. Here, we obtained nine species of Drosophila with paired populations of laboratory‐maintained and freshly collected flies. These species, representing a range of ecotypes, were assayed for four stress‐tolerance, two body‐size traits and six life‐history traits. For all of these traits, we observed small differences in species‐specific comparisons between field and laboratory populations; however, these differences were unsystematic and laboratory maintenance did not eclipse fundamental species characteristics. To investigate whether laboratory maintenance influence the general patterns in comparative studies, we correlated stress tolerance and life‐history traits with environmental traits for the laboratory‐maintained and freshly collected populations. Based on this analysis, we found that the comparative physiological and ecological trait correlations are similar irrespective of provenience. This finding is important for comparative biology in general because it validates comparative meta‐analyses based on laboratory‐maintained populations.
Secondary Prevention of Alcohol Problems in Rural Areas Using a Bibliotherapy-Based Approach

This study investigated the relative effects of 3 12-week secondary prevention interventions for problem drinking men and women in rural counties in New York State. The participants were 111 self-referred men and women without severe dependence on alcohol who nevertheless reported heavy drinking and a desire to reduce their alcohol consumption. They were assigned randomly to 1 of 3 12-week interventions focused on reducing alcohol intake: bibliotherapy (a self-directed manual) alone, bibliotherapy with 1 telephone-administered motivational interview, or bibliotherapy with 1 telephone-administered motivational interview and 6 biweekly telephone therapy sessions. Results showed that, across conditions, participants significantly increased their abstinent and light drinking days and significantly decreased their heavy drinking days over the course of treatment and a 12-month follow-up period. In addition, participants reported moderate reductions in alcohol consequences and increases in confidence not to drink heavily across a variety of situations from pre- to posttreatment, with these changes remaining stable across the course of the follow-up. Use of the drinking reduction strategies presented in the self-directed manual also remained stable from posttreatment to the 12-month follow-up. These results provide support for consideration of bibliotherapy for rural problem drinkers who are not severely dependent on alcohol, with or without the addition of telephone contacts.
Amino acid modulation of dopamine in the nucleus accumbens mediates sex differences in nicotine withdrawal

The aversive effect of nicotine withdrawal is greater in female versus male rats, and we postulate that this sex difference is mediated in the nucleus accumbens (NAc). Nicotine withdrawal induces decreases in NAc dopamine and increases in acetylcholine (ACh) levels in male rats. To our knowledge, these neurochemical markers of nicotine withdrawal have not been compared in female versus male rats. Given the role of amino acids in modulating NAc dopaminergic and cholinergic transmission, concomitant measures of gamma‐aminobutyric acid (GABA) and glutamate levels were also compared across sex. Rats received continuous nicotine exposure for 14 days, and then NAc dialysate was collected during baseline and following administration of the nicotinic receptor antagonist mecamylamine to precipitate withdrawal. Chronic nicotine exposure was associated with larger increases in baseline dopamine, GABA and glutamate levels in the NAc of female versus male rats, whereas baseline ACh was only increased in male rats. During withdrawal, both sexes displayed equivalent increases in NAc ACh levels. As expected, male rats displayed decreases in dopamine, coupled with increases in GABA and decreases in glutamate levels, suggesting the possibility of increased inhibitory tone in the NAc during withdrawal. Relative to males, female rats displayed larger decreases in NAc dopamine and related increases in GABAergic transmission. As female rats also showed elevated glutamate levels that persist during withdrawal, it is suggested that sex differences may arise from increased glutamatergic drive of inhibitory tone in the NAc. The findings provide a potential mechanism whereby the aversive effects of nicotine withdrawal are enhanced in female rats.
Cognitive Impairment, Dementia, and Personality Stability Among Older Adults

There is contrasting evidence on personality stability in advanced age, and limited knowledge on the impact of cognitive impairment and dementia on trait stability. Group- and individual-level longitudinal analyses of the five major dimensions of personality assessed twice over 4 years (N = 9,935) suggest that rank-order stability was progressively lower with advancing age (from rtt = 0.68 for age 50 to 60 years to rtt = 0.58 for age >80 years). Stability was low in the dementia group (rtt = 0.43), and this was not simply due to lower reliability given that internal consistency remained adequate in the dementia group. Among individuals with no cognitive impairment or dementia, there was no association between stability and age (rtt = 0.70 even for age >80 years). These results suggest that the lower personality stability in older adults is not due to age but cognitive impairment and dementia.
Resting-State Functional Connectivity in the Infant Brain: Methods, Pitfalls, and Potentiality

Early brain development is characterized by rapid growth and perpetual reconfiguration, driven by a dynamic milieu of heterogeneous processes. Postnatal brain plasticity is associated with increased vulnerability to environmental stimuli. However, little is known regarding the ontogeny and temporal manifestations of inter- and intra-regional functional connectivity that comprise functional brain networks. Resting-state functional magnetic resonance imaging (rs-fMRI) has emerged as a promising non-invasive neuroinvestigative tool, measuring spontaneous fluctuations in blood oxygen level dependent (BOLD) signal at rest that reflect baseline neuronal activity. Over the past decade, its application has expanded to infant populations providing unprecedented insight into functional organization of the developing brain, as well as early biomarkers of abnormal states. However, many methodological issues of rs-fMRI analysis need to be resolved prior to standardization of the technique to infant populations. As a primary goal, this methodological manuscript will (1) present a robust methodological protocol to extract and assess resting-state networks in early infancy using independent component analysis (ICA), such that investigators without previous knowledge in the field can implement the analysis and reliably obtain viable results consistent with previous literature; (2) review the current methodological challenges and ethical considerations associated with emerging field of infant rs-fMRI analysis; and (3) discuss the significance of rs-fMRI application in infants for future investigations of neurodevelopment in the context of early life stressors and pathological processes. The overarching goal is to catalyze efforts toward development of robust, infant-specific acquisition, and preprocessing pipelines, as well as promote greater transparency by researchers regarding methods used.
Importance of Fluctuations in Light on Plant Photosynthetic Acclimation1[CC-BY]

Fluctuating light influences acclimation in Arabidopsis independently of light intensity. The acclimation of plants to light has been studied extensively, yet little is known about the effect of dynamic fluctuations in light on plant phenotype and acclimatory responses. We mimicked natural fluctuations in light over a diurnal period to examine the effect on the photosynthetic processes and growth of Arabidopsis (Arabidopsis thaliana). High and low light intensities, delivered via a realistic dynamic fluctuating or square wave pattern, were used to grow and assess plants. Plants subjected to square wave light had thicker leaves and greater photosynthetic capacity compared with fluctuating light-grown plants. This, together with elevated levels of proteins associated with electron transport, indicates greater investment in leaf structural components and photosynthetic processes. In contrast, plants grown under fluctuating light had thinner leaves, lower leaf light absorption, but maintained similar photosynthetic rates per unit leaf area to square wave-grown plants. Despite high light use efficiency, plants grown under fluctuating light had a slow growth rate early in development, likely due to the fact that plants grown under fluctuating conditions were not able to fully utilize the light energy absorbed for carbon fixation. Diurnal leaf-level measurements revealed a negative feedback control of photosynthesis, resulting in a decrease in total diurnal carbon assimilated of at least 20%. These findings highlight that growing plants under square wave growth conditions ultimately fails to predict plant performance under realistic light regimes and stress the importance of considering fluctuations in incident light in future experiments that aim to infer plant productivity under natural conditions in the field.
Demography of a forest elephant population

African forest elephants face severe threats from illegal killing for ivory and bushmeat and habitat conversion. Due to their cryptic nature and inaccessible range, little information on the biology of this species has been collected despite its iconic status. Compiling individual based monitoring data collected over 20 years from the Dzanga Bai population in Central African Republic, we summarize sex and age specific survivorship and female age specific fecundity for a cohort of 1625 individually identified elephants. Annual mortality (average = 3.5%) and natality (average = 5.3%) were lower and markedly less variable relative to rates reported for savanna elephant populations. New individuals consistently entered the study system, leading to a 2.5% average annual increase in the registered population. Calf sex ratios among known birth did not differ from parity. A weak seasonal signal in births was detected suggesting increased conceptions during the wet season. Inter-calf intervals and age of primiparity were longer relative to savanna elephant populations. Within the population, females between the ages of 25–39 demonstrated the shortest inter-calf intervals and highest fecundity, and previous calf sex had no influence on the interval. Calf survivorship was high (97%) the first two years after birth and did not differ by sex. Male and female survival began to differ by the age of 13 years, and males demonstrated significantly lower survival relative to females by the age of 20. It is suspected these differences are driven by human selection for ivory. Forest elephants were found to have one of the longest generation times recorded for any species at 31 years. These data provide fundamental understanding of forest elephant demography, providing baseline data for projecting population status and trends.
The Selective Serotonin Reuptake Inhibitor Fluoxetine Directly Inhibits Osteoblast Differentiation and Mineralization During Fracture Healing in Mice

Chronic use of selective serotonin reuptake inhibitors (SSRIs) for the treatment of depression has been linked to osteoporosis. In this study, we investigated the effect of chronic SSRI use on fracture healing in two murine models of bone regeneration. First, we performed a comprehensive analysis of endochondral bone healing in a femur fracture model. C57/BL6 mice treated with fluoxetine, the most commonly prescribed SSRI, developed a normal cartilaginous soft‐callus at 14 days after fracture and demonstrated a significantly smaller and biomechanically weaker bony hard‐callus at 28 days. In order to further dissect the mechanism that resulted in a smaller bony regenerate, we used an intramembranous model of bone healing and revealed that fluoxetine treatment resulted in a significantly smaller bony callus at 7 and 14 days postinjury. In order to test whether the smaller bony regenerate following fluoxetine treatment was caused by an inhibition of osteogenic differentiation and/or mineralization, we employed in vitro experiments, which established that fluoxetine treatment decreases osteogenic differentiation and mineralization and that this effect is serotonin‐independent. Finally, in a translational approach, we tested whether cessation of the medication would result in restoration of the regenerative potential. However, histologic and μCT analysis revealed non‐union formation in these animals with fibrous tissue interposition within the callus. In conclusion, fluoxetine exerts a direct, inhibitory effect on osteoblast differentiation and mineralization, shown in two disparate murine models of bone repair. Discontinuation of the drug did not result in restoration of the healing potential, but rather led to complete arrest of the repair process. Besides the well‐established effect of SSRIs on bone homeostasis, our study provides strong evidence that fluoxetine use negatively impacts fracture healing. © 2017 American Society for Bone and Mineral Research.
Frameless stereotactic body radiation therapy for multiple lung metastases

Two patients with multiple lung metastases (≥ 5) were treated using frameless stereotactic body radiation therapy (SBRT) on an Elekta Axesse linear accelerator equipped with an interdigitation‐capable multileaf collimator and four‐dimensional cone‐beam CT (4D CBCT). The technique and the early clinical outcomes were evaluated. Patient A with five lung metastases and Patient B with seven lung metastases underwent SBRT (48 Gy/8 fractions for Patient A, 42 Gy/7 fractions for Patient B). The treatments were administered using a 6 MV photon beam. The nominal dose rate was 660 MUs/min. Patients were positioned and immobilized using thermoplastic masks and image guidance was done using 4D CBCT. The targets were delineated on the images of the 4D CT, and the positron emission tomography‐computed tomography (PET‐CT) images were taken as references. A two‐step, volumetric‐modulated arc therapy (VMAT) plan was designed for each patient. Step 1: the lesions in one lung were irradiated by a 210° arc field; Step 2: the rest of the lesions in the other lung were irradiated by a 120° arc field. Plans were evaluated using conformity index (CI) and homogeneity index (HI). Patients were followed up and adverse events were graded according to the Common Terminology Criteria for Adverse Events v4.0 (CTCAE v4.0). The beam‐on time of each treatment was less than 10 min. The CI and HI for the two plans were 0.562, 0.0709 and 0.513, 0.0794, respectively. Pulmonary function deteriorated slightly in both patients, and the patient with seven lung lesions was confirmed to have Grade 1 radiation pneumonitis. The technique was fast, accurate, and well tolerated by patients, and the two‐step plan is a helpful design in reducing the dose to the lungs. PACS numbers: 87.55‐x, 87.56. J‐, 87.56. ‐v, 87.56. nk, 87.57. qp
Use of Hydroxychloroquine Is Associated With Improved Lipid Profile in Rheumatoid Arthritis Patients

Background/Purpose We examined the association between hydroxychloroquine (HCQ) and plasma lipid and glucose levels in rheumatoid arthritis (RA) cohort. Methods This is a retrospective cohort analysis of 1261 RA patients comparing fasting lipid profiles and plasma glucose between patients who were and were not taking HCQ. We divided patients into 3 groups based on HCQ exposure during follow-up: those who had never taken HCQ, those who took it intermittently, and those who took it continuously. We used multivariable models and propensity scoring to compensate for the effect of nonrandom treatment assignment. Results We followed 1261 RA patients for a total of 4605 observations between 1996 and 2014. After adjusting for age, sex, ethnicity, other disease-modifying antirheumatic drugs (DMARDs), lipid-lowering medications, body mass index (BMI), and smoking, patients taking HCQ at baseline had significantly lower total cholesterol (TC) (P ⩽ 0.001), low-density lipoprotein (LDL) (P ⩽ 0.001), triglycerides (P = 0.013), and lipid profile ratios TC/high-density lipoprotein (HDL) (P ⩽ 0.001) and LDL/HDL (P ⩽ 0.001), as well as higher HDL (P ⩽ 0.001). In longitudinal analyses, after adjusting for confounders, patients who continuously took HCQ showed significantly lower TC, LDL, TC/HDL, and LDL/HDL and higher HDL (P ⩽ 0.01). Fasting plasma glucose levels were not significantly associated with HCQ exposure. Conclusions Hydroxychloroquine use was associated with lower lipid levels but not with the plasma glucose in this RA cohort. These findings support the need for a randomized trial to establish the role of HCQ in cardiovascular disease prevention in RA patients.
Increased fire frequency promotes stronger spatial genetic structure and natural selection at regional and local scales in Pinus halepensis Mill

Background and Aims The recurrence of wildfires is predicted to increase due to global climate change, resulting in severe impacts on biodiversity and ecosystem functioning. Recurrent fires can drive plant adaptation and reduce genetic diversity; however, the underlying population genetic processes have not been studied in detail. In this study, the neutral and adaptive evolutionary effects of contrasting fire regimes were examined in the keystone tree species Pinus halepensis Mill. (Aleppo pine), a fire-adapted conifer. The genetic diversity, demographic history and spatial genetic structure were assessed at local (within-population) and regional scales for populations exposed to different crown fire frequencies. Methods Eight natural P. halepensis stands were sampled in the east of the Iberian Peninsula, five of them in a region exposed to frequent crown fires (HiFi) and three of them in an adjacent region with a low frequency of crown fires (LoFi). Samples were genotyped at nine neutral simple sequence repeats (SSRs) and at 251 single nucleotide polymorphisms (SNPs) from coding regions, some of them potentially important for fire adaptation. Key Results Fire regime had no effects on genetic diversity or demographic history. Three high-differentiation outlier SNPs were identified between HiFi and LoFi stands, suggesting fire-related selection at the regional scale. At the local scale, fine-scale spatial genetic structure (SGS) was overall weak as expected for a wind-pollinated and wind-dispersed tree species. HiFi stands displayed a stronger SGS than LoFi stands at SNPs, which probably reflected the simultaneous post-fire recruitment of co-dispersed related seeds. SNPs with exceptionally strong SGS, a proxy for microenvironmental selection, were only reliably identified under the HiFi regime. Conclusions An increasing fire frequency as predicted due to global change can promote increased SGS with stronger family structures and alter natural selection in P. halepensis and in plants with similar life history traits.
Comparison of Rumen and Manure Microbiomes and Implications for the Inoculation of Anaerobic Digesters

Cattle manure is frequently used as an inoculum for the start-up of agricultural biogas plants or as a co-substrate in the anaerobic digestion of lignocellulosic feedstock. Ruminal microbiota are considered to be effective plant fiber degraders, but the microbes contained in manure do not necessarily reflect the rumen microbiome. The aim of this study was to compare the microbial community composition of cow rumen and manure with respect to plant fiber-digesting microbes. Bacterial and methanogenic communities of rumen and manure samples were examined by 454 amplicon sequencing of bacterial 16S rRNA genes and mcrA genes, respectively. Rumen fluid samples were dominated by Prevotellaceae (29%), whereas Ruminococcaceae was the most abundant family in the manure samples (31%). Fibrobacteraceae (12%) and Bacteroidaceae (13%) were the second most abundant families in rumen fluid and manure, respectively. The high abundances of fiber-degrading bacteria belonging to Prevotellaceae and Fibrobacteraceae might explain the better performance of anaerobic digesters inoculated with rumen fluid. Members of the genus Methanobrevibacter were the predominant methanogens in the rumen fluid, whereas methanogenic communities of the manure samples were dominated by the candidate genus Methanoplasma. Our results suggest that inoculation or bioaugmentation with fiber-digesting rumen microbiota can enhance the anaerobic digestion of lignocellulosic biomass.
A Multicenter Retrospective Analysis Evaluating Performance of Synovial Biopsy Techniques in Patients With Inflammatory Arthritis

To evaluate whether the choice of synovial biopsy technique (arthroscopy, blind needle [BN] biopsy, ultrasound [US]–guided portal and forceps [P&F], or US‐guided needle biopsy [NB]) translates to significant variation in synovial tissue quality and quantity, with the aim of informing recommendations for the choice of synovial sampling technique within clinical trials.
High endothelial venules associated with T cell subsets in the inflamed gut of newly diagnosed inflammatory bowel disease patients

Naive and central memory T lymphocytes (TN and TCM) can infiltrate the inflamed gut mucosa in inflammatory bowel disease (IBD) patients. Homing of these subsets to the gut might be explained by ectopic formation of tertiary lymphoid organs (TLOs), containing high endothelial venules (HEVs). We aimed to evaluate the presence of HEVs and TLOs in inflamed intestinal mucosa of newly diagnosed, untreated IBD patients in relation to the presence of TN and TCM lymphocytes. IBD patients (n = 39) and healthy controls (n = 8) were included prospectively. Biopsy samples of inflamed and normal intestine, respectively, were analysed by immunohistochemistry for lymphocytes (CD3/CD20), blood vessels (CD31) and peripheral lymph node addressin (PNAd) expression (MECA‐79). TN and TCM lymphocyte subsets were identified by flow cytometric immunophenotyping. A higher number of HEVs was found in the inflamed colon of patients with ulcerative colitis [median 3·05 HEV/mm2; interquartile range (IQR) = 0–6·39] and ileum of Crohn's disease patients (1·40; 0‐4·34) compared to healthy controls (both 0; P = 0·033). A high density of colonic HEVs (HEVhigh) was associated with increased infiltration of TN and TCM in the inflamed gut (median 87%; IQR = 82–93% of T cell population), compared to HEVlow patients (58%; 38–81%; P = 0·003). The number of colonic follicles was higher in HEVhigh patients (median 0·54/mm2; IQR 0·28–0·84) compared to HEVlow patients (0·25/mm2; 0·08–0·45; P = 0·031) and controls (0·31/mm2; 0·23–0·45; P = 0·043). Increased homing of TN and TCM lymphocytes to inflamed gut tissue in IBD patients might be facilitated by ectopic formation of extrafollicular HEVs and TLOs in a subgroup of patients.