Miracle-dz/UniFAR-FTUs huggingface dataset:
Long-term empirical evidence of ocean warming leading to tropicalization of fish communities, increased herbivory, and loss of kelp

Significance Most studies of the impact of global warming focus on the direct physiological impacts of climate change. However, global warming is shifting the distribution of many species and leading to novel interactions between previously separated species that have the potential to transform entire ecological communities. This study shows that an increase in the proportion of warmwater species (“tropicalization”) as oceans warm is increasing fish herbivory in kelp forests, contributing to their decline and subsequent persistence in alternate “kelp-free” states. These tropical and subtropical herbivores are increasingly impacting temperate algal communities worldwide, posing a significant threat to the long-term stability of these iconic ecosystems and the valuable services they provide. Some of the most profound effects of climate change on ecological communities are due to alterations in species interactions rather than direct physiological effects of changing environmental conditions. Empirical evidence of historical changes in species interactions within climate-impacted communities is, however, rare and difficult to obtain. Here, we demonstrate the recent disappearance of key habitat-forming kelp forests from a warming tropical–temperate transition zone in eastern Australia. Using a 10-y video dataset encompassing a 0.6 °C warming period, we show how herbivory increased as kelp gradually declined and then disappeared. Concurrently, fish communities from sites where kelp was originally abundant but subsequently disappeared became increasingly dominated by tropical herbivores. Feeding assays identified two key tropical/subtropical herbivores that consumed transplanted kelp within hours at these sites. There was also a distinct increase in the abundance of fishes that consume epilithic algae, and much higher bite rates by this group at sites without kelp, suggesting a key role for these fishes in maintaining reefs in kelp-free states by removing kelp recruits. Changes in kelp abundance showed no direct relationship to seawater temperatures over the decade and were also unrelated to other measured abiotic factors (nutrients and storms). Our results show that warming-mediated increases in fish herbivory pose a significant threat to kelp-dominated ecosystems in Australia and, potentially, globally.
Regulation of sodium transport in M-1 cells.

The M-1 cell line, derived from the mouse cortical collecting duct (CCD), is being used as a mammalian model of the CCD to study Na+ transport. The present studies aimed to further define the role of various hormones in affecting Na+ transport in M-1 cells grown in defined media. M-1 cells on permeable support, in serum-free media, developed amiloride-sensitive current 4-5 days after seeding. As expected for the involvement of epithelial Na+ channels, α-, β-, and γ-subunits of the epithelial Na+ channel were identified by RT-PCR. Either dexamethasone (Dex, 10-100 nM) or aldosterone (Aldo, 10-6-10-7M) for 24 h stimulated transport. Cells grown in the presence of Aldo and Dex had higher transport than with Dex alone. Spironolactone added to Dex media decreased transport. The acute effects of hormones reported to inhibit Na+ transport in CCD were also examined. Epidermal growth factor, phorbol esters, and increased intracellular Ca2+ with thapsigargin did not alter transport. Arginine vasopressin caused a transient increase in transport (probably Cl- secretion), which was not amiloride sensitive. Also, the protease inhibitor aprotinin decreased Na+ transport; in aprotinin-treated cells, trypsin stimulated transport. This study demonstrates that adrenal steroids (Dex > Aldo) stimulate Na+ transport in M-1 cells. At least part of this response may represent activation of mineralocorticoid receptors based on an additive effect of Dex and Aldo, as well as inhibition by spironolactone. Responses to immediate-acting hormones is limited. However, an endogenous protease activity, which activates Na+ transport, is present in these cells.
Fast, Flexible, Polyglot Instrumentation Support for Debuggers and other Tools

Context: Software development tools that interact with running programs such as debuggers, profilers, and dynamic analysis frameworks are presumed to demand difficult tradeoffs among implementation complexity (cost), functionality, usability, and performance. Among the many consequences, tools are often delivered late (if ever), have limited functionality, require non-standard configurations, and impose serious performance costs on running programs. Inquiry: Can flexible tool support become a practical, first class, intrinsic requirement for a modern highperformance programming language implementation framework? Approach: We extended the Truffle Language Implementation Framework, which together with the GraalVM execution environment makes possible very high performance language implementations. Truffle's new Instrumentation Framework is language-agnostic and designed to derive high performance from the same technologies as do language implementations. Truffle Instrumentation includes: (1) low overhead capture of execution events by dynamically adding "wrapper" nodes to executing ASTs; (2) extensions to the Language Implementation Framework that allow per-language specialization, primarily for visual display of values and names, among others; and (3) versatile APIs and support services for implementing many kinds of tools without VM modification. Knowledge: It is now possible for a client in a production environment to insert (dynamically, with thread safety) an instrumentation probe that captures and reports abstractly specified execution events. A probe in fully optimized code imposes very low overhead until actually used to access (or modify) execution state. Event capture has enabled construction of numerous GraalVM services and tools that work for all implemented languages, either singly or in combination. Instrumentation has also proved valuable for implementing some traditionally tricky language features, as well as some GraalVM services such as placing bounds on resources consumed by running programs. Grounding: Tools for debugging (via multiple clients), profiling, statement counting, dynamic analysis, and others are now part of GraalVM or are in active development. Third parties have also used Truffle Instrumentation for innovative tool implementations. Importance: Experience with Truffle Instrumentation validates the notion that addressing developer tools support as a forethought can change expectations about the availability of practical, efficient tools for high-performance languages. Tool development becomes a natural part of language implementation, requiring little additional effort and offering the advantage of early and continuous availability.
A novel bioassay to evaluate the potential of Beauveria bassiana strain NI8 and the insect growth regulator novaluron against Lygus lineolaris on a non-autoclaved solid artificial diet

Abstract A non-autoclaved solid diet was used to evaluate the entomopathogenic fungus Beauveria bassiana (Balsamo) Vuillemin (Hypocreales: Clavicipitaceae) strain NI8 and the insect growth regulator novaluron (Diamond® 0.83EC insecticide) for control of the tarnished plant bug, Lygus lineolaris (Palisot de Beauvois) (Hemiptera: Miridae). The diet was composed of toasted wheat germ, ground lima bean meal, soy flour, yolk of chicken eggs, inhibitor, and agar. It was prepared in one step by blending the ingredients in boiling water. The diet was used to bioassay L. lineolaris from the second instar to the adult stage. Fourth and fifth instars and adults of L. lineolaris were more susceptible than second and third instars to infection by B. bassiana, whereas second, third, and fourth instars had higher mortality than fifth instars 10 days after exposure to novaluron. No effects on longevity were observed in adults treated with novaluron when compared with the control, but longevity was significantly different from that of adults exposed to B. bassiana. Adults of L. lineolaris were maintained for over a month without changing the diet. The nonautoclaved diet is semi-liquid before it cools, which facilitates the mechanics of diet packaging similar to food packaging or lepidopteran diet preparation. This solid artificial diet for Lygus bugs provides improved research capacity for studying the ecology and susceptibility of Lygus spp. to a number of different control agents, including beneficial organisms, insect pathogens, and insecticidal toxins being developed for transgenic technologies.
Modeling of Patient-Derived Xenografts in Colorectal Cancer

Developing realistic preclinical models using clinical samples that mirror complex tumor biology and behavior are vital to advancing cancer research. While cell line cultures have been helpful in generating preclinical data, the genetic divergence between these and corresponding primary tumors has limited clinical translation. Conversely, patient-derived xenografts (PDX) in colorectal cancer are highly representative of the genetic and phenotypic heterogeneity in the original tumor. Coupled with high-throughput analyses and bioinformatics, these PDXs represent robust preclinical tools for biomarkers, therapeutic target, and drug discovery. Successful PDX engraftment is hypothesized to be related to a series of anecdotal variables namely, tissue source, cancer stage, tumor grade, acquisition strategy, time to implantation, exposure to prior systemic therapy, and genomic heterogeneity of tumors. Although these factors at large can influence practices and patterns related to xenotransplantation, their relative significance in determining the success of establishing PDXs is uncertain. Accordingly, we systematically examined the predictive ability of these factors in establishing PDXs using 90 colorectal cancer patient specimens that were subcutaneously implanted into immunodeficient mice. Fifty (56%) PDXs were successfully established. Multivariate analyses showed tissue acquisition strategy [surgery 72.0% (95% confidence interval (CI): 58.2–82.6) vs. biopsy 35% (95% CI: 22.1%–50.6%)] to be the key determinant for successful PDX engraftment. These findings contrast with current empiricism in generating PDXs and can serve to simplify or liberalize PDX modeling protocols. Better understanding the relative impact of these factors on efficiency of PDX formation will allow for pervasive integration of these models in care of colorectal cancer patients. Mol Cancer Ther; 16(7); 1435–42. ©2017 AACR.
Novel ABCG2 Antagonists Reverse Topotecan-Mediated Chemotherapeutic Resistance in Ovarian Carcinoma Xenografts

Chemotherapeutic resistance remains a challenge in the treatment of ovarian carcinoma, especially in recurrent disease. Despite the fact that most patients with newly diagnosed tumors attain complete remission following cytoreductive surgery and chemotherapy, ovarian carcinoma has a recurrence rate that exceeds 75%. The ATP-binding cassette family G member 2 (ABCG2) efflux protein has been described as one mechanism that confers multiple-drug resistance to solid tumors and contributes to topotecan resistance in ovarian carcinoma. In fact, one clinical trial demonstrated ABCG2 expression in all patients with primary or recurrent ovarian carcinoma. On the basis of our previous work, we hypothesized that three compounds (CID44640177, CID1434724, and CID46245505), which represent a new piperazine-substituted pyrazolo[1,5]pyrimidine substructure class of ABCG2-specific antagonists, would restore chemosensitivity to drug-resistant ovarian cancer in vitro and in vivo. To address the treatment difficulties associated with chemotherapeutic resistance in ovarian cancer, we combined each compound (CID44640177, CID1434724, and CID46245505) with topotecan and administered the mixture to chemoresistant Igrov1/T8 ovarian cancer cells in vitro and Igrov1/T8 xenografts in CB-17 SCID mice. We found that only nanomolar concentrations of each ABCG2 inhibitor in combination with topotecan were required to restore chemosensitivity to Igrov1/T8 cells in vitro. In vivo, substantial tumor reduction was achieved with each compound in 4 days, with CID1434724 causing the largest reduction in excess of 60%. No signs of secondary toxic effects were observed with the ABCG2 antagonists. These novel compounds should be viewed as promising drug candidates to reverse ABCG2-mediated chemoresistance. Mol Cancer Ther; 15(12); 2853–62. ©2016 AACR.
Quantitative parameters and ecological implications of a specialized tritrophic interaction involving a seed-feeding tortricid, Pseudargyrotoza conwagana, a braconid parasitoid, Bracon otiosus, and the wild privet, Ligustrum vulgare

Abstract Little is known about tritrophic interactions involving seed-feeding insects, parasitoid wasps, and wild fleshy fruits. Here, we examine relationships between Pseudargyrotoza conwagana (F.) (Lepidoptera: Tortricidae), Bracon otiosus Marshall (Hymenoptera: Braconidae), and the wild privet, Ligustrum vulgare L. (Lamiales: Oleaceae), after collecting fruits in a hedgerow habitat in northwest Spain and rearing insects indoors. No other insect species was detected in this trophic system. Each fruit contained one to four seeds, each infested fruit contained only one seedfeeding tortricid caterpillar, and each parasitized caterpillar was affected by a single braconid individual, i.e., B. otiosus was a solitary parasitoid. Almost half of the wild privet shrubs were infested by P. conwagana, and infestation ranged from 2 to 32% of fruits per infested shrub. The general effect of P.conwagana on wild privet dispersal can be considered low, as the overall rate of seed infestation was low (6% of seeds). The infestation rate was higher in wild privet shrubs with a larger number of seeds per fruit, and tortricid caterpillars that left the fruits successfully ate >80% of seeds. In total, the parasitism rate was moderate (25% of caterpillars), but varied considerably (0–75%) among shrubs where P. conwagana infestation was detected. Parasitism only occurred in shrubs showing high infestation rates (19–32% infested fruits), i.e., with high host densities; however, the parasitism rate was densityindependent in these shrubs. The wild privets benefited from the action of B. otiosus in two ways: the tortricid caterpillar population was partly eliminated, and the caterpillars were prevented from eating more than one seed per fruit. The B. otiosus sex ratio was very balanced (1 male to 1.18 females). Winter diapause and protandry were prevalent in B. otiosus.
Extracting aerobic system dynamics during unsupervised activities of daily living using wearable sensor machine learning models.

Physical activity levels are related through algorithms to the energetic demand, with no information regarding the integrity of the multiple physiological systems involved in the energetic supply. Longitudinal analysis of the oxygen uptake (V̇o2) by wearable sensors in realistic settings might permit development of a practical tool for the study of the longitudinal aerobic system dynamics (i.e., V̇o2 kinetics). This study evaluated aerobic system dynamics based on predicted V̇o2 data obtained from wearable sensors during unsupervised activities of daily living (μADL). Thirteen healthy men performed a laboratory-controlled moderate exercise protocol and were monitored for ≈6 h/day for 4 days (μADL data). Variables derived from hip accelerometer (ACCHIP), heart rate monitor, and respiratory bands during μADL were extracted and processed by a validated random forest regression model to predict V̇o2. The aerobic system analysis was based on the frequency-domain analysis of ACCHIP and predicted V̇o2 data obtained during μADL. Optimal samples for frequency domain analysis (constrained to ≤0.01 Hz) were selected when ACCHIP was higher than 0.05 g at a given frequency (i.e., participants were active). The temporal characteristics of predicted V̇o2 data during μADL correlated with the temporal characteristics of measured V̇o2 data during laboratory-controlled protocol ([Formula: see text] = 0.82, P < 0.001, n = 13). In conclusion, aerobic system dynamics can be investigated during unsupervised activities of daily living by wearable sensors. Although speculative, these algorithms have the potential to be incorporated into wearable systems for early detection of changes in health status in realistic environments by detecting changes in aerobic response dynamics. NEW & NOTEWORTHY The early detection of subclinical aerobic system impairments might be indicative of impaired physiological reserves that impact the capacity for physical activity. This study is the first to use wearable sensors in unsupervised activities of daily living in combination with novel machine learning algorithms to investigate the aerobic system dynamics with the potential to contribute to models of functional health status and guide future individualized health care in the normal population.
Validity, Reliability, and Inertia of Four Different Temperature Capsule Systems

Purpose Telemetric temperature capsule systems are wireless, relatively noninvasive, and easily applicable in field conditions and have therefore great advantages for monitoring core body temperature. However, the accuracy and responsiveness of available capsule systems have not been compared previously. Therefore, the aim of this study was to examine the validity, reliability, and inertia characteristics of four ingestible temperature capsule systems (i.e., CorTemp, e-Celsius, myTemp, and VitalSense). Methods Ten temperature capsules were examined for each system in a temperature-controlled water bath during three trials. The water bath temperature gradually increased from 33°C to 44°C in trials 1 and 2 to assess the validity and reliability, and from 36°C to 42°C in trial 3 to assess the inertia characteristics of the temperature capsules. Results A systematic difference between capsule and water bath temperature was found for CorTemp (0.077°C ± 0.040°C), e-Celsius (−0.081°C ± 0.055°C), myTemp (−0.003°C ± 0.006°C), and VitalSense (−0.017°C ± 0.023°C; P < 0.010), with the lowest bias for the myTemp system (P < 0.001). A systematic difference was found between trial 1 and trial 2 for CorTemp (0.017°C ± 0.083°C; P = 0.030) and e-Celsius (−0.007°C ± 0.033°C; P = 0.019), whereas temperature values of myTemp (0.001°C ± 0.008°C) and VitalSense (0.002°C ± 0.014°C) did not differ (P > 0.05). Comparable inertia characteristics were found for CorTemp (25 ± 4 s), e-Celsius (21 ± 13 s), and myTemp (19 ± 2 s), whereas the VitalSense system responded more slowly (39 ± 6 s) to changes in water bath temperature (P < 0.001). Conclusions Although differences in temperature and inertia were observed between capsule systems, an excellent validity, test–retest reliability, and inertia was found for each system between 36°C and 44°C after removal of outliers.
Interactive graph-cut segmentation for fast creation of finite element models from clinical ct data for hip fracture prediction

Abstract In this study, we propose interactive graph cut image segmentation for fast creation of femur finite element (FE) models from clinical computed tomography scans for hip fracture prediction. Using a sample of N = 48 bone scans representing normal, osteopenic and osteoporotic subjects, the proximal femur was segmented using manual (gold standard) and graph cut segmentation. Segmentations were subsequently used to generate FE models to calculate overall stiffness and peak force in a sideways fall simulations. Results show that, comparable FE results can be obtained with the graph cut method, with a reduction from 20 to 2–5 min interaction time. Average differences between segmentation methods of 0.22 mm were not significantly correlated with differences in FE derived stiffness (R2 = 0.08, p = 0.05) and weakly correlated to differences in FE derived peak force (R2 = 0.16, p = 0.01). We further found that changes in automatically assigned boundary conditions as a consequence of small segmentation differences were significantly correlated with FE derived results. The proposed interactive graph cut segmentation software MITK-GEM is freely available online at https://simtk.org/home/mitk-gem.
Blood biomarkers in chronic airways diseases and their role in diagnosis and management

ABSTRACT Introduction: The complexity and heterogeneous nature of asthma and chronic obstructive pulmonary disease (COPD) results in difficulties in diagnosing and treating patients. Biomarkers that can identify underlying mechanisms, identify patient phenotypes and to predict treatment response could be of great value for adequate treatment. Areas covered: Biomarkers play an important role for the development of novel targeted therapies in airways disease. Blood biomarkers are relatively non-invasive, easy to obtain and easy to apply in routine care. Several blood biomarkers are being used to diagnose and monitor chronic airways diseases, as well as to predict response to treatment and long-term prognosis. Blood eosinophils are the best studied biomarker, the most applied in clinical practice, and until now the most promising of all blood biomarkers. Other blood biomarkers, including serum periostin, IgE and ECP and plasma fibrinogen are less studied and less relevant in clinical practice. Recent developments include the use of antibody assays of many different cytokines at the same time, and ‘omics’ techniques and systems medicine. Expert commentary: With the exception of blood eosinophils, the use of blood biomarkers in asthma and COPD has been rather disappointing. Future research using new technologies like big-data analysis of blood samples from real-life patient cohorts will probably gain better insight into underlying mechanisms of different disease phenotypes. Identification of specific molecular pathways and associated biomarkers will then allow the development of new targets for precision medicine.
Language Development of Three- to Twelve-Year-Old Twins Compared to Singletons

Objective: The language development of twins tends to lag behind in comparison to that of singletons. The purpose of this study was to compare expressive and receptive language skills of 3- to 12-year-old twins with singletons. Secondly, correlations between language differences between twins and singletons and age were investigated. Patients and Methods: Twenty-four twins with a mean age of 5.1 years participated in the study. The control group consisted of 24 singletons who were matched for gender and age. Language development was investigated using the Clinical Evaluation of Language Fundamentals. Results: Twins scored significantly lower for expressive and receptive language skills compared to singletons. Even when excluding preterm-born children, twins still scored significantly lower for expressive language skills. There was no correlation between age and language differences between twins and their matched singletons. Conclusion: Twins score lower for expressive and receptive language skills compared to singletons, and preterm birth cannot be regarded as the main cause for the language delay. The language delay in twins is rather mild but does not seem to decrease with increasing age.