Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting poaching for wildlife Protection

Wildlife species such as tigers and elephants are under the threat of poaching. To combat poaching, conservation agencies (“defenders”) need to 1) anticipate where the poachers are likely to poach and 2) plan effective patrols. We propose an anti-poaching tool CAPTURE (Comprehensive Anti-Poaching tool with Temporal and observation Uncertainty REasoning), which helps the defenders achieve both goals. CAPTURE builds a novel hierarchical model for poacher-patroller interaction. It considers the patroller's imperfect detection of signs of poaching, the complex temporal dependencies in the poacher's behaviors, and the defender's lack of knowledge of the number of poachers. Further, CAPTURE uses a new game-theoretic algorithm to compute the optimal patrolling strategies and plan effective patrols. This paper investigates the computational challenges that CAPTURE faces. First, we present a detailed analysis of parameter separation and cell abstraction, two novel approaches used by CAPTURE to efficiently learn the parameters in the hierarchical model. Second, we propose two heuristics—piecewise linear approximation and greedy planning—to speed up the computation of the optimal patrolling strategies. In this paper, we discuss the lessons learned from using CAPTURE to analyze real-world poaching data collected over 12 years in Queen Elizabeth National Park in Uganda.
Investigation of the BOLD and CBV fMRI responses to somatosensory stimulation in awake marmosets (Callithrix jacchus)

Understanding the spatiotemporal features of the hemodynamic response function (HRF) to brain stimulation is essential for the correct application of neuroimaging methods to study brain function. Here, we investigated the spatiotemporal evolution of the blood oxygen level‐dependent (BOLD) and cerebral blood volume (CBV) HRF in conscious, awake marmosets (Callithrix jacchus), a New World non‐human primate with a lissencephalic brain and with growing use in biomedical research. The marmosets were acclimatized to head fixation and placed in a 7‐T magnetic resonance imaging (MRI) scanner. Somatosensory stimulation (333‐μs pulses; amplitude, 2 mA; 64 Hz) was delivered bilaterally via pairs of contact electrodes. A block design paradigm was used in which the stimulus duration increased in pseudo‐random order from a single pulse up to 256 electrical pulses (4 s). For CBV measurements, 30 mg/kg of ultrasmall superparamagnetic ironoxide particles (USPIO) injected intravenously, were used. Robust BOLD and CBV HRFs were obtained in the primary somatosensory cortex (S1), secondary somatosensory cortex (S2) and caudate at all stimulus conditions. In particular, BOLD and CBV responses to a single 333‐μs‐long stimulus were reliably measured, and the CBV HRF presented shorter onset time and time to peak than the BOLD HRF. Both the size of the regions of activation and the peak amplitude of the HRFs grew quickly with increasing stimulus duration, and saturated for stimulus durations greater than 1 s. Onset times in S1 and S2 were faster than in caudate. Finally, the fine spatiotemporal features of the HRF in awake marmosets were similar to those obtained in humans, indicating that the continued refinement of awake non‐human primate models is essential to maximize the applicability of animal functional MRI studies to the investigation of human brain function.
Impact of transposable elements on polyploid plant genomes.

Background The growing wealth of knowledge on whole-plant genome sequences is highlighting the key role of transposable elements (TEs) in plant evolution, as a driver of drastic changes in genome size and as a source of an important number of new coding and regulatory sequences. Together with polyploidization events, TEs should thus be considered the major players in evolution of plants. Scope This review outlines the major mechanisms by which TEs impact plant genome evolution and how polyploidy events can affect these impacts, and vice versa. These include direct effects on genes, by providing them with new coding or regulatory sequences, an effect on the epigenetic status of the chromatin close to genes, and more subtle effects by imposing diverse evolutionary constraints to different chromosomal regions. These effects are particularly relevant after polyploidization events. Polyploidization often induces bursts of transposition probably due to a relaxation in their epigenetic control, and, in the short term, this can increase the rate of gene mutations and changes in gene regulation due to the insertion of TEs next to or into genes. Over longer times, TE bursts may induce global changes in genome structure due to inter-element recombination including losses of large genome regions and chromosomal rearrangements that reduce the genome size and the chromosome number as part of a process called diploidization. Conclusions TEs play an essential role in genome and gene evolution, in particular after polyploidization events. Polyploidization can induce TE activity that may explain part of the new phenotypes observed. TEs may also play a role in the diploidization that follows polyploidization events. However, the extent to which TEs contribute to diploidization and fractionation bias remains unclear. Investigating the multiple factors controlling TE dynamics and the nature of ancient and recent polyploid genomes may shed light on these processes.
Explaining Recollection Without Remembering

Recollection without remembering is a counterintuitive phenomenon that violates a traditional assumption of source memory models—namely, that accurate item memory is a necessary precondition for remembering source details that accompanied an item’s presentation. The dual-recollection model explains recollection without remembering as a by-product of the contrasting effects of target and context recollection on item tests versus source tests. We pitted that explanation against 2 others that preserve the traditional assumption, one based on hypothesized testing artifacts and the other derived from multivariate signal detection theory. Our experiments focused on a manipulation that, according to dual-recollection theory, should drive source memory and item memory in opposite directions. In 2 experiments, studied items were tagged with 3 source details (voice gender, taxonomic category, and list), such that either (a) the 3 details were consistent with each other or (b) 1 detail was inconsistent with the other 2. As predicted, source memory was better but item memory was worse when source details were consistent with each other. The recollection without remembering effect was observed in both experiments, and as predicted by dual-recollection theory, it was more robust when item memory was worse than when it was better. A further instance of recollection without remembering was detected that involved distractors rather than presented items.
Transcriptome and Proteome Dynamics of a Light-Dark Synchronized Bacterial Cell Cycle

Background Growth of the ocean's most abundant primary producer, the cyanobacterium Prochlorococcus, is tightly synchronized to the natural 24-hour light-dark cycle. We sought to quantify the relationship between transcriptome and proteome dynamics that underlie this obligate photoautotroph's highly choreographed response to the daily oscillation in energy supply. Methodology/Principal Findings Using RNA-sequencing transcriptomics and mass spectrometry-based quantitative proteomics, we measured timecourses of paired mRNA-protein abundances for 312 genes every 2 hours over a light-dark cycle. These temporal expression patterns reveal strong oscillations in transcript abundance that are broadly damped at the protein level, with mRNA levels varying on average 2.3 times more than the corresponding protein. The single strongest observed protein-level oscillation is in a ribonucleotide reductase, which may reflect a defense strategy against phage infection. The peak in abundance of most proteins also lags that of their transcript by 2–8 hours, and the two are completely antiphase for some genes. While abundant antisense RNA was detected, it apparently does not account for the observed divergences between expression levels. The redirection of flux through central carbon metabolism from daytime carbon fixation to nighttime respiration is associated with quite small changes in relative enzyme abundances. Conclusions/Significance Our results indicate that expression responses to periodic stimuli that are common in natural ecosystems (such as the diel cycle) can diverge significantly between the mRNA and protein levels. Protein expression patterns that are distinct from those of cognate mRNA have implications for the interpretation of transcriptome and metatranscriptome data in terms of cellular metabolism and its biogeochemical impact.
The Impact of the Internet on Health Consultation Market Concentration: An Econometric Analysis of Secondary Data

Background Many markets have traditionally been dominated by a few best-selling products, and this is also the case for the health care industry. However, we do not know whether the market will be more or less concentrated when health care services are delivered online (known as E-consultation), nor do we know how to reduce the concentration of the E-consultation market. Objective The aim of this study was to investigate the concentration of the E-consultation market and how to reduce its concentration through information disclosure mechanisms (online reputation and self-representation). Methods We employed a secondary data econometric analysis using transaction data obtained from an E-consultation Website (haodf.com) for three diseases (infantile pneumonia, diabetes, and pancreatic cancer) from 2008 to 2015. We included 2439 doctors in the analysis. Results The E-consultation market largely follows the 20/80 principle, namely that approximately 80% of orders are fulfilled by nearly 20% of doctors. This is much higher than the offline health care market. Meanwhile, the market served by doctors with strong online reputations (beta=0.207, P<.001) or strong online self-representation (beta=0.386, P<.001) is less concentrated. Conclusions When health care services are delivered online, the market will be more concentrated (known as the “Superstar” effect), indicating poor service efficiency for society as a whole. To reduce market concentration, E-consultation websites should provide important design elements such as ratings of doctors (user feedback), articles contributed by doctors, and free consultation services (online representation). A possible and important way to reduce the market concentration of the E-consultation market is to accumulate enough highly rated or highly self-represented doctors.
Relationship between onset of spontaneous pneumothorax and weather conditions

OBJECTIVES Spontaneous pneumothorax (SP) results from the rupture of blebs or bullae. It has been suggested that changes in weather conditions may trigger the onset of SP. Our aim was to examine the association between the onset of primary SP with weather changes in the general population in Sapporo, Japan. METHODS From January 2008 through September 2013, 345 consecutive cases with a diagnosis of primary SP were reviewed. All cases of primary SP developed in the area within 40 km from the Sapporo District Meteorological Observatory. Climatic measurements were obtained from the Observatory, which included 1‐h readings of weather conditions. Logistic regression model was used to obtain predicted risks for the onset of SP with respect to weather conditions. RESULTS SP occurred significantly when the atmospheric pressure decreased by − 18 hPa or less during 96 h before the survey date (odds ratio = 1.379, P = 0.026), when the pressure increased by 15 hPa or more during 72 h before the survey date (odds ratio = 1.095, P = 0.007) and when maximum fluctuation in atmospheric pressure over 22 hPa was observed during 96 h before the survey date (odds ratio = 1.519, P = 0.001). Other weather conditions, including the presence of thunderstorms, were not significantly correlated with the onset of pneumothorax. CONCLUSIONS Changes in atmospheric pressure influence the onset of SP. Future studies on the relationship between the onset of SP and weather conditions on days other than before the onset and with large number of patients may enable us to predict the onset of SP in various regions and weather conditions.
Percutaneous short-term active mechanical support devices in cardiogenic shock: a systematic review and collaborative meta-analysis of randomized trials

Aims Evidence on the impact on clinical outcome of active mechanical circulatory support (MCS) devices in cardiogenic shock (CS) is scarce. This collaborative meta-analysis of randomized trials thus aims to investigate the efficacy and safety of percutanzeous active MCS vs. control in CS. Methods and results Randomized trials comparing percutaneous active MCS to control in patients with CS were identified through searches of medical literature databases. Risk ratios (RR) and 95% confidence intervals (95% CI) were calculated to analyse the primary endpoint of 30-day mortality and device-related complications including bleeding and leg ischaemia. Mean differences (MD) were calculated for mean arterial pressure (MAP), cardiac index (CI), pulmonary capillary wedge pressure (PCWP), and arterial lactate. Four trials randomizing 148 patients to either TandemHeart™ or Impella® MCS (n = 77) vs. control (n = 71) were identified. In all four trials intra-aortic balloon pumping (IABP) served as control. There was no difference in 30-day mortality (RR 1.01, 95% CI 0.70 to 1.44, P = 0.98, I2 = 0%) for active MCS compared with control. Active MCS significantly increased MAP (MD 11.85 mmHg, 95% CI 3.39 to 20.31, P = 0.02, I2 = 32.7%) and decreased arterial lactate (MD - 1.36 mmol/L, 95% CI - 2.52 to - 0.19, I2 = 0%, P = 0.02) at comparable CI (MD 0.32, 95% CI - 0.24 to 0.87, P = 0.14, I2 = 44.1%) and PCWP (MD - 5.59, 95% -15.59 to 4.40, P = 0.14, I2 = 81.1%). No significant difference was observed in the incidence of leg ischaemia (RR 2.64, 95% CI 0.83 to 8.39, P = 0.10, I2 = 0%), whereas the rate of bleeding was significantly increased in MCS compared to IABP (RR 2.50, 95% CI 1.55 to 4.04, P < 0.001, I2 = 0%). Conclusion Results of this collaborative meta-analysis do not support the unselected use of active MCS in patients with CS complicating AMI.
GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models

Motivation Mathematical modeling using ordinary differential equations is used in systems biology to improve the understanding of dynamic biological processes. The parameters of ordinary differential equation models are usually estimated from experimental data. To analyze a priori the uniqueness of the solution of the estimation problem, structural identifiability analysis methods have been developed. Results We introduce GenSSI 2.0, an advancement of the software toolbox GenSSI (Generating Series for testing Structural Identifiability). GenSSI 2.0 is the first toolbox for structural identifiability analysis to implement Systems Biology Markup Language import, state/parameter transformations and multi‐experiment structural identifiability analysis. In addition, GenSSI 2.0 supports a range of MATLAB versions and is computationally more efficient than its previous version, enabling the analysis of more complex models. Availability and implementation GenSSI 2.0 is an open‐source MATLAB toolbox and available at https://github.com/genssi‐developer/GenSSI. Supplementary information Supplementary data are available at Bioinformatics online.
The safety and efficacy of carboplatin plus nanoparticle albumin-bound paclitaxel in the treatment of non-small cell lung cancer patients with interstitial lung disease

Background The optimal chemotherapy regimen for non-small cell lung cancer patients with interstitial lung disease is unclear. We therefore investigated the safety and efficacy of carboplatin plus nab-paclitaxel as a first-line regimen for non-small cell lung cancer in patients with interstitial lung disease. Methods We retrospectively reviewed advanced non-small cell lung cancer patients with interstitial lung disease who received carboplatin plus nab-paclitaxel as a first-line chemotherapy regimen at Hyogo Cancer Center between February 2013 and August 2016. interstitial lung disease was diagnosed according to the findings of pretreatment chest high-resolution computed tomography. Results Twelve patients were included (male, n = 11; female, n = 1). The overall response rate was 67% and the disease control rate was 100%. The median progression free survival was 5.1 months (95% CI: 2.9-8.3 months) and the median overall survival was 14.9 months (95% CI: 4.8-not reached). A chemotherapy-related acute exacerbation of interstitial lung disease was observed in one patient; the extent of this event was Grade 2. There were no treatment-related deaths. Conclusions Carboplatin plus nab-paclitaxel, as a first-line chemotherapy regimen for non-small cell lung cancer, showed favorable efficacy and safety in patients with preexisting interstitial lung disease.
Biogeosciences Effect of CO 2 on the properties and sinking velocity of aggregates of the coccolithophore Emiliania huxleyi

Coccolithophores play an important role in organic matter export due to their production of the mineral calcite that can act as ballast. Recent studies indicated that calcification in coccolithophores may be affected by changes in seawater carbonate chemistry. We investigated the influence of CO2 on the aggregation and sinking behaviour of the coccolithophoreEmiliania huxleyi(PML B92/11) during a laboratory experiment. The coccolithophores were grown under low (∼180 μatm), medium ( ∼380 μatm), and high (∼750 μatm) CO2 conditions. Aggregation of the cells was promoted using roller tables. Size and settling velocity of aggregates were determined during the incubation using video image analysis. Our results indicate that aggregate properties are sensitive to changes in the degree of ballasting, as evoked by ocean acidification. Average sinking velocity was highest for low CO2 aggregates ( ∼1292 m d−1) that also had the highest particulate inorganic to particulate organic carbon (PIC/POC) ratio. Lowest PIC/POC ratios and lowest sinking velocity (∼366 m d−1) at comparable sizes were observed for aggregates of the high CO 2 treatment. Aggregates of the high CO2 treatment showed a 4-fold lower excess density (∼4.2×10−4 g cm−3) when compared to aggregates from the medium and low CO2 treatments ( ∼1.7 g×10−3 cm−3). We also observed that more aggregates formed in the high CO 2 treatment, and that those aggregates contained more bacteria than aggregates in the medium and low CO 2 treatment. If applicable to the future ocean, our findings suggest that a CO2 induced reduction of the calcite content of aggregates could weaken the deep export of organic matter in the ocean, particularly in areas dominated by coccolithophores. Correspondence to: A. Biermann (abiermann@ifm-geomar.de)
Web-Based Tools for Text-Based Patient-Provider Communication in Chronic Conditions: Scoping Review

Background Patients with chronic conditions require ongoing care which not only necessitates support from health care providers outside appointments but also self-management. Web-based tools for text-based patient-provider communication, such as secure messaging, allow for sharing of contextual information and personal narrative in a simple accessible medium, empowering patients and enabling their providers to address emerging care needs. Objective The objectives of this study were to (1) conduct a systematic search of the published literature and the Internet for Web-based tools for text-based communication between patients and providers; (2) map tool characteristics, their intended use, contexts in which they were used, and by whom; (3) describe the nature of their evaluation; and (4) understand the terminology used to describe the tools. Methods We conducted a scoping review using the MEDLINE (Medical Literature Analysis and Retrieval System Online) and EMBASE (Excerpta Medica Database) databases. We summarized information on the characteristics of the tools (structure, functions, and communication paradigm), intended use, context and users, evaluation (study design and outcomes), and terminology. We performed a parallel search of the Internet to compare with tools identified in the published literature. Results We identified 54 papers describing 47 unique tools from 13 countries studied in the context of 68 chronic health conditions. The majority of tools (77%, 36/47) had functions in addition to communication (eg, viewable care plan, symptom diary, or tracker). Eight tools (17%, 8/47) were described as allowing patients to communicate with the team or multiple health care providers. Most of the tools were intended to support communication regarding symptom reporting (49%, 23/47), and lifestyle or behavior modification (36%, 17/47). The type of health care providers who used tools to communicate with patients were predominantly allied health professionals of various disciplines (30%, 14/47), nurses (23%, 11/47), and physicians (19%, 9/47), among others. Over half (52%, 25/48) of the tools were evaluated in randomized controlled trials, and 23 tools (48%, 23/48) were evaluated in nonrandomized studies. Terminology of tools varied by intervention type and functionality and did not consistently reflect a theme of communication. The majority of tools found in the Internet search were patient portals from 6 developers; none were found among published articles. Conclusions Web-based tools for text-based patient-provider communication were identified from a wide variety of clinical contexts and with varied functionality. Tools were most prevalent in contexts where intended use was self-management. Few tools for team-based communication were found, but this may become increasingly important as chronic disease care becomes more interdisciplinary.
Psychometric Evaluation of the Young Children's Participation and Environment Measure (YC-PEM) for use in Singapore

ABSTRACT Aims: To estimate the psychometric properties of a culturally adapted version of the Young Children's Participation and Environment Measure (YC-PEM) for use among Singaporean families. Methods: This is a prospective cohort study. Caregivers of 151 Singaporean children with (n = 83) and without (n = 68) developmental disabilities, between 0 and 7 years, completed the YC-PEM (Singapore) questionnaire with 3 participation scales (frequency, involvement, and change desired) and 1 environment scale for three settings: home, childcare/preschool, and community. Setting-specific estimates of internal consistency, test-retest reliability, and construct validity were obtained. Results: Internal consistency estimates varied from . 59 to . 92 for the participation scales and . 73 to . 79 for the environment scale. Test-retest reliability estimates from the YC-PEM conducted on two occasions, 2–3 weeks apart, varied from . 39 to . 89 for the participation scales and from . 65 to . 80 for the environment scale. Moderate to large differences were found in participation and perceived environmental support between children with and without a disability. Conclusions: YC-PEM (Singapore) scales have adequate psychometric properties except for low internal consistency for the childcare/preschool participation frequency scale and low test-retest reliability for home participation frequency scale. The YC-PEM (Singapore) may be used for population-level studies involving young children with and without developmental disabilities.