Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of oil palm sustainability certification on deforestation and fire in Indonesia

Significance Demand for agricultural commodities is the leading driver of tropical deforestation. Many corporations have pledged to eliminate forest loss from their supply chains by purchasing only certified “sustainable” products. To evaluate whether certification fulfills such pledges, we applied statistical analyses to satellite-based estimates of tree cover loss to infer the causal impact of a third-party certification system on deforestation and fire within Indonesian oil palm plantations. We found that certification significantly reduced deforestation, but not fire or peatland clearance, among participating plantations. Moreover, certification was mostly adopted in older plantations that contained little remaining forest. Broader adoption by oil palm growers is likely needed for certification to have a large impact on total forest area lost to oil palm expansion. Many major corporations and countries have made commitments to purchase or produce only “sustainable” palm oil, a commodity responsible for substantial tropical forest loss. Sustainability certification is the tool most used to fulfill these procurement policies, and around 20% of global palm oil production was certified by the Roundtable on Sustainable Palm Oil (RSPO) in 2017. However, the effect of certification on deforestation in oil palm plantations remains unclear. Here, we use a comprehensive dataset of RSPO-certified and noncertified oil palm plantations (∼188,000 km2) in Indonesia, the leading producer of palm oil, as well as annual remotely sensed metrics of tree cover loss and fire occurrence, to evaluate the impact of certification on deforestation and fire from 2001 to 2015. While forest loss and fire continued after RSPO certification, certified palm oil was associated with reduced deforestation. Certification lowered deforestation by 33% from a counterfactual of 9.8 to 6.6% y−1. Nevertheless, most plantations contained little residual forest when they received certification. As a result, by 2015, certified areas held less than 1% of forests remaining within Indonesian oil palm plantations. Moreover, certification had no causal impact on forest loss in peatlands or active fire detection rates. Broader adoption of certification in forested regions, strict requirements to avoid all peat, and routine monitoring of clearly defined forest cover loss in certified and RSPO member-held plantations appear necessary if the RSPO is to yield conservation and climate benefits from reductions in tropical deforestation.
pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions

Motivation Hydrogen bonds (H-bonds) play an essential role for many molecular interactions but are also often transient, making visualising them in a flexible system challenging. Results We provide pyHVis3D which allows for an easy to interpret 3D visualisation of H-bonds resulting from molecular simulations. We demonstrate the power of pyHVis3D by using it to explain the changes in experimentally measured binding affinities for three T-cell receptor/peptide/MHC complexes and mutants of each of these complexes. Availability and implementation pyHVis3D can be downloaded for free from http://opig.stats. ox.ac. uk/resources. Contact science.bernhard. knapp@gmail.com. Supplementary information Supplementary data are available at Bioinformatics online.
Differences in cell death and cell cycle following fucoidan treatment in high-density HT-29 colon cancer cells

Fucoidan, a sulfated polysaccharide present in marine brown seaweed, has been demonstrated to inhibit in vivo and in vitro growth of cells. The present study was conducted in HT-29 human colon cancer cells cultured at a high density, and examined the potential underlying mechanisms by which fucoidan exerts its anti-proliferative effects, which remain poorly understood. Fucoidan treatment of high-density HT-29 cells resulted in the inhibition of cell growth and increased apoptotic cell death. Flow cytometric analysis revealed that fucoidan treatment led to sub-G1 phase cell cycle arrest. This was associated with decreased protein expression levels of Retinoblastoma protein and E2 factor protein. In conclusion, the results of the present study demonstrated that fucoidan possesses anticancer activity against high density HT-29 cells by inhibiting cell growth and cell cycle progression.
Whole abdomen irradiation in epithelial ovarian cancer – state of the art

a malignancy which poses multiple challenges has led to growing attention and concern during recent years. The not very noteworthy treatment results achieved during the last three decades with contemporary chemotherapeutic schemes have led to the need for research and development of new therapeutic approaches, as well as to a resurgence of interest in radiotherapy (RT) as part of a combined modality approach and as salvage therapy for patients with small volume persistent disease after primary cytoreductive surgery and chemotherapy. This article reviews the state of the art of whole abdomen irradiation (WAI) (excluding the moving strip field technique) as part of the complex treatment of epithelial OC. The prognostic factors and risk groups of epithelial OC are discussed as indicators for WAI, giving in detail the applied treatment modalities, fractionation and total doses. Toxicity and second primary malignancies following WAI are analyzed. The clinical experience accumulated during the last decades, as adjuvant, consolidative, salvage and palliative WAI in combined treatment of epithelial OC, is presented. Current issues in the radiotherapeutic management are discussed along with ideas for future clinical research directions.
Thyroid Stimulating Hormone Reference Range and Prevalence of Thyroid Dysfunction in the Korean Population: Korea National Health and Nutrition Examination Survey 2013 to 2015

Background No nationwide epidemiological study evaluating the prevalence of subclinical and overt forms of hypothyroidism and hyperthyroidism has yet been conducted in Korea. This study aimed to evaluate the reference range of serum thyroid stimulating hormone (TSH) and the national prevalence of thyroid dysfunctions in Korea. Methods Nation-wide cross-sectional data were analyzed from a representative sample of the civilian, non-institutionalized Korean population (n=6,564) who underwent blood testing for thyroid function and anti-thyroid peroxidase antibody (TPOAb) as part of the Korea National Health and Nutrition Examination Survey VI (2013 to 2015). Results The reference interval of serum TSH in the Korean reference population was 0.62 to 6.68 mIU/L. Based on this reference interval, the prevalence of overt and subclinical hypothyroidism was 0.73% (males 0.40%, females 1.10%) and 3.10% (males 2.26%, females 4.04%), respectively. The prevalence of hypothyroidism increased with age until the age group between 50 to 59 years. Positive TPOAb were found in 7.30% of subjects (males 4.33%, females 10.62%). The prevalence of overt and subclinical hypothyroidism TPOAb-positive subjects was 5.16% and 10.88%, respectively. The prevalence of overt and subclinical hyperthyroidism was 0.54% (males 0.30%, females 0.81%) and 2.98% (males 2.43%, females, 3.59%), respectively. Conclusion The Serum TSH reference levels in the Korean population were higher than the corresponding levels in Western countries. Differences were found in the prevalence of hypothyroidism and hyperthyroidism according to age, sex, and TPOAb positivity. This study provides important baseline information for understanding patterns of thyroid dysfunction and diseases in Korea.
Differential Rate of Return of the Emerging Market Economies

An emerging market economy (EME) is a developing economy where the investment has a potential to attain a higher expected rate of return but is associated with a higher risk. In this paper, an EME is characterized by the bottleneck parameter, which measures the inability of the foreign investor to invest in a particular EME. This paper develops a model to endogenously determine the relationship between the bottleneck parameter and the rate of return of investment in an EME. The equilibrium rate of return and the equilibrium bottleneck parameter is determined by the intersection of the upward sloping profit maximizing rate of return and the downward sloping profitable investment rate of return. An EME with lower bottleneck parameter attracts smaller foreign investment scale, thereby provides a lower equilibrium rate of return to the foreign investor and vice versa. The social planner of the EME can set the bottleneck parameter low or high to drive or deter competition, respectively.
Influence of Morbid Obesity on the Clinical Pharmacokinetics of Various Anti-Infective Drugs: Reappraisal Using Recent Case Studies—Issues, Dosing Implications, and Considerations

Owing to availability of scanty pharmacokinetic data, dosing decisions in morbid obesity is increasingly challenging in the field of anti-infective drugs. However, in recent years data are emerging that describe the pharmacokinetics of anti-infective drugs in morbidly obese subjects. The objectives of the present work were: (1) to collate the recent reports pertaining to the pharmacokinetics in morbidly obese subjects for several anti-infective drugs and provide an overview of the pharmacokinetic data along with the applicable pharmacodynamics and/or clinical outcome; (2) to perform regression analysis on limited dataset for a few drugs to verify the existence of relationships between Cmax/Ctrough versus steady-state volume of distribution (Vss)/clearance to enable data prediction in morbid obesity subjects; (3) to provide a general discussion on issues and dosing implications. The key findings of this review were: (a) drugs such as vancomycin, ethambutol, and fluconazole, where the VSS is substantially greater in morbidly obese patients, need a dosing strategy with the appropriate body mass descriptors; (b) other drugs such as moxifloxacin, linezolid, doripenem, meropenem, voriconazole, oseltamivir, tigecycline, levofloxacin may not ordinarily need dosing adjustments; (c) using regression analysis of limited data, it seemed that drugs such as vancomycin, voriconazole, oseltamivir, and oseltamivir carboxylate may be amenable for the prediction of VSS and/or clearance in morbid obesity patients.
AMPK activity regulates trafficking of mitochondria to the leading edge during cell migration and matrix invasion

Mitochondria infiltrate leading edge lamellipodia, increasing local mitochondrial mass and relative ATP concentration. AMPK regulates infiltration of mitochondria into the leading edge of 2D lamellipodia and 3D invadopodia, coupling local metabolic sensing to subcellular targeting of mitochondria during cell movement.
The oncogenic role of the spliced somatostatin receptor sst5TMD4 variant in prostate cancer

sst5TMD4, a splice variant of the sst5 gene, is overexpressed and associated with aggressiveness in various endocrine‐related tumors, but its presence, functional role, and mechanisms of actions in prostate cancer (PCa)—the most common cancer type in males—is completely unexplored. In this study, formalin‐fixed, paraffin‐embedded prostate pieces from patients with localized PCa, which included tumoral and nontumoral adjacent regions (n = 45), fresh biopsies from patients with high‐risk PCa (n = 52), and healthy fresh prostates from cystoprostatectomies (n = 14) were examined. In addition, PCa cell lines and xenograft models were used to determine the presence and functional role of sst5TMD4. Results demonstrated that sst5TMD4 is overexpressed (mRNA/protein) in PCa samples, and this is especially drastic in metastatic and/or high Gleason score tumor samples. Remarkably, sst5TMD4 expression was associated with an altered frequency of 2 single‐nucleotide polymorphisms: rs197055 and rs12599155. In addition, PCa cell lines and xenograft models were used to demonstrate that sst5TMD4 overexpression increases cell proliferation and migration in PCa cells and induces larger tumors in nude mice, whereas its silencing decreased proliferation and migration. Remarkably, sst5TMD4 overexpression activated multiple intracellular pathways (ERK/JNK, MYC/MAX, WNT, retinoblastoma), altered oncogenes and tumor suppressor gene expression, and disrupted the normal response to somatostatin analogs in PCa cells. Altogether, we demonstrate that sst5TMD4 is overexpressed in PCa, especially in those patients with a worse prognosis, and plays an important pathophysiologic role in PCa, which suggesting its potential as a biomarker and/or therapeutic target. —Hormaechea‐Agulla, D. , Jiménez‐Vacas, J. M. , Gómez‐Gómez, E. , L. ‐López, F. , Carrasco‐Valiente, J., Valero‐Rosa, J., Moreno, M. M. , Sánchez‐Sánchez, R. , Ortega‐Salas, R. , Gracia‐Navarro, F. , Culler, M. D. , Ibáñez‐Costa, A. , Gahete, M. D. , Requena, M. J., Castaño, J. P., Luque, R. M. The oncogenic role of the spliced somatostatin receptor sst5TMD4 variant in prostate cancer. FASEB J. 31, 4682–4696 (2017). www.fasebj. org
Multi-scroll and hypercube attractors from Josephson junctions

In this paper Josephson junctions are used in order to generate n-scroll and n-scroll hypercube attractors. We propose to use of the Josephson junction in a general Jerk circuit in such a way that there is no need for synthesizing the nonlinearity towards n-scroll and n-scroll hypercube attractors. The results are illustrated with computer simulations
CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets

High-dimensional mass and flow cytometry (HDCyto) experiments have become a method of choice for high-throughput interrogation and characterization of cell populations. Here, we present an updated R-based pipeline for differential analyses of HDCyto data, largely based on Bioconductor packages. We computationally define cell populations using FlowSOM clustering, and facilitate an optional but reproducible strategy for manual merging of algorithm-generated clusters. Our workflow offers different analysis paths, including association of cell type abundance with a phenotype or changes in signalling markers within specific subpopulations, or differential analyses of aggregated signals. Importantly, the differential analyses we show are based on regression frameworks where the HDCyto data is the response; thus, we are able to model arbitrary experimental designs, such as those with batch effects, paired designs and so on. In particular, we apply generalized linear mixed models or linear mixed models to analyses of cell population abundance or cell-population-specific analyses of signaling markers, allowing overdispersion in cell count or aggregated signals across samples to be appropriately modeled. To support the formal statistical analyses, we encourage exploratory data analysis at every step, including quality control (e.g., multi-dimensional scaling plots), reporting of clustering results (dimensionality reduction, heatmaps with dendrograms) and differential analyses (e.g., plots of aggregated signals).
Relative biological effectiveness (RBE) values for proton beam therapy. Variations as a function of biological endpoint, dose, and linear energy transfer

Proton therapy treatments are based on a proton RBE (relative biological effectiveness) relative to high-energy photons of 1.1. The use of this generic, spatially invariant RBE within tumors and normal tissues disregards the evidence that proton RBE varies with linear energy transfer (LET), physiological and biological factors, and clinical endpoint. Based on the available experimental data from published literature, this review analyzes relationships of RBE with dose, biological endpoint and physical properties of proton beams. The review distinguishes between endpoints relevant for tumor control probability and those potentially relevant for normal tissue complication. Numerous endpoints and experiments on sub-cellular damage and repair effects are discussed. Despite the large amount of data, considerable uncertainties in proton RBE values remain. As an average RBE for cell survival in the center of a typical spread-out Bragg peak (SOBP), the data support a value of ~1.15 at 2 Gy/fraction. The proton RBE increases with increasing LETd and thus with depth in an SOBP from ~1.1 in the entrance region, to ~1.15 in the center, ~1.35 at the distal edge and ~1.7 in the distal fall-off (when averaged over all cell lines, which may not be clinically representative). For small modulation widths the values could be increased. Furthermore, there is a trend of an increase in RBE as (α/β)x decreases. In most cases the RBE also increases with decreasing dose, specifically for systems with low (α/β)x. Data on RBE for endpoints other than clonogenic cell survival are too diverse to allow general statements other than that the RBE is, on average, in line with a value of ~1.1. This review can serve as a source for defining input parameters for applying or refining biophysical models and to identify endpoints where additional radiobiological data are needed in order to reduce the uncertainties to clinically acceptable levels.
Humanoid robot learning and game playing using PC-based vision

This paper describes humanoid robot learning from observation and game playing using information provided by a real-time PC-based vision system. To cope with extremely fast motions that arise in the environment, a visual system capable of perceiving the motion of several objects at 60 fields per second was developed. We have designed a suitable error recovery scheme for our vision system to ensure successful game playing over longer periods of time. To increase the learning rate of the robot it is given domain knowledge in the form of primitives. The robot learns how to perform primitives from data collected while observing a human. The robot control system and primitive use strategy are also explained.
Personalized Dose Finding Using Outcome Weighted Learning

ABSTRACT In dose-finding clinical trials, it is becoming increasingly important to account for individual-level heterogeneity while searching for optimal doses to ensure an optimal individualized dose rule (IDR) maximizes the expected beneficial clinical outcome for each individual. In this article, we advocate a randomized trial design where candidate dose levels assigned to study subjects are randomly chosen from a continuous distribution within a safe range. To estimate the optimal IDR using such data, we propose an outcome weighted learning method based on a nonconvex loss function, which can be solved efficiently using a difference of convex functions algorithm. The consistency and convergence rate for the estimated IDR are derived, and its small-sample performance is evaluated via simulation studies. We demonstrate that the proposed method outperforms competing approaches. Finally, we illustrate this method using data from a cohort study for warfarin (an anti-thrombotic drug) dosing. Supplementary materials for this article are available online.
VERY LOW INFLUENZA A VIRUS PREVALENCE IN CERVIDS IN GERMAN NATIONAL PARKS

Abstract Influenza A viruses are one of the most important and most studied pathogens in humans and domestic animals but little is known about viral prevalence in non-avian wildlife. Serum samples from three free-ranging cervid species (red [Cervus elaphus], fallow [Dama dama], and roe deer [Capreolus capreolus]) were collected from six German national parks between 2000 and 2002. The serum was tested for the presence of influenza A antibodies using a commercial competitive enzyme-linked immunosorbent assay. Only one of 137 samples tested positive.
Point-of-care testing in primary care patients with acute cardiopulmonary symptoms: a systematic review

Background Point-of-care tests (POCT) can assist general practitioners (GPs) in diagnosing and treating patients with acute cardiopulmonary symptoms, but it is currently unknown if POCT impact relevant clinical outcomes in these patients. Objective To assess whether using POCT in primary care patients with acute cardiopulmonary symptoms leads to more accurate diagnosis and impacts clinical management. Methods We performed a systematic review in four bibliographic databases. Articles published before February 2016 were screened by two reviewers. Studies evaluating the effect of GP use of POCT on clinical diagnostic accuracy and/or effect on treatment and referral rate in patients with cardiopulmonary symptoms were included. Results Our search yielded nine papers describing data from seven studies, on the clinical diagnostic accuracy of POCT in a total of 2277 primary care patients with acute cardiopulmonary symptoms. Four papers showed data on GP use of D-dimer POCT in pulmonary embolism (two studies); two studies on Troponin T in acute coronary syndrome; one on heart-type fatty acid-binding protein (H-FABP) in acute coronary syndrome; one on B-type natriuretic peptide (BNP) in heart failure; one on 3-in-1 POCT (Troponin T, BNP, D-dimer) in acute coronary syndrome, heart failure and/or pulmonary embolism. Only one study assessed the effect of GP use of POCT on treatment initiation and one on actual referral rates. Conclusion There is currently limited and inconclusive evidence that actual GP use of POCT in primary care patients with acute cardiopulmonary symptoms leads to more accurate diagnosis and affects clinical management. However, some studies show promising results, especially when a POCT is combined with a clinical decision rule.
Neuroimaging in the Evaluation of Epilepsy

Abstract Neuroimaging has provided extraordinary insight into the pathologic substrate of epilepsy. The excellent spatial resolution and soft tissue contrast of magnetic resonance imaging (MRI) allows identification of a substantial number of pathologies including hippocampal sclerosis, malformations of cortical development, low grade tumors, and vascular abnormalities, among others. Complementary imaging modalities such as positron emission tomography, single photon emission computed tomography, and magnetoencephalography can be diagnostically helpful as well. Identification of a pathologic substrate is particularly important in patients with medically refractory epilepsy who are undergoing evaluation for surgery, and essential in determining the likelihood of seizure freedom after surgical intervention. This article reviews current and emerging neuroimaging techniques in the field of epilepsy.
DEVELOPMENT, OPTIMIZATION AND COMPARATIVE IN-VIVO EVALUATION OF SALBUTAMOL FLOATING CAPSULE FORMULATION

In this study different contents of low viscosity grade hydroxypropyl methylcellulose (HPMC, 50cps) and Tragacanth were conceived to develop and optimize salbutamol gastric floating capsules capable to sustain the release of loaded drug over a prolonged time duration through consecutive application of full factorial and composite index based mathematical designs. Tragacanth content was established to have a more influence on floating duration of developed capsule formulations whilst content of both HPMC and Tragacanth were found to affect the rate and kinetics of the drug release. Significant increase (p< 0.05) in floating duration and drug release rate was monitored with increasing content of HPMC in capsule formulations composed of polymer combination. Formulation composed of 16% w/w HPMC and 36% w/w Tragacanth (F8) was considered as best ranked formulation that fulfill preset constraints for floating duration, % drug release in the first hour and % drug release within 4 hours. Upon optimization of F8 with regard to drug release kinetics, a formulation comprised of 8% and 36% w/w HPMC and Tragacanth, respectively, was achieved and measured floating duration of 6.8 hr, 30% drug release at the first hour, 72% of loaded drug release after 4 hours with a diffusion exponent of 0.7888. Compared to an immediate release non floating capsule formulation, in vivo investigation in 8 dogs has shown that there was significant increase (p≤0.05) in Tmax, AUC0-∞, elimination t½ and mean resident time of salbutamol associated with the optimized salbutamol floating capsule formulation, indicating the improved W