Miracle-dz/UniFAR-FTUs huggingface dataset:
Title: Cytokeratin-18 has potential as a biomarker of drug-induced liver injury in European and African patients on treatment for tuberculosis Running Title: K18 in tuberculosis treatment Keywords: cytokeratin-18, K18, drug-induced liver injury, tuberculosis

1. Pharmacology, Therapeutics and Toxicology, Centre for Cardiovascular Science, University of Edinburgh, The Queen’s Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ 2. School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TF 3. Edinburgh University/Infection Medicine, Chancellor’s Building, 49 Little France Crescent, Edinburgh, EH16 4SB 4. Edinburgh University/Centre for Inflammation Research, The Queen’s Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ 5. Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda.
A 3D Iris Scanner From a Single Image Using Convolutional Neural Networks

A 3D model of the human iris provides an additional degree of freedom in iris recognition, which could help identify people in larger databases, even when only a piece of the iris is available. Previously, we reported developing a 3D iris scanner that uses 2D images of the iris from multiple perspectives to reconstruct a 3D model of the iris. This paper focuses on the development of a 3D iris scanner from a single image by means of a Convolutional Neural Network (CNN). The method is based on a depth-estimation CNN for the 3D iris model. A dataset of 26,520 real iris images from 120 subjects, and a dataset of 72,000 synthetic iris images with their aligned depthmaps were created. With these datasets, we trained and compared the depth estimation capabilities of available CNN architectures. We analyzed the performance of our method to estimate the iris depth in multiple ways: using real step pyramid printed 3D models, comparing the results to those of a test set of synthetic images, comparing the results to those of the OCT scans from both eyes of one subject, and generating the 3D rubber sheet from the 3D iris model proving the correspondence with the resulting 2D rubber sheet and binary codes. On a preliminary test the proposed 3D rubber sheet model increased iris recognition performance by 48% with respect to the standard 2D iris code. Other contributions include assessing the scanning resolution, reducing the acquisition and processing time to produce the 3D iris model, and reducing the complexity of the image acquisition system.
Foods of Elk and Other Ungulates at Low Elevations in Northwestern Colorado

In northwestern Colorado on areas where elk (Cervus canadenzis) and wild horses have been increasing in recent years, the diets of elk, cattle and wild horses consisted mainly of sedges and grasses. On the same areas mule deer (Odocoileus hemionus) have been decreasing steadily recently, and their diets were mostly browse. The foods of elk, wild horses, and cattle were much more similar to each other than any one of the herbivore diets was to that of mule deer. Cattle and wild horses have strikingly similar diets, and if forage was limited they would compete strongly for forage. There appears to be no large herbivore on the study areas that competes significantly for foods with mule deer. J. WILDL. MANAGE. 41(1):76-80 During the past 30 years elk in Colorado have been increasing slowly. During the past 15 years mule deer have declined rapidly. Record high numbers (23,946) of elk and near record low (46,666) deer numbers were harvested in 1974 (Riffel 1975:1). According to the most recent summary for 1975, the deer harvest was 14 percent less in 1975 than in 1974 (Lashnits 1975:1). In some low elevational ranges in northwestern Colorado, nonmigratory herds of elk have become established where they are not legally hunted or where only a few hunting permits are issued. Some of these same ranges also have increasing herds of wild horses (Cook 1975). There is growing concern for multiple use management of rangelands, and information pertaining to foods shared among different herbivores using a particular range is relatively limited. When provided protection from predators and man, large herbivores not only tolerate but may thrive within broad limits of climate, soil, topography, and vegetation. The food habits of large herbivores are generalized. Precise predictions of the botanical composition of diets of a species of herbivore may differ significantly between areas occurring wit in the same vegetation type. The purpose of this study was to determine the botanical composition of the diets of elk, mule de , wild horses, and cattle on the same
Dietary Habits, Anthropometric Features and Daily Performance in Two Independent Long-Lived Populations from Nicoya peninsula (Costa Rica) and Ogliastra (Sardinia)

(1) Background: Longevity Blue Zones (LBZs) are populations characterized by exceptional longevity. The purpose of this cross-sectional study was to compare the food habits of two representative samples of the oldest old subjects from the population residing in the LBZs of Nicoya peninsula (Costa Rica) and in the mountainous part of Ogliastra (Sardinia, Italy). (2) Methods: Data were collected using validated tools, including a food frequency questionnaire, Basic Activities of Daily Living (BADL) and Instrumental Activities of Daily Living (IADL) scales for functional autonomy, body mass index, and waist and limbs circumferences. (3) Results: A total of 210 subjects, 60 (31 male) from Nicoya (age range 80–109 years), and 150 (61 male) from Ogliastra (age 90–101 years) were included in the study. In both populations, the highest frequencies of consumption were recorded for plant-derived foods (cereals 60–80% daily, legumes ≥ 80% daily in Nicoya, ≥ 60% 2–5 servings/week in Ogliastra), followed by those of animal origin (dairy products, meat) ≥60% and 80% daily, in Nicoya and Ogliastra, respectively. The frequency of milk consumption showed a positive correlation with BADL (ρ = 0.268 for Nicoya and ρ = 0.214 for Ogliastra) and IADL scores (ρ = 0.466 for Nicoya and ρ = 0.471 for Ogliastra), whereas legumes consumption correlated negatively with self-rated health (ρ = −0.264) and IADL (ρ = −0.332). (4) Conclusions: Our results indicate that the dominant dietary model among the elderly of Nicoya and Ogliastra is a plant-based diet complemented by a non-negligible consumption of animal products, mostly dairy products. Further prospective studies are needed to ascertain a possible cause–effect relationship between food habits and increased likelihood of reaching advanced age.
PIQMEE: Bayesian Phylodynamic Method for Analysis of Large Data Sets with Duplicate Sequences

Abstract Next-generation sequencing of pathogen quasispecies within a host yields data sets of tens to hundreds of unique sequences. However, the full data set often contains thousands of sequences, because many of those unique sequences have multiple identical copies. Data sets of this size represent a computational challenge for currently available Bayesian phylogenetic and phylodynamic methods. Through simulations, we explore how large data sets with duplicate sequences affect the speed and accuracy of phylogenetic and phylodynamic analysis within BEAST 2. We show that using unique sequences only leads to biases, and using a random subset of sequences yields imprecise parameter estimates. To overcome these shortcomings, we introduce PIQMEE, a BEAST 2 add-on that produces reliable parameter estimates from full data sets with increased computational efficiency as compared with the currently available methods within BEAST 2. The principle behind PIQMEE is to resolve the tree structure of the unique sequences only, while simultaneously estimating the branching times of the duplicate sequences. Distinguishing between unique and duplicate sequences allows our method to perform well even for very large data sets. Although the classic method converges poorly for data sets of 6,000 sequences when allowed to run for 7 days, our method converges in slightly more than 1 day. In fact, PIQMEE can handle data sets of around 21,000 sequences with 20 unique sequences in 14 days. Finally, we apply the method to a real, within-host HIV sequencing data set with several thousand sequences per patient.
LDL Receptor Regulates the Reverse Transport of Macrophage-Derived Unesterified Cholesterol via Concerted Action of the HDL-LDL Axis

Supplemental Digital Content is available in the text. Rationale: The HDL (high-density lipoprotein)-mediated stimulation of cellular cholesterol efflux initiates macrophage-specific reverse cholesterol transport (m-RCT), which ends in the fecal excretion of macrophage-derived unesterified cholesterol (UC). Early studies established that LDL (low-density lipoprotein) particles could act as efficient intermediate acceptors of cellular-derived UC, thereby preventing the saturation of HDL particles and facilitating their cholesterol efflux capacity. However, the capacity of LDL to act as a plasma cholesterol reservoir and its potential impact in supporting the m-RCT pathway in vivo both remain unknown. Objective: We investigated LDL contributions to the m-RCT pathway in hypercholesterolemic mice. Methods and Results: Macrophage cholesterol efflux induced in vitro by LDL added to the culture media either alone or together with HDL or ex vivo by plasma derived from subjects with familial hypercholesterolemia was assessed. In vivo, m-RCT was evaluated in mouse models of hypercholesterolemia that were naturally deficient in CETP (cholesteryl ester transfer protein) and fed a Western-type diet. LDL induced the efflux of radiolabeled UC from cultured macrophages, and, in the simultaneous presence of HDL, a rapid transfer of the radiolabeled UC from HDL to LDL occurred. However, LDL did not exert a synergistic effect on HDL cholesterol efflux capacity in the familial hypercholesterolemia plasma. The m-RCT rates of the LDLr (LDL receptor)-KO (knockout), LDLr-KO/APOB100, and PCSK9 (proprotein convertase subtilisin/kexin type 9)-overexpressing mice were all significantly reduced relative to the wild-type mice. In contrast, m-RCT remained unchanged in HAPOB100 Tg (human APOB100 transgenic) mice with fully functional LDLr, despite increased levels of plasma APO (apolipoprotein)-B–containing lipoproteins. Conclusions: Hepatic LDLr plays a critical role in the flow of macrophage-derived UC to feces, while the plasma increase of APOB-containing lipoproteins is unable to stimulate m-RCT. The results indicate that, besides the major HDL-dependent m-RCT pathway via SR-BI (scavenger receptor class B type 1) to the liver, a CETP-independent m-RCT path exists, in which LDL mediates the transfer of cholesterol from macrophages to feces.
Membrane biogenesis in the sprouting neuron. I. Selective transfer of newly synthesized phospholipid into the growing neurite

Our goal was to elucidate the pathway of newly synthesized phospholipid into the growing neurite. This was accomplished in pulse-chase studies with the phospholipid precursor [3H]glycerol, using sprouting explant cultures of rat superior cervical ganglion as an experimental system. After the pulse with the precursor and various chase periods, we separated perikarya and neurites microsurgically and extracted their phospholipids. The phospholipid extract from the perikarya exhibited a steep rise followed by a rapid decline in specific radioactivity. In contrast, an increase in neuritic specific radioactivity of phospholipid was observed only after a lag period of approximately 60 min. Nearly quantitative transfer of newly synthesized phospholipid from the perikarya into the neurites could be demonstrated. Both the decline in perikaryal specific radioactivity and the increase in its neuritic counterpart, i.e., the proximodistal transfer, could be blocked with the microtubule drug colchicine and the metabolic uncoupler, 2,4-dinitrophenol. These observations indicate preferential export of newly synthesized phospholipid from the perikaryon (the major or exclusive site of synthesis) into the growing neurites, most likely by rapid axoplasmic transport of formed elements.
Diet breadth and host plant diversity of tropical‐ vs. temperate‐zone herbivores: South‐East Asian and West Palaearctic butterflies as a case study

1. Data on host plant associations of butterflies (Papilionoidea, excluding Hesperiidae) from two biogeographical regions were used to investigate (1) whether tropical herbivores are more narrowly specialized with regard to host plant choice than those of northern temperate zones, and (2) whether tropical butterflies show a greater diversity of host plant affiliations.
A 28-GHz Cascode Inverse Class-D Power Amplifier Utilizing Pulse Injection in 22-nm FDSOI

Current Mode Class-D (CMCD) Power Amplifiers are of particular interest in outphasing transmitters or Doherty configuration. This is because the output capacitance can be absorbed in the RLC output matching network and 100% theoretical efficiency. In this paper, a 28 GHz current mode (inverse) Class-D power amplifier was simulated, implemented, and measured in 22nm FDSOI. In order to overcome the breakdown voltages of the devices, the amplifier employs a stacked topology, which enables higher output powers and efficiency. The stacked transistors are also pulse injected to further increase the efficiency. Measurement results shows a peak PAE of 46%, peak drain efficiency (DE) of 71% and a saturated output power of 19 dBm. The implemented CMCD PA reports the best performance in literature compared to other CMOS based CMCD PAs.
CHEMICAL ROUTES TO MATERIALS Phase separation in wurtzite CuInxGa12xS2 nanoparticles

It has earlier been reported that that the gallium incorporation in wurtzite CuInS2 (CIS) results in structural distortion, non-homogeneous shape, and distribution of particles. However, a detailed study of the effect of Ga substitution on the structure and morphology has not been reported. Here, we report the synthesis of nanocrystalline CuInxGa1-xS2 (x = 1, 0.7, 0.5, 0.3, and 0) wurtzite particles by solution processing in a nitrogen atmosphere. Structural analyses by X-ray diffraction (XRD) and transmission electron microscopy (TEM) showed that the as-synthesized CuInS2 (CIS) and CuGaS2 (CGS) nanoparticle were single-phase wurtzite structures, whereas CuIn0.7Ga0.3S2, CuIn0.5Ga0.5S2, and CuIn0.3Ga0.7S2 had three wurtzite phases having In-rich, In–Ga, and Ga-rich compositions. The shape of the resulting nanoparticles was either elongated, polygonal, or tadpole depending on the phase composition. In-rich particles had elongated rod-like morphology, the In–Ga particles were irregular hexagonal/ equiaxed, while the Ga-rich phase formed with a tadpole morphology. The bandgap of the wurtzite-CuInxGa1-xS2 increased with Ga substitution: from 1.49 eV for CIS to 2.0 eV for CGS.
MOTIVATION AND LEARNING MODES: TOWARDS AN AUTOMATIC INTELLIGENT EVALUATION OF LEARNER MOTIVATION

This paper presents an experimental learning environment to analyze research questions related to learner’s motivation. Three learning modes are available for the learners; all of them are about the same topic: designing entity-relationship data models. The first learning mode is a hypermedia, the second a set of navigable learning videos with an annotated timeline, and the third one is a graphical design environment offering a range of social activities including assessment of peers’ solutions. Our goal is to study the motivational aspects that come into play in different learning modes to design an intelligent system for automatic evaluation of the learner motivation. We are currently exploring the Hidden Markov Models (HMMs) from artificial intelligence techniques.
Densification-Induced Structure Changes in Basolite MOFs: Effect on Low-Pressure CH4 Adsorption

Metal-organic frameworks’ (MOFs) adsorption potential is significantly reduced by turning the original powder into pellets or granules, a mandatory step for their use at industrial scale. Pelletization is commonly performed by mechanical compression, which often induces the amorphization or pressure-induced phase transformations. The objective of this work is the rigorous study of the impact of mechanical pressure (55.9, 111.8 and 186.3 MPa) onto three commercial materials (Basolite C300, F300 and A100). Phase transformations were determined by powder X-ray diffraction analysis, whereas morphological changes were followed by nitrogen physisorption. Methane adsorption was studied in an atmospheric fixed bed. Significant crystallinity losses were observed, even at low applied pressures (up to 69.9% for Basolite C300), whereas a structural change occurred to Basolite A100 from orthorhombic to monoclinic phases, with a high cell volume reduction (13.7%). Consequently, adsorption capacities for both methane and nitrogen were largely reduced (up to 53.6% for Basolite C300), being related to morphological changes (surface area losses). Likewise, the high concentration of metallic active centers (Basolite C300), the structural breathing (Basolite A100) and the mesopore-induced formation (Basolite F300) smooth the dramatic loss of capacity of these materials.
Distribution Shift Metric Learning for Fine-Grained Ship Classification in SAR Images

Fine-grained ship classification in synthetic aperture radar (SAR) images is a challenging task, since SAR images can only provide limited discriminative information due to the limitation of SAR imaging mechanism. Distance metric learning (DML) methods have the ability to improve the discriminative ability of the feature representations through preserving the supervisory information of ship samples. In this article, we proposed a novel DML method, termed as distribution shift metric learning (DML-ds), which improves the original Laplacian regularized metric learning by adding an interclass distribution shift regularization term. Extensive experiments and in-depth analysis demonstrate that the proposed DML-ds can effectively increase the interclass separability and the intraclass compactness, thereby improving the fine-grained ship classification performance in SAR images, and outperforms most of state-of-the-art methods.
Carbenium ion-mediated oligomerization of methylglyoxal for secondary organic aerosol formation

Significance Secondary organic aerosol (SOA) from photochemical oxidation of volatile organic compounds represents one of the most dominant constituents of fine particulate matter in the troposphere, with profound implications for air quality and climate. However, the fundamental chemical mechanisms leading to SOA formation remain highly uncertain. Here, we show oligomer formation from methylglyoxal with the carbenium ions as the key intermediate using quantum chemical calculations. This cationic oligomerization is demonstrated to proceed via barrierless pathways and occurs at fast rates on weakly acidic aqueous aerosols and/or cloud droplets under typical tropospheric conditions. In contrast to a previously proposed hydration mechanism, out results reveal that the carbenium ion-mediated oligomerization of methylglyoxal provides a major SOA source from anthropogenic and biogenic emissions. Secondary organic aerosol (SOA) represents a major constituent of tropospheric fine particulate matter, with profound implications for human health and climate. However, the chemical mechanisms leading to SOA formation remain uncertain, and atmospheric models consistently underpredict the global SOA budget. Small α-dicarbonyls, such as methylglyoxal, are ubiquitous in the atmosphere because of their significant production from photooxidation of aromatic hydrocarbons from traffic and industrial sources as well as from biogenic isoprene. Current experimental and theoretical results on the roles of methylglyoxal in SOA formation are conflicting. Using quantum chemical calculations, we show cationic oligomerization of methylglyoxal in aqueous media. Initial protonation and hydration of methylglyoxal lead to formation of diols/tetrol, and subsequent protonation and dehydration of diols/tetrol yield carbenium ions, which represent the key intermediates for formation and propagation of oligomerization. On the other hand, our results reveal that the previously proposed oligomerization via hydration for methylglyoxal is kinetically and thermodynamically implausible. The carbenium ion-mediated mechanism occurs barrierlessly on weakly acidic aerosols and cloud/fog droplets and likely provides a key pathway for SOA formation from biogenic and anthropogenic emissions.
Response of Equatorial Ionization in Indian Longitudes to HSSW Driven Geomagnetic Storm

The paper reports the effects of a moderate High Speed Solar Wind (HSSW) driven Corotating Interaction Region (CIR) geomagnetic storm (minimum Dst ≤ -53 nT) on the ionosphere at Hyderabad (17.42°N, 78.55°E geographic, 8.93°N, 152.65°E geomagnetic) during August 4-8, 2019. Hyderabad is situated at geophysically sensitive Equatorial Ionization Anomaly (EIA) region between geomagnetic equator and northern crest of EIA. The results yield positive enhancement of Total Electron Content (TEC) during the main phase of the storm (August 5, 2019, increment of VTEC: 8.17 TECU). The effects of Disturbed Dynamo Electric Field (DDEF) were also observed during the recovery phase of the storm (August 6, 2019, decrement of VTEC: 7.56 TECU). Another TEC enhancement was observed during the recovery phase of the storm (August 7, 2019, increment of VTEC: 4.25 TECU). This could possibly be explained by the day-to-day variabilities of TEC at low latitudes and the impact of fading geomagnetic storm intensity coupled with strong solar wind.
The Warburg Effect Promotes Mitochondrial Injury Regulated by Uncoupling Protein-2 in Septic Acute Kidney Injury

Supplemental Digital Content is available in the text ABSTRACT Background: Evidence implying that metabolism reprogramming plays an important role in the regulation of sepsis is increasing; however, whether it has a similar role in septic organ dysfunction remains unclear. Here, we provide evidence to support a new role of uncoupling protein-2 (UCP2)-regulated Warburg effect, i.e., aerobic glycolysis, in promoting mitochondrial injury in the kidney. Methods: To imitate sepsis condition, male C57BL/6 mice were operated by the cecal ligation puncture in vivo, whereas a normal human kidney cell line (HK-2) was treated with lipopolysaccharide in vitro. UCP2 small interfering RNA pretreatment was performed to knock down UCP2 expression in vitro. The glycolysis metabolite was detected by liquid chromatography/tandem mass spectrometry in vivo and detected by commercial kits in vitro. Oxidative phosphorylation level and glycolysis level were monitored by measuring the oxygen consumption rate (indicative of respiration) and extracellular acidification rate (indicative of glycolysis) in vitro. Exogenous lactate was supplied to stimulate HK-2 cells and indicators of mitochondrial dysfunction were also assessed. Results: Aerobic glycolysis is enhanced in septic tubular epithelial cells, and the glycolysis inhibitor 2-deoxyglucose can partially restore mitochondrial membrane potential and decrease the reactive oxygen species production. With the knockdown of UCP2, the aerobic glycolysis level upregulates, and mitochondrial injury increases. Conclusions: These results provide insights on a new mechanism of metabolic regulation of mitochondrial injury and the importance of targeting aerobic glycolysis for the treatment of septic acute kidney injury.