Miracle-dz/UniFAR-FTUs huggingface dataset:
Epidemiology of clinically suspected and laboratory-confirmed bloodstream infections at a South African neonatal unit.

INTRODUCTION Data from Africa reporting the epidemiology of infection in hospitalised neonates are limited. METHODOLOGY A prospective study with convenience sampling was conducted to characterise neonates investigated with blood culture/s for suspected infection at a 132-bed neonatal unit in Cape Town, South Africa (1 February-31 October 2018). Enrolled neonates were classified as having proven bloodstream infection (BSI) (blood culture-positive with a pathogen) or presumed infection (clinically suspected but blood culture-negative) or as potentially at risk of infection (maternal risk factors at birth). RESULTS Of 1299 hospitalised neonates with >1 blood culture sampling episode, 712 (55%) were enrolled: 126 (17.7%) had proven BSI; 299 (42%) had presumed infection and 287 (40.3%) were potentially at risk of infection. Neonates with proven BSI had lower birth weight and higher rates of co-existing surgical conditions versus the presumed/potential infection groups (p < 0.001). Median onset of proven BSI versus presumed infection was at 8 (IQR = 5-13) and 1 (IQR = 0-5) days respectively (p < 0.001). Most proven BSI were healthcare-associated (114/126; 90.5%), with Klebsiella pneumoniae (80.6% extended-spectrum β-lactamase producers) and Staphylococcus aureus (66.7% methicillin-resistant) predominating. Mortality from proven BSI (34/126; 27%) was substantially higher than that observed in presumed (8/299; 2.7%) and potential infections (3/287; 1.0%) (p < 0.001). The odds of death from proven BSI was 3-fold higher for Gram-negatives than for Gram-positive/fungal pathogens (OR = 3.23; 95% CI = 1.17-8.92). CONCLUSIONS Proven BSI episodes were predominantly healthcare-associated and associated with a high case fatality rate. Most neonates with presumed infection or at potential risk of infection had favourable 30-day outcomes.
Prediction of Liver Transplant Rejection With a Biologically Relevant Gene Expression Signature

Background. Noninvasive biomarkers distinguishing early immune activation before acute rejection (AR) could more objectively inform immunosuppression management in liver transplant recipients (LTRs). We previously reported a genomic profile distinguishing LTR with AR versus stable graft function. This current study includes key phenotypes with other causes of graft dysfunction and uses a novel random forest approach to augment the specificity of predicting and diagnosing AR. Methods. Gene expression results in LTRs with AR versus non-AR (combination of other causes of graft dysfunction and normal function) were analyzed from single and multicenter cohorts. A 70:30 approach (61 ARs; 162 non-ARs) was used for training and testing sets. Microarray data were normalized using a LT-specific vector. Results. Random forest modeling on the training set generated a 59-probe classifier distinguishing AR versus non-AR (area under the curve 0.83; accuracy 0.78, sensitivity 0.70, specificity 0.81, positive predictive value 0.54, negative predictive value [NPV] 0.89; F-score 0.61). Using a locked threshold, the classifier performed well on the testing set (accuracy 0.72, sensitivity 0.67, specificity 0.73, positive predictive value 0.48, NPV 0.86; F-score 0.56). Probability scores increased in samples preceding AR versus non-AR, when liver function tests were normal, and decreased following AR treatment (P < 0.001). Ingenuity pathway analysis of the genes revealed a high percentage related to immune responses and liver injury. Conclusions. We have developed a blood-based biologically relevant biomarker that can be detected before AR-associated graft injury distinct from LTR never developing AR. Given its high NPV (“rule out AR”), the biomarker has the potential to inform precision-guided immunosuppression minimization in LTRs.
Dysregulation of energy homeostasis in amyotrophic lateral sclerosis

Purpose of review Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease targeting upper and lower motor neurons, inexorably leading to an early death. Defects in energy metabolism have been associated with ALS, including weight loss, increased energy expenditure, decreased body fat mass and increased use of lipid nutrients at the expense of carbohydrates. We review here recent findings on impaired energy metabolism in ALS, and its clinical importance. Recent findings Hypothalamic atrophy, as well as alterations in hypothalamic peptides controlling energy metabolism, have been associated with metabolic derangements. Recent studies showed that mutations causing familial ALS impact various metabolic pathways, in particular mitochondrial function, and lipid and carbohydrate metabolism, which could underlie these metabolic defects in patients. Importantly, slowing weight loss, through high caloric diets, is a promising therapeutic strategy, and early clinical trials indicated that it might improve survival in at least a subset of patients. More research is needed to improve these therapeutic strategies, define pharmacological options, and refine the population of ALS patients that would benefit from these approaches. Summary Dysfunctional energy homeostasis is a major feature of ALS clinical picture and emerges as a potential therapeutic target.
Salt‐tolerant cation exchanger‐containing sulfate groups as a viable alternative for mixed‐mode type and heparin‐based affinity resins

Ion‐exchange chromatography is still one of the most popular protein separation techniques. Before chromatographic separation, the high salt concentration in various samples necessitates additional steps. Therefore, low salt tolerance of ion‐exchange resins is a drawback that needs to be addressed. Herein, the differences in salt tolerance and hydrophobicity of strong cation‐exchange TOYOPEARL resins of sulfonium and sulfate‐types were investigated. Despite only a minor structural difference, differences in selectivity and salt tolerance between the sulfate and sulfonic groups were detected. In silico calculations were also carried out for model substances representing the sulfonium and sulfate groups, wherein significant differences in hydrophobicity was observed. These experiments confirmed the hypothesis that the salt tolerance, higher affinity, and selectivity for certain vitamin K dependent clotting factors are interrelated and dependent on the presence of the sulfate group. Separation of clotting factor IX from the prothrombin complex concentrate further to confirmed the affinity for these proteins. The results show that the use of only a resin with the sulfate ligand and not with the sulfonic acid ligand allows for a facile and rapid separation of clotting factor IX and other vitamin K dependent clotting factors.
Net energy value of canola meal, field pea, and wheat millrun fed to growing-finishing pigs.

Two experiments were conducted to (1) determine NE values of soybean meal (SBM), Napus canola meal (NCM), Juncea canola meal (JCM), field pea, and wheat millrun (WM) using indirect calorimetry, and (2) compare the determined NE values with the calculated NE values of the same feedstuffs based on a prediction equation. In Experiment 1, 6 ileal-cannulated barrows (31 kg) were fed 5 diets in 5 × 6 Youden square to give 6 replicates per diet. Diets were cornstarch-based diets containing soybean meal (SBM), NCM, JCM, field pea, or WM. The SBM was included as a reference. In Experiment 2, 6 ileal-cannulated barrows (70 kg) were fed a N-free diet for determining energy digestibility and NE values of test feedstuffs fed in Experiment 1 by difference method. The NE values of test feedstuffs were also calculated from the DE values and analyzed macronutrient content of the test feedstuffs (NRC, 2012). On DM basis, SBM, NCM, JCM, field pea, and WM contained 51, 41, 42, 28, and 18% CP; 1.52, 2.95, 2.36, 1.33, and 3.12% ether extract; 2.93, 0.14, 1.44; 36.7, and 28.7% starch; and 5.30, 21.0, 13.4, 9.49, and 16.1% ADF, respectively. The determined NE value for SBM (2.29 Mcal/kg) did not differ from that of NCM (1.72 Mcal/kg DM) or JCM (2.14 Mcal/kg DM). The NCM and JCM did not differ in NE value. Also, the determined NE value did not differ between field pea (2.00 Mcal/kg) and WM (2.55 Mcal/kg). The calculated NE values for SBM (2.18 Mcal/kg DM), NCM (1.73 Mcal/kg DM), and JCM (1.86 Mcal/kg DM) did not differ from the corresponding determined NE values of the same feedstuffs. However, the calculated NE value for field pea (2.51 Mcal/kg DM) was greater (P = 0.004) than the determined NE value of field pea, whereas the calculated NE value for WM (2.27 Mcal/kg DM) tended to be lower (P = 0.054) than the determined NE value of WM. In conclusion, the NE value for SBM and canola meals can be predicted based on the DE value and the macronutrient composition of the same feedstuffs. However, the NE value for field pea and WM may not be predicted precisely based on the DE value and the macronutrient composition of the same feedstuffs.
Ambient Temperature as a Strong Zeitgeber of Circadian Rhythms in Response to Temperature Sensitivity and Poor Heat Dissipation Abilities in Subterranean African Mole-Rats

Mammals have evolved circadian rhythms in internal biological processes and behaviors, such as locomotor activity (LA), to synchronize to the environmental conditions they experience. Photic entrainment of LA has been well established; however, non-photic entrainment, such as ambient temperature (Ta), has received much less attention. To address this dearth of knowledge, we exposed two subterranean endothermic-homeothermic African mole-rat species, the solitary Cape mole-rat (Georychus capensis [GC]) and social Mahali mole-rat (Cryptomys hottentotus mahali [CHM]), to varying Ta cycles in the absence of light. We showed that the LA rhythms of these two species entrain to Ta cycles and that the majority of LA occurred during the coolest 12-h period. LA confined to the coolest Ta periods may be the direct consequence of the poor heat dissipation abilities of African mole-rats brought about by physiological and ecological constraints. Recently, it has been hypothesized that Ta is only a strong zeitgeber for circadian rhythms in species whose thermoregulatory abilities are sensitive to changes in Ta (i.e., heterotherms and ectotherms), which previously has excluded endothermic-homeothermic mammals. However, this study demonstrates that Ta is a strong zeitgeber or entrainer for circadian rhythms of LA in subterranean endothermic-homeothermic mammals as a consequence of their sensitivity to changes in Ta brought about by their poor heat dissipation abilities. This study reinforces the intimate link between circadian rhythms and thermoregulation and conclusively, for the first time, provides evidence that Ta is a strong zeitgeber for endothermic-homeothermic mammals.
Identification of four gastric cancer subtypes based on genetic analysis of cholesterogenic and glycolytic pathways

ABSTRACT Warburg phenomenon refers to the development of unique metabolic patterns during the growth of tumor cells. This study stratified gastric cancer into prognostic metabolic subgroups according to changes in gene expressions related to glycolysis and cholesterol synthesis. The RNA-seq expression data, single nucleotide variants (SNV), short insertions and deletions (InDel) mutation data, copy number variation (CNV) data and clinical follow-up information data of gastric cancer tissues were downloaded from The Cancer Genome Atlas (TCGA) database. ConsensusClusterPlus was used to stratify the metabolic subtypes of gastric cancer. Four metabolic subtypes (Cholesterogenic, Glycolytic, Mixed and Quiescent) of gastric cancer were identified, and patients with cholesterogenic tumors had the longest disease-specific survival (DSS). Genome-wide analysis showed that aberrant amplification of TP53 and MYC in gastric cancer was associated with abnormal cholesterol anabolic metabolism. The mRNA levels of mitochondrial pyruvate carriers 1 and 2 (MPC1/2) differed among the four subtypes. Tumors in the glycolytic group showed a higher PDCD1. A genomic signature based on tumor metabolism of different cancer types was established. This study showed that genes related to glucose and lipid metabolism play an important role in gastric cancer and facilitate a personalized treatment of gastric cancer. GRAPHICAL ABSTRACT
Dual targeting of CTLA-4 and CD47 on Treg cells promotes immunity against solid tumors

Selective CD47 blockade on CTLA-4high tumor-infiltrating Treg cells reduces systemic toxicity and enhances antitumor immunity. Targeting Treg cells Depletion of regulatory T (Treg) cells is an attractive strategy to promote antitumor immunity. One strategy that could deplete Treg cells is blockade of the “do not eat me” signal, CD47, which prevents Treg cells from being targets of phagocytosis. However, CD47 is broadly expressed, making Treg cell–specific targeting difficult. To selectively deplete Treg cells, Zhang et al. designed a heterodimer that combines an anti–cytotoxic T lymphocyte antigen 4 (CTLA-4) antibody, which targets intratumoral Treg cells, and the CD47 ligand, signal regulatory protein α (SIRPα). Treatment with this heterodimer increased phagocytosis of Treg cells, leading to their depletion, and promoted antitumor immunity in mouse models. Thus, dual targeting of CD47 and CTLA-4 selectively depletes Treg cells and can promote immune responses against solid tumors. Blockade of CD47, the “do not eat me” signal, has limited effects in solid tumors despite its potent antitumor effects in hematopoietic malignancies. Taking advantage of the high expression of cytotoxic T lymphocyte–associated protein 4 (CTLA-4) on Treg cells and abundant Fc receptor–expressing active phagocytes inside the tumor microenvironment (TME), we designed and tested a heterodimer combining an anti–CTLA-4 antibody, which targets Treg cells, with the CD47 ligand, signal regulatory protein α (SIRPα), to selectively block CD47 on intratumoral Treg cells. We hypothesized that heterodimer treatment would increase antibody-dependent cellular phagocytosis of the targeted Treg cells. We found that anti–CTLA-4×SIRPα preferentially depleted ICOShigh immunosuppressive Treg cells in the TME and enhanced immunity against solid tumors, including MC38 and CT26 murine colon cancers. Mechanistically, we found that CD47 expression on Treg cells limited anti–CTLA-4–mediated depletion and Fc on the heterodimer-enhanced depletion. Furthermore, anti-human CTLA-4×SIRPα depleted tumor Treg cells and exhibits less toxicity than anti-human CTLA-4 in a humanized mouse model. Collectively, these results demonstrate that simultaneously modulating both “eat me” and do not eat me signals induces Treg cell depletion inside the TME and may be an effective strategy for treating solid tumors.
A satellite selection algorithm based on adaptive simulated annealing particle swarm optimization for the BeiDou Navigation Satellite System/Global Positioning System receiver

In this article, we propose a new particle swarm optimization–based satellite selection algorithm for BeiDou Navigation Satellite System/Global Positioning System receiver, which aims to reduce the computational complexity of receivers under the multi-constellation Global Navigation Satellite System. The influences of the key parameters of the algorithm—such as the inertia weighting factor, acceleration coefficient, and population size—on the performance of the particle swarm optimization satellite selection algorithm are discussed herein. In addition, the algorithm is improved using the adaptive simulated annealing particle swarm optimization (ASAPSO) approach to prevent converging to a local minimum. The new approach takes advantage of the adaptive adjustment of the evolutionary parameters and particle velocity; thus, it improves the ability of the approach to escape local extrema. The theoretical derivations are discussed. The experiments are validated using 3-h real Global Navigation Satellite System observation data. The results show that in terms of the accuracy of the geometric dilution of precision error of the algorithm, the ASAPSO satellite selection algorithm is about 86% smaller than the greedy satellite selection algorithm, and about 80% is less than the geometric dilution of precision error of the particle swarm optimization satellite selection algorithm. In addition, the speed of selecting the minimum geometric dilution of precision value of satellites based on the ASAPSO algorithm is better than that of the traditional traversal algorithm and particle swarm optimization algorithm. Therefore, the proposed ASAPSO algorithm reduces the satellite selection time and improves the geometric dilution of precision using the selected satellite algorithm.
Thermal Properties of Fullerene С56

The behavior of С56 fullerene when heated in a nitrogen atmosphere at a pressure of 105 Pa was studied using computer thermodynamic modeling. The modeling consisted in a complete thermodynamic analysis of the system using the TERRA software package, which is one of the most developed and efficient ones that implements such thermodynamic calculations. Experiment temperature ranges are from 273 to 3373 К. Based on the calculated data, a graph of the carbon balance in the С56-N2 system was constructed, the ongoing physicochemical processes were described, divided into four classes: sublimation, dissociation in the gas phase, chemical reactions occurring in the gas phase, dissociation and chemical reaction in the gas phase. Temperature intervals of reactions are identified. The equilibrium constants of the reactions are calculated and described, as well as the coefficients of these constants are found using the least squares method. The temperature interval of thermal stability of the condensed C56 fullerene and C56 vapors is defined. This work is one of the series of works on the properties of nanoparticles, in the future it is planned to study the thermal properties of higher fullerenes. The data obtained can be used to determine the explosive and fire hazardous properties of fullerenes as a dispersed solid.
Support Vector Machine (SVM)-Based Optimal Design Procedure of Fly Ash Blended Concrete

A support vector machine (SVM) is widely used for predicting the properties of fly ash blended concrete. However, the studies about the optimal design of fly ash blended concrete based on SVM are very limit. This study shows an SVM-based optimal design procedure of fly ash blended concrete. First, we built an SVM model and evaluated the compressive strength of fly ash blended concrete considering the effects of water to binder ratio, fly ash replacement ratio, and test ages. Second, we made parameter studies based on the SVM model. The parameter studies show that fly ash can improve the late age strength of concrete. This improvement is obvious for concrete with lower water to binder ratio. The optimal fly ash replacement ratio increases as the water to binder ratio decreases.
Utilization of Fly Ash in the Synthesis of Refractory Forsterite-Spinel Ceramics

Forsterite refractory ceramics is utilized in the metallurgical and cement industries as a lining of metallurgical furnaces and rotary kilns for its high refractoriness up to 1850°C and refractoriness under load above 1600°C. Another significant property of forsterite is its coefficient of linear thermal expansion utilized in the electrotechnical industry for ceramic-metal joints. Addition of aluminium oxide into the raw material mixture results in creation of magnesium-alumina spinel (MgO·Al2O3) which improves sintering, thermal shock resistance and mechanical properties in comparison with pure forsterite ceramics. Inexpensive source of aluminium oxide is fly ash. Utilization of fly ash, secondary energetic product of coal-burning power plants, is important for the environment and sustainable development. This paper evaluated properties of fly ash-based forsterite-spinel ceramics in comparison with alumina-based forsterite-spinel ceramics. Forsterite-spinel ceramics was synthesized from olivine, calcined magnesite and fly ash/alumina powders. XRD analysis was used to determine mineralogical composition, thermal analyses were used to determine the behaviour during firing and scanning electron microscopy to determine the morphology of crystal phases. Refractoriness of pyrometric cones, refractoriness under load, thermal shock resistance, coefficient of linear thermal expansion, water absorption, porosity and modulus of rupture were also determined on fired test samples.
In silico gene knockout prediction using a hybrid of Bat algorithm and minimization of metabolic adjustment

Abstract Microorganisms commonly produce many high-demand industrial products like fuels, food, vitamins, and other chemicals. Microbial strains are the strains of microorganisms, which can be optimized to improve their technological properties through metabolic engineering. Metabolic engineering is the process of overcoming cellular regulation in order to achieve a desired product or to generate a new product that the host cells do not usually need to produce. The prediction of genetic manipulations such as gene knockout is part of metabolic engineering. Gene knockout can be used to optimize the microbial strains, such as to maximize the production rate of chemicals of interest. Metabolic and genetic engineering is important in producing the chemicals of interest as, without them, the product yields of many microorganisms are normally low. As a result, the aim of this paper is to propose a combination of the Bat algorithm and the minimization of metabolic adjustment (BATMOMA) to predict which genes to knock out in order to increase the succinate and lactate production rates in Escherichia coli (E. coli).
The effect of nonlinear drag on the rise velocity of bubbles in turbulence

Abstract We investigate how turbulence in liquid affects the rising speed of gas bubbles within the inertial range. Experimentally, we employ stereoscopic tracking of bubbles rising through water turbulence created by the convergence of turbulent jets and characterized with particle image velocimetry performed throughout the measurement volume. We use the spatially varying, time-averaged mean water velocity field to consider the physically relevant bubble slip velocity relative to the mean flow. Over a range of bubble sizes within the inertial range, we find that the bubble mean rise velocity $\left \langle v_z \right \rangle$ decreases with the intensity of the turbulence as characterized by its root-mean-square fluctuation velocity, $u'$. Non-dimensionalized by the quiescent rise velocity $v_{q}$, the average rise speed follows $\left \langle v_z \right \rangle /v_{q}\propto 1/{\textit {Fr}}$ at high ${\textit {Fr}}$, where ${\textit {Fr}}=u'/\sqrt {dg}$ is a Froude number comparing the intensity of the turbulence to the bubble buoyancy, with $d$ the bubble diameter and $g$ the acceleration due to gravity. We complement these results by performing numerical integration of the Maxey–Riley equation for a point bubble experiencing nonlinear drag in three-dimensional, homogeneous and isotropic turbulence. These simulations reproduce the slowdown observed experimentally, and show that the mean magnitude of the slip velocity is proportional to the large-scale fluctuations of the flow velocity. Combining the numerical estimate of the slip velocity magnitude with a simple theoretical model, we show that the scaling $\left \langle v_z \right \rangle /v_{q}\propto 1/{\textit {Fr}}$ originates from a combination of the nonlinear drag and the nearly isotropic behaviour of the slip velocity at large ${\textit {Fr}}$ that drastically reduces the mean rise speed.