Miracle-dz/UniFAR-FTUs huggingface dataset:
Experimental investigation of dynamic response of acoustically forced turbulent premixed CH 4 /CO 2 /air flames

Increasing demand for energy and continuing increase in environmental as well as financial cost of use of fossil fuels drive the need for utilization of fuels from sustainable sources for power generation. Development of fuel-flexible combustion systems is vital in enabling the use of sustainable fuels. It is also important that these sustainable combustion systems meet the strict governmental emission legislations. Biogas is considered as one of the viable sustainable fuels that can be used to power modern gas turbines: However, the change in chemical, thermal and transport properties as well as change in Wobbe index due to the variation of the fuel constituents can have a significant effect on the performance of the combustor. It is known that the fuel properties have strong influence on the dynamic flame response; however there is a lack of detailed information regarding the effect of fuel compositions on the sensitivity of the flames subjected to flow perturbations. In this study, we describe an experimental effort investigating the response of premixed biogas-air turbulent flames with varying proportions of CH 4 and CO 2 to velocity perturbations. The flame was stabilized using a centrally placed conical bluff body. Acoustic perturbations were imposed to the flow using loud speakers. The flame dynamics and the local heat release rate of these acoustically excited biogas flames were studied using simultaneous measurements of OH and H 2 CO planar laser induced fluorescence. OH* chemiluminescence along with acoustic pressure measurements were also recorded to estimate the total flame heat release modulation and the velocity fluctuations. The measurements were carried out by keeping the theoretical laminar flame speed constant while varying the bulk velocity and the fuel composition. The results indicate that the flame sensitivity to perturbations increased with increased dilution of CH 4 by CO 2 at low amplitude forcing, while at high amplitude forcing conditions the magnitude of the flame response was independent of dilution.
Tadpole species have variable roles in litter breakdown, sediment removal, and nutrient cycling in a tropical stream

Quantifying the influence of biodiversity on ecosystem function is an increasingly important goal as biodiversity declines. Tadpoles can be important contributors to ecosystem processes in streams, so amphibian declines over recent decades may have far-reaching ecosystem effects. We, therefore, used artificial channels located near an Australian rainforest stream to assess how the tadpoles of 2 frog species affect leaf litter decay, sediment bioturbation, and nutrient cycling in the presence and absence of invertebrates. Mixophyes coggeri (Myobatrachidae) tadpoles did not increase leaf mass loss, but were important in sediment removal, which benefits smaller consumers. In contrast, high densities of Litoria serrata (Hylidae) tadpoles increased leaf mass loss, possibly because their excretion of nutrients facilitated decomposition, but were not important in sediment removal. However, we found no effect of nutrient excretion by L. serrata tadpoles on the nutrient quality of leaves and sediments, or on biofilm growth, even though L. serrata tadpoles and invertebrates together appeared to remove significant quantities of nutrients from sediment. Our results show that tadpoles of different species can have different functional roles in the ecosystem, which need to be taken into account when assessing the influence of amphibian declines on ecosystem processes.
Automatic Facial Landmark Localization in Clinical Populations - Improving Model Performance with a Small Dataset

Background Automatic facial landmark localization in videos is an important first step in many computer vision applications, including the objective assessment of orofacial function. Convolutional neural networks (CNN) for facial landmarks localization are typically trained on faces of healthy and young adults, so model performance is inferior when applied to faces of older adults or people with diseases that affect facial movements, a phenomenon known as algorithmic bias. Fine-tuning pre-trained CNN models with representative data is a well-known technique used to reduce algorithmic bias and improve performance on clinical populations. However, the question of how much data is needed to properly fine-tune the model remains. Methods In this paper, we fine-tuned a popular CNN model for automatic facial landmarks localization using different number of manually annotated photographs from patients with facial palsy and evaluated the effects of the number of photographs used for model fine-tuning in the model performance by computing the normalized root mean squared error between the facial landmarks positions predicted by the model and those provided by manual annotators. Furthermore, we studied the effect of annotator bias by fine-tuning and evaluating the model with data provided by multiple annotators. Results Our results showed that fine-tuning the model with as little as 8 photographs from a single patient significantly improved the model performance on other individuals from the same clinical population, and that the best performance was achieved by fine-tuning the model with 320 photographs from 40 patients. Using more photographs for fine-tuning did not improve the model performance further. Regarding the annotator bias, we found that fine-tuning a CNN model with data from one annotator resulted in models biased against other annotators; our results also showed that this effect can be diminished by averaging data from multiple annotators. Conclusions It is possible to remove the algorithmic bias of a\textbf{depth} CNN model for automatic facial landmark localization using data from only 40 participants (total of 320 photographs). These results pave the way to future clinical applications of CNN models for the automatic assessment of orofacial function in different clinical populations, including patients with Parkinson’s disease and stroke.
Characterization and Function of Islet Antigen Presenting Cells during NOD Diabetes

Autoimmune diabetes is characterized by inflammatory infiltration; however, the initiating events are poorly understood. We found that the islets of Langerhans in young nonobese diabetic (NOD) mice contained two antigen-presenting cell (APC) populations: a major macrophage and a minor CD103 dendritic cell (DC) population. By 4 weeks of age, CD4 T cells entered islets coincident with an increase in CD103 DCs. In order to examine the role of the CD103 DCs in diabetes, we examined Batf3-deficient NOD mice that lacked the CD103 DCs in islets and pancreatic lymph nodes. This led to a lack of autoreactive T cells in islets and, importantly, no incidence of diabetes. Additional examination revealed that presentation of major histocompatibility complex (MHC) class I epitopes in the pancreatic lymph nodes was absent with a partial impairment of MHC class II presentation. Altogether, this study reveals that CD103 DCs are essential for autoimmune diabetes development.
Fish conservation in the land of steppe and sky: Evolutionarily significant units of threatened salmonid species in Mongolia mirror major river basins

Abstract Mongolia's salmonids are suffering extensive population declines; thus, more comprehensive fisheries management and conservation strategies are required. To assist with their development, a better understanding of the genetic structure and diversity of these threatened species would allow a more targeted approach for preserving genetic variation and ultimately improve long‐term species recoveries. It is hypothesized that the unfragmented river basins that have persisted across Mongolia provide unobstructed connectivity for resident salmonid species. Thus, genetic structure is expected to be primarily segregated between major river basins. We tested this hypothesis by investigating the population structure for three salmonid genera (Hucho, Brachymystax and Thymallus) using different genetic markers to identify evolutionarily significant units (ESUs) and priority rivers to focus conservation efforts. Fish were assigned to separate ESUs when the combined evidence of mitochondrial and nuclear data indicated genetic isolation. Hucho taimen exhibited a dichotomous population structure forming two ESUs, with five priority rivers. Within the Brachymystax genus, there were three B. lenokESUs and one B. tumensisESU, along with six priority rivers. While B. tumensiswas confirmed to display divergent mtDNA haplotypes, haplotype sharing between these two congeneric species was also identified. For T. baicalensis,only a single ESU was assigned, with five priority rivers identified plus Lake Hovsgol. Additionally, we confirmed that T. nigrescens from Lake Hovsgol is a synonym of T. baicalensis. Across all species, the most prominent pattern was strong differentiation among major river basins with low differentiation and weak patterns of isolation by distance within river basins, which corroborated our hypothesis of high within‐basin connectivity across Mongolia. This new genetic information provides authorities the opportunity to distribute resources for management between ESUs while assigning additional protection for the more genetically valuable salmonid rivers so that the greatest adaptive potential within each species can be preserved.
Biochemical evidence that the Dlk1 and Grb10 signalling proteins interact through a common growth regulatory pathway

• Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.
Modulation of rpoS fitness by loss of cpdA activity during stationary-phase in Escherichia coli

Experimental evolution of Escherichia coli in one month long stationary-phase in lysogeny broth batch cultures repeatedly selected mutations in the genes for the stationary-phase sigma factor RpoS and the cAMP phosphodiesterase CpdA. The founder strain carried a previously identified allele of rpoS, referred to as rpoS819, a partially functional variant that confers growth advantage in stationary-phase (GASP). The 46 base duplication at the 3’ end of rpoS819 produces a longer protein present at very low levels compared to wild type RpoS. A new rpoS variant rpoS92, carrying a re-duplication of the original duplication in rpoS819, arose during the first week of our evolution experiment. In rpoS92, an in-frame stop codon truncated RpoS819 creating a shorter RpoS92 whose levels are restored to that of wild type RpoS. Transcription profiling of rpoS92 indicated a shift in gene-expression to that of wild-type rpoS, reversing some of the expression trends of rpoS819. Δ3cpdA, carrying an in-frame three base deletion, had arisen late in our evolution experiment. It is a loss of function mutation, which elevates cAMP levels. Using mixed culture competition experiments, we demonstrate that rpoS92 confers GASP, whereas Δ3cpdA confers relatively modest GASP in comparison to the ancestral rpoS819. Δ3cpdA mediates epistatic repression of rpoS92 GASP. The original survivor carrying both rpoS92 and Δ3cpdA besides other mutations displays robust GASP, highlighting the role of these additional mutations in reversing the epistatic interaction between Δ3cpdA and rpoS92. In 10- and 20-day old spent media, there is a reduction in the competitive fitness of rpoS92, which is arrested by Δ3cpdA. Thus the activity of RpoS fluctuates via genetic mutations in deep stationary phase, and additional mutations in CpdA helps modulate the competitive fitness of RpoS variants.
Assessment of minerals composition of natural salt licks, in Kainji Lake National Park, Nigeria

The study was carried out to determine the quantities of essential elements composition of natural salt lick, at the three (3) different horizons in Oli range, Borgu sector of Kainji lake national park. Field survey and focus group discussion were used through the help of experienced park rangers to locate the commonly utilized saltlick spots. Nine (9) samples of soil were collected from three (3) different spots, two (2) saltlick spots and one (1) control spot each from three horizons (O, A, & E). Mineral element were determined for soil pH. , potassium, sodium, calcium, magnesium, organic carbon, organic matter nitrogen were used respectively. Analysis of variance (ANOVA) and Duncan Multiple Range test was used to compare themeans. Results indicated that calcium content of the saltlick at second horizon (A layer) was (15.13± 0.81b) differs significantly (p<0.05) from calcium content of the saltlick at first and third horizon (O layer) (4.03±0.81a) and E layers (1.53 ± 0.81a) respectively. Magnesium content followed the same trend. Layer (A) was where high concentration of salt-licking was observed in all the spots sampled. The study also revealed that natural licks had higher level of essential elements than the control samples. Keywords: Salt lick, Mineral elements, Horizon and Soil Profile
Comparison of Approaches to the identification of Symptom Burden in Hemodialysis Patients Utilizing Electronic Health Records

Background Identification of symptoms is challenging with surveys, which are time-intensive and low-throughput. Natural language processing (NLP) could be utilized to identify symptoms from narrative documentation in the electronic health record (EHR). Methods We utilized NLP to parse notes for maintenance hemodialysis (HD) patients from two EHR databases (BioMe and MIMIC-III) to identify fatigue, nausea/vomiting, anxiety, depression, cramping, itching, and pain. We compared NLP performance with International Classification of Diseases (ICD) codes and validated the performance of both NLP and codes against manual chart review in a representative subset. Results We identified 1034 and 929 HD patients from BioMe and MIMIC-III respectively. The most frequently identified symptoms by NLP from both cohorts were fatigue, pain, and nausea and/or vomiting. NLP was significantly more sensitive than ICD codes for nearly all symptoms. In the BioMe dataset, sensitivity for NLP ranged from 0.85-0.99 vs. 0.09-0.59 for ICD codes. In the MIMIC-III dataset, NLP sensitivity was 0.8-0.98 vs. 0.02-0.53 for ICD. ICD codes were significantly more specific for nausea and/or vomiting (NLP 0.57 vs. ICD 0.97, P=0.03) in BioMe and for depression (NLP 0.67 vs. ICD 0.99, P=0.002) in MIMIC-III. A majority of patients in both cohorts had ? 4 symptoms. The more encounters available for a patient the more likely NLP was to identify a symptom. Conclusions NLP out performed ICD codes for identification of symptoms on several tests parameters including sensitivity for a majority of symptoms. NLP may be useful for the high-throughput identification of patient centered outcomes from EHR. Significance Statement Patients on maintenance hemodialysis experience a high frequency of symptoms. However, symptoms have been measured utilizing time-intensive surveys. This paper compares natural language processing (NLP) to administrative codes for the identification of seven key symptoms from two cohorts with electronic health records and validation through manual chart review. NLP identified high rates of symptoms; the most common were fatigue, pain, and nausea and/or vomiting. A majority of patients had ≥4 symptoms. NLP was significantly more sensitive at identifying symptoms compared to administrative codes for nearly all symptoms but specificity was not significantly different compared to codes. This paper demonstrates utility of a high throughput method of identifying symptoms from EHR which may advance the field of patient centered research in nephrology.
Elucidation of Codon Usage Signatures across the Domains of Life

Due to the degeneracy of the genetic code, multiple codons are translated into the same amino acid. Despite being ‘synonymous’, these codons are not equally used. Selective pressures are thought to drive the choice among synonymous codons within a genome, while GC content, which is generally attributed to mutational drift, is the major determinant of interspecies codon usage bias. Here we find that in addition to the bias caused by GC content, inter-species codon usage signatures can also be detected. More specifically, we show that a single amino acid, arginine, is the major contributor to codon usage bias differences across domains of life. We then exploit this finding, and show that the identified domain-specific codon bias signatures can be used to classify a given sequence into its corresponding domain with high accuracy. Considering that species belonging to the same domain share similar tRNA decoding strategies, we then wondered whether the inclusion of codon autocorrelation patterns might improve the classification performance of our algorithm. However, we find that autocorrelation patterns are not domain-specific, and surprisingly, are unrelated to tRNA reusage, in contrast to the common belief. Instead, our results reveal that codon autocorrelation patterns are a consequence of codon optimality throughout a sequence, where highly expressed genes display autocorrelated ‘optimal’ codons, whereas lowly expressed genes display autocorrelated ‘non-optimal’ codons.
Thermal sensitivity of performance of Phymaturus palluma (Liolaemidae) in the highlands of Aconcagua: vulnerability to global warming in the Andes

Ectotherms are especially vulnerable to climate change due to their dependence on environmental thermal conditions to obtain adequate body temperatures for physiological performance. An approach to predict the impact of global warming in ectotherms is quantifying their locomotor sensitivities to temperature across the thermal performance curves (TPCs) owing to the crucial role running plays on most of their activities, like dispersion, reproduction, and foraging. Here, we have examined the relationship between body temperature (Tb) and locomotor performance in juveniles and adults of the high-mountain lizard Phymaturus palluma. We have determined the speed in long (LR) and sprint runs (SR) at five different body temperatures, and their relationship with morphological traits. In addition, we have measured the operative temperatures in the microenvironments used by P. palluma to evaluate their vulnerability to global warming. For this, we have estimated the thermal safety margin and warming tolerance. Phymaturus palluma showed a left-skewed TPCs for LR and SR. The optimal temperature (To) matched the set point of preferred temperatures and the performance breadth was correlated with the variance in Tb registered in the field, as the thermal coadaptation hypothesis predicts. The rising temperatures projected by the study site could represent a threat for the species, because currently P. palluma experiences operative temperatures that include their performance breadth and To. Moreover, we have demonstrated that the species currently exhibit negative thermal safety margins, thus an increase in ambient temperatures will reduce the amount of time in which lizards could achieve an optimal performance.
Dynamic Aha1 co‐chaperone binding to human Hsp90

Hsp90 is an essential chaperone that requires large allosteric changes to determine its ATPase activity and client binding. Because of the inherent low ATPase activity of human Hsp90, the co-chaperone Aha1, which is the only known ATPase stimulator in eukaryotes, is important for regulation of Hsp90’s allosteric timing. Little is known, however, about the structure of the Hsp90/Aha1 full-length complex. Here, we characterize the solution structure of unmodified human Hsp90 in complex with Aha1 using NMR spectroscopy. We show that the 214 kDa complex adopts multiple conformations in the absence of nucleotide. Interaction with Aha1 induces structural changes near the nucleotide-binding site in Hsp90’s N-terminal domain, providing a basis for its ATPase-enhancing activity. Moreover, the E67K mutation in Aha1 strongly diminishes the interaction, supporting a two-step binding mechanism. Our data reveal important aspects of this pivotal chaperone/co-chaperone interaction and emphasize the relevance of characterizing dynamic chaperone structures in solution.
Energy expenditure and body composition changes after an isocaloric ketogenic diet in overweight and obese men: A secondary analysis of energy expenditure and physical activity

Background Hall et al. (1) tested competing models for the etiology of obesity by measuring the change in energy expenditure (EE) of overweight and obese subjects after being switched from a baseline high-carbohydrate diet (BD) to an isocaloric low-carbohydrate ketogenic diet (KD). EE measured using metabolic chambers increased transiently and by what was considered a relatively small extent after the switch to the KD, whereas EE measured using doubly labeled water (EEDLW) after the response in the chambers had waned increased more substantially. Objective Using the publicly available Hall et al. dataset, we examined the effect of housing conditions on the magnitude of the increase in EEDLW after the switch to the KD and the role of physical activity in that response. Design The 14-day EEDLW measurement period included 4 days when subjects were confined to chambers instead of living on wards. To determine the effect on EEDLW only for the days subjects were living on the wards, we used a formula in Hall et al. to calculate non-chamber EE (EEnonchamber). To assess the role of physical activity in the response to the KD, we analyzed accelerometer data from the BD and KD EEDLW measurement periods. Results In comparison with the increase in 14-day EEDLW of 151 kcal/d ± 63 (P = 0.03) after the switch to the KD, EEnonchamber increased by 203 ± 89 kcal/d (P = 0.04) or, with inclusion of a questionable outlier, by 283 ± 116 kcal/d (P = 0.03). Hip accelerometer counts decreased significantly (P = 0.01) after the switch to the KD, whereas wrist accelerometer counts did not change. Conclusion Switching to the KD increased EEDLW only on non-chamber days to an extent substantially greater than that originally reported. Increased physical activity as measured by accelerometry does not appear to account for this effect.
Investigation of the latitudinal occurrence rate of ionospheric plasma bubble in case of strong and weak pre–reversal enhancement in Southeast Asia

We used ionosonde and GPS receivers during March–April in 2004–2005 and 2011–2015 to investigate the latitudinal variation of equatorial plasma bubble (EPB) occurrence rate in cases of strong and weak pre-reversal enhancement (PRE). The ionosonde at Chumphon in Thailand was used to estimate the PRE strength. Ten GPS receivers in Southeast Asia, ranging from magnetic latitude (ML) of 4.4°S to 21.6°S, were used to investigate the latitudinal variation of EPB occurrence rate. In the case of strong PRE, the EPB occurrence rates decrease from 38.9% to 34.9% at ML of 4.4°S–7.2°S. Continuously, the occurrence rate increases and reaches the peak (44%) at ML of 9.3°S; afterward, the occurrence rate rapidly decreases and reaches below 5% at ML of 21.6°S. In the case of weak PRE, the occurrence rate decreases from 21.8% at ML of 4.4°S, seems constant (15.3%–16%) at ML of 8.2°S–12.1°S, and reaches less than 5% at ML of 16.1°S. Generally, the EPB occurrence rate and its latitudinal extension in case of strong PRE are higher than that in case of weak PRE. Interestingly, we found that the latitudinal occurrence rate peak of the EPB in case of strong is farther than that in case of weak PRE.