Miracle-dz/UniFAR-FTUs huggingface dataset:
Surveillance of small, solid pulmonary nodules at digital chest tomosynthesis: data from a cohort of the pilot Swedish CArdioPulmonary bioImage Study (SCAPIS)

Background Digital tomosynthesis (DTS) might be a low-dose/low-cost alternative to computed tomography (CT). Purpose To investigate DTS relative to CT for surveillance of incidental, solid pulmonary nodules. Material and Methods Recruited from a population study, 106 participants with indeterminate solid pulmonary nodules on CT underwent surveillance with concurrently performed CT and DTS. Nodule size on DTS was assessed by manual diameter measurements and semi-automatic nodule segmentations were independently performed on CT. Measurement agreement was analyzed according to Bland–Altman with 95% limits of agreement (LoA). Detection of nodule volume change > 25% by DTS in comparison to CT was evaluated with receiver operating characteristics (ROC). Results A total of 81 nodules (76%) were assessed as measurable on DTS by two independent observers. Inter- and intra-observer LoA regarding change in average diameter were ± 2 mm. Calculation of relative volume change on DTS resulted in wide inter- and intra-observer LoA in the order of ± 100% and ± 50%. Comparing relative volume change between DTS and CT resulted in LoA of –58% to 67%. The area under the ROC curve regarding the ability of DTS to detect volumetric changes > 25% on CT was 0.58 (95% confidence interval [CI] = 0.40–0.76) and 0.50 (95% CI = 0.35–0.66) for the two observers. Conclusion The results of the present study show that measurement variability limits the agreement between DTS and CT regarding nodule size change for small solid nodules.
Contribution of a GATA4-Expressing Hematopoietic Progenitor Lineage to the Adult Mouse Endothelium

Different sources have been claimed for the embryonic origin of the coronary endothelium. Recently, the potential of circulating cells as progenitors of the cardiac endothelium has also been suggested. In a previous study we have shown that circulating progenitors are recruited by the embryonic endocardium and incorporated into the coronary vessels. These progenitors derive from a mesodermal lineage characterized by the expression of Gata4 under control of the enhancer G2. Herein, we aim to trace this specific lineage throughout postnatal stages. We have found that more than 50% of the adult cardiac endothelium derives from the G2-GATA4 lineage. This percentage increases from embryos to adults probably due to differential proliferation and postnatal recruitment of circulating endothelial progenitors. In fact, injection of fetal liver or placental cells in the blood stream of neonates leads to incorporation of G2-GATA4 lineage cells to the coronary endothelium. On the other hand, labeling of the hematopoietic lineage by the stage E7.5 also resulted in positive coronary endothelial cells from both, embryos and adults. Our results suggest that early hematopoietic progenitors recruited by the embryonic ventricular endocardium can become the predominant source of definitive endothelium during the vascularization of the heart.
Photobiomodulation Therapy on Orthodontic Movement: Analysis of Preliminary Studies with a New Protocol

This study aimed to investigate the effectiveness of photobiomodulation therapy (PBMT) on the acceleration of orthodontic movements, deriving from its biostimulating and regenerative capacity on soft tissues, consequent to the increase in differentiation, proliferation, and activity of cells that are involved with alveolar bone remodeling. The present randomized controlled trial was conducted on six patients who required extractive orthodontic therapy because their ectopic canines had erupted. A total of eight canines were analyzed, four of which received laser irradiation (i.e., experimental group). Two weeks after the extractions, all canines of the experimental and placebo groups were distalized simultaneously and symmetrically with the laceback retraction technique. The PBMT protocol consisted of four cycles of laser applications, one each on days 0, 3, 7, and 14 of the study, with session treatment durations of 2–4 min. The results of the descriptive analysis on the distal displacement speed of the canines after 1 month of follow-up indicate an average displacement of 1.35 mm for the non-irradiated group and 1.98 mm for the irradiated group. Through inferential analysis, a statistically significant difference (p < 0.05) was found between the average speed of the irradiated canines and the control canines. The low energy density laser used in this study, with the parameters set, was found to be a tool capable of statistically significantly accelerating the distal displacement of canines.
Incidence and severity of sorghum anthracnose in Ethiopia.

A two year survey was conducted to determine incidence and severity of sorghum anthracnose in different sorghum growing regions in Ethiopia. A total of 487 fields in 49 districts were surveyed in each of the 2005 and 2007 production season. Incidence of sorghum anthracnose was assessed as the percentage of plants with visible symptoms in a field and anthracnose severity was evaluated as the percentage of leaf area with symptoms. Also, the relationship of the incidence and severity of the disease to the altitude of the fields and weather conditions were determined. Results from the 2 years survey revealed that sorghum anthracnose is present in most (84%) of the survey districts. However, both incidence and severity of the disease varied significantly (p<0.0001) among the survey areas. Anthracnose incidence ranged from 0 to 77% and severity of the disease varied between 0 and 59% on average for the two years. The two year average anthracnose severity classes ranged from trace (<5%) to severe (up to 59%) and the disease was generally more severe in the Southwest and South regions. However, some districts in the East and North Ethiopia also had fields with severe anthracnose infection. It was also found out that the prevailing weather conditions especially rainfall has a significant impact on both anthracnose incidence and severity.
Bioinformatic and experimental evidence for suicidal and catalytic plant THI4s

Like fungi and some prokaryotes, plants use a thiazole synthase (THI4) to make the thiazole precursor of thiamin. Fungal THI4s are suicide enzymes that destroy an essential active-site Cys residue to obtain the sulfur atom needed for thiazole formation. In contrast, certain prokaryotic THI4s have no active-site Cys, use sulfide as sulfur donor, and are truly catalytic. The presence of a conserved active-site Cys in plant THI4s and other indirect evidence implies that they are suicidal. To confirm this, we complemented the Arabidopsis tz-1 mutant, which lacks THI4 activity, with a His-tagged Arabidopsis THI4 construct. LC-MS analysis of tryptic peptides of the THI4 extracted from leaves showed that the active-site Cys was predominantly in desulfurated form, consistent with THI4 having a suicide mech-anism in planta. Unexpectedly, transcriptome datamining and deep proteome profiling showed that barley, wheat, and oat have both a widely expressed canonical THI4 with an active-site Cys, and a THI4-like paralog (non-Cys THI4) that has no active-site Cys and is the major type of THI4 in devel-oping grains. Transcriptomic evidence also indicated that barley, wheat, and oat grains synthesize thiamin de novo, implying that their non-Cys THI4s synthesize thiazole. Structure modeling supported this inference, as did demonstration that non-Cys THI4s have significant capacity to complement thia-zole auxotrophy in Escherichia coli. There is thus a prima facie case that non-Cys cereal THI4s, like their prokaryotic counterparts, are catalytic thiazole synthases. Bioenergetic calculations show that, relative to suicide THI4s, such enzymes could save substantial energy during the grain filling period. Abbreviations DHAla, dehydroalanine; EST, expressed sequence tag; FDR, false discovery rate; IPTG, β-D-1-thiogalactopyranoside
Numerical Analysis and Experimental Study of the Thermal Field in a Power Distribution Block

This paper considers the heating in a closed low-voltage power distribution block by simulation and experiment. For the simulation, Coupled problem electric field-thermal field-fluid mechanics has been solved by means of a computer model, developed in the COMSOL software package. The model takes into account both the thermodynamic processes and the heat exchange through radiation in the volume of the power distribution block, and the heat exchange through radiation and convection towards the environment. Experimental studies have been carried out by means of specially developed computer-controlled experimental setup. Comparison has been made between the obtained numerical and experimental results, related to the heating in the distribution block, and good agreement has been achieved.
Towards a Generic Framework for Lumped Parameters Modelling

This contribution describes some developments towards the construction of a generic framework for reluctance networks. This tool is used for the study of a permanent magnet (PM) machine. The focus will be put on the modelling methodology, and software implementation. More precisely, the aspects related to genericity will be discussed. In order to validate the developed tool, results obtained from this framework are compared to corresponding finite element analyses (FEA).
Talin1 controls dendritic cell activation by regulating TLR complex assembly and signaling

Lim et al. show that the integrin adaptor talin1 controls dendritic cell activation and maturation by promoting the formation of preassembled TLR complexes in steady state and signalosome assembly upon ligand binding via novel direct interactions with MyD88 and PIP5K. Talin1 controls TLR-signaling pathways through scaffolding Myddosome in DCs and thereby influences inflammatory responses in vivo.
Fine-grained Scheduling in FPGA-Based Convolutional Neural Networks

FPGA has been considered as a promising solution to accelerate Convolutional Neural Networks (CNNs) for its excellent performance in energy efficiency and programmability. However, prior designs are usually designed for inference only as designers can map pre-trained models to the hardware in a very efficient way. However, those approaches may not be suitable for training CNN models. In this paper, we propose FConv, in which the CPU and FPGA work together in a fine-grained manner. The FPGA accelerator in FConv uses one Winograd-based convolver, which reduces the design complexity and improves performance. We apply double-buffer for output routine to effectively overlap computation and data transfer. We also integrate multiple PEs to improve data parallelism. We propose our analytical model for prediction and use it as a guide in task scheduling. We find the upper limit of performance under the current design based on the analytical model. We evaluate our design on VGG-16 and Densnet-40 on ImageNet and CIFAR-10. We achieve 262.43 GOP/s on the VGG-16 model, which is $2.13 \times$ of the performance compared to FFT-based implementation on the same platform. We also achieve at most $4 \times$+ performance improvement compared MKL with 20 threads running on 10 core Intel processors.
Laboratory Studies on Effects of Temperature and Delayed Initial Feeding on Development of Striped Bass Larvae

Abstract Rearing temperature and the time of first feeding interacted to determine the degree of survival and rate of growth of larval striped bass (Morone saxatilis) in laboratory experiments. Between 15 and 24 C, lower temperatures reduced the rate of growth and development of fed larvae, and increased the time to death by starvation of unfed larvae. Striped bass larvae survived for several weeks without food following yolk absorption. Unfed groups survived up to 22 days after hatching at 24 C and 32 days at 15 C. Although unfed larvae decreased in length and dry weight during starvation, many recovered and continued development after food was provided. Among starved larvae the rate of loss in weight and length increased with increasing temperature. The growth rate among early and delayed feeding groups was also temperature related. Larvae that survived delayed feeding were indistinguishable on the basis of size and external morphology from younger but well-fed individuals. It is suggested that size alo.
whISOBAXTM Inhibits Bacterial Pathogenesis and Enhances the Effect of Antibiotics

As bacteria are becoming more resistant to commonly used antibiotics, alternative therapies are being sought. whISOBAX (WH) is a witch hazel extract that is highly stable (tested up to 2 months in 37 °C) and contains a high phenolic content, where 75% of it is hamamelitannin and traces of gallic acid. Phenolic compounds like gallic acid are known to inhibit bacterial growth, while hamamelitannin is known to inhibit staphylococcal pathogenesis (biofilm formation and toxin production). WH was tested in vitro for its antibacterial activity against clinically relevant Gram-positive and Gram-negative bacteria, and its synergy with antibiotics determined using checkerboard assays followed by isobologram analysis. WH was also tested for its ability to suppress staphylococcal pathogenesis, which is the cause of a myriad of resistant infections. Here we show that WH inhibits the growth of all bacteria tested, with variable efficacy levels. The most WH-sensitive bacteria tested were Staphylococcus epidermidis, Staphylococcus aureus, Enterococcus faecium and Enterococcus faecalis, followed by Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, Streptococcus agalactiae and Streptococcus pneumoniae. Furthermore, WH was shown on S. aureus to be synergistic to linezolid and chloramphenicol and cumulative to vancomycin and amikacin. The effect of WH was tested on staphylococcal pathogenesis and shown here to inhibit biofilm formation (tested on S. epidermidis) and toxin production (tested on S. aureus Enterotoxin A (SEA)). Toxin inhibition was also evident in the presence of subinhibitory concentrations of ciprofloxacin that induces pathogenesis. Put together, our study indicates that WH is very effective in inhibiting the growth of multiple types of bacteria, is synergistic to antibiotics, and is also effective against staphylococcal pathogenesis, often the cause of persistent infections. Our study thus suggests the benefits of using WH to combat various types of bacterial infections, especially those that involve resistant persistent bacterial pathogens.
Enhancing bacterial survival through phenotypic heterogeneity

The ability of bacterial populations to develop phenotypically heterogeneous subpopulations has been recognized for decades. A recent study found that genetic hallmarks of phenotypic heterogeneity are ubiquitous among bacterial species of the intestinal microbiota [1], underscoring that this is a broadly employed, underappreciated survival strategy for both pathogenic and commensal bacterial species. Phenotypic heterogeneity—functional diversity among genetically identical cells—can permit division of labor and cooperative behaviors or serve as a bet-hedging strategy to help ensure the survival of the population as a whole. Division of labor occurs when biological processes are separated among subpopulations, conferring an overall fitness advantage to the population. For example, the opportunistic pathogen Pseudomonas aeruginosa forms multiple unique cell types that perform specialized roles in the formation of biofilm. Some cells contribute to biofilm extracellular matrix production and initiate biofilm development, while others exhibit surface motility and allow biofilm expansion [2]. In the bet-hedging strategy, incorporating phenotypic variants into a population increases the likelihood that some members will survive a stress. In settings where environmental changes are rapid and stark, phenotypic heterogeneity helps ensure the survival of the population at the expense of individuals not well suited to the current environment, which are selected against and lost. This strategy is advantageous over traditional senseand-respond mechanisms, which require an adaptation time that may be insufficient in the face of sudden or severe environmental changes. Mechanisms of phenotypic heterogeneity may be particularly important in the context of disease, as these mechanisms are more common in hostassociated bacteria than in aquatic or terrestrial species [1].
Ultraviolet-absorbing plastic sheets protect crops from insect pests and from virus diseases vectored by insects.

Crops grown in walk-in tunnels covered with UV-absorbing plastic sheets were highly protected from infestation with sweetpotato whitefly, Bemisia tabaci (Gennadius); western flower thrips, Frankliniella occidentalis (Pergande); and cotton aphid, Aphis gossypii Glover. Protection against B. tabaci was associated with a dramatic reduction in the spread of the whitefly-borne geminivirus tomato yellow leaf curl (TYLCV) and with a pronounced delay in plant infection and disease severity. Two months after transplantation, the average TYLCV disease incidence under 3 different UV-absorbing plastic sheets was 50, 30, and 20% compared with 93% under UV-nonabsorbing polyethylene sheets. In additional experiments, it was shown that the UV-absorbing sheets were also highly effective in the protection of cucumbers against F. occidentalis and A. gossypii . Filtration of full spectrum and monochromatic UV light by UV-absorbing plastic sheets reduced significantly the attraction of B. tabaci to these light sources. The association of the described phenomena with the UV vision of insects is discussed.
Exposure of Intestinal Epithelial Cells to 2′-Fucosyllactose and CpG Enhances Galectin Release and Instructs Dendritic Cells to Drive Th1 and Regulatory-Type Immune Development

Intestinal epithelial cells (IEC) release immunomodulatory galectins upon exposure to CpG DNA (mimicking bacterial triggers) and short-chain galacto- and long-chain fructo-oligosaccharides (GF). This study aims to investigate the immunomodulatory properties of 2′-fucosyllactose (2′-FL), a non-digestible oligosaccharide (NDO) abundantly present in human milk, using a co-culture model developed to study the crosstalk between IEC and innate and adaptive immune cells. IECs, co-cultured with αCD3/CD28-activated peripheral blood mononuclear cells (PBMC), were apically exposed to NDOs and CpG, washed and co-cultured with immature monocyte-derived dendritic cells (moDC). Subsequently, moDC were co-cultured with naïve CD4+ T-cells. In the presence of CpG, both 2′-FL or GF-exposed IEC enhanced Th1-type IFNγ and regulatory IL-10 secretion of PBMCs, compared to CpG alone, while Th2-type IL-13 was reduced. Both NDOs increased IEC-derived galectin-3, -4, -9 and TGF-β1 of CpG-exposed IEC. Only galectin-9 correlated with all modified immune parameters and TGF-β1 secretion. MoDCs exposed to 2′-FL and CpG-conditioned IEC instructed IFNγ and IL-10 secretion by CD4+ T-cells, suggesting the development of a regulatory Th1 response. These results reveal that 2′-FL and GF could contribute to the mucosal immune development by supporting the effect of microbial CpG DNA associated with the modulation of epithelial galectin and TGF-β1 secretion.
Changes in functional status and health-related quality of life in older adults after surgical, interventional, or medical management of acute myocardial infarction.

OBJECTIVES Functional status and health-related quality of life (HRQoL) are important outcomes, particularly among older patients. However, data on such patient-centered outcomes after cardiac surgery are limited. We evaluated the incidence and predictors of decline in functional status and HRQoL among older patients hospitalized for acute myocardial infarction (AMI). METHODS Participants were age 75 years or older hospitalized for AMI at 94 U.S. sites. We examined decline in functional status (defined as decline in 1 or more activities of daily living, ADLs), as well as mental (MCS) and physical component scales (PCS) of the SF-12 to assess HRQoL (5-point decline or greater in each scale) between 1 month prior to the hospitalization and 6 months after. Multivariable model compared the risk of decline after CABG, percutaneous coronary intervention (PCI) and medical management. RESULTS Among 3041 patients (1,708 PCI, 362 CABG, 971 medical management), 1,525 (50.2%) experienced decline in 1 or more domain: 633 (20.8%) declined in ADLs, 786 (25.9%) declined in the MCS, and 1,078 (35.5%) declined in the PCS. The unadjusted incidence of ADL decline was the lowest among patients who underwent CABG (n=50, 13.8%) compared with PCI (n=271, 15.9%) or medical management (n=312, 32.1%). Patients who underwent CABG and PCI had lower adjusted risk of decline in functional and HRQoL compared with those who received medical therapy. The risks after CABG and PCI were not significantly different. CONCLUSIONS Over half of older patients significantly declined in function or HRQoL after AMI. Compared with medical management, risk of decline was lower in those who underwent revascularization.
Ultrasensitive detection of malignant melanoma using PET molecular imaging probes

Significance With the emergence of new therapeutic modalities, the diagnosis of melanoma at the earliest practicable stage has become more important for improving the survival of patients. We developed a positron emission tomography (PET) imaging probe, N-(2-(dimethylamino)ethyl)-5-[18F]fluoropicolinamide ([18F]DMPY2) and evaluated diagnostic performance in animal models. [18F]DMPY2 PET exhibited excellent performance in detecting primary and metastatic melanomas, demonstrating strong/prolonged tumoral uptake and rapid background clearance. This suggests that this radiotracer could be used as a novel PET imaging agent to obtain outstanding image quality in the diagnosis of melanoma. This is the pioneering report of pyridine-based benzamide derivative with reduced alkyl chains in the amine residue and ultrasensitive detection of melanoma lesions in living subjects compared to conventional PET imaging agents. Malignant melanoma has one of the highest mortality rates of any cancer because of its aggressive nature and high metastatic potential. Clinical staging of the disease at the time of diagnosis is very important for the prognosis and outcome of melanoma treatment. In this study, we designed and synthesized the 18F-labeled pyridine-based benzamide derivatives N-(2-(dimethylamino)ethyl)-5-[18F]fluoropicolinamide ([18F]DMPY2) and N-(2-(dimethylamino)ethyl)-6-[18F]fluoronicotinamide ([18F]DMPY3) to detect primary and metastatic melanoma at an early stage and evaluated their performance in this task. [18F]DMPY2 and [18F]DMPY3 were synthesized by direct radiofluorination of the bromo precursor, and radiochemical yields were ∼15–20%. Cell uptakes of [18F]DMPY2 and [18F]DMPY3 were >103-fold and 18-fold higher, respectively, in B16F10 (mouse melanoma) cells than in negative control cells. Biodistribution studies revealed strong tumor uptake and retention of [18F]DMPY2 (24.8% injected dose per gram of tissue [ID/g] at 60 min) and [18F]DMPY3 (11.7%ID/g at 60 min) in B16F10 xenografts. MicroPET imaging of both agents demonstrated strong tumoral uptake/retention and rapid washout, resulting in excellent tumor-to-background contrast in B16F10 xenografts. In particular, [18F]DMPY2 clearly visualized almost all metastatic lesions in lung and lymph nodes, with excellent image quality. [18F]DMPY2 demonstrated a significantly higher tumor-to-liver ratio than [18F]fluorodeoxyglucose ([18F]FDG) and the previously reported benzamide tracers N-[2-(diethylamino)-ethyl]-5-[18F]fluoropicolinamide ([18F]P3BZA) and N-[2-(diethylamino)-ethyl]-4-[18F]fluorobenzamide ([18F]FBZA) in B16F10-bearing or SK-MEL-3 (human melanoma)-bearing mice. In conclusion, [18F]DMPY2 might have strong potential for the diagnosis of early stage primary and metastatic melanoma using positron emission tomography (PET).