Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Association Mapping for Heat Stress Responsive Traits in Field Pea

Environmental stress hampers pea productivity. To understand the genetic basis of heat resistance, a genome-wide association study (GWAS) was conducted on six stress responsive traits of physiological and agronomic importance in pea, with an objective to identify the genetic loci associated with these traits. One hundred and thirty-five genetically diverse pea accessions from major pea growing areas of the world were phenotyped in field trials across five environments, under generally ambient (control) and heat stress conditions. Statistical analysis of phenotype indicated significant effects of genotype (G), environment (E), and G × E interaction for all traits. A total of 16,877 known high-quality SNPs were used for association analysis to determine marker-trait associations (MTA). We identified 32 MTAs that were consistent in at least three environments for association with the traits of stress resistance: six for chlorophyll concentration measured by a soil plant analysis development meter; two each for photochemical reflectance index and canopy temperature; seven for reproductive stem length; six for internode length; and nine for pod number. Forty-eight candidate genes were identified within 15 kb distance of these markers. The identified markers and candidate genes have potential for marker-assisted selection towards the development of heat resistant pea cultivars.
An adaptive window motion blurred star restoration based on energy equalization

The accuracy of star centroid extraction and identified star number is both crucial features for star sensor precision. Motion blur and fracture are introduced when star sensor works under high dynamic conditions, which affect the accuracy of star centroid extraction and further reduce the precision of the star sensor. To improve the precision of star sensor, this paper proposes an adaptive window star map restoration method based on energy equalization. The local degradation function is estimated for the star point energy distribution region, and dynamic star map simulation and restoration are performed. The simulation process is divided into three steps. Firstly, establish the motion trajectory of the star point centroid in the detector plane during the exposure time, according to the trailing trajectory size and direction adaptive selection window. Secondly, accumulate the star image point energy in the adaptive window to achieve star point recovery, and finally the recovery effect was evaluated by star extraction results.
Effects of diversity and coalescence of species assemblages on ecosystem function at the margins of an environmental shift

Sea level rise is mixing formerly isolated freshwater communities with saltwater communities. The structure of these new aquatic communities is jointly controlled by pre- and post-colonization processes. Similarly, since salinity is a strong abiotic determinant of post-colonization survival in coastal systems, changes in salinity will likely impact community composition. In this study, we examine how a strong abiotic gradient affects the diversity and structure of bacterial and zooplankton communities and associated ecosystem functions (decomposition and carbon mineralization). We ran a six week dispersal experiment using mesocosm ponds with four distinct salinity profiles (0, 5, 9, and 13 psu). We find that salinity is the primary driver of both bacterial and zooplankton community composition. We find evidence that as bacterial richness increases so does the amount of decomposition. A phenomenological model suggests carbon mineralization may decrease at mid-salinities; this warrants future work into possible mechanisms for this apparent loss of function. Understanding how salinization changes community structure and ecosystem function may be paramount for managing and conserving coastal plain ecosystems where salinity is increasing due to sea level rise, saltwater intrusion, storm surges, and drought.
Direct measurement of vertical forces shows correlation between mechanical activity and proteolytic ability of invadopodia

A microscopy technique based on interference of light measures the piconewton forces that cancer cells exert during invasion. Mechanobiology plays a prominent role in cancer invasion and metastasis. The ability of a cancer to degrade extracellular matrix (ECM) is likely connected to its invasiveness. Many cancer cells form invadopodia—micrometer-sized cellular protrusions that promote invasion through matrix degradation (proteolysis). Although it has been hypothesized that invadopodia exert mechanical force that is implicated in cancer invasion, direct measurements remain elusive. Here, we use a recently developed interferometric force imaging technique that provides piconewton resolution to quantify invadopodial forces in cells of head and neck squamous carcinoma and to monitor their temporal dynamics. We compare the force exerted by individual protrusions to their ability to degrade ECM and investigate the mechanical effects of inhibiting invadopodia through overexpression of microRNA-375. By connecting the biophysical and biochemical characteristics of invadopodia, our study provides a new perspective on cancer invasion that, in the future, may help to identify biomechanical targets for cancer therapy.
QuantMed: Component-based deep learning platform for translational research

QuantMed is a platform consisting of software components enabling clinical deep learning, together forming the QuantMed infrastructure. It addresses numerous challenges: systematic generation and accumulation of training data; the validation and utilization of quantitative diagnostic software based on deep learning; and thus, providing support for more reliable, accurate, and efficient clinical decisions. QuantMed provides learning and expert correction capabilities on large, heterogeneous datasets. The platform supports collaboration to extract medical knowledge from large amounts of clinical data among multiple partner institutions via a two- stage learning approach: the sensitive patient data remains on premises and is analyzed locally in a first step in so-called QuantMed nodes. Support for GPU clusters accelerates the learning process. The knowledge is then accumulated through the QuantMed hub, and can be re-distributed afterwards. The resulting knowledge modules – algorithmic solution components which contain trained deep learning networks as well as specifications of input data and output parameters - do not contain any personalized data, and thus, are safe to share under data protection law. This way, our modular infrastructure makes it possible to efficiently carry out translational research in the context of deep learning, and deploy results seamlessly into prototypes or third-party software.
Changes in the faecal microbiota of horses and ponies during a two-year body weight gain programme

Obesity is a major health concern in many domesticated equids animals since it is related to metabolic abnormalities such as insulin dysregulation, hyperlipidaemia or laminitis. Ponies especially are known as “easy keepers” and are often affected by obesity and its related metabolic disorders. Research in the last decade indicated that the intestinal microbiota may play an important role in the development of obesity, at least in humans. Therefore, the objective of our study was to characterize changes in the faecal microbiota during a two-year weight gain programme which compared ponies and warmblood horses. For this purpose, 10 Shetland ponies and ten warmblood horses were fed a ration which provided 200% of their maintenance energy requirement over two years. Feed intake, body weight, body condition and cresty neck score were recorded weekly. At three standardized time points faecal samples were collected to characterize the faecal microbiota and its fermentation products such as short chain fatty acids and lactate. Next generation sequencing was used for the analysis of the faecal microbiota. During body weight gain the richness of the faecal microbiota decreased in ponies. Besides changes in the phylum Firmicutes in ponies that were already described in human studies, we found a decrease of the phylum Fibrobacteres in horses and an increase of the phylum Actinobacteria. We were also able to show that the phylum Fibrobacteres is more common in the microbiota of horses than in the microbiota of ponies. Therefore, the fibrolytic phylum Fibrobacteres seems to be an interesting phylum in the equine microbiota that should receive more attention in future studies.
RpoS-regulated SEN1538 gene promotes resistance to stress and influences Salmonella enterica serovar enteritidis virulence

ABSTRACT Salmonella enterica serovar Enteritidis (S. Enteritidis; wild type (WT)) is a major cause of foodborne illness globally. The ability of this pathogen to survive stress inside and outside the host, such as encountering antimicrobial peptides and heat stress, determines the efficiency of enteric infection. These stressors concertedly trigger virulence factors encoded on Salmonella pathogenicity islands (SPIs). Although RpoS is a well-known central transcriptional stress and virulence regulator, functional information regarding the genes of the regulon is currently limited. Here, we identified SEN1538 as a conserved RpoS-regulated gene belonging to the KGG protein superfamily. We further assessed its role in pathogenic stress responses and virulence. When SEN1538 was deleted (Δ1538), the pathogen showed reduced survival during antimicrobial peptide introduction and heat stress at 55°C compared to WT. The mutant displayed 70% reduced invasion in the HCT116 colon epithelial cell line, 5-fold attenuated phagocytic survival in RAW264.7 cells, and downregulation of several SPI-1 and SPI-2 genes encoding the three secretion system apparatus and effector proteins. Δ1538 also showed decreased virulence compared to WT, demonstrated by its reduced bacterial counts in the feces, mLN, spleen, and cecum of C57BL/6 mice. Comparative transcriptomic analysis of Δ1538 against WT revealed 111 differentially regulated genes, 103 of which were downregulated (fold change ≤ −1.5, P < 0.05). The majority of these genes were in clusters for metabolism, transporters, and pathogenesis, driving pathogenic stress responses and virulence. SEN1538 is, therefore, an important virulence determinant contributing to the resilience of S. Enteritidis to stress factors during infection.
Small Object Augmentation of Urban Scenes for Real-Time Semantic Segmentation

Semantic segmentation is a key step in scene understanding for autonomous driving. Although deep learning has significantly improved the segmentation accuracy, current high-quality models such as PSPNet and DeepLabV3 are inefficient given their complex architectures and reliance on multi-scale inputs. Thus, it is difficult to apply them to real-time or practical applications. On the other hand, existing real-time methods cannot yet produce satisfactory results on small objects such as traffic lights, which are imperative to safe autonomous driving. In this paper, we improve the performance of real-time semantic segmentation from two perspectives, methodology and data. Specifically, we propose a real-time segmentation model coined Narrow Deep Network (NDNet) and build a synthetic dataset by inserting additional small objects into the training images. The proposed method achieves 65.7% mean intersection over union (mIoU) on the Cityscapes test set with only 8.4G floating-point operations (FLOPs) on $1024\times 2048$ inputs. Furthermore, by re-training the existing PSPNet and DeepLabV3 models on our synthetic dataset, we obtained an average 2% mIoU improvement on small objects.
A fiber-based photodetector linearity measurement system from classic to single photon level

It is important to measure the spectral transmission characteristics of materials when the spatial density of classical optical power (that is, the laser or attenuated light is a small spot, but the optical power hits a fixed position) is different from the spatial density of weak optical power. The most important scientific problem (research or experimental objective) is to distinguish the difference between the probability of photons passing through a sample with a specific absorption rate collectively and the probability of approaching a single photon passing through the same sample. We design an optical fiber system that can measure weak optical power. We use many methods to expand the linear measurement range so that it can measure its linearity in the power range of 1 fA-1 mA. In addition, the system can also verify the linearity of photon counter, starting from 0.1 pA block - essentially, when the detector is adjusted to 0.1 pA, the verification and evaluation of photon counting at the photomultiplier tube level is started. From the power measurement level of cryogenic radiometer to the photon counting level, the optical fiber measurement system covers 12 orders of magnitude, which also shows that the spectral transmittance and reflection ratio can cover a wide range, that is, it can be used to measure the characteristic materials with high transmittance.
Foodborne Transmission and Clinical Symptoms of Honey Bee Viruses in Ants Lasius spp.

Emerging infectious diseases are often the products of host shifts, where a pathogen jumps from its original host to a novel species. Viruses in particular cross species barriers frequently. Acute bee paralysis virus (ABPV) and deformed wing virus (DWV) are viruses described in honey bees (Apis mellifera) with broad host ranges. Ants scavenging on dead honey bees may get infected with these viruses via foodborne transmission. However, the role of black garden ants, Lasius niger and Lasius platythorax, as alternative hosts of ABPV and DWV is not known and potential impacts of these viruses have not been addressed yet. In a laboratory feeding experiment, we show that L. niger can carry DWV and ABPV. However, negative-sense strand RNA, a token of virus replication, was only detected for ABPV. Therefore, additional L. niger colonies were tested for clinical symptoms of ABPV infections. Symptoms were detected at colony (fewer emerging workers) and individual level (impaired locomotion and movement speed). In a field survey, all L. platythorax samples carried ABPV, DWV-A and –B, as well as the negative-sense strand RNA of ABPV. These results show that L. niger and L. platythorax are alternative hosts of ABPV, possibly acting as a biological vector of ABPV and as a mechanical one for DWV. This is the first study showing the impact of honey bee viruses on ants. The common virus infections of ants in the field support possible negative consequences for ecosystem functioning due to host shifts.
Immunologic Dose-Response to Adenovirus-Vectored Vaccines in Animals and Humans: A Systematic Review of Dose-Response Studies of Replication Incompetent Adenoviral Vaccine Vectors when Given via an Intramuscular or Subcutaneous Route

Optimal vaccine dosing is important to ensure the greatest protection and safety. Analysis of dose-response data, from previous studies, may inform future studies to determine the optimal dose. Implementing more quantitative modelling approaches in vaccine dose finding have been recently suggested to accelerate vaccine development. Adenoviral vectored vaccines are in advanced stage of development for a variety of prophylactic and therapeutic indications, however dose-response has not yet been systematically determined. To further inform adenoviral vectored vaccines dose identification, historical dose-response data should be systematically reviewed. A systematic literature review was conducted to collate and describe the available dose-response studies for adenovirus vectored vaccines. Of 2787 papers identified by Medline search strategy, 35 were found to conform to pre-defined criteria. The majority of studies were in mice or humans and studied adenovirus serotype 5. Dose-response data were available for 12 different immunological responses. The majority of papers evaluated three dose levels, only two evaluated more than five dose levels. The most common dosing range was 107–1010 viral particles in mouse studies and 108–1011 viral particles in human studies. Data were available on adenovirus vaccine dose-response, primarily on adenovirus serotype 5 backbones and in mice and humans. These data could be used for quantitative adenoviral vectored vaccine dose optimisation analysis.
Machine-learning-assisted design of depth-graded multilayer x-ray structure

Depth-graded multilayer structures are widely used in X-ray related applications. In this paper, we propose an optimization approach using machine learning principles to accelerate depth-graded multilayer structures design. We use Monte Carlo tree search (MCTS) to find optimal thickness for each layer in the structure that achieves maximum mean reflectivity in an angular range at a specific beam energy. We obtained 0.78 mean reflectivity in an angular range 0.4~0.55° for Cu Kα radiation using this approach. For a at top structure, we could achieve a small standard deviation of 0.016 within the same range. MCTS is an iterative design method that employs tree search with guided randomization that showed exceptional performance in computer games. MCTS expands towards the promising areas of the search space making it able to search large spaces efficiently and systematically. This approach offers flexibility for multiple design purposes without the need to data availability in advance.
Lidocaine Binding Enhances Inhibition of Nav1.7 Channels by the Sulfonamide PF-05089771

PF-05089771 is an aryl sulfonamide Nav1.7 channel blocker that binds to the inactivated state of Nav1.7 channels with high affinity but binds only weakly to channels in the resting state. Such aryl sulfonamide Nav1.7 channel blockers bind to the extracellular surface of the S1-S4 voltage-sensor segment of homologous Domain 4, whose movement is associated with inactivation. This binding site is different from that of classic sodium channel inhibitors like lidocaine, which also bind with higher affinity to the inactivated state than the resting state but bind at a site within the pore of the channel. The common dependence on gating state with distinct binding sites raises the possibility that inhibition by aryl sulfonamides and by classic local anesthetics might show an interaction mediated by their mutual state dependence. We tested this possibility by examining the state-dependent inhibition by PF-05089771 and lidocaine of human Nav1.7 channels expressed in human embryonic kidney 293 cells. At −80 mV, where a small fraction of channels are in an inactivated state under drug-free conditions, inhibition by PF-05089771 was both enhanced and speeded in the presence of lidocaine. The results suggest that lidocaine binding to the channel enhances PF-05089771 inhibition by altering the equilibrium between resting states (with D4S4 in the inner position) and inactivated states (with D4S4 in the outer position). The gating state–mediated interaction between the compounds illustrates a principle applicable to many state-dependent agents. SIGNIFICANCE STATEMENT The results show that lidocaine enhances the degree and rate of inhibition of Nav1.7 channels by the aryl sulfonamide compound PF-05089771, consistent with state-dependent binding by lidocaine increasing the fraction of channels presenting a high-affinity binding site for PF-05089771 and suggesting that combinations of agents targeted to the pore-region binding site of lidocaine and the external binding site of aryl sulfonamides may have synergistic actions.
Relationship between healthcare seeking and pain expansion in patients with nonspecific chronic low back pain

Objectives Low back pain (LBP) is the most prevalent musculoskeletal problem, which implies a high rate of chronicity. The chronicity of symptoms can lead to pain expansion. The main objective of this study was to assess whether there were differences between patients with nonspecific chronic LBP (CLBP) who sought healthcare compared to those who did not in terms of pain expansion. Methods Ninety individuals participated in the study and were divided into three groups: 30 patients who sought care; 30 patients who did not seek care; and 30 asymptomatic individuals. The primary variable analyzed was pain expansion. Secondary physical and psychological variables were assessed later, and a regression analysis was performed. Results Patients who sought help showed significant differences in pain expansion and pain intensity compared with the group who did not seek help, with a medium effect size (0.50–0.79). The regression model for the care-seeking group showed that dynamic balance with the left leg and depression were predictors of percentage pain surface area (34.6%). The combination of dynamic balance, range of movement in flexoextension and depression were predictors of widespread pain (48.5%). Conclusion Patients who soughtcare presented greater pain expansion than patients whodidnot. A combination of functional and psychological variables can significantly predict pain expansion in patients with nonspecific CLBP who seek help.
Influence of temperature on volume, weight and density changes of i-gel masks

Background The i-gel mask is a second-generation, single-use supraglottic airway device which does not have an inflatable cuff. The cuff consists of a thermoplastic elastomer and its mechanism of sealing still remains unclear. Various theories such as temperature-dependent changes in hardness and volume expansion as well as fluid absorption have been discussed. The aim of the present study is to investigate changes in volume, weight and density caused by temperature changes. Material and methods Three i-gel masks (sizes 3, 4 and 5) were heated in a water bath from 10°C to 50°C in 5°C steps. The changes in weight, volume, and density were measured at each temperature step. In a second study, the identical parameters of masks (n = 5 of sizes 3, 4 and 5) used in patients were investigated. Results of volume and density between benchtop and patient measurements were examined for correlation. Results All masks investigated, regardless of the size, showed a significant linear temperature-dependent volume expansion (sizes 3, 4 and 5: P < 0.001), a weight increase (sizes 3: P = 0.018; 4: P = 0.027; and 5: P = 0.006) and a linear decrease in density (sizes 3, 4 and 5: P < 0.001). There was a very strong correlation between the results of benchtop and patient measurements (volume: P < 0.001; density: P < 0.001). Conclusions We observed significant changes in all three properties investigated. Thus, a temperature-dependent volume expansion and weight increasement was observed, which can be considered as a further explanation for improved sealing after insertion.