bluuebunny/crossref_metadata_2025 huggingface dataset:
An Automatic Wound Detection System Empowered by Deep Learning
Authors: Adnan Muhammad , Asif Muhammad , Ahmad Maaz Bin , Mahmood Toqeer , Masood Khalid , Ashraf Rehan , Nadeem Faisal C.M.
Published: August 2023

The wound can be defined as a breakdown in the protective function of the skin. Perceiving the types of wounds at the initial stages can be more viable in the treatment process. The paramedical staff usually examines the wound with its size and healing status is determined through visual assessment. Telemedicine and rest of the healthcare services delivered through digital means aim to ensure the availability of health facilities at doorstep. Especially, in COVID-19 period these services played significant role where physical examination of patient in hospital may enhance the spread of the disease. The remote assessment of wound demands high quality of medical images or videos and localization of wound area. The manual diagnosis is not very robust and reliable because of variability in the appearance of wound site. Whereas an automatic wound detection, localization and classification may assist a physician with more accuracy and robustness. In this work, an automatic wound detection technique using YOLO v3 model is proposed. The proposed technique detects, localizes and classifies the wound into four main categories containing stitch-wound, cut-wound, open-wound and normal-skin. The experimental results show that the proposed technique is more efficient and robust with 99% accuracy and outperforms other counter parts.
Medical Image Segmentation Based on U-Net
Authors: Chen Zhihao
Published: August 2023

Traditional statistical methods, although having a solid theoretical foundation, have been challenged in terms of their efficiency as well as their generalization ability in the face of the ever-increasing amount of massive data. With the rise of deep learning in recent years, the use of new tools such as convolutional neural networks to get information from data has become a new option. In particular, in the field of imaging, segmentation of medical images is important for tasks such as determining the type of disease and the location of lesions, which are excellent application areas for deep learning. U-Net is a particularly important deep model structure with good results for segmentation of medical images. However, there is a lack of discussions on the application of U-Net in the clinical field. In this paper, we introduce traditional image segmentation methods and U-Net, analyze the advantages of deep learning techniques in the field of image segmentation. In addition, we applied U-Net to the problem of cell segmentation and segmentation of covid-19 CT images, showing the potential of U-Net for clinical applications.
CAM-TMIL: A Weakly-Supervised Segmentation Framework for Histopathology based on CAMs and MIL
Authors: Feng Jiahao , Li Ce , Wang Jin
Published: August 2023

Semantic segmentation plays a significant role in histopathology by assisting pathologists in diagnosis. Although fully-supervised learning achieves excellent success on segmentation for histopathological images, it costs pathologists and experts great efforts on pixel-level annotation in the meantime. Thus, to reduce the annotation workload, we proposed a weakly-supervised learning framework called CAM-TMIL, which assembles methods based on class activation maps (CAMs) and multiple instance learning (MIL) to perform segmentation with image-level labels. By leveraging the MIL method, we effectively alleviate the influence caused by that CAMs only focus on discriminative regions. As a result, we achieved comparable performance with fully-supervised learning on Camelyon 16 only with image-level labels.
Improved Causal Bayesian Optimization Algorithm with Counter-noise Acquisition Function and Supervised Prior Estimation
Authors: Li Zheng , Li Yongxuan , Lian Zongqiang , Zheng Rui
Published: August 2023

Causality is an important element in decision-making and interventions are required to optimize results of target values. In this paper, based on the model of Causal Bayesian Optimization, a counter-noise version of acquisition function is proposed and new prior estimation algorithms including Support Vector Regression, Ridge Regression and Random Forest are evaluated. This paper provides an improved framework to facilitate causal inference and optimization processes.
Driving Assist: A Supervised-Learning Method for Parking Lot Detection
Authors: Huo Mingxiao
Published: August 2023

In the driving process, the parking lot detection can instruct drivers to get an appropriate place to get the car parking. Therefore, this study attempts to use computer vision methods to guide drivers to park. In this paper, we first divide all the parking lots into single parking spot by the Hough transform. Then a supervised learning method is proposed to classify every single parking spot into car spots and non-car spots. In this classification problem, we adopt the CNN (convolution neural network) method to extract every single spot’s features and put the spot into the corresponding category. For the whole network, VGG-19, which can extract a deeper feature, is adopted to get a more precise classification. Also, we adopt the Adam optimizer replacing the SGD optimizer in the former work, which relies little on the learning rate. It shows that the Adam optimizer gets better loss convergence in the training process. After collecting the results of the prediction for the test videos, it shows that the deeper network VGG-19 improves the accuracy of predicting a driver spot.
Logistics Robot Path Planning: A* Algorithm Operation and Analysis
Authors: Gui Yihan
Published: August 2023

With the rapid development of the e-commerce market, traditional logistics and warehousing methods are far from meeting the needs of the industry. Logistics robots have great potential in the area of intelligent warehousing. Inspired by this, this paper introduces the path planning principle of A* algorithm and the application of A* algorithm to find the path in the field of logistics robots. The principle of the A* algorithm is to select the grid with the least cost for each step from the starting point until the end point is reached. And it can be applied to the motion control of AGV and other logistics robots.
Predicting mortality index for ICU inpatients based on clinical data extracted from electronic health record
Authors: Dawood Aisha , Saba Tanzila
Published: August 2023

Predicting ICU inpatients mortality index needs to be improved to incorporate clinical data. It is also helpful to reflect the patient’s recovery and hospitals standards. In this research machine learning model LightGBM was trained and assessed. This study used a dataset for ICU admissions for adult patients from six countries. And a total of 130,000 patient records were included in the study. The final model achieved AUROC (95% CI) of 0.97, an accuracy of 0.95, and an F1 score of 0.81 on the dataset. Based on results, it is observed that machine learning models with the support of conventional mortality scoring indices can provide a successful and useful model for predicting the outcome of critical and severe cases in the ICU.
Multi-bubble Bourgain-Wang solutions to nonlinear Schrödinger equations
Authors: Röckner Michael , Su Yiming , Zhang Deng
Published: August 2023

We study a general class of focusing

L
2

L^2

-critical nonlinear Schrödinger equations with lower order perturbations, in the possible absence of the pseudo-conformal symmetry and the conservation law of energy. In dimensions one and two, we construct multi-bubble Bourgain-Wang type blow-up solutions, which behave like a sum of pseudo-conformal blow-up solutions that concentrate at

K
K

distinct singularities,

1
≤
K
>

∞

1\leq K>{\infty }

, and a regular profile. Moreover, we obtain the uniqueness in the energy class where the convergence rate is within the order

(
T
−
t

)

4
+

(T-t)^{4+}

, for

t
t

close to the blow-up time

T
T

. These results in particular apply to the canonical nonlinear Schrödinger equations and, through the pseudo-conformal transform, yield the existence and conditional uniqueness of non-pure multi-solitons, which behave asymptotically as a sum of multi-solitons and a dispersive part. Thus, the results provide new examples of the mass quantization conjecture and the soliton resolution conjecture. Furthermore, through a Doss-Sussman type transform, we obtain multi-bubble Bourgain-Wang solutions for stochastic nonlinear Schrödinger equations, where the driving noise is taken in the sense of controlled rough path.
How should we be using biomarkers in trials of disease modification in Parkinson’s disease?
Authors: Vijiaratnam Nirosen , Foltynie Thomas
Published: August 2023

The recent validation of the α-synuclein seed amplification assay as a biomarker with high sensitivity and specificity for the diagnosis of Parkinson’s disease has formed the backbone for a proposed staging system for incorporation in Parkinson’s disease clinical studies and trials. The routine use of this biomarker should greatly aid in the accuracy of diagnosis during recruitment of Parkinson’s disease patients into trials (as distinct from patients with non-Parkinson’s disease parkinsonism or non-Parkinson’s disease tremors). There remain, however, further challenges in the pursuit of biomarkers for clinical trials of disease modifying agents in Parkinson’s disease, namely: optimizing the distinction between different α-synucleinopathies; the selection of subgroups most likely to benefit from a candidate disease modifying agent; a sensitive means of confirming target engagement; and the early prediction of longer-term clinical benefit. For example, levels of CSF proteins such as the lysosomal enzyme β-glucocerebrosidase may assist in prognostication or allow enrichment of appropriate patients into disease modifying trials of agents with this enzyme as the target; the presence of coexisting Alzheimer’s disease-like pathology (detectable through CSF levels of amyloid-β42 and tau) can predict subsequent cognitive decline; imaging techniques such as free-water or neuromelanin MRI may objectively track decline in Parkinson’s disease even in its later stages. The exploitation of additional biomarkers to the α-synuclein seed amplification assay will, therefore, greatly add to our ability to plan trials and assess the disease modifying properties of interventions. The choice of which biomarker(s) to use in the context of disease modifying clinical trials will depend on the intervention, the stage (at risk, premotor, motor, complex) of the population recruited and the aims of the trial. The progress already made lends hope that panels of fluid biomarkers in tandem with structural or functional imaging may provide sensitive and objective methods of confirming that an intervention is modifying a key pathophysiological process of Parkinson’s disease. However, correlation with clinical progression does not necessarily equate to causation, and the ongoing validation of quantitative biomarkers will depend on insightful clinical-genetic-pathophysiological comparisons incorporating longitudinal biomarker changes from those at genetic risk with evidence of onset of the pathophysiology and those at each stage of manifest clinical Parkinson’s disease.
Early sensory gain control is dominated by obligatory and global feature-based attention in top-down shifts of combined spatial and feature-based attention
Authors: Gundlach Christopher , Wehle Sebastian , Müller Matthias M
Published: August 2023

What are the dynamics of global feature-based and spatial attention, when deployed together? In an attentional shifting experiment, flanked by three control experiments, we investigated neural temporal dynamics of combined attentional shifts. For this purpose, orange- and blue-frequency-tagged spatially overlapping Random Dot Kinematograms were presented in the left and right visual hemifield to elicit continuous steady-state-visual-evoked-potentials. After being initially engaged in a fixation cross task, participants were at some point in time cued to shift attention to one of the Random Dot Kinematograms, to detect and respond to brief coherent motion events, while ignoring all such events in other Random Dot Kinematograms. The analysis of steady-state visual-evoked potentials allowed us to map time courses and dynamics of early sensory-gain modulations by attention. This revealed a time-invariant amplification of the to-be attended color both at the attended and the unattended side, followed by suppression for the to-be-ignored color at attended and unattended sides. Across all experiments, global and obligatory feature-based selection dominated early sensory gain modulations, whereas spatial attention played a minor modulatory role. However, analyses of behavior and neural markers such as alpha-band activity and event-related potentials to target- and distractor-event processing, revealed clear modulations by spatial attention.
Exploring exposure to multiple psychosocial work factors: prospective associations with depression and sickness absence
Authors: Lunen Jonas Christian , Rugulies Reiner , Sørensen Jeppe K , Andersen Lars L , Clausen Thomas
Published: August 2023

Background

Most studies on the psychosocial working environment have focused on evaluating the isolated effect of individual psychosocial work factors or looked at effects through a lens of theories such as job strain or effort–reward imbalance. However, to fathom the intricate nature of workers’ experience of occupational strain, there is a need to investigate the combined and cumulative effects of multiple exposures to psychosocial work factors on workers’ health.

Methods

In this prospective cohort study, we created an additive index (range 0–4) on number of baseline exposures to quantitative demands, emotional demands, role conflicts, and workplace bullying. Via logistic regression and Cox regression, we estimated the association between the additive index of psychosocial work factors and depressive disorder and long-term sickness absence (LTSA). We assessed the onset of depressive disorder using the Major Depression Inventory at 6-month follow-up and the onset of LTSA using a national register during 12-month follow-up.

Results

For onset of depressive disorder, high exposure to any one [odds ratio (OR) 2.98], two (OR 3.14), three (OR 6.44) and all four (OR 9.62) adverse psychosocial work factors predicted a statistically significant increased risk. For onset of LTSA, high exposure to any one [hazard ratio (HR) 1.13], two (HR 1.67), three (HR 2.31) and all four (HR 4.04) psychosocial work factors predicted an increased risk. The two latter associations were statistically significant. Trend tests indicated an exposure–response relationship for both outcomes.

Conclusions

Workers reporting exposure to multiple adverse psychosocial work factors had a higher risk of developing depressive disorder and LTSA.
Musculoskeletal corticosteroid injection and risk of acute coronary syndrome: a case control study
Authors: Thomas Katharine , Schonmann Yochai
Published: August 2023

Background

Musculoskeletal corticosteroid injection (CSI) is a frequently used treatment, considered safe with a low incidence of minor side effects.

Objective

To investigate whether the incidence of acute coronary syndrome (ACS) is increased following corticosteroid injection for musculoskeletal conditions.

Methods

Data were reviewed from 41,276 patients aged over 40 years and hospitalised with ACS between January 2015 and December 2019. Each ACS case was allocated up to 10 control patients from their primary care clinic, matched for age and sex. The cases and controls were reviewed for orthopaedic or rheumatological consultation including a CSI procedure and occurring prior to the hospital admission date. The incidence of CSI was compared between the case and control groups.

Results

Data from a total of 413,063 patients were reviewed, 41,276 ACS cases and 371,787 controls. The mean age was 68.1, standard deviation (SD) = 13.1, 69.4% male. In the week prior to their hospital admission, 118 ACS patients were treated with CSI compared with 495 patients in the control group; odds ratio (OR) = 1.95 (1.56–2.43). In total, 98% of CSI procedures were carried out by orthopaedic specialists. An association between ACS and prior CSI was strongest in the days immediately prior to hospitalisation: OR = 3.11 (2.10–4.61) for patients who were injected 1 day before ACS. The association between ACS and CSI declined with increasing time between injection and hospital admission: at 90 days OR = 1.08 (0.98–1.18). The association remained robust when cardiovascular risk factors, history of rheumatological disease, and other co-morbidity were taken into consideration.

Conclusions

Musculoskeletal corticosteroid injection appears to substantially increase the risk of acute coronary syndrome.
Cardiac rehabilitation: pedagogical education strategies have positive effect on long-term patient-reported outcomes
Authors: Pedersen C G , Nielsen C V , Lynggaard V , Zwisler A D , Maribo T
Published: August 2023

This study examined whether patients attending cardiac rehabilitation (CR) based on the pedagogical strategy learning and coping (LC) led to improved health-related quality of life (HRQL), reduced symptoms of anxiety and depression and improved self-management 6 and 12 months after the completion of CR compared with patients attending CR based on the pedagogical strategy ‘Empowerment, Motivation and Medical Adherence’ (EMMA). A pragmatic cluster-controlled trial of two pedagogical strategies, LC and EMMA, including 10 primary health care settings and 555 patients diagnosed with ischaemic heart disease and referred to CR between August 2018 and July 2019 was conducted. In total, 312 patients replied to the questionnaires collected at baseline, 12 weeks, 6 months and 12 months after completing CR. Linear regression analyses adjusted for potential confounder variables and cluster effects were performed. We found clinically relevant and statistically significant improvements in HRQL, anxiety, depression and self-management after completing CR. The improvements were sustained at 6 and 12 months after the completion of CR. We found no differences between the two evidence-based patient education strategies. In conclusion, this study supports the use of evidence-based patient education strategies, but there is no evidence to suggest that one pedagogical strategy is superior to the other.
Exploring the determinants of successful implementation of a preventive mental health and wellness intervention for Afghan refugee families: a qualitative analysis
Authors: Rosenberg Julia , McDonough Ryan Patricia , Brown Camille , Schaffer Rachel , O’Brien Caroline , Ganjavi Fereshteh , Sharifi Mona
Published: August 2023

Many refugee children experience trauma in early childhood. Effective, tailored interventions are needed to improve refugee children’s access to preventive mental health. We interviewed refugee-serving stakeholders and parents participating in an evidence-based preventive mental health and wellness intervention adapted for Afghan refugee children and families who may have experienced trauma. Interview guide development was informed by two implementation science frameworks: the Consolidated Framework for Implementation Research and the Model for Adaptation Design and Impact. A three-person team coded transcripts via rapid qualitative analysis, and the study team reached consensus on themes. Six refugee-serving facilitators and five refugee parents discussed key determinants of successful implementation. Themes included: (i) modeling cultural humility to promote communication about emotions; (ii) needed linguistic support and referral networks to avoid miscommunications and missed communications; (iii) bridging connections between children, families and schools; (iv) different takeaways, or differing goals and expectations between facilitators and participants; and (v) timely, specific cultural considerations to overcome participation barriers. Overall, we found key determinants of successful implementation of a preventive mental health and wellness intervention for refugee children and families included adaptations to enhance cultural humility and sensitivity to cultural context while strengthening communication among facilitators, children and families.
Arginine methylation of RNA-binding proteins is impaired in Huntington’s disease
Authors: Ratovitski Tamara , Kamath Siddhi V , O'Meally Robert N , Gosala Keerthana , Holland Chloe D , Jiang Mali , Cole Robert N , Ross Christopher A
Published: August 2023

Huntington’s disease (HD) is a progressive neurodegenerative disorder caused by a CAG repeat expansion in the HD gene, coding for huntingtin protein (HTT). Mechanisms of HD cellular pathogenesis remain undefined and likely involve disruptions in many cellular processes and functions presumably mediated by abnormal protein interactions of mutant HTT. We previously found HTT interaction with several protein arginine methyl-transferase (PRMT) enzymes. Protein arginine methylation mediated by PRMT enzymes is an important post-translational modification with an emerging role in neurodegeneration. We found that normal (but not mutant) HTT can facilitate the activity of PRMTs in vitro and the formation of arginine methylation complexes. These interactions appear to be disrupted in HD neurons. This suggests an additional functional role for HTT/PRMT interactions, not limited to substrate/enzyme relationship, which may result in global changes in arginine protein methylation in HD. Our quantitative analysis of striatal precursor neuron proteome indicated that arginine protein methylation is significantly altered in HD. We identified a cluster highly enriched in RNA-binding proteins with reduced arginine methylation, which is essential to their function in RNA processing and splicing. We found that several of these proteins interact with HTT, and their RNA-binding and localization are affected in HD cells likely due to a compromised arginine methylation and/or abnormal interactions with mutant HTT. These studies reveal a potential new mechanism for disruption of RNA processing in HD, involving a direct interaction of HTT with methyl-transferase enzymes and modulation of their activity and highlighting methylation of arginine as potential new therapeutic target for HD.
Exclusive Enteral Nutrition Alleviates Th17-Mediated Inflammation via Eliminating Mechanical Stress–Induced Th17-Polarizing Cytokines in Crohn’s-like Colitis
Authors: Geesala Ramasatyaveni , Zhang Ke , Lin You-Min , Johnson John C , Cong Yingzi , Cohn Steven , Shi Xuan-Zheng
Published: August 2023

Background and Aims

Exclusive enteral nutrition (EEN) with a liquid diet is the only established dietary treatment for Crohn’s’ disease (CD). However, the mechanism of action of EEN in CD is unclear. T helper 17 (Th17) immune response plays a critical role in CD. We hypothesized that EEN alleviates Th17 response by eliminating mechanical stress–induced expression of Th17-polarizing cytokines.

Methods

A rat model of Crohn’s-like colitis was established by intracolonic instillation of TNBS (65 mg/kg in 250 µL of 40% ethanol). Control rats were treated with saline. We characterized immunophenotypes and molecular changes of the colon in control and colitis rats with and without EEN treatment. Th17 differentiation was determined using coculture assays.

Results

TNBS instillation induced transmural inflammation with stenosis in the inflammation site and a marked increase of Th17-polarizing cytokines interleukin (IL)-6 and osteopontin and the Th17 cell population in the mechanically distended preinflammation site (P-site). EEN treatment eliminated mechanical distention and the increase of IL-6, osteopontin, and Th17 response in the P-site. IL-6 and osteopontin expression was found mainly in the muscularis externa. Mechanical stretch of colonic smooth muscle cells in vitro induced a robust increase of IL-6 and osteopontin. When naïve T cells were cultured with conditioned media from the P-site tissue or stretched cells, Th17 differentiation was significantly increased. Inhibition of IL-6, but not deletion of osteopontin, blocked the increase of Th17 differentiation.

Conclusions

Mechanical stress induces Th17-polarizing cytokines in the colon. EEN attenuates Th17 immune response by eliminating mechanical stress–induced IL-6 in Crohn’s-like colitis.
Group Equations With Abelian Predicates
Authors: Ciobanu Laura , Garreta Albert
Published: August 2023

In this paper, we begin the systematic study of group equations with abelian predicates in the main classes of groups where solving equations is possible. We extend the line of work on word equations with length constraints, and more generally, on extensions of the existential theory of semigroups, to the world of groups. We use interpretability by equations to establish model-theoretic and algebraic conditions, which are sufficient to get undecidability. We apply our results to (non-abelian) right-angled Artin groups and show that the problem of solving equations with abelian predicates is undecidable for these. We obtain the same result for hyperbolic groups whose abelianisation has torsion-free rank at least two. By contrast, we prove that in groups with finite abelianisation, the problem can be reduced to solving equations with recognisable constraints, and so this is decidable in right-angled Coxeter groups, or more generally, graph products of finite groups, as well as hyperbolic groups with finite abelianisation.
Feeding dietary fermentable fiber improved fecal microbial composition and increased acetic acid production in a nursery pig model
Authors: Zhang Gang , Zhao Jinbiao , Song Xiaoming , Yang Meiyu , Wang Haotian , Wu Yi
Published: August 2023

The objective of this study was to determine the fermentable fiber (FF) content of several common fibrous ingredients fed to nursery pigs, and then evaluate the effect of dietary FF level on growth performance and fecal microbial composition. In experiment 1, 54 nursery pigs were randomly allotted to be fed nine diets with six replicate pigs per diet. Dietary treatments included a corn–soybean meal basal diet and eight test diets based on a mixture of the corn–soybean meal diet and corn distillers dried grains with solubles, sunflower meal, oat bran, wheat bran, corn bran, sugar beet pulp (SBP), apple pomace (AP) or soybean hulls (SH). In experiment 2, 180 nursery pigs were housed in 30 pens (six pigs per pen) and randomly allotted to be fed five diets with different FF to total dietary fiber (TDF) ratios, which were 0.52, 0.55, 0.58, 0.61, and 0.64, respectively. Results showed that the FF content in SBP, AP, and SH was greater (P < 0.01) than that in other ingredients. Water binding capacity of fibrous ingredients was positively correlated (P < 0.05) to the digestibility of TDF, acid detergent fiber, and non-starch polysaccharides in test ingredients. Pigs fed the SBP, AP and SH diets had greater (P < 0.05) fecal acetic acid and total short-chain fatty acids (SCFAs) concentrations compared with pigs fed other diets. Fecal acetic acid and total SCFAs concentrations were positively correlated (P < 0.05) with FF content in experimental diets. Average daily weight gain and average daily feed intake of pigs quadratically increased (P < 0.01) as the ratios of FF to TDF increased. Pigs in FF64% group showed higher (P < 0.05) ACE index and fecal acetic acid concentration compared with pigs fed the dietary FF/TDF ratio of 0.52 to 0.61. Compared with the classification system of soluble dietary fiber and insoluble dietary fiber, FF could better describe the mechanism by which dietary fiber has beneficial effects on pig gut health.
Prediction of available energy and amino acid digestibility of Chinese sorghum fed to growing–finishing pigs
Authors: Feng Ganyi , Li Rui , Jiang Xianji , Yang Gang , Tian Mingzhou , Xiang Qiang , Liu Xiaojie , Ouyang Qing , Long Cimin , Huang Ruilin , Yin Yulong
Published: August 2023

Two experiments were conducted to determine digestible energy (DE), metabolizable energy (ME), as well as the standardized ileal digestibility (SID) of crude protein (CP) and amino acids (AA) in 10 sorghum samples fed to pigs. In experiment 1, 22 crossbred barrows (Duroc × Yorkshire × Landrace, Initial body weight [BW]: 70.0 ± 1.8 kg) were selected and allotted to a replicated 11 × 3 incomplete Latin square design, including a basal diet and 10 sorghum energy diets and three consecutive periods. Each period had 7 d adaptation and 5 d total feces and urine collection. The DE and ME were determined by the total collection and the difference method. In experiment 2, 22 crossbred barrows (Duroc × Yorkshire × Landrace, Initial BW: 41.3 ± 1.2 kg) that had a T-cannula installed in the distal ileum were assigned to a replicated 11 × 3 incomplete Latin square design, including an N-free diet and 10 sorghum diets. Each period had 5 d adaptation and 2 d ileal digesta collection. The basal endogenous N losses were measured by the N-free diet method. All diets in experiment 2 were added 0.30% titanium dioxide as an indigestible marker for calculating the ileal CP and AA digestibility. On an as-fed basis, the DE and ME contents in sorghum were 3,410 kcal/kg (2,826 to 3,794 kcal/kg) and 3,379 kcal/kg (2,785 to 3,709 kcal/kg), respectively. The best-fit prediction equation for DE and ME were DE = 6,267.945 − (1,271.154 × % tannin) − (1,109.720 × % ash) (R2 = 0.803) and ME = 51.263 + (0.976 × DE) (R2 = 0.994), respectively. The SID of CP, Lys, Met, Thr, and Trp (SIDCP, SIDLys, SIDMet, SIDThr, and SIDTrp) in 10 sorghum samples were 78.48% (69.56% to 84.23%), 74.27% (61.11% to 90.60%), 92.07% (85.16% to 95.40%), 75.46% (66.39% to 80.80%) and 87.99% (84.21% to 92.37%), respectively. The best prediction equations for SID of CP and the first four limiting AAs were as following: SIDCP = 93.404 − (21.026 × % tannin) (R2 = 0.593), SIDCP = 42.922 − (4.011 × % EE) + (151.774 × % Met) (R2 = 0.696), SIDLys = 129.947 − (670.760 × % Trp) (R2 = 0.821), SIDMet = 111.347 − (232.298 × % Trp) (R2 = 0.647), SIDThr = 55.187 + (3.851 × % ADF) (R2 = 0.609) and SIDTrp = 95.676 − (10.824 × % tannin) (R2 = 0.523), respectively. Overall, tannin and ash are the first and second predictors of DE and ME values of sorghum, respectively, and the tannin, EE, Trp, ash, CF, and ADF can be used as the key predictors for SID of CP and first four limiting AAs.
Iron requirements of broiler chickens as affected by supplemental phytase
Authors: Feijo Julmar Costa , Vieira Sergio Luiz , Horn Raquel Medeiros , Altevogt Walter Edmundo , Tormes Giovane
Published: August 2023

Iron is routinely supplemented in broiler feeds intending to prevent dietary deficiencies. The present research was conducted with the objective of assessing Fe requirements of broilers when fed supplemental phytase. A total of 1,280 1-d-old male Cobb × Cobb 500 were distributed in a 2 × 5 factorial arrangement (phytase-supplemented feeds × 5 graded increases of supplemental Fe) in 80 battery cages, eight replications of eight chicks each. The trial was replicated once. Chicks were fed a Fe-deficient diet without phytase (Fe analyzed at 31.30 ± 3.79 mg/kg) from placement to 7 d and then randomly distributed into battery cages with corresponding dieting treatments with or without phytase and graded increases of supplemental Fe. Feeds were formulated with corn and soybean meal (SBM), laboratory-grade calcium carbonate, and phosphoric acid; therefore, the vast majority of dietary Fe originated from corn and SBM (analyzed diet had 53.3 ± 1.41 mg/kg Fe). Phytase was added in excess to the producer recommendation of 1,000 FYT (4,452 ± 487 FYT/kg analyzed) such that phytate degradation was expected to be maximized. Supplemental Fe was from laboratory-grade ferrous sulfate heptahydrate (FeSO47H2O) which was increasingly added to the feeds (analyzed Fe in the supplemented feeds were: 53.3 ± 1.41, 65.5 ± 0.59, 77.2 ± 1.97, 87.6 ± 1.72, 97.7 ± 1.33 mg/kg). There were no interactions between phytase and dietary Fe for any response throughout the study (P > 0.05). Supplementing phytase had no effects on Fe intake or Fe excretion, as well as on hematocrit (Ht), hemoglobin (Hb), ferritin, Fe contents in the liver or thigh muscle color (P > 0.05). However, phytase-supplemented feeds produced better live performance as well as higher ileal digestible energy and Fe digestibility (P < 0.05). No effects were found for dietary Fe in live performance at day 28 (P > 0.05). On the other hand, increasing dietary Fe led to linear increases in Fe retention and excretion, Fe contents in livers, as well as Ht and Hb at 14 d (P < 0.05). Quadratic responses (P < 0.05) were observed for Hb at 21 d, serum ferritin on days 14, 21, and 28 (maximum responses were 83.3, 104.0, 91.9, and 88.3 mg/kg Fe, respectively). In conclusion, supplementing Fe adding to a total of 97.7 mg/kg dietary Fe did not affect live performance traits. However, the average of Fe-related blood parameters was maximized at 91.9 mg/kg dietary Fe. Supplementing phytase provided a significant increase in Fe digestibility.
An approximate method for calculating anisotropy parameters and reflectivity of shales with horizontal fractures
Authors: Chen Chao , Yin Xingyao , Chen Zuqing , Liu Xiaojing , Wang Jingbo
Published: August 2023

Shale is a typical medium of transverse isotropy with a vertical axis of symmetry (VTI), and its strong anisotropy is mainly due to the combined effect of intrinsic anisotropy and that induced by horizontal fractures. To calculate the anisotropy parameters of shale, a physical rock model is built based on Hudson's thin-coin fracture model and Schoenberg's linear-sliding model, and an approximate theoretical calculation method for Thomsen's anisotropy parameters of VTI media with horizontal fractures is proposed. These calculation results using the proposed method confirm that this anisotropy contributed to by horizontal fractures cannot be ignored to the overall anisotropy of shale. To simplify Rüger's formula that is an approximate theoretical formula for calculating the anisotropic reflection coefficients of VTI media, a new four-term approximate formula is derived in a standard reflectivity form based on Rüger's and Aki–Richards’ formulas. The simulation results of a VTI theoretical model and logging data of shale reservoirs show that there is only a small difference between the newly derived four-term formula and Rüger's formula for incidence angles <40°, and the new four-term formula can correctly reveal the seismic amplitude-versus-offset (AVO) characteristics of VTI media and fully retain the corresponding anisotropic seismic responses. Compared to Rüger's formula, the proposed new formula only has four terms of unknown parameters and can directly decouple Thomsen's anisotropy parameter ε from them, which helps to alleviate the ill-posed problems of simultaneous inversion of multiple parameters and enhance its application potential in seismic inversion of VTI media as shale.
A non-parametric panel model for climate data with seasonal and spatial variation
Authors: Gao Jiti , Linton Oliver , Peng Bin
Published: August 2023

We consider a panel data model that allows for heterogeneous time trends at different locations. The model is well suited to identifying trends in climate data recorded at multiple stations. We propose a new estimation method for the model and derive an asymptotic theory for the proposed estimation method. For inferential purposes, we develop a bootstrap method for the case where weak correlation presents in both dimensions of the error terms. We examine the finite-sample properties of the proposed model and estimation method through extensive simulated studies. Finally, we use the newly proposed model and method to investigate monthly rainfall, temperature, and sunshine data of the UK, respectively. Overall, we find spring and winter have changed significantly over the past 50 years. Changes vary with respect to locations for the other seasons.
The dynamic duo: how DNA methylation and gene transcription help diatoms thrive in modern oceans
Authors: Lin Xin , Tirichine Leila , Zhang Xu
Published: August 2023

This article comments on:

Wan J, Zhou Y, Beardall J, Raven JA, Lin J, Huang J, Lu Y, Liang S, Ye M, Xiao M, Zhao J, Dai X, Xia J, Jin P. 2023. DNA methylation and gene transcription act cooperatively in driving the adaptation of a marine diatom to global change. Journal of Experimental Botany74, 4259–4276.
Star cluster classification using deep transfer learning with PHANGS-HST
Authors: Hannon Stephen , Whitmore Bradley C , Lee Janice C , Thilker David A , Deger Sinan , Huerta E A , Wei Wei , Mobasher Bahram , Klessen Ralf , Boquien Médéric , Dale Daniel A , Chevance Mélanie , Grasha Kathryn , Sanchez-Blazquez Patricia , Williams Thomas , Scheuermann Fabian , Groves Brent , Kim Hwihyun , Kruijssen J M Diederik ,   the PHANGS-HST Team
Published: August 2023

Currently available star cluster catalogues from the Hubble Space Telescope (HST) imaging of nearby galaxies heavily rely on visual inspection and classification of candidate clusters. The time-consuming nature of this process has limited the production of reliable catalogues and thus also post-observation analysis. To address this problem, deep transfer learning has recently been used to create neural network models that accurately classify star cluster morphologies at production scale for nearby spiral galaxies (D ≲ 20 Mpc). Here, we use HST ultraviolet (UV)–optical imaging of over 20 000 sources in 23 galaxies from the Physics at High Angular resolution in Nearby GalaxieS (PHANGS) survey to train and evaluate two new sets of models: (i) distance-dependent models, based on cluster candidates binned by galaxy distance (9–12, 14–18, and 18–24 Mpc), and (ii) distance-independent models, based on the combined sample of candidates from all galaxies. We find that the overall accuracy of both sets of models is comparable to previous automated star cluster classification studies (∼60–80 per cent) and shows improvement by a factor of 2 in classifying asymmetric and multipeaked clusters from PHANGS-HST. Somewhat surprisingly, while we observe a weak negative correlation between model accuracy and galactic distance, we find that training separate models for the three distance bins does not significantly improve classification accuracy. We also evaluate model accuracy as a function of cluster properties such as brightness, colour, and spectral energy distribution (SED)-fit age. Based on the success of these experiments, our models will provide classifications for the full set of PHANGS-HST candidate clusters (N ∼ 200 000) for public release.
The unseen host galaxy and high dispersion measure of a precisely localized fast radio burst suggests a high-redshift origin
Authors: Marnoch Lachlan , Ryder Stuart D , James Clancy W , Gordon Alexa C , Sammons Mawson W , Prochaska J Xavier , Tejos Nicolas , Deller Adam T , Scott Danica R , Bhandari Shivani , Glowacki Marcin , Mahony Elizabeth K , McDermid Richard M , Sadler Elaine M , Shannon Ryan M , Qiu Hao
Published: August 2023

FRB 20210912A is a fast radio burst (FRB), detected and localized to subarcsecond precision by the Australian Square Kilometre Array Pathfinder. No host galaxy has been identified for this burst despite the high precision of its localization and deep optical and infrared follow-up, to 5σ limits of R = 26.7 mag and Ks = 24.9 mag with the Very Large Telescope. The combination of precise radio localization and deep optical imaging has almost always resulted in the secure identification of a host galaxy, and this is the first case in which the line of sight is not obscured by the Galactic disc. The dispersion measure of this burst, DMFRB = 1233.696 ± 0.006 pc cm−3, allows for a large source redshift of z > 1 according to the Macquart relation. It could thus be that the host galaxy is consistent with the known population of FRB hosts, but is too distant to detect in our observations (z > 0.7 for a host like that of the first repeating FRB source, FRB 20121102A); that it is more nearby with a significant excess in DMhost, and thus dimmer than any known FRB host; or, least likely, that the FRB is truly hostless. We consider each possibility, making use of the population of known FRB hosts to frame each scenario. The fact of the missing host has ramifications for the FRB field: even with high-precision localization and deep follow-up, some FRB hosts may be difficult to detect, with more distant hosts being the less likely to be found. This has implications for FRB cosmology, in which high-redshift detections are valuable.
Mapping pediatric brain tumors to their origins in the developing cerebellum
Authors: Okonechnikov Konstantin , Joshi Piyush , Sepp Mari , Leiss Kevin , Sarropoulos Ioannis , Murat Florent , Sill Martin , Beck Pengbo , Chan Kenneth Chun-Ho , Korshunov Andrey , Sah Felix , Deng Maximilian Y , Sturm Dominik , DeSisto John , Donson Andrew M , Foreman Nicholas K , Green Adam L , Robinson Giles , Orr Brent A , Gao Qingsong , Darrow Emily , Hadley Jennifer L , Northcott Paul A , Gojo Johannes , Kawauchi Daisuke , Hovestadt Volker , Filbin Mariella G , von Deimling Andreas , Zuckermann Marc , Pajtler Kristian W , Kool Marcel , Jones David T W , Jäger Natalie , Kutscher Lena M , Kaessmann Henrik , Pfister Stefan M
Published: August 2023

Background

Distinguishing the cellular origins of childhood brain tumors is key for understanding tumor initiation and identifying lineage-restricted, tumor-specific therapeutic targets. Previous strategies to map the cell-of-origin typically involved comparing human tumors to murine embryonal tissues, which is potentially limited due to species-specific differences. The aim of this study was to unravel the cellular origins of the 3 most common pediatric brain tumors, ependymoma, pilocytic astrocytoma, and medulloblastoma, using a developing human cerebellar atlas.

Methods

We used a single-nucleus atlas of the normal developing human cerebellum consisting of 176 645 cells as a reference for an in-depth comparison to 4416 bulk and single-cell transcriptome tumor datasets, using gene set variation analysis, correlation, and single-cell matching techniques.

Results

We find that the astroglial cerebellar lineage is potentially the origin for posterior fossa ependymomas. We propose that infratentorial pilocytic astrocytomas originate from the oligodendrocyte lineage and MHC II genes are specifically enriched in these tumors. We confirm that SHH and Group 3/4 medulloblastomas originate from the granule cell and unipolar brush cell lineages. Radiation-induced gliomas stem from cerebellar glial lineages and demonstrate distinct origins from the primary medulloblastoma. We identify tumor genes that are expressed in the cerebellar lineage of origin, and genes that are tumor specific; both gene sets represent promising therapeutic targets for future study.

Conclusion

Based on our results, individual cells within a tumor may resemble different cell types along a restricted developmental lineage. Therefore, we suggest that tumors can arise from multiple cellular states along the cerebellar “lineage of origin.”
LESION SIMULATING DISEASE 3 regulates disease resistance via fine-tuning histone acetylation in cassava
Authors: Zeng Hongqiu , Xu Haoran , Tan Mengting , Zhang Bowen , Shi Haitao
Published: August 2023

Bacterial blight seriously affects the growth and production of cassava (Manihot esculenta Crantz), but disease resistance genes and the underlying molecular mechanism remain unknown. In this study, we found that LESION SIMULATING DISEASE 3 (MeLSD3) is essential for disease resistance in cassava. MeLSD3 physically interacts with SIRTUIN 1 (MeSRT1), inhibiting MeSRT1-mediated deacetylation modification at the acetylation of histone 3 at K9 (H3K9Ac). This leads to increased H3K9Ac levels and transcriptional activation of SUPPRESSOR OF BIR1 (SOBIR1) and FLAGELLIN-SENSITIVE2 (FLS2) in pattern-triggered immunity, resulting in immune responses in cassava. When MeLSD3 was silenced, the release of MeSRT1 directly decreased H3K9Ac levels and inhibited the transcription of SOBIR1 and FLS2, leading to decreased disease resistance. Notably, DELLA protein GIBBERELLIC ACID INSENSITIVE 1 (MeGAI1) also interacted with MeLSD3, which enhanced the interaction between MeLSD3 and MeSRT1 and further strengthened the inhibition of MeSRT1-mediated deacetylation modification at H3K9Ac of defense genes. In summary, this study illustrates the mechanism by which MeLSD3 interacts with MeSRT1 and MeGAI1, thereby mediating the level of H3K9Ac and the transcription of defense genes and immune responses in cassava.
Development of a Tool to Determine Excellence in the Provision of Physical Therapist Clinical Education: A Modified Delphi Study
Authors: Timmerberg Jean Fitzpatrick , Pelletier Deborah , Harding Elizabeth , Recker-Hughes Carol , Wetherbee-McDevitt Ellen , Stolfi Angela
Published: August 2023

Objective

The purpose of this study was to create a Site of Excellence in Clinical Education (SECE-PT) tool with the essential criteria used to determine excellence in the provision of physical therapist clinical education at a clinical site using a consensus-building approach.

Methods

The development of the SECE-PT tool was divided into 2 parts. Part 1 involved the development of an initial set of proposed criteria, whereas part 2 employed a modified Delphi approach for consensus building. Purposive selection and snowball sampling techniques were used to recruit clinical instructors, recent graduates, site coordinators of clinical education, and directors of clinical education who met the inclusion criteria for the modified Delphi study. Three web-based survey rounds were used to achieve consensus, defined as a mean score of ≥7 on the 11-point Likert scale. The first round gathered demographic information on participants and collected information about clarity and redundancy in the criteria provided, the second gathered information once again about clarity and redundancy on the revised criteria provided, and the third asked participants to rate how essential it was for a site of excellence to demonstrate each of the final criteria.

Results

A total of 123 participants, equally representing clinical and academic perspectives, completed the demographic survey and round 1. Ninety-four participants completed round 2, and 80 participants completed the third and final round. Consensus revealed that 44 criteria were deemed essential for a SECE-PT to demonstrate.

Conclusion

This study provides a measure to evaluate clinical sites providing clinical education. The SECE-PT tool should be widely adopted to evaluate the quality of the clinical site providing the education to student physical therapists.

Impact

The SECE-PT tool can be used by clinical sites for self-assessment to examine aspects of their clinical education programs and determine whether parts of their program should be further developed. This can provide a framework for discussion and collaboration between clinical and academic partners, as well as regional consortia.