bluuebunny/crossref_metadata_2025 huggingface dataset:
BloodNet: An attention-based deep network for accurate, efficient, and costless bloodstain time since deposition inference
Authors: Li Huiyu , Shen Chen , Wang Gongji , Sun Qinru , Yu Kai , Li Zefeng , Liang XingGong , Chen Run , Wu Hao , Wang Fan , Wang Zhenyuan , Lian Chunfeng
Published: December 2022

The time since deposition (TSD) of a bloodstain, i.e., the time of a bloodstain formation is an essential piece of biological evidence in crime scene investigation. The practical usage of some existing microscopic methods (e.g., spectroscopy or RNA analysis technology) is limited, as their performance strongly relies on high-end instrumentation and/or rigorous laboratory conditions. This paper presents a practically applicable deep learning-based method (i.e., BloodNet) for efficient, accurate, and costless TSD inference from a macroscopic view, i.e., by using easily accessible bloodstain photos. To this end, we established a benchmark database containing around 50,000 photos of bloodstains with varying TSDs. Capitalizing on such a large-scale database, BloodNet adopted attention mechanisms to learn from relatively high-resolution input images the localized fine-grained feature representations that were highly discriminative between different TSD periods. Also, the visual analysis of the learned deep networks based on the Smooth Grad-CAM tool demonstrated that our BloodNet can stably capture the unique local patterns of bloodstains with specific TSDs, suggesting the efficacy of the utilized attention mechanism in learning fine-grained representations for TSD inference. As a paired study for BloodNet, we further conducted a microscopic analysis using Raman spectroscopic data and a machine learning method based on Bayesian optimization. Although the experimental results show that such a new microscopic-level approach outperformed the state-of-the-art by a large margin, its inference accuracy is significantly lower than BloodNet, which further justifies the efficacy of deep learning techniques in the challenging task of bloodstain TSD inference. Our code is publically accessible via https://github.com/shenxiaochenn/BloodNet. Our datasets and pre-trained models can be freely accessed via https://figshare.com/articles/dataset/21291825.
An evolution-based machine learning to identify cancer type-specific driver mutations
Authors: Kim Donghyo , Ha Doyeon , Lee Kwanghwan , Lee Heetak , Kim Inhae , Kim Sanguk
Published: December 2022

Identifying cancer type-specific driver mutations is crucial for illuminating distinct pathologic mechanisms across various tumors and providing opportunities of patient-specific treatment. However, although many computational methods were developed to predict driver mutations in a type-specific manner, the methods still have room to improve. Here, we devise a novel feature based on sequence co-evolution analysis to identify cancer type-specific driver mutations and construct a machine learning (ML) model with state-of-the-art performance. Specifically, relying on 28 000 tumor samples across 66 cancer types, our ML framework outperformed current leading methods of detecting cancer driver mutations. Interestingly, the cancer mutations identified by sequence co-evolution feature are frequently observed in interfaces mediating tissue-specific protein–protein interactions that are known to associate with shaping tissue-specific oncogenesis. Moreover, we provide pre-calculated potential oncogenicity on available human proteins with prediction scores of all possible residue alterations through user-friendly website (http://sbi.postech.ac.kr/w/cancerCE). This work will facilitate the identification of cancer type-specific driver mutations in newly sequenced tumor samples.
Biophysical informatics reveals distinctive phenotypic signatures and functional diversity of single-cell lineages
Authors: Chan Trevor J , Zhang Xingjian , Mak Michael
Published: December 2022

Motivation

In this work, we present an analytical method for quantifying both single-cell morphologies and cell network topologies of tumor cell populations and use it to predict 3D cell behavior.

Results

We utilized a supervised deep learning approach to perform instance segmentation on label-free live cell images across a wide range of cell densities. We measured cell shape properties and characterized network topologies for 136 single-cell clones derived from the YUMM1.7 and YUMMER1.7 mouse melanoma cell lines. Using an unsupervised clustering algorithm, we identified six distinct morphological subclasses. We further observed differences in tumor growth and invasion dynamics across subclasses in an in vitro 3D spheroid model. Compared to existing methods for quantifying 2D or 3D phenotype, our analytical method requires less time, needs no specialized equipment and is capable of much higher throughput, making it ideal for applications such as high-throughput drug screening and clinical diagnosis.

Availability and implementation

https://github.com/trevor-chan/Melanoma_NetworkMorphology.

Supplementary information

Supplementary data are available at Bioinformatics online.
Expression patterns of NKCC1 in neurons and non-neuronal cells during cortico-hippocampal development
Authors: Kurki Samu N , Uvarov Pavel , Pospelov Alexey S , Trontti Kalevi , Hübner Antje K , Srinivasan Rakenduvadhana , Watanabe Masahiko , Hovatta Iiris , Hübner Christian A , Kaila Kai , Virtanen Mari A
Published: December 2022

The Na-K-2Cl cotransporter NKCC1 is widely expressed in cells within and outside the brain. However, our understanding of its roles in brain functions throughout development, as well as in neuropsychiatric and neurological disorders, has been severely hindered by the lack of reliable data on its developmental and (sub)cellular expression patterns. We provide here the first properly controlled analysis of NKCC1 protein expression in various cell types of the mouse brain using custom-made antibodies and an NKCC1 knock-out validated immunohistochemical procedure, with parallel data based on advanced mRNA approaches. NKCC1 protein and mRNA are expressed at remarkably high levels in oligodendrocytes. In immature neurons, NKCC1 protein was located in the somata, whereas in adult neurons, only NKCC1 mRNA could be clearly detected. NKCC1 immunoreactivity is also seen in microglia, astrocytes, developing pericytes, and in progenitor cells of the dentate gyrus. Finally, a differential expression of NKCC1 splice variants was observed, with NKCC1a predominating in non-neuronal cells and NKCC1b in neurons. Taken together, our data provide a cellular basis for understanding NKCC1 functions in the brain and enable the identification of major limitations and promises in the development of neuron-targeting NKCC1-blockers.
Single voxel autocorrelation uncovers gradients of temporal dynamics in the hippocampus and entorhinal cortex during rest and navigation
Authors: Bouffard Nichole R , Golestani Ali , Brunec Iva K , Bellana Buddhika , Park Jun Young , Barense Morgan D , Moscovitch Morris
Published: December 2022

During navigation, information at multiple scales needs to be integrated. Single-unit recordings in rodents suggest that gradients of temporal dynamics in the hippocampus and entorhinal cortex support this integration. In humans, gradients of representation are observed, such that granularity of information represented increases along the long axis of the hippocampus. The neural underpinnings of this gradient in humans, however, are still unknown. Current research is limited by coarse fMRI analysis techniques that obscure the activity of individual voxels, preventing investigation of how moment-to-moment changes in brain signal are organized and how they are related to behavior. Here, we measured the signal stability of single voxels over time to uncover previously unappreciated gradients of temporal dynamics in the hippocampus and entorhinal cortex. Using our novel, single voxel autocorrelation technique, we show a medial-lateral hippocampal gradient, as well as a continuous autocorrelation gradient along the anterolateral-posteromedial entorhinal extent. Importantly, we show that autocorrelation in the anterior-medial hippocampus was modulated by navigational difficulty, providing the first evidence that changes in signal stability in single voxels are relevant for behavior. This work opens the door for future research on how temporal gradients within these structures support the integration of information for goal-directed behavior.
Associations among body mass index, working memory performance, gray matter volume, and brain activation in healthy children
Authors: Zhang Yaqi , Ji Weibin , Jiang Fukun , Wu Feifei , Li Guanya , Hu Yang , Zhang Wenchao , Wang Jia , Fan Xiao , Wei Xiaorong , Manza Peter , Tomasi Dardo , Volkow Nora D , Gao Xinbo , Wang Gene-Jack , Zhang Yi
Published: December 2022

To investigate the neural mechanisms underlying the association between poorer working memory performance and higher body mass index (BMI) in children. We employed structural-(sMRI) and functional magnetic resonance imaging (fMRI) with a 2-back working memory task to examine brain abnormalities and their associations with BMI and working memory performance in 232 children with overweight/obesity (OW/OB) and 244 normal weight children (NW) from the Adolescent Brain Cognitive Development dataset. OW/OB had lower working memory accuracy, which was associated with higher BMI. They showed smaller gray matter (GM) volumes in the left superior frontal gyrus (SFG_L), dorsal anterior cingulate cortex, medial orbital frontal cortex, and medial superior frontal gyrus, which were associated with lower working memory accuracy. During the working memory task, OW/OB relative to NW showed weaker activation in the left superior temporal pole, amygdala, insula, and bilateral caudate. In addition, caudate activation mediated the relationship between higher BMI and lower working memory accuracy. Higher BMI is associated with smaller GM volumes and weaker brain activation in regions involved with working memory. Task-related caudate dysfunction may account for lower working memory accuracy in children with higher BMI.
Knowledge of Strategies to Teach Reading Components among Teachers of Hard of Hearing Students
Authors: Alasim Khalid N
Published: December 2022

This study investigated Saudi Arabian elementary school teachers’ knowledge of strategies to teach reading components to hard of hearing students. The study focused on four of the five reading components the National Reading Panel (NPR, 2000) identified: phonemic awareness; phonics; vocabulary; and reading comprehension, and explored the relation between teachers’ demographic characteristics and their knowledge of the strategies as well. An explanatory sequential mixed methods design was used that included two phases. The quantitative phase examined the knowledge of these Arabic reading components among 89 elementary school teachers of hard of hearing students, and the qualitative phase consisted of interviews with 10 teachers. The results indicated that the teachers have a great deal of knowledge (above the mean score) of strategies to teach reading components. Specifically, teachers’ knowledge of strategies to teach the vocabulary component was the highest. The results also showed no significant association between teachers’ demographic characteristics and their knowledge of strategies to teach reading components. The qualitative analysis revealed two themes: (1) teachers’ lack of basic knowledge of strategies to teach reading components, and (2) the absence of in-service courses and training programs in reading for teachers.
Coaching Caregivers of Children who are Deaf or Hard of Hearing
Authors: Brock Aleah S , Bass-Ringdahl Sandie M
Published: December 2022

This study explored the impact of a caregiver training intervention on caregivers’ use of individually selected facilitative language techniques (FLTs) with their children (ranging from 14 to 27 months of age) who were deaf or hard of hearing. In addition, the study sought to identify real-time relationships between caregiver input and child output. Finally, the Language ENvironment Analysis (LENA) system was used to assess generalization of intervention gains to the natural environment. Intervention was delivered via a telehealth approach to train four caregivers to utilize a targeted FLT with their child. Pre-baseline LENA recordings guided selection of treatment targets, and post-intervention LENA recordings were used to assess generalization to the natural environment. All caregivers demonstrated increases in use of their targeted FLT in structured intervention sessions and maintained them 2–6 weeks after the conclusion of intervention. All children demonstrated an increase in their developmentally appropriate vocalizations in tandem with caregiver FLT increases. Results indicate that coaching can be used to increase caregiver responsiveness, changes which were found to carry over into the home environment.
Insights for Foreign Policy Analysis from European Union External Action Studies
Authors: Gstöhl Sieglinde , Schunz Simon
Published: December 2022

The European Union (EU) has increasingly become a foreign policy actor in its own right, sparking the emergence of EU External Action Studies (EU EAS). Although this thriving field at the intersection of EU Studies and International Relations has gradually matured, the interaction of EU EAS with Foreign Policy Analysis (FPA) has so far remained limited. This contribution discusses whether concepts and approaches from EU EAS hold valuable theoretical insights for FPA, and how these could be exploited. It argues that there is a largely untapped potential for cross-fertilization between the two fields. This claim is illustrated with several examples as well as two short instructive cases that show how the approach to studying the EU's “external effectiveness” helps addressing FPA's blind spot regarding foreign policy impacts, and how the critical agenda on “decentering” EU external action directs much-needed attention to the “foreign” in FPA.
Development of Prognostic Prediction Model to Estimate Mortality for Frail Oldest Old: Prospective Cohort Study
Authors: Gu Yaohua , Wu Wenwen , Kong Chan , Luo Qiaoqian , Ran Li , Tan Xiaodong , Zhang Qing
Published: December 2022

Background

This study was performed to derive and validate a prognostic prediction model for individualized estimation of mortality risk among the frail oldest old (aged 80 years or older).

Methods

This analysis was based on the prospective open cohort study from the Chinese Longevity and Health Longitudinal Survey. A total of 14 118 frail oldest old were included from the 2002 wave to 2014 waves; the study outcome was all-cause mortality. Available predictors included frailty, demographics, and social factors. Cox models were used to estimate the coefficients of the predictors and least absolute shrinkage and selection operator was used for selecting predictors. Model performance was measured by discrimination and calibration with internal validation by bootstrapping. We also developed a nomogram to visualize and predict the 3-year mortality risk based on the obtained prognostic prediction model.

Results

During the 16-years follow-up, 10 410 (76.42%) deaths were identified. The final model comprises the following factors: frailty, age, sex, race, birthplace, education, occupation, marital status, residence, economic condition, number of children, and the question “who do you ask for help first when in trouble.” The model has valid predictive ability as measured and validated by Harrell’s C statistic (0.602) and calibration plots.

Conclusions

This study provides a basic prognostic prediction model to quantify absolute mortality risk for the frail oldest old. Future studies are needed, firstly, to update, adjust, and perform external validation of the present model by using phenotypic frailty, and secondly, to add biomarkers, environmental, and psychological factors to the prediction model.
Shear wave velocity structure and crustal lithology beneath the ultraslow spreading Southwest Indian Ridge at 50° E
Authors: Niu Xiongwei , Minshull T A , Li Jiabiao , Ruan Aiguo , Wu Zhenli , Wei Xiaodong , Wang Wei , Li Yan , Bayrakci G , Dong Chongzhi , Ding Weiwei , Fang Yinxia , Zhang Jie
Published: December 2022

Shear wave velocities provide an important constraint on crustal lithology. Limited crustal shear wave data are available from the ultraslow spreading mid-ocean ridges. We combine observations of both compressional (P) and shear (S) waves in ocean–bottom seismometer data from the Southwest Indian Ridge to determine crustal P-wave velocity (Vp), S-wave velocity (Vs), Vp/Vs and Poisson's ratio variations along the ridge at 49°17′E–50°49′E. Similar layered crustal structures were revealed beneath both the magmatically robust segment centres (Vp/Vs of 1.76–1.94, Poisson's ratio of 0.26–0.32) and the non-transform discontinuity (NTD) between them (Vp/Vs of 1.76–2.03 and Poisson's ratio of 0.26–0.34). Because laboratory measurements show an overlap in Poisson's ratio between mafic igneous and ultramafic rocks, particularly at Vp values typical of oceanic Layer 3, it can be difficult to distinguish crustal composition using this parameter only. However, our observed Vp gradients of 0.1 ± 0.1 s−1 suggest that in this area, oceanic Layer 3 consists primarily of mafic igneous rocks both at segment centres and at the NTD. Oceanic crustal Layers 2A and 2B above are likely also to consist of mafic igneous rocks, with some evidence for increased fracturing at the NTD.
Effect ofMAOADNA Methylation on Human in Vivo Protein Expression Measured by [11C]harmine Positron Emission Tomography
Authors: Handschuh Patricia A , Murgaš Matej , Vraka Chrysoula , Nics Lukas , Hartmann Annette M , Winkler-Pjrek Edda , Baldinger-Melich Pia , Wadsak Wolfgang , Winkler Dietmar , Hacker Marcus , Rujescu Dan , Domschke Katharina , Lanzenberger Rupert , Spies Marie
Published: December 2022

Background

Epigenetic modifications like DNA methylation are understood as an intermediary between environmental factors and neurobiology. Cerebral monoamine oxidase A (MAO-A) levels are altered in depression, as are DNA methylation levels within the MAOA gene, particularly in the promoter/exon I/intron I region. An effect of MAOA methylation on peripheral protein expression was shown, but the extent to which methylation affects brain MAO-A levels is not fully understood.

Methods

Here, the influence of MAOA promoter/exon I/intron I region DNA methylation on global MAO-A distribution volume (VT), an index of MAO-A density, was assessed via [11C]harmine positron emission tomography in 22 patients (14 females) suffering from seasonal affective disorder and 30 healthy controls (17 females).

Results

No significant influence of MAOA DNA methylation on global MAO-A VT was found, despite correction for health status, sex, season, and MAOA variable number of tandem repeat genotype. However, season affected average methylation in women, with higher levels in spring and summer (Puncorr = .03). We thus did not find evidence for an effect of MAOA DNA methylation on brain MAO-A VT.

Conclusions

In contrast to a previous study demonstrating an effect of methylation of a MAOA promoter region located further 5’ on brain MAO-A, MAOA methylation of the region assessed here appears to affect brain protein levels to a limited extent at most. The observed effect of season on methylation levels is in accordance with extensive evidence for seasonal effects within the serotonergic system.

Clinicaltrials.gov Identifier

NCT02582398 (https://clinicaltrials.gov/ct2/show/NCT02582398).
Remembering the Shared History of (Eur)Asia: Is This a Good Idea in the Twenty-First Century?
Authors: Zarakol Ayşe
Published: December 2022

If we assume the premise of this forum that we are indeed moving from a Transatlantic to an Afro-Eurasian World, it still remains to be seen what role ‘Asia’ will play in shaping that world. And what one imagines ‘Asia’ can do has much to do with what one imagines ‘Asia’ to be. In this research note, I argue first that the geographical space we call Asia today does have a connected history that goes back almost a millennium (if not longer) and then also consider the reasons why that history is not invoked more in contemporary debates.
Evaluation of Outcomes Following Surgical Treatment of Hidradenitis Suppurativa
Authors: Romanowski Kathleen S , Galet Colette , Torres Marlon , Wibbenmeyer Lucy
Published: December 2022

Hidradenitis suppurativa (HS), a chronic disease of the apocrine bearing skin causing induration, pain, draining sinuses, and subcutaneous abscesses, significantly impairs patients’ quality of life (QOL). Full-thickness excision followed by skin grafting of the involved area can be curative. Herein, we evaluated the impact of this surgical treatment on QOL and depression symptomatology. Adult patients (≥18 years) who consented to participate filled out the dermatology quality of life (DLQI) and the Patient History Questionnaire (PHQ-9) at consent and at 1, 6, and 12 months post-initial evaluation and surgery. Demographics, HS, admission, and operative information were collected. Sixteen patients were included. Subjects were mainly white (81.3 %) and female (56.3%) with a median age of 38.2 (Interquartile range: 34.2–54.5); 62.5% were obese (BMI= 39.7 [28.4–50.6]). Half of the subjects presented with HS in 2 or more areas. Six patients were still undergoing surgeries at 6 months. One-, six-, and 12-month follow-up surveys were obtained from 14, 11, and 8 subjects for DQLI and from 14, 9, and 5 subjects for PHQ9. DLQI scores significantly decreased at 6 months compared to baseline, which indicates QOL improvement (10 [4–20] vs 15.5 [12–21.8], P = .036). Although not significant, PHQ9 scores tended to decrease. For those with the worst disease, DLQI significantly decreased at both 6 (P = .049) and 12 months (P = .047) compared to baseline. Despite a small sample size, our data suggest that aggressive surgical treatment improves the QOL of HS patients. Further studies are warranted to confirm our findings.
Randomized phase III study of daratumumab versus bortezomib plus daratumumab as maintenance therapy after D-MPB for transplant-ineligible patients with untreated multiple myeloma (JCOG1911, B-DASH study)
Authors: Suzuki Tomotaka , Terada Mitsumi , Machida Ryunosuke , Kataoka Tomoko , Ito Yuta , Kataoka Keisuke , Maruyama Dai , Nagai Hirokazu ,   Lymphoma Study Group of the Japan Clinical Oncology Group
Published: December 2022

Daratumumab, melphalan, prednisolone and bortezomib followed by daratumumab maintenance is a standard regimen for transplant-ineligible newly diagnosed multiple myeloma. A large-scale clinical trial demonstrated that progression-free survival declined more sharply during the maintenance phase than during the daratumumab, melphalan, prednisolone and bortezomib induction phase, which suggests the necessity of reinforcing maintenance therapy. This randomized phase III trial aims to confirm the superiority of daratumumab plus bortezomib to daratumumab as maintenance therapy in terms of progression-free survival for transplant-ineligible newly diagnosed multiple myeloma (JCOG1911, B-DASH). First registration (222 patients, within 5 years) was before daratumumab, melphalan, prednisolone and bortezomib administration; those who responded to daratumumab, melphalan, prednisolone and bortezomib were included in the second registration. They were randomized to the daratumumab or daratumumab plus bortezomib maintenance arm. This trial is registered in the Japan Registry for Clinical Trials as jRCT031200320 (https://jrct.niph.go.jp/). An ancillary study examining the association of genetic alterations in myeloma cells with prognosis and drug resistance, using next-generation sequencing, is ongoing.
Analyzing the synchronism of stacking-fault formation in side-by-side SiC nanowire pairs using the Levenshtein distance: stochastic versus deterministic processes
Authors: Moriuchi Fuka , Kohno Hideo
Published: December 2022

Pairs of silicon carbide nanowires were grown side by side synchronously from the same metal catalyst nanoparticles. The stacking sequences of each pair were read by high-resolution transmission electron microscopy, and the similarity of each stacking sequence was measured using the Levenshtein distance. No synchronism was detected in the pairs of stacking sequences, and the results indicated that the formation of stacking faults in silicon carbide nanowires was not deterministic, but purely stochastic.
Hemiarthroplasty for tumor-induced osteomalacia caused by tumor localized in femoral head: a case report
Authors: Arita Sayaka , Nishino Tomofumi , Mitani Yuuki , Sakashita Kotaro , Totsuka Sho , Watanabe Ryunosuke , Mishima Hajime , Kawai Hitomi , Matsubara Daisuke , Oda Yoshionao , Yamazaki Masashi
Published: December 2022

Tumor-induced osteomalacia (TIO) is a rare tumor-associated syndrome in which osteomalacia is induced by a tumor. A 67-year-old male patient presented for the first time with low back pain, weakness of the lower extremities and difficulty in walking. Six years earlier, he had nonspecific symptoms such as low back pain, and blood tests showed high alkaline phosphatase and low phosphorus. In addition, fibroblast growth factor 23 (FGF23) was abnormally high at 454 pg/mL. A diagnosis of FGF23-related hypophosphatemic osteomalacia was made. Somatostatin receptor scintigraphy, venous sampling and MRI were performed to localize and diagnose TIO. The tumor was found to be confined to the right femoral head and hemiarthroplasty was performed. Pathological examination revealed a phosphaturic mesenchymal tumor. Postoperatively, symptoms and blood test data improved. Although resection of the lesion and osteochondral transplantation or total hip arthroplasty were considered, hemiarthroplasty was chosen over concerns about treatment failure due to seeding.
Left-sided gallbladder ‘sinistroposition’ associated with an anatomical variant of cystic duct insertion: case report
Authors: Guachilema Ribadeneira Alex , Palacios Gordon Mauricio , Morocho Sandra , Bahamonde Edwin Guillermo , Basantes Andrea Daniela , Parra Valverde Estefanía
Published: December 2022

True left-sided gallbladder (LSGB) is a rare congenital anomaly with an incidence of 0.1–1.2%. It is more common in women than in men at a ratio of 5:1. Its etiology is unknown, although several theories have been proposed. The symptoms are similar to those of a normal gallbladder, which makes the preoperative diagnosis difficult despite imaging studies. In most cases, the diagnosis is achieved intraoperatively. LSGB is associated with biliary anomalies, and the incidence of biliary tract lesions is high. Four-port laparoscopic cholecystectomy is a safe procedure for LSGB. Surgical technique varies according to each case. Preoperative imaging studies have low sensitivity for diagnosis, and the surgeon should be familiar with ductal and vascular anatomical variants in addition to possessing the ability to change the conventional surgical technique to optimize the exposure and minimize the risk of bile duct injury.
FRB–SRB–XRB: Geometric and relativistic beaming constraints of fast radio bursts from the Galactic magnetar SGR J1935+2154
Authors: Chen Connery J , Zhang Bing
Published: December 2022

The detection of a fast radio burst (FRB), FRB 200428, coincident with an X-ray burst (XRB) from the Galactic magnetar soft gamma repeater (SGR) SGR J1935+2154 suggests that magnetars can produce FRBs. Many XRBs have been detected from the source, but very few were found to be associated with bursty radio emission. Meanwhile, a number of weaker radio bursts have been detected from the source, which could in principle be slow radio bursts (SRBs): FRBs detected at viewing angles outside the FRB jet cone. In this paper, we use these X-ray and radio observations to constrain the geometric and relativistic beaming factors of FRBs under two hypotheses. First, we assume that all SRBs should be associated with XRBs like FRB 200428. We use the FRB–SRB closure relations to identify two SRBs and derive that FRB beaming must be geometrically narrow, θj ≲ 10−2 rad and follow θjΓ ∼ 2. Second, we assume a less stringent constraint for SRBs by not requiring that they are associated with XRBs. We identify a total of seven SRBs, five of which have Gaussian-like spectra, and derive that FRB beaming factors again follow θjΓ ∼ 2.
A probabilistic deep learning model to distinguish cusps and cores in dwarf galaxies
Authors: Expósito-Márquez J , Brook C B , Huertas-Company M , Di Cintio A , Macciò A V , Grand R J J , Battaglia G , Arjona-Gálvez E
Published: December 2022

Numerical simulations within a cold dark matter (DM) cosmology form haloes whose density profiles have a steep inner slope (‘cusp’), yet observations of galaxies often point towards a flat central ‘core’. We develop a convolutional mixture density neural network model to derive a probability density function (PDF) of the inner density slopes of DM haloes. We train the network on simulated dwarf galaxies from the NIHAO and AURIGA projects, which include both DM cusps and cores: line-of-sight velocities and 2D spatial distributions of their stars are used as inputs to obtain a PDF representing the probability of predicting a specific inner slope. The model recovers accurately the expected DM profiles: $\sim 82{{\ \rm per\ cent}}$ of the galaxies have a derived inner slope within ±0.1 of their true value, while $\sim 98{{\ \rm per\ cent}}$ within ±0.3. We apply our model to four Local Group dwarf spheroidal galaxies and find results consistent with those obtained with the Jeans modelling based code GravSphere: the Fornax dSph has a strong indication of possessing a central DM core, Carina and Sextans have cusps (although the latter with large uncertainties), while Sculptor shows a double peaked PDF indicating that a cusp is preferred, but a core cannot be ruled out. Our results show that simulation-based inference with neural networks provide a innovative and complementary method for the determination of the inner matter density profiles in galaxies, which in turn can help constrain the properties of the elusive DM.
Black software — the energy unsustainability of software systems in the 21st century
Authors: Manner Jukka
Published: December 2022

Climate change is happening, and the information and communication technology (ICT) industry is providing solutions to enable a more sustainable future. ICT enables enhanced manufacturing processes, optimized logistics, solutions supporting environmental protection and solutions facilitating climate change adaptation, for example. The performance of ICT hardware and electronics has increased tremendously. The capabilities of microchips have increased ~100,000-fold in the past 30 years and the power efficiency has increased a million-fold. Yet, various reports show that the ICT sector increases its carbon footprint and energy consumption, while other sectors are lowering their impact on our planet. Thus, there seems to be an adverse development ongoing where most industry sectors can lower their carbon footprint while the ICT sector increases its consumption. This paper looks at the development of the ICT sector and seeks to understand the current development. We argue that a major reason for the rebound effect we are seeing within the ICT sector is the lack of understanding in energy consumption and the cost pressures of developing digital services. The results are software and services that could be much greener and energy efficient but seem to rather go toward a darker direction. The ICT industry and software engineering needs to do a clear change of course and take accountability of their activities.
Using probiotics in paediatric populations
Authors: Schneider Rilla , Sant’Anna Ana
Published: December 2022

This statement defines probiotics and reviews the most recent literature on their use in paediatrics. Many studies have examined the potential benefit of probiotics, but significant variation in the strains and doses of probiotics used, the patient populations studied, and in study design, have led to heterogeneous results. Present evidence suggests that probiotics can decrease mortality and lower incidence of necrotizing enterocolitis in preterm and low birth weight neonates. Probiotics may also be beneficial in reducing feeding intolerance. In infants, probiotics may be considered to reduce symptoms of colic. In older children, probiotics can be considered to prevent antibiotic-associated diarrhea and Clostridium difficile-associated diarrhea. Probiotic supplements used in conjunction with standard therapy can help with Helicobacter pylori eradication and decrease the side effects of treatment. Lactobacillus species can be considered to treat irritable bowel syndrome. Probiotics can also be considered to help prevent atopic dermatitis and eczema. To optimize paediatric policy and practice, large, quality studies are needed to determine what types and combinations of probiotics are most efficacious.
The diversity of substrates for plant respiration and how to optimize their use
Authors: Le Xuyen H , Millar A Harvey
Published: December 2022

Plant respiration is a foundational biological process with the potential to be optimized to improve crop yield. To understand and manipulate the outputs of respiration, the inputs of respiration—respiratory substrates—need to be probed in detail. Mitochondria house substrate catabolic pathways and respiratory machinery, so transport into and out of these organelles plays an important role in committing substrates to respiration. The large number of mitochondrial carriers and catabolic pathways that remain unidentified hinder this process and lead to confusion about the identity of direct and indirect respiratory substrates in plants. The sources and usage of respiratory substrates vary and are increasing found to be highly regulated based on cellular processes and environmental factors. This review covers the use of direct respiratory substrates following transport through mitochondrial carriers and catabolism under normal and stressed conditions. We suggest the introduction of enzymes not currently found in plant mitochondria to enable serine and acetate to be direct respiratory substrates in plants. We also compare respiratory substrates by assessing energetic yields, availability in cells, and their full or partial oxidation during cell catabolism. This information can assist in decisions to use synthetic biology approaches to alter the range of respiratory substrates in plants. As a result, respiration could be optimized by introducing, improving, or controlling specific mitochondrial transporters and mitochondrial catabolic pathways.
Abscisic acid increases hydrogen peroxide in mitochondria to facilitate stomatal closure
Authors: Postiglione Anthony E , Muday Gloria K
Published: December 2022

Abscisic acid (ABA) drives stomatal closure to minimize water loss due to transpiration in response to drought. We examined the subcellular location of ABA-increased accumulation of reactive oxygen species (ROS) in guard cells, which drive stomatal closure, in Arabidopsis (Arabidopsis thaliana). ABA-dependent increases in fluorescence of the generic ROS sensor, dichlorofluorescein (DCF), were observed in mitochondria, chloroplasts, cytosol, and nuclei. The ABA response in all these locations was lost in an ABA-insensitive quintuple receptor mutant. The ABA-increased fluorescence in mitochondria of both DCF- and an H2O2-selective probe, Peroxy Orange 1, colocalized with Mitotracker Red. ABA treatment of guard cells transformed with the genetically encoded H2O2 reporter targeted to the cytoplasm (roGFP2-Orp1), or mitochondria (mt-roGFP2-Orp1), revealed H2O2 increases. Consistent with mitochondrial ROS changes functioning in stomatal closure, we found that guard cells of a mutant with mitochondrial defects, ABA overly sensitive 6 (abo6), have elevated ABA-induced ROS in mitochondria and enhanced stomatal closure. These effects were phenocopied with rotenone, which increased mitochondrial ROS. In contrast, the mitochondrially targeted antioxidant, MitoQ, dampened ABA effects on mitochondrial ROS accumulation and stomatal closure in Col-0 and reversed the guard cell closure phenotype of the abo6 mutant. ABA-induced ROS accumulation in guard cell mitochondria was lost in mutants in genes encoding respiratory burst oxidase homolog (RBOH) enzymes and reduced by treatment with the RBOH inhibitor, VAS2870, consistent with RBOH machinery acting in ABA-increased ROS in guard cell mitochondria. These results demonstrate that ABA elevates H2O2 accumulation in guard cell mitochondria to promote stomatal closure.
Dark accumulation of downstream glycolytic intermediates initiates robust photosynthesis in cyanobacteria
Authors: Tanaka Kenya , Shirai Tomokazu , Vavricka Christopher J , Matsuda Mami , Kondo Akihiko , Hasunuma Tomohisa
Published: December 2022

Photosynthesis must maintain stability and robustness throughout fluctuating natural environments. In cyanobacteria, dark-to-light transition leads to drastic metabolic changes from dark respiratory metabolism to CO2 fixation through the Calvin–Benson–Bassham (CBB) cycle using energy and redox equivalents provided by photosynthetic electron transfer. Previous studies have shown that catabolic metabolism supports the smooth transition into CBB cycle metabolism. However, metabolic mechanisms for robust initiation of photosynthesis are poorly understood due to lack of dynamic metabolic characterizations of dark-to-light transitions. Here, we show rapid dynamic changes (on a time scale of seconds) in absolute metabolite concentrations and 13C tracer incorporation after strong or weak light irradiation in the cyanobacterium Synechocystis sp. PCC 6803. Integration of this data enabled estimation of time-resolved nonstationary metabolic flux underlying CBB cycle activation. This dynamic metabolic analysis indicated that downstream glycolytic intermediates, including phosphoglycerate and phosphoenolpyruvate, accumulate under dark conditions as major substrates for initial CO2 fixation. Compared with wild-type Synechocystis, significant decreases in the initial oxygen evolution rate were observed in 12 h dark preincubated mutants deficient in glycogen degradation or oxidative pentose phosphate pathways. Accordingly, the degree of decrease in the initial oxygen evolution rate was proportional to the accumulated pool size of glycolytic intermediates. These observations indicate that the accumulation of glycolytic intermediates is essential for efficient metabolism switching under fluctuating light environments.
Evaluation of the agreement between the ACR 1990 fibromyalgia tender points and an enthesitis score in patients with axial spondyloarthritis
Authors: Hamitouche Faten , Lopez-Medina Clementina , Gossec Laure , Perrot Serge , Dougados Maxime , Moltó Anna
Published: December 2022

Objectives

Coexistence of FM represents a challenge in the evaluation of enthesitis in patients with axial spondyloarthritis (axSpA) due to a possible overlap between the tender points (TP) due to enthesitis and those of FM. The objective was to assess the agreement between the MASES enthesitis score and the tender points of the ACR 1990 criteria in patients with axSpA.

Methods

This was a cross-sectional ancillary analysis of the Predict-SpA study (NCT03039088). Patients had a diagnosis of axSpA according to their rheumatologist and an indication to start a TNFα blocker. All patients were screened for FM according to the FiRST questionnaire. A physician was asked to assess 31 anatomically described sites in a random order without knowing to which instrument the site belonged (i.e. the 18 ACR 1990 TP and the 13 MASES sites). Agreement between the MASES and the ACR 1990 TPs by the intraclass correlation coefficient (ICC), also stratified by the presence/absence of concomitant FM according to the FiRST.

Results

Among the 526 patients, 53% were men and 202 (38%) had FM. Radiographic sacroiliitis and MRI sacroiliitis were present in 56% and 68% patients, respectively. Patients were mostly men (53.4%) with radiographic and MRI sacroiliitis in 56% and 68% patients, respectively. Mean number of ACR 1990 TP was 5.4 (s.d. 4.6) and mean MASES was 4.2 (s.d. 3.6). ICC between both scores was 0.7 [95% CI (0.6, 0.8)]. ICC between both scores was 0.6 [95% CI (0.3, 0.8)] and 0.7 [95% CI (0.6, 0.7)] for patients with and without FM, respectively.

Conclusion

These results suggest a significant overlap between both scores in patients with axSpA, including in those without concomitant FM.

Trial registration

clinicaltrials.gov, https://clinicaltrials.gov, NCT03039088
Diagnostic and therapeutic algorithms for monogenic autoinflammatory diseases presenting with recurrent fevers among adults
Authors: Delplanque Marion , Fayand Antoine , Boursier Guilaine , Grateau Gilles , Savey Léa , Georgin-Lavialle Sophie
Published: December 2022

Autoinflammatory diseases (AIDs) are defined as disorders of innate immunity. They were initially defined in contrast to autoimmune diseases because of the lack of involvement of the adaptive immune system and circulating autoantibodies. The four monogenic AIDs first described are called the ‘historical’ AIDs and include FMF (associated with MEFV mutations), cryopyrinopathies (associated with NLRP3 mutations), TNF receptor–associated periodic syndrome (associated with TNFRSF1A mutations) and mevalonate kinase deficiency (MKD; associated with MVK mutations). In the last 10 years, >50 new monogenic AIDs have been discovered due to genetic advances. The most important discovery for adult patients is VEXAS syndrome associated with somatic UBA1 mutations leading to an AID affecting mostly elderly men. Diagnosis of monogenic AIDs is based on personal and family history and detailed analysis of symptoms associated with febrile attacks in the context of elevated peripheral inflammatory markers. This review proposes a practical approach for the diagnosis of the main monogenic AIDs among adult patients.
A Phosphate Uptake System Is Required for Xanthomonas citri pv. glycines Virulence in Soybean
Authors: Sattrapai Nutthakan , Chaiprom Usawadee , Lindow Steven E. , Chatnaparat Tiyakhon
Published: December 2022

The genes encoding the phosphate uptake system in Xanthomonas citri pv. glycines 12-2 were previously found to be upregulated when in soybean leaves. This study thus explored the role of the phosphate uptake system on its virulence to soybean. While phoB and pstSCAB mutants were greatly impaired in both inciting disease symptoms and growth in soybean, the virulence and growth in soybean of a phoU mutant was not reduced when compared with the wild-type strain. The expression of phoB and pstSCAB was highly induced in phosphate-deficient media. In addition, the expression of phoB, assessed with a fusion to a promoterless ice nucleation reporter gene, was greatly increased in soybean leaves, confirming that the soybean apoplast is a phosphorus-limited habitat for X. citri pv. glycines. Global gene expression profiles of phoB and phoU mutants of X. citri pv. glycines conducted under phosphate-limitation conditions in vitro, using RNA-seq, revealed that PhoB positively regulated genes involved in signal transduction, the xcs cluster type II secretion system, cell motility, and chemotaxis, while negatively regulating cell wall and membrane biogenesis, DNA replication and recombination and repair, and several genes with unknown function. PhoU also positively regulated the same genes involved in cell motility and chemotaxis. The severity of bacterial pustule disease was decreased in soybean plants grown under high phosphate fertilization conditions, demonstrating that high phosphate availability in soybean plants can affect infection by X. citri pv. glycines by modulation of the expression of phosphate uptake systems.

[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
A curious case of a blue finger
Authors: Trotter Kristine , Espinosa James , Lucerna Alan
Published: December 2022

This article describes an unusual presentation of a blue finger in a middle-aged woman with no significant past medical history. The patient was diagnosed with Achenbach syndrome, a rare condition that is generally considered transient and benign. The underlying pathophysiology of this condition is unclear, but may be related to transient subcutaneous ecchymosis, possibly from microtrauma. If the condition recurs, a workup can include laboratory tests for autoimmune diseases such as rheumatoid arthritis. Clinician awareness of this presentation may reduce patient anxiety and unnecessary testing.
Early identification of Lyme disease complications
Authors: Eckenrode Kristin
Published: December 2022

Complications of Lyme disease including Lyme arthritis, Lyme carditis, and Lyme neuroborreliosis, typically occur during the early disseminated and late phases of the disease. Clinicians must maintain a high index of suspicion so they can recognize and treat complications promptly. Early treatment with appropriate antibiotics often leads to improved clinical outcomes.
Which four medication classes have important pharmacogenetic considerations?
Authors: Smith Susan M.
Published: December 2022

Medications often are prescribed without knowledge of a patient's pharmacogenetic profile. Initial therapy may require subsequent modification due to adverse reactions or lack of efficacy. Although many variables, including changes in pharmacokinetics, pharmacodynamics, or patient nonadherence, may account for these outcomes, information about a patient's ability to metabolize or transport drugs across membranes may be used to optimize therapy, resulting in improved medication outcomes.
New Zealand PA profession gains momentum with regulation in sight
Authors: deWolfe Lisa Fitzgerald
Published: December 2022

This article offers an update on physician associate (PA) growth and development in the New Zealand healthcare system. New Zealand has a shortage of healthcare workers and PAs offer a solution. Regulation is in process and will allow a full scope of practice for PAs. A New Zealand-based PA training program also is being considered when regulation has progressed.
Tailoring the mental health assessment to older adults
Authors: Davies Tracy Lynn
Published: December 2022

This article discusses selected considerations for mental health assessment in older adults. Adopting a biopsychosocial model and trauma-informed approach to care creates a safe structure for a more comprehensive assessment. Selecting appropriate tools to improve diagnostic reasoning sets the foundation for further workup and tailored interventions.
35th Annual APRN Legislative Update
Authors: Haney Beth
Published: December 2022

Advanced practice registered nurses (APRNs) continue to make history by being at the forefront of legislative victories that have culminated in increased patient access to care. Modernization of APRN practice in various states, some influenced by the COVID-19 pandemic, has resulted in easing of regulations, including those relating to supervision, collaboration, license renewal, and portability, in reduced and restricted practice settings.
Autonomic dysreflexia in patients with spinal cord injury
Authors: Harmison Lauren E. , Beckham James W. , Adelman Deborah S.
Published: December 2022

Patients with traumatic spinal cord injury have a vast array of secondary pathophysiologic effects, one of which is autonomic dysreflexia (AD). It can be triggered by noxious stimuli and cause severe and fatal consequences that require rapid intervention. This article examines AD and its implications for nursing care.
Creating a friendly healthcare environment for LGBTQIA+ patients
Authors: Bingham Karilee W. , Heavey Elizabeth
Published: December 2022

Persons who identify as Lesbian, Gay, Bisexual, Transgender, Queer or Questioning, Intersex, and Asexual (LGBTQIA+) are diverse in gender, gender identification, sexual orientation, race and ethnicity, and socioeconomic status. They face unique disparities in healthcare. This article discusses how to create a welcoming healthcare environment for these individuals.