bluuebunny/crossref_metadata_2025 huggingface dataset:
A surrogate molecular approach for the detection of Philadelphia chromosome–like B‐acute lymphoblastic leukemia
Authors: Gupta Dikshat Gopal , Varma Neelam , Abdulkadir Sarki Abba , Sreedharanunni Sreejesh , Sachdeva Man Updesh Singh , Naseem Shano , Bose Parveen , Binota Jogeshwar , Malhotra Pankaj , Khadwal Alka , Trehan Amita , Varma Subhash
Published: October 2023

Background

Philadelphia chromosome (Ph)–like B‐acute lymphoblastic leukemia (B‐ALL) is a clinically significant, high‐risk genetic subtype of B‐ALL cases. There are few data on the incidence, characterization, and treatment outcomes of Ph‐like ALL cases from low‐ and middle‐income countries. There is a pressing need to establish a well‐organized/cost‐effective approach for identifying Ph‐like ALL instances.

Methods

Multiplex reverse transcriptase polymerase chain reaction, nCounter NanoString, and fluorescence in situ hybridization were used to detect and characterize Ph‐like ALL cases among recurrent genetic abnormalities (RGA)neg B‐ALL cases. At the end of induction therapy, flow cytometry‐minimal residual disease (MRD) assay was used to quantify MRD positivity in Ph‐like ALL cases.

Results

Of 130 newly diagnosed B‐ALL cases, 25% (BCR::ABL1), 4% (ETV6::RUNX1), 5% (TCF3::PBX1), 2% (KM2TA::AFF1), and 65% RGAneg B‐ALL cases were revealed by multiplex reverse transcriptase polymerase chain reaction. Among RGAneg B‐ALL cases, 24% Ph‐like ALL cases using nCounter NanoString were identified, with 48% CRLF2high cases with 45% CRLF2::P2RY8 and 18% CRLF2::IGH rearrangements(∼r) revealed by fluorescence in situ hybridization. In 52% of CRLF2low cases, 17% ABL1 and JAK2∼r 8% EPOR::IGH & PDGRFB∼r were identified. Ph‐like ALL cases had higher total leukocyte count (p < .05), male preponderance (p < .05), and high MRD‐positivity/induction failure compared with RGAneg B‐ALL cases. Furthermore, in Ph‐like ALL cases, 11 significant genes using quantitative polymerase chain reaction were identified and validated. CRLF2, IGJ, CEACAM6, MUC4, SPATS2L and NRXN3 genes were overexpressed and show statistical significance (p < .05) in Ph‐like ALL cases.

Conclusions

This study showed the high incidence of Ph‐like ALL cases with kinase activating alterations and treatment outcomes from low‐ and middle‐income region. Furthermore, a surrogate cost‐effective multiplex panel of 11 overexpressed genes for the prompt detection of Ph‐like ALL cases is proposed.

Plain Language Summary

Identification of recurrent gene abnormalities (RGA)neg B‐acute lymphoblastic leukemia (B‐ALL) cases using multiplex‐reverse transcriptase polymerase chain reaction.

Identification and characterization of Philadelphia (Ph)–like ALL cases using nCounter NanoString gene expression profiling and fluorescence in situ hybridization.

Furthermore, Ph‐like ALL cases were characterized according to CRLF2 expression and kinase‐activating genomic alterations. Minimal residual disease of Ph‐like ALL cases were quantified using flow cytometry‐minimal residual disease assay.

A surrogate molecular approach was established to detect Ph‐like ALL cases from low‐ and middle‐income countries.
SMAD4 loss predicts worse overall and distant metastasis‐free survival in patients with resected pancreatic adenocarcinoma
Authors: Anstadt Emily J. , Carmona Ruben , Berlin Eva , Yegya‐Raman Nikhil , Venigalla Sriram , Reddy Vishruth , Williams Graeme R. , Leibensperger Mark R. , Wojcieszynski Andrzej , Baumann Brian C. , Lee Major K. , Plastaras John P. , Furth Emma E. , Mell Loren K. , Metz James M. , Ben‐Josef Edgar
Published: October 2023

Background

In select patients, pancreatic adenocarcinoma remains a local disease, yet there are no validated biomarkers to predict this behavior and who may benefit from aggressive local treatments. This study sought to determine if SMAD4 (mothers against decapentaplegic homolog 4) messenger RNA–sequencing (RNA‐seq) expression is a robust method for predicting overall survival (OS) and distant metastasis‐free survival (DMFS) in patients with resected pancreatic adenocarcinoma.

Methods

Utilizing The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), 322 patients with resected stage I–III pancreatic adenocarcinoma were identified. In TCGA, multivariable proportional hazards models were used to determine the association of SMAD4 genomic aberrations and RNA‐seq expression with OS and DMFS. In the ICGC, analysis sought to confirm the predictive performance of RNA‐seq via multivariable models and receiver operator characteristic curves.

Results

In TCGA, the presence of SMAD4 genomic aberrations was associated with worse OS (hazard ratio [HR], 1.55; 95% CI, 1.00–2.40; p = .048) but not DMFS (HR, 1.33; 95% CI, .87–2.03; p = .19). Low SMAD4 RNA‐seq expression was associated with worse OS (HR, 1.83; 95% CI, 1.17–2.86; p = .008) and DMFS (HR, 1.70; 95% CI, 1.14–2.54; p = .009). In the ICGC, increased SMAD4 RNA‐seq expression correlated with improved OS (area under the curve [AUC], .92; 95% CI, .86–.94) and DMFS (AUC, .84; 95% CI, .82–.87).

Conclusions

In patients with resected pancreatic adenocarcinoma, SMAD4 genomic aberrations are associated with worse OS but do not predict for DMFS. Increased SMAD4 RNA‐seq expression is associated with improved OS and DMFS in patients with resected pancreatic adenocarcinoma. This reproducible finding suggests SMAD4 RNA‐seq expression may be a useful marker to predict metastatic spread.
Muscle channelopathies: A review
Authors: McGowan Bridget R. , Schwaede Abigail N. , De Simone Lenika , Rao Vamshi K.
Published: October 2023

Background

Muscle channelopathies are a rare and heterogeneous group of disorders that can be clinically challenging and functionally disabling. These disorders can present in both adult and pediatric age groups. These disorders have been known since the turn of the 20th century, with a steady evolution in terms of understanding the pathophysiology, phenotype, diagnostic, and treatment modalities over the last three decades.

Methods

We present a comprehensive review of muscle channelopathies that includes nondystrophic myotonias and periodic paralyses. The disorders in this review have been classified based on the presence or absence of myotonia on either the clinical exam or on electrophysiological testing. The historical background, genetics, pathophysiology, phenotypic presentations, and treatment modalities of each disorder reveal similarities as well as specific nuances in the disease phenotypes. Neurophysiologic testing shows differences in responses on routine and exercise testing and can narrow the differential within subsets of nondystrophic myotonias and periodic paralyses. The advances in genetics further aid in specifying which of the putative channels are at fault. Management can then be guided by knowledge of the causative gene and involves either avoidance of triggers or channel‐based therapeutics.

Conclusion

Muscle channelopathies are rare, but a high index of suspicion along with a knowledge of the phenotype will help guide neurophysiological and genetic testing. A muscle channelopathy diagnosis, subsequently, can assist in avoiding triggers and directing treatments.
Tracing task‐based runtime systems: Feedbacks from theStarPUcase
Authors: Denis Alexandre , Jeannot Emmanuel , Swartvagher Philippe , Thibault Samuel
Published: October 2023

Given the complexity of current supercomputers and applications, being able to trace application executions to understand their behavior is not a luxury. As constraints, tracing systems have to be as little intrusive as possible in the application code and performances, and be precise enough in the collected data. In this article, we present how works the tracing system used by the task‐based runtime systemStarPU. We study the different sources of performance overhead coming from the tracing system and how to reduce these overheads. Then, we evaluate the accuracy of distributed traces with different clock synchronization techniques. Finally, we summarize our experiments and conclusions with the lessons we learned to efficiently trace applications, and the list of characteristics each tracing system should feature to be competitive. The reported experiments and implementation details comprise a feedback of integrating into a task‐based runtime system state‐of‐the‐art techniques to efficiently and precisely trace application executions. We highlight the points every application developer or end‐user should be aware of to seamlessly integrate a tracing system or just trace application executions.
Object‐aware deep feature extraction for feature matching
Authors: Li Zuoyong , Wang Weice , Lai Taotao , Xu Haiping , Keikhosrokiani Pantea
Published: October 2023

Feature extraction is a fundamental step in the feature matching task. A lot of studies are devoted to feature extraction. Recent researches propose to extract features by pre‐trained neural networks, and the output is used for feature matching. However, the quality and the quantity of the features extracted by these methods are difficult to meet the requirements for the practical applications. In this article, we propose a two‐stage object‐aware‐based feature matching method. Specifically, the proposed object‐aware block predicts a weighted feature map through a mask predictor and a prefeature extractor, so that the subsequent feature extractor pays more attention to the key regions by using the weighted feature map. In addition, we introduce a state‐of‐the‐art model estimation algorithm to align image pair as the input of the object‐aware block. Furthermore, our method also employs an advanced outlier removal algorithm to further improve matching quality. Experimental results show that our object‐aware‐based feature matching method improves the performance of feature matching compared with several state‐of‐the‐art methods.
Synthesis of Organic Optoelectronic Materials Using Direct C−H Functionalization
Authors: Kuwabara Junpei , Kanbara Takaki
Published: October 2023

Small molecules and polymers with conjugated structures can be used as organic optoelectronic materials. These molecules have conventionally been synthesized by cross‐coupling reactions; however, in recent years, direct functionalization of C−H bonds has been used to synthesize organic optoelectronic materials. Representative reactions include direct arylation reactions (C−H/C−X couplings, with X being halogen or pseudo‐halogen) and cross‐dehydrogenative coupling (C−H/C−H cross‐coupling) reactions. Although these reactions are convenient for short‐step synthesis, they require regioselectivity in the C−H bonds and suppression of undesired homo‐coupling side reactions. This review introduces examples of the synthesis of organic optoelectronic materials using two types of direct C−H functionalization reactions. In addition, we summarize our recent activities in the development of direct C−H functionalization reactions using fluorobenzenes as substrates. This review covers the reaction mechanism and material properties of the resulting products.
Hybrid simulation of the plasma characteristics in a dual‐frequency dual‐antenna inductively coupled plasma discharge
Authors: Sun Xiao‐Yan , Yang Ming‐Hui , Shao Wei‐Li , Tao Xin , Li Long‐Wei
Published: October 2023

Dual‐frequency (DF) dual‐antenna inductively coupled plasma (ICP) sources have been proposed as one of the methods to produce large‐area uniform plasma. In this study, a hybrid model, consisting of a fluid module and an electron Monte Carlo (eMC) module, is used to further investigate the modulation of the plasma characteristics (i.e., induced electric field, electron energy distribution, electron heating mechanism, electron temperature, and plasma density) by the low‐frequency (LF) and high‐frequency (HF) currents in a DF argon discharge. When the inner LF current increases from 12 to 22 A at a fixed outer HF current of 10 A, the induced electric field is strengthened near the LF coil and weakened near the HF coil. The fraction of high‐energy electrons at different spatial positions increases with the increase of LF current, which is caused by the sufficient collision heating in the skin layer of LF source, leading to an increase in electron temperature. When the outer HF current rises from 7 to 13 A with the inner LF current fixed at 17 A, the induced electric field is enhanced near the HF coil and weakened near the LF coil. The fraction of low‐energy electrons at different positions increases with the increase of HF current since the energetic electrons from the skin layer of HF source are cooled due to the ionization, excitation, and stepwise ionization collisions between electrons and neutral particles, as well as the weakened induced electric field near the LF coil. As a result, the electron temperature drops with the increase of HF current. Moreover, when the LF and HF currents increase, the plasma density increases, and the distribution of plasma density is also significantly modulated.
OMIP‐099: 31‐color spectral flow cytometry panel to investigate the steady‐state phenotype of human T cells
Authors: Zacharias Zeb R. , Houtman Jon C. D.
Published: October 2023

We have developed a 31‐color panel to define the steady‐state phenotype of T cells in human peripheral blood (Table 1). The panel presented here was optimized using cryopreserved peripheral blood mononuclear cells (PBMC). The markers included in this panel were chosen in order to characterize the steady‐state phenotype of T cells and includes markers (CD45RA, CD45RO, CCR7, CD95) to distinguish the main subsets (e.g., naïve, TEM, TCM, TEMRA, TSCM etc.) of CD4, CD8, and γδ T cells. This panel also includes markers for the identification of differentiation status (CD27, CD28), activation/antigen experience status (CD11a, CD49d, CD38, HLA‐DR, CD56, and CD39), co‐inhibitory marker expression (PD‐1, TIM‐3), and CD4 T helper subsets (CXCR3, CXCR5, CCR4, CCR6, Foxp3, CD25, and CD127). This optimized panel provides a broad assessment of the steady‐state phenotype of human T cells.
Timing‐deviation and frequency‐offset estimations for multicarrier transmission in high mobility environments using deep neural network
Authors: Wu Hong , Geng Xue , Chen Zhuo , Zhao Yingxin
Published: October 2023

The multicarrier technology used in fourth‐generation (4G) and fifth‐generation (5G) communications is quite susceptible to multipath fading and Doppler frequency shift, which is more prominent in high mobility environments. Therefore, the accuracy of timing and frequency synchronization impacts the overall system performance significantly. Existing synchronization methods rely on the correlation of the preamble sequences and are, hence, vulnerable to severe multipath effect and Doppler effect. In this article, we propose a novel scheme leveraging deep neural network (DNN) to achieve high‐precision synchronization in high mobility environments. Concretely, a convolutional neural network (CNN) architecture is proposed to extract the hidden features of received signals for timing deviation estimation. In the following, a fully connected (FC) model is demonstrated to classify the optimal carrier frequency offset (CFO) estimate from several CFO candidates. The proposed synchronization scheme is assessed under extended vehicular A (EVA) channel with various Doppler frequency shifts. Simulation results corroborate that the proposed DNN‐based scheme achieves a significant performance gain over the conventional correlation methods, and the proposed timing deviation estimation scheme exhibits an excellent complexity reduction; wherefore, it is extremely promising for multicarrier transmission systems in high mobility environments.
Colloid and pigmented histiocytes in lymph node aspirates as a clue to metastasis in patients with a history of papillary thyroid carcinoma
Authors: Ng Joanna K. M. , Chan Amy B. W. , Li Joshua J. X.
Published: October 2023

Introduction

Cystic changes, calcification, colloid material, and multinucleated giant cells are frequently associated with primary and metastatic papillary thyroid carcinoma (PTC). These features are sometimes present in negative lymph node fine‐needle aspiration cytology (FNAC). This study aims to review nodal aspirates of PTC to elucidate the significance of these cytological features in aspirates without tumor cells.

Methods

FNAC specimens from patients with PTC confirmed on thyroidectomy were reviewed for cystic changes, tumor‐associated features, and lymphoid components. Histologic follow‐up of the lymph nodes were retrieved for correlation.

Results

A total of 113 aspirates were retrieved, of which 79 showed tumor cells on the FNAC specimen, and 95 were matched to a positive lymph node histology. At univariable analysis, calcification (n = 18/113, p = .044), colloid material (n = 40/113, p = .001), multinucleated giant cells (n = 29/113, p = .028), tumor cells (n = 79/133, p < .001), foamy histiocytes (n = 36/113, p = .002) and pigmented histiocytes (n = 62/113, p < .001) were associated with a positive histology. Presence of lymphoid fragments (n = 11/113, p < .001) and abundant background lymphocytes correlated with a negative histologic follow‐up (n = 45/113, p = .005). In aspirates without tumor cells, multivariable analysis demonstrated colloid material (p < .001) and pigmented histiocytes (p = .003) to be independently predictive of metastatic PTC, whereas lymphoid fragments (p < .001) were independently associated with a negative histologic follow up.

Conclusion

Colloid material and pigmented histiocytes, and to lesser degree calcification and multinucleated giant cells, when seen in an aspirate without tumor cells, raises suspicion metastatic disease. On the contrary, the lymphoid fragments can be regarded as supportive evidence of adequate sampling and a true negative result.
Cognitive development from infancy to young adulthood in common marmosets (Callithrix jacchus): Effect of age, sex, and hormones on learning and affective state
Authors: Ash Hayley , Goy Robinson W. , Spaulding Abigail , Colman Ricki J. , Corbett Cody J. , Ziegler Toni E.
Published: October 2023

Studies looking at individual variability in cognition have increased in recent years. We followed 43 marmosets (21 males, 22 females) from infancy to young adulthood. At 3‐months old, marmosets were trained to touch a rewarded stimulus. At 9‐, 15‐, and 21‐months old, they were given visual discrimination and cognitive bias tests, and urine samples were collected to examine hormone levels. Marmosets were significantly more successful learners at 15 months than 9 months. Individuals who were more successful learners at 9 months were also more successful at 15 months, with more male learners than expected at 15 months. At 9 months, learning success was associated with higher cortisol levels. At 15 months, males with higher estradiol levels were more successful learners, whereas at 21 months, females with higher estradiol and cortisol levels tended to be less successful learners and more pessimistic. Nine months, therefore, appears to be an important developmental timepoint for acquiring cognitive control, which has developed by 15 months. Steroids may have differential effects on each sex, with complex interactions between gonadal and adrenal hormones having an influence on cognitive function over the lifespan. This longitudinal study offers new insight into cognition, including its development and biological underpinnings.
New physics of supersonic ruptures
Authors: Tarasov Boris G.
Published: October 2023

Until recently, it is believed that the rupture speed above the pressure wave is impossible since spontaneously propagating ruptures are driven by the energy released due to the rupture motion, which is transferred through the medium to the rupture tip region at the maximum speed equal to the pressure wave speed. However, the apparent violation of classic theories has been revealed by new experimental results demonstrating supersonic shear ruptures. This paper presents a detailed analysis of the recently discovered shear rupture mechanism (fan hinged), which suggests a new physics of energy supply to the tip of supersonic ruptures. The key element of this mechanism is the fan‐shaped structure of the head of extreme ruptures, which is formed as a result of an intense tensile cracking process with the creation of intercrack slabs that act as hinges between the shearing rupture faces. The fan structure is featured with the following extraordinary properties: extremely low friction approaching zero; amplification of shear stresses above the material strength at low applied shear stresses; creation of a self‐disbalancing stress state causing a spontaneous rupture growth; abnormally high energy release; generation of driving energy directly at the rupture tip which excludes the need to transfer energy through the medium. The fan mechanism operates in intact rocks at stress conditions corresponding to seismogenic depths and in pre‐existing extremely smooth interfaces due to identical tensile cracking processes at these conditions. This is Paper 1 (of two companion papers) which discusses the fan theory and extreme ruptures in experiments on extremely smooth interfaces. Paper 2 entitled “Fan‐hinged shear instead of frictional stick‐slip as the main and most dangerous mechanism of natural, induced and volcanic earthquakes in the earth's crust” considers extreme ruptures in intact rocks. Further study of this subject is a major challenge for deep underground science, earthquake and fracture mechanics, physics, and tribology.
A randomized, controlled pilot study of positive affect treatment adapted for anorexia nervosa
Authors: Haynos Ann F. , Anderson Lisa M. , Askew Autumn J. , Liu Chassidie , Venables Kira , Craske Michelle G. , Peterson Carol B.
Published: October 2023

Objective

Novel treatments for adults with anorexia nervosa (AN) are sorely needed. Although psychological interventions have been developed for AN, none have been identified as superior to one another or nonspecific treatments. Common comorbidities (e.g., mood and anxiety disorders) are rarely targeted in AN treatments, possibly impairing long‐term clinical improvement. AN is associated with reward processing dysfunctions paralleling those identified in affective disorders; however, few treatments directly target these processes.

Method

We adapted Positive Affect Treatment, a neuroscience‐informed behavioral treatment developed for affective disorders, to the treatment of AN (PAT‐AN). Adults with AN (N = 20) were randomized to 20 weeks of PAT‐AN or waitlist to investigate the feasibility, acceptability, preliminary efficacy, and target engagement (on reward mechanisms) of PAT‐AN.

Results

PAT‐AN demonstrated strong retention (100%) and acceptability ratings (M = 5.67–5.95 on a 7‐point scale). BMI (p = .006) and eating disorder symptoms (p < .001) improved over PAT‐AN sessions. The PAT‐AN group showed medium to large pre‐to‐post‐treatment improvements in BMI, eating disorder symptoms and impairment, depressive and anxiety symptoms, and some reward indices (ds = .56–.87); changes were largely sustained at 3‐month follow‐up. Waitlist showed negligible changes (ds < .20) on nearly all measures.

Discussion

PAT‐AN holds promise as an innovative treatment with capability to simultaneously improve eating disorder symptoms, affective symptoms, and underlying reward mechanisms. Findings should be interpreted cautiously due to small sample size and permitted concurrent enrollment in other treatments. Future, larger‐scale research is warranted to establish the efficacy of PAT‐AN.

Public Significance

This study provided a preliminary evaluation of Positive Affect Treatment for anorexia nervosa (PAT‐AN), a novel, neuroscience‐informed treatment aimed at increasing rewarding life experiences outside of one's eating disorder. Initial results suggest that PAT‐AN is considered acceptable and may alleviate eating disorder, depressive, and anxiety symptoms. Therefore, this study presents promising data on a treatment that may hold potential for improving the lives of individuals with this disorder.
A pathogen's spatial range is not constrained by geographical features in the flax rust pathosystem
Authors: Duggal Keenan , Miller Ian , Jiranek Juliana , Metcalf Jessica
Published: October 2023

Climate change and shifting environmental conditions can allow pathogens to spread into previously unburdened areas. For plant pathogens, this dynamic has the potential to disrupt natural ecosystem equilibria and human agriculture, making predicting plant pathogen range shifts increasingly important. Although such predictions will hinge on an accurate understanding of the determinants of pathogen range—namely the environmental, geographical, and host range characteristics that modulate local pathogen habitation—few studies to date have probed these in natural plant populations. Here, we characterize range determinants for the model system of Lewis flax (Linum lewisii) and its pathogen, flax rust (Melampsora lini), in the Rocky Mountains. Transect surveys were performed to assess three relationships: (i) the effect of geographical features—elevation, slope aspect, slope grade, and land cover—on flax presence and density, (ii) the effect of geographical features on flax rust presence and prevalence, and (iii) the effects of flax's local population density and metapopulation structure on flax rust presence and prevalence. We found that flax population density, but not host metapopulation structure, influences the distribution of flax rust. Additionally, we showed that, while the distribution of flax was broadly constrained to a relatively narrow range of geographical and resulting environmental features, flax rust was evenly distributed across the full range of settings measured. These results indicate that a warming environment, which is expected to modulate such features, may restrict the optimal range of the plant more than that of its pathogen. Importantly, our results also suggest that even if flax shifts its spatial range to escape increasing climatic pressures, flax rust will not face any significant barriers to track this movement.
Chigger mite (Eutrombicula alfreddugesi) ectoparasitism does not contribute to sex differences in growth rate in eastern fence lizards (Sceloporus undulatus)
Authors: Conrad Hailey , Pollock Nicholas B. , John‐Alder Henry
Published: October 2023

Parasitism is nearly ubiquitous in animals and is frequently associated with fitness costs in host organisms, including reduced growth, foraging, and reproduction. In many species, males tend to be more heavily parasitized than females and thus may bear greater costs of parasitism. Sceloporus undulatus is a female‐larger, sexually size dimorphic lizard species that is heavily parasitized by chigger mites (Eutrombicula alfreddugesi). In particular, the intensity of mite parasitism is higher in male than in female juveniles during the period of time when sex differences in growth rate lead to the development of sexual size dimorphism (SSD). Sex‐biased differences in fitness costs of parasitism have been documented in other species. We investigated whether there are growth costs of mite ectoparasitism, at a time coinciding with sex differences in growth rate and the onset of SSD. If there are sex‐biased growth costs of parasitism, then this could suggest a contribution to the development of SSD in S. undulatus. We measured growth and mite loads in two cohorts of unmanipulated, field‐active yearlings by conducting descriptive mark‐recapture studies during the activity seasons of 2016 and 2019. Yearling males had consistently higher mid‐summer mite loads and consistently lower growth rates than females. However, we found that growth rate and body condition were independent of mite load in both sexes. Furthermore, growth rates and mite loads were higher in 2019 than in 2016. Our findings suggest that juveniles of S. undulatus are highly tolerant of chigger mites and that any costs imposed by mites may be at the expense of functions other than growth. We conclude that sex‐biased mite ectoparasitism does not contribute to sex differences in growth rate and, therefore, does not contribute to the development of SSD.
DNA barcodes provide insights into the diversity and biogeography of the non‐biting midge Polypedilum (Diptera, Chironomidae) in South America
Authors: da Silva Fabio Laurindo , Pinho Luiz Carlos , Stur Elisabeth , Nihei Silvio Shigueo , Ekrem Torbjørn
Published: October 2023

South America, particularly within its tropical belt, is renowned for its unparalleled high levels of species richness, surpassing other major biomes. Certain neotropical areas harbor fragmented knowledge of insect diversity and face imminent threats from biodiversity loss and climate change. Hence, there is an urgent need for rapid estimation methods to complement slower traditional taxonomic approaches. A variety of algorithms for delimiting species through single‐locus DNA barcodes have been developed and applied for rapid species diversity estimates across diverse taxa. However, tree‐based and distance‐based methods may yield different group assignments, leading to potential overestimation or underestimation of putative species. Here, we investigate the performance of different DNA‐based species delimitation approaches to rapidly estimate the diversity of Polypedilum (Chironomidae, Diptera) in South America. Additionally, we test the hypothesis that significant differences exist in the community structure of Polypedilum fauna between South America and its neighboring regions, particularly the Nearctic. Our analysis encompasses a dataset of 1492 specimens from 598 locations worldwide, with a specific focus on South America. Within this region, we analyzed a subset of 247 specimens reported from 37 locations. Using various methods including the Barcode Index Number (BIN), Bayesian Poisson tree processes (bPTP), multi‐rate Poisson tree processes (mPTP), single‐rate Poisson tree processes (sPTP), and generalized mixed Yule coalescent (sGMYC), we identify molecular operational taxonomic units (MOTUs) ranging from 267 to 520. Our results indicate that the sGMYC method is the most suitable for estimating putative species in our dataset, resulting in the identification of 75 species in the Neotropical region, particularly in South America. Notably, this region exhibited higher species richness in comparison to the Palearctic and Oriental realms. Additionally, our findings suggest potential differences in species composition of Polypedilum fauna between the Neotropical and the adjacent Nearctic realms, highlighting high levels of endemism and species richness in the first. These results support our hypothesis that there are substantial differences exist in species composition between the Polypedilum fauna in South America and the neighboring regions.
Development of a stand‐alone portable respiratory rate monitor using a Doppler radar
Authors: Katoh Miyu , Kanazawa Takeru , Abe Yoshifusa , Sun Guanghao , Matsui Takemi
Published: October 2023

Respiratory rate (RR) is known to be a more accurate predictor of clinical deterioration than other vital signs. However, there were few respiration measurement devices certified as medical devices that could be used in daily clinical settings. Therefore, using a bult‐in microcontroller (72×57×12 mm) instead of a personal computer, we developed a portable stand‐alone respiration measurement device with minimum workload in computing that can be used for non‐contact measurement in 30 s using a Doppler radar. In this study, the problems of respiration measurement using a Doppler radar, such as miscounting of respiratory peaks were clarified, and proposed device with respiratory peaks miscount prevention algorithm achieved high accuracy RR measurement. Clinical testing was conducted on pediatric outpatients of Children's Medical Center, Showa University Koto Toyosu Hospital. The measurement accuracy of the system was confirmed to be comparable to the respiration measurement accuracy of stationary certified medical devices used in hospital, such as capnometers and the chest wall impedance method used in bedside monitors.
Fatty liver biomarkers and insulin resistance indices in the prediction of non‐alcoholic fatty liver disease in Ghanaian patients
Authors: Bockarie A. S. , Nartey Y. A. , Nsiah P. , Edzie E. K. M. , Tuoyire D. , Acquah S. , Eliason S. , Nkum B.
Published: October 2023

Background

Scant West African data on non‐alcoholic fatty liver disease (NAFLD) means there is little representation of this population in the modelling used to derive biomarkers and predictive indices for risk stratification of patients for the presence of hepatic steatosis. This study evaluates the performance of the fatty liver index (FLI), hepatic steatosis index (HSI) and triglyceride‐glucose (TyG) index and its derivatives in predicting ultrasound detected NAFLD in a locally resident population of Ghanaian participants.

Methods and Findings

A post hoc analysis of data from a cross sectional assessment of NAFLD and cardiovascular risk was performed. Data from 210 participants without significant alcohol intake, or secondary causes of fatty liver and not on steatogenic drugs was evaluated. A structured questionnaire had been used to collect demographic data, medical and drug history. Anthropometry, blood sampling for liver chemistry and fasting lipids were performed. Hepatic steatosis was detected by ultrasonography. A retrospective analysis involving multivariate binary logistic regression assessed FLI, HIS, TyG (and its derivatives) as predictors of NAFLD with p < .05 considered statistically significant. Sensitivity, specificity, predictive values, likelihood ratios were calculated and accuracy of the proxies evaluated from area under the receiver operating characteristics curve (AUROC).

All the biomarkers and indices were significantly associated with NAFLD (p ≤ .001). All the lipid and fatty liver indices assessed performed acceptably as predictors of NAFLD. FLI (AUC = 0.8, 95% CI [0.74–0.87]), TyG‐WC (AUC = 0.81, 95% CI [0.75–0.88]) and TyG‐WHtR (AUC = 0.81, 95% CI [0.74–0.88]) performed best at predicting NAFLD. Whilst in all cases the markers had good specificity (>90%) they lacked sufficient sensitivity with FLI having the highest sensitivity of 36.7%. Their overall accuracy was greater than 70% in each case.

Conclusion

The overall accuracy of HSI, FLI, TyG index and its derivatives (TyG WHtR, TyG BMI, TyG WC) was acceptable for predicting NAFLD in this population. Given their performance in this study and in light of their low cost, accessibility, easy interpretation and non‐invasive nature; they are suitable tools for screening in the Ghanaian population.
How much is enough? Examining the sampling effort necessary to estimate mean eDNA concentrations in lentic systems
Authors: Yates M. C. , Gaudet‐Boulay M. , Garcia Machado E. , Côté G. , Gilbert A. , Bernatchez L.
Published: October 2023

The concentration of eDNA in an environment can provide important ecological information of relevance for management and conservation, but little research has explored optimizing sampling strategies to estimate mean eDNA concentrations in natural environments. Inter‐replicate eDNA concentrations often exhibit right‐skewed “clustered” or “clumped” distributions, likely due to the stochastic capture of large “aggregate” particles with high eDNA copy numbers. This has important potential implications for modeling the resulting sampling effort necessary to accurately quantify eDNA concentrations. In a previous study, 17–20 Brook Charr eDNA samples were collected from 28 lakes in Québec, Canada. We explored how variation in eDNA concentrations within a lake was affected by several habitat characteristics. We then conducted a power analysis to determine the sampling effort (“minimum n”) necessary to accurately quantify mean lake eDNA concentrations and, using simulations, explored how a bimodal distribution of eDNA particle copy count could affect inter‐replicate variability. The median sample size such that 90% of sample mean estimates were within 20% of the “true” mean was 12.5; a sample size of 20 was sufficient to quantify mean concentrations in 21/28 lakes. We found no evidence that temperature or lake size impacted sample variability. We also found that variance among replicates was non‐linearly related to mean lake eDNA concentration across years: variability was lowest at low and high concentrations and highest at intermediate concentrations. We hypothesize that this resulted from the stochastic capture of large “aggregate” particles at intermediate concentrations; at low concentrations, aggregates were likely rarely captured and at high concentrations may represent a consistent component of total eDNA. Simulations demonstrated that these patterns can emerge from some bimodal eDNA particle “size” distributions. Overall, we conclude that sampling efforts in many previous studies (notably including the authors' own) were potentially low, emphasizing the need to increase spatial replication in lentic surveys.
Capturing drifting species and molecules—Lessons learned from integrated approaches to assess marine metazoan diversity in highly dynamic waters
Authors: Ohnesorge Alica , John Uwe , Taudien Sarah , Neuhaus Stefan , Kuczynski Lucie , Laakmann Silke
Published: October 2023

Marine community diversity surveys require a reliable assessment to estimate ecosystem functions and their dynamics. For these, non‐invasive environmental DNA (eDNA) metabarcoding is increasingly applied in zoological studies to complement or even replace traditional morphological identification methods. However, uncertainties remain about the accuracy of the diversity detected with eDNA to capture the actual diversity in the field. Here, we validate the reliability of eDNA metabarcoding in identifying metazoan biodiversity in highly dynamic marine waters of the North Sea. We analyzed biodiversity from water (eDNA) and zooplankton samples with cytochrome c oxidase subunit 1 (COI) and 18S rRNA (18S) metabarcoding at Helgoland Roads and validated the optimal molecular resolution by morphological and molecular zooplankton identification (metabarcoding) with the result of merely a few false‐negative detections. eDNA and zooplankton metabarcoding resolved 354 species from all major and in total 16 metazoan phyla. This molecular genetic species inventory overlapped by 95.9% (COI) and 81.9% (18S) with published inventories of local, morphologically identified species, among them neozoa and rediscovered species. Even though half of all species were detected by both eDNA and zooplankton metabarcoding, the methods differed significantly in their detected diversity. eDNA metabarcoding performed very well in cnidarians and annelids, whereas zooplankton metabarcoding identified higher numbers of fish and malacostraca. Species assemblages significantly differed between the individual sampling events and the cumulative number of identified species increased steadily over the sampling period and did not reach saturation. About a third of the species were detected only once while a core community of 22 species was identified continuously. Our study confirms eDNA metabarcoding to be a powerful tool to identify and analyze North Sea fauna in highly dynamic waters and we recommend investing in high sampling efforts by repetitive sampling and replication using at least 0.45 μm filters to increase filtration volume.
Clinical characteristics and prognosis of patients with isolated cardiac sarcoidosis: Insights from the ILLUMINATE‐CS study
Authors: Maeda Daichi , Matsue Yuya , Dotare Taishi , Sunayama Tsutomu , Iso Takashi , Yoshioka Kenji , Nabeta Takeru , Naruse Yoshihisa , Kitai Takeshi , Taniguchi Tatsunori , Tanaka Hidekazu , Okumura Takahiro , Baba Yuichi , Minamino Tohru
Published: October 2023

Aim

Data on the clinical features and prognosis of patients with isolated cardiac sarcoidosis (iCS) are limited. This study evaluated the clinical characteristics and prognostic impact of iCS.

Methods and results

This was a secondary analysis of the ILLUMINATE‐CS study, a multicentre, retrospective registry investigating the clinical characteristics and prognosis of cardiac sarcoidosis. iCS was diagnosed according to the 2016 Japanese Circulation Society (JCS) guidelines. Clinical characteristics and prognosis were compared between patients with iCS and systemic cardiac sarcoidosis (sCS). The primary outcome was a combined endpoint of all‐cause death, hospitalization for heart failure, or fatal ventricular arrhythmia events. Among 475 patients with CS (mean age, 62.0 ± 10.9 years; female ratio, 59%) diagnosed by the JCS guidelines, 119 (25.1%) were diagnosed with iCS. Patients with iCS had a higher prevalence of a history of atrial fibrillation or hospitalization for heart failure, or lower left ventricular ejection fraction than those with sCS. During a median follow‐up of 42.3 (interquartile range, 22.8–72.5) months, 141 primary outcomes (29.7%) occurred. Cox proportional hazard analysis revealed that iCS was a significant risk factor for the primary outcome in the unadjusted model (hazard ratio [HR] 1.62; 95% confidence interval [CI] 1.12–2.34; p = 0.011). However, this association was not retained after adjustment for other covariates (adjusted HR 1.27; 95% CI 0.86–1.88; p = 0.226).

Conclusions

Patients with iCS had more impaired cardiovascular function at the time of diagnosis than those with sCS. However, iCS was not independently associated with poor prognosis after adjustment for prognostic factors.
System failure: Systemic inflammation following spinal cord injury
Authors: DiSabato Damon J. , Marion Christina M. , Mifflin Katherine A. , Alfredo Anthony N. , Rodgers Kyleigh A. , Kigerl Kristina A. , Popovich Phillip G. , McTigue Dana M.
Published: October 2023

Spinal cord injury (SCI) affects hundreds of thousands of people in the United States, and while some effects of the injury are broadly recognized (deficits to locomotion, fine motor control, and quality of life), the systemic consequences of SCI are less well‐known. The spinal cord regulates systemic immunological and visceral functions; this control is often disrupted by the injury, resulting in viscera including the gut, spleen, liver, bone marrow, and kidneys experiencing local tissue inflammation and physiological dysfunction. The extent of pathology depends on the injury level, severity, and time post‐injury. In this review, we describe immunological and metabolic consequences of SCI across several organs. Since infection and metabolic disorders are primary reasons for reduced lifespan after SCI, it is imperative that research continues to focus on these deleterious aspects of SCI to improve life span and quality of life for individuals with SCI.
Structuring of 2‐oleodipalmitin at the air interface from all‐atom, united‐atom, and coarse‐grained molecular dynamics simulations
Authors: Kindlein Moritz , Elts Ekaterina , Horlacher Peter , Briesen Heiko , Koch Tobias
Published: October 2023

This study employs classical molecular dynamics (MD) simulations to investigate the behavior of 1,3‐dipalmitoyl‐2‐oleoyl glycerol (POP), a typical triglyceride found in food at the air interface. The investigation utilizes three force fields (FF) with varying levels of detail, including all‐atom, united‐atom, and coarse‐grained simulations, to elucidate the structural evolution of POP at the air interface. The results confirm that the structuring processes observed in nonfood triglyceride systems also occur in POP. Aliphatic chains orient toward the air phase, while glycerol backbones face the inner triglyceride phase. Additionally, the study observes the formation of clusters of glycerol head groups at the interface, and the choice of the FF significantly affects the simulated morphological structure. The Berger FF exhibits the most substantial structuring effects after 200 ns of simulation, followed by the General AMBER FF, while the Martini FF shows the weakest effects. Number density plots of aliphatic chains and glycerol backbones at different temperatures monitor the evolution of structuring effects over time and determine the approach toward equilibrium conditions. The temperatures investigated include the solid state of POP at ambient temperature (293 K), the liquid state at human body temperature (310 K), and a typical processing temperature of the chocolate conching process (333 K).

Practical Applications: Tailored molecular design of interfaces according to their purpose in food.
To conceal or reveal: Identity‐conscious diversity ideologies facilitate sexual minority identity disclosure
Authors: Kirby Teri A. , Barreto Manuela , Korine Raphael , Hendy James , Osman Laura , Stadie Sophie , Tan Darren
Published: October 2023

Sexual minorities continue to face workplace discrimination, which leads to them experiencing concerns about disclosing their own sexual identities. Despite the benefits of disclosure, relatively little research has examined what organizational factors can work together to foster disclosure of a sexual minority identity. Across five experiments (N = 1662), we examined two main factors: diversity ideologies and information about diversity climate. Sexual minorities were more willing to disclose in organizations with diversity messages conveying that they value group differences (an identity‐conscious ideology) relative to those that downplay differences (an identity‐blind ideology). Identity‐conscious ideologies also increased belonging, perceptions of fair treatment and perceptions of LGBTQ+ representation. Despite expectations that contradictory evidence demonstrating a negative diversity climate might create mistrust and impede disclosure, the benefits of an identity‐conscious ideology persisted in the face of a negative diversity climate. These findings point to the complexities of facilitating visible sexual minority representation in many workplace environments.
Examining change in social dominance and authoritarianism during New Zealand's nationwide COVID‐19 lockdown
Authors: Zubielevitch Elena , Sibley Chris G. , Osborne Danny
Published: October 2023

We investigated mean‐level changes in social dominance orientation (SDO) and right‐wing authoritarianism (RWA) during (vs before) New Zealand's nationwide coronavirus disease 2019 (COVID‐19) lockdown at a time when New Zealand was led by a left‐leaning government. The number of participants in the study ranged from (Ns = 25,065–24,653). Using propensity score matching to approximate experimental conditions, results show that both ideological motivations decreased slightly during the lockdown but rebounded after restrictions were removed several months later. We also tested whether the lockdown differentially moderated the associations SDO and RWA had with institutional attitudes. Lockdown conditions exacerbated the negative association between SDO and government satistfaction but attenuated the negative association between RWA and government satisfaction. Similar patterns emerged for trust in police and politicians but not trust in science. Although SDO and RWA fluctuated in similar directions during New Zealand's nationwide lockdown, our results indicate that people high in RWA may become more supportive of the government and police under such conditions—even in countries with a left‐leaning political leader helming the pandemic response.