bluuebunny/crossref_metadata_2025 huggingface dataset:
Machine learning concepts applied to oral pathology and oral medicine: A convolutional neural networks' approach
Authors: Araújo Anna Luíza Damaceno , da Silva Viviane Mariano , Kudo Maíra Suzuka , de Souza Eduardo Santos Carlos , Saldivia‐Siracusa Cristina , Giraldo‐Roldán Daniela , Lopes Marcio Ajudarte , Vargas Pablo Agustin , Khurram Syed Ali , Pearson Alexander T. , Kowalski Luiz Paulo , de Carvalho André Carlos Ponce de Leon Ferreira , Santos‐Silva Alan Roger , Moraes Matheus Cardoso
Published: January 2023

Introduction

Artificial intelligence models and networks can learn and process dense information in a short time, leading to an efficient, objective, and accurate clinical and histopathological analysis, which can be useful to improve treatment modalities and prognostic outcomes. This paper targets oral pathologists, oral medicinists, and head and neck surgeons to provide them with a theoretical and conceptual foundation of artificial intelligence‐based diagnostic approaches, with a special focus on convolutional neural networks, the state‐of‐the‐art in artificial intelligence and deep learning.

Methods

The authors conducted a literature review, and the convolutional neural network's conceptual foundations and functionality were illustrated based on a unique interdisciplinary point of view.

Conclusion

The development of artificial intelligence‐based models and computer vision methods for pattern recognition in clinical and histopathological image analysis of head and neck cancer has the potential to aid diagnosis and prognostic prediction.
Evaluation of candidemia in children at a university hospital: A retrospective cohort
Authors: Guner Ozenen Gizem , Sahbudak Bal Zumrut , Avcu Gulhadiye , Ozkaya Yazici Pinar , Karakoyun Miray , Metin Dilek Yesim , Hilmioglu Polat Suleyha
Published: January 2023

Background

Candidemia is a life‐threatening infection in hospitalied children. This study aimed to evaluate candidemia's demographic and clinical characteristics and identify the risk factors and outcomes of Candida albicans (CA) and non‐albicans Candida (NAC) spp.

Methods

A retrospective cohort was designed to evaluate paediatric patients with candidemia between January 2008 and December 2020.

Results

A total of 342 episodes in 311 patients were evaluated. The median age of the patients was 2.1 years (1 month–17 years and 6 months), and 59.6% were male. The prevalence of NAC (67.5%) candidemia was higher than that of CA (32.5%). The most commonly isolated Candida species was Candida parapsilosis (43.3%), followed by C. albicans (32.5%), Candida glabrata (6.1%) and Candida tropicalis (5.0%). The length of hospital stay prior to the positive culture and the total length of hospital stay were longer in the NAC group (p = .003 and p = .006). The neutrophil count was lower in the NAC group (p = .007). In the multivariate analysis, total parenteral nutrition, antifungal prophylaxis and a history of coagulase‐negative staphylococci (CoNS) culture positivity in the past month were risk factors for developing candidemia due to NAC (p values were .003, .003 and .045). C. albicans and C. parapsilosis fluconazole resistance were 9.5% and 46.6%, respectively. The rates of amphotericin B resistance were 1.1% and 7.6% in C. albicans and C. parapsilosis, respectively. Mortality (14‐day and 30‐day) rates did not differ between the groups.

Conclusions

A history of CoNS culture positivity in the past month, total parenteral nutrition, and antifungal prophylaxis increases the risk of NAC candidemia.
Pathogenesis, immunology, and immune‐targeted management of the multisystem inflammatory syndrome in children (MIS‐C) or pediatric inflammatory multisystem syndrome (PIMS): EAACI Position Paper
Authors: Feleszko Wojciech , Okarska‐Napierała Magdalena , Buddingh Emilie Pauline , Bloomfield Marketa , Sediva Anna , Bautista‐Rodriguez Carles , Brough Helen A. , Eigenmann Philippe A. , Eiwegger Thomas , Eljaszewicz Andrzej , Eyerich Stefanie , Gomez‐Casado Cristina , Fraisse Alain , Janda Jozef , Jiménez‐Saiz Rodrigo , Kallinich Tilmann , Krohn Inge Kortekaas , Mortz Charlotte G. , Riggioni Carmen , Sastre Joaquin , Sokolowska Milena , Strzelczyk Ziemowit , Untersmayr Eva , Tramper‐Stranders Gerdien ,   for the Immunology Section and Working Group Infections of the EAACI
Published: January 2023

Multisystem inflammatory syndrome in children (MIS‐C) is a rare, but severe complication of coronavirus disease 2019 (COVID‐19). It develops approximately 4 weeks after severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection and involves hyperinflammation with multisystem injury, commonly progressing to shock. The exact pathomechanism of MIS‐C is not known, but immunological dysregulation leading to cytokine storm plays a central role. In response to the emergence of MIS‐C, the European Academy of Allergy and Clinical Immunology (EAACI) established a task force (TF) within the Immunology Section in May 2021. With the use of an online Delphi process, TF formulated clinical statements regarding immunological background of MIS‐C, diagnosis, treatment, follow‐up, and the role of COVID‐19 vaccinations. MIS‐C case definition is broad, and diagnosis is made based on clinical presentation. The immunological mechanism leading to MIS‐C is unclear and depends on activating multiple pathways leading to hyperinflammation. Current management of MIS‐C relies on supportive care in combination with immunosuppressive and/or immunomodulatory agents. The most frequently used agents are systemic steroids and intravenous immunoglobulin. Despite good overall short‐term outcome, MIS‐C patients should be followed‐up at regular intervals after discharge, focusing on cardiac disease, organ damage, and inflammatory activity. COVID‐19 vaccination is a safe and effective measure to prevent MIS‐C. In anticipation of further research, we propose a convenient and clinically practical algorithm for managing MIS‐C developed by the Immunology Section of the EAACI.
The reputational dividends of collaborating with a highly reputable agency: The case of interagency collaboration between the U.S. FDA and its domestic partner agencies
Authors: Maor Moshe , Sulitzeanu‐Kenan Raanan , Balmas Meital
Published: January 2023

What reputational dividends in the media, if any, do federal agencies reap from collaboration with a highly reputable agency, such as the U.S. Food and Drug Administration (FDA)? Utilizing a dataset covering 30 U.S. federal agencies over a period of 34 years (1980–2013), we estimate the short and long‐term reputational effects of interagency collaboration. Collaboration is measured by the number of memorandums of understanding in effect between each agency and the FDA, while agency reputation in the media is assessed using an automated measure of media‐coverage valence (positive/negative tone) for each agency‐year. To account for potential reverse and reciprocal causality, we utilize cross‐lagged fixed‐effects models. We find evidence of moderate rises in reputation in the media due to increased collaboration with the FDA. These effects persist significantly for 2 years following the end of the collaboration, before declining to null after 4 years. Employing similar analyses, we furthermore estimate reverse causality—of reputation in the media on the level of consequent collaboration—finding no evidence of such effects.
Successful use of peritoneal dialysis after abdominal surgery in a patient with factor XI deficiency: A case report
Authors: Li Xueying , Chen Ming , Wang Yong , Zhou Xuelei , Wang Min , Zou Lihua
Published: January 2023

Factor XI (FXI) deficiency is a rare bleeding disorder of unpredictable severity that correlates poorly with FXI coagulation activity and that poses great challenges for perioperative hemostatic management and the dialysis methods potentially available to new end‐stage renal disease (ESRD) patients. We describe an individual with both ESRD and severe FXI deficiency, who successfully underwent peritoneal dialysis (PD) after emergency abdominal surgery. In the traditional concept, recent abdominal surgery is a contraindication to PD, especially for patients with bleeding risk. However, this case report highlights that PD can still be an possible option for patients with FXI deficiency who have just undergone abdominal surgery; laparoscopic PD catheter placement offers a chance to establish PD access in patients traditionally viewed as noncandidates for this method. Careful perioperative management and fresh frozen plasma transfusion ensure successful surgery. This case should be of help to clinicians and patients considering PD in similar situations.
Impact of maize straw biochar and tied‐ridge‐furrow rainwater harvesting on soil erosion and soil quality in a semiarid region
Authors: Mak‐Mensah Erastus , Zhao Wucheng , Zhou Xujiao , Zhang Dengkui , Zhao Xiaole , Wang Qi , Obour Peter Bilson
Published: January 2023

In dryland areas, integrating biochar soil amendment with in situ rainwater harvesting systems may decrease soil erosion, improve soil quality, and increase crop productivity and yield. This study was conducted to investigate the effect of maize straw biochar amendment and ridge‐furrow rainwater harvesting systems on run‐off, sediment yield and the physico‐chemical properties of a Calcic Cambisol soil in semiarid areas. The experiment was conducted on alfalfa (Medicago sativa) production land at the Anjiagou Catchment experimental station in Gansu province, China. The experimental layout was a split‐plot design with three replications. Biochar was applied at a rate of 0 and 30 t ha−1, respectively. The tillage treatments were flat planting, open‐ridging, and tied‐ridging (TR). Overall, the integration of maize straw biochar with TR decreased soil bulk density at 0–40 cm depth. Biochar application reduced run‐off by 37.8% and soil loss by 55.5% during alfalfa‐growing seasons compared to the control. In general, biochar addition increased soil total potassium, but the same effect was not observed for soil pH, total nitrogen, total phosphorus, and available phosphorus. These findings demonstrate the potential of integrating maize straw biochar and tillage systems to reduce soil erosion and improve soil quality for rainfed crop production in semiarid areas. Further studies on the effect of biochar‐tillage system interaction are warranted to improve soil conditions for plant growth and increase crop yield in dryland areas.
Evolution of calling songs in the grasshopper subfamily Gomphocerinae (Orthoptera, Acrididae)
Authors: Sevastianov Nikita , Neretina Tatiana , Vedenina Varvara
Published: January 2023

The evolution of the calling songs in Gomphocerinae was evaluated via estimating a phylogenetic signal of the song characters and an ancestral character state reconstruction. Analyses of the calling songs in 80 palearctic gomphocerine species allowed us to define 24 characters describing the temporal pattern of the sound and the stridulatory leg‐movement pattern. The ancestral song of Gomphocerinae was shown to consist of numerous short echemes lasting on average 0.9 s; each echeme comprised only one syllable produced by movements of only one leg. The next step of the song evolution could be producing longer echemes or longer echeme‐sequence. Later, echeme duration again decreased, but this was accompanied by increasing of echeme or syllable complexity. The characters describing the echeme structure were found to be conservative in their evolution. By contrast, most characters of the syllable temporal structure were shown to be relatively labile and more likely under natural or sexual selection. Our study shows that the song evolution in Gomphocerinae implied not only increasing but also decreasing complexity of the syllable temporal structure.
On strong chains of sets and functions
Authors: Inamdar Tanmay C.
Published: January 2023

Shelah has shown that there are no chains of length ω3increasing modulo finite in . We improve this result to sets. That is, we show that there are no chains of length ω3in increasing modulo finite. This contrasts with results of Koszmider who has shown that there are, consistently, chains of length ω2increasing modulo finite in as well as in . More generally, we study the depth of function spaces quotiented by the ideal where are infinite cardinals.
Myonuclear alterations associated with exercise are independent of age in humans
Authors: Battey E. , Ross J. A. , Hoang A. , Wilson D. G. S. , Han Y. , Levy Y. , Pollock R. D. , Kalakoutis M. , Pugh J. N. , Close G. L. , Ellison‐Hughes G. M. , Lazarus N. R. , Iskratsch T. , Harridge S. D. R. , Ochala J. , Stroud M. J.
Published: January 2023

Age‐related decline in skeletal muscle structure and function can be mitigated by regular exercise. However, the precise mechanisms that govern this are not fully understood. The nucleus plays an active role in translating forces into biochemical signals (mechanotransduction), with the nuclear lamina protein lamin A regulating nuclear shape, nuclear mechanics and ultimately gene expression. Defective lamin A expression causes muscle pathologies and premature ageing syndromes, but the roles of nuclear structure and function in physiological ageing and in exercise adaptations remain obscure. Here, we isolated single muscle fibres and carried out detailed morphological and functional analyses on myonuclei from young and older exercise‐trained individuals. Strikingly, myonuclei from trained individuals were more spherical, less deformable, and contained a thicker nuclear lamina than those from untrained individuals. Complementary to this, exercise resulted in increased levels of lamin A and increased myonuclear stiffness in mice. We conclude that exercise is associated with myonuclear remodelling, independently of age, which may contribute to the preservative effects of exercise on muscle function throughout the lifespan.

image

Key points

The nucleus plays an active role in translating forces into biochemical signals.

Myonuclear aberrations in a group of muscular dystrophies called laminopathies suggest that the shape and mechanical properties of myonuclei are important for maintaining muscle function.

Here, striking differences are presented in myonuclear shape and mechanics associated with exercise, in both young and old humans.

Myonuclei from trained individuals were more spherical, less deformable and contained a thicker nuclear lamina than untrained individuals.

It is concluded that exercise is associated with age‐independent myonuclear remodelling, which may help to maintain muscle function throughout the lifespan.
WHOLE GENOME SEQUENCING AND GENOTYPING PROTOCOL OF RABIES VIRUS ISOLATES
Authors: Yessembekova G. , Abenova A. , Amirgazin A. , Karibayev T. , Shevtsov A. , Abdrakhmanov S.
Published: January 2023

This study describes the developed protocol for whole genome sequencing of clinical Rabies virus RNA samples on the Illumina MiSeq platform. Previously, genotyping of the rabies virus circulating in Kazakhstan was based on the nucleoprotein gene sequence (N gene). The protocol describes the methods of sample preparation, whole genome sequencing and genotyping currently used for epidemiological analysis not only of Rabies virus, but also for other viral pathogens such as SARS-CoV-2, Influenza and others. The aim of the work was to develop and test a protocol for whole genome sequencing and genetyping of rabies virus isolates for further use in epidemiological monitoring. As a result of the research, whole genome sequences of 31 isolates of Rabies virus isolated from various infected animals and regions of Kazakhstan were obtained for the first time. All the isolates belong to the major steppe-type clade – Cosmopolitan (30 isolates belong to the minor clade CA1, while 1 isolate belongs to an unassigned minor clade). 2 local outbreaks and 6 separated rabies virus lineages were identified. Estimated dates of divergence from a common ancestor were calculated for both the Cosmopolitan clade and the minor clade CA1.
Self-Debonding of Adhesive Thin Films on Convex Cylindrical Surfaces and Spherical Surfaces
Authors: Ma Xiaojie , Long Hao , Wei Yueguang
Published: January 2023

The emerging skin-integrated devices have been embedded with various functions, whose ideal implementation typically relies on intact bonding to curved substrates. However, the predeformation, which originates from the attachment of a thin film to a curved substrate, attempts to peel the film (i.e., self-debonding). It calls for strong enough interfacial adhesion in applications. On the other hand, too strong adhesion can destroy the surfaces of devices and substrates when the devices are peeled off after service. Therefore, seeking critical conditions becomes essential. Herein, we study the self-debonding of an adhesive thin film on a convex cylindrical surface. Taking Dugdale’s constant-stress law to describe the interfacial traction–separation relationship, we analytically unveil that the self-debonding behaviors are not solely determined by the interfacial energy. Instead, both the interfacial strength and critical interfacial separation are decisive. We thus obtain a phase diagram consisting of two critical conditions correspondingly. Similar results appear in the finite element analysis with the trapezoidal cohesive law, quantitatively showing the evolution of deflection and interfacial detachment force. Furthermore, we find that the circular film, symmetrically adhering to a spherical surface with small deflection, can still share similar self-debonding behavior. Our results provide guidance on how to stick a thin film on a convex cylindrical or spherical surface well with proper interfacial adhesion.
Independence or Interaction? Understanding the Benefits and Limitations of Nominally Inspired and Interacting Sub-Structured Teams in a Virtual and Interdisciplinary Engineering Design Task
Authors: Gyory Joshua T. , Soria Zurita Nicolás F. , Cagan Jonathan , McComb Christopher
Published: January 2023

Teams are common throughout engineering practice and industry when solving complex, interdisciplinary problems. Previous works in engineering problem solving have studied the effectiveness of teams and individuals, showing that in some circumstances, individuals can outperform collaborative teams working on the same task. The current work extends these insights to novel team configurations in virtual, interdisciplinary teams. In these team configurations, the whole meta-team can interact, but the sub-teams within them may or may not. Here, team performance and process are studied within the context of a complex drone design and path-planning problem. Via a collaborative research platform called HyForm, communication and behavioral patterns can be tracked and analyzed throughout problem solving. This work shows that nominally inspired sub-structured teams, where members work independently, outperform interacting sub-structured teams. While problem-solving actions remain consistent, communication patterns significantly differ, with nominally inspired sub-structured teams communicating significantly less. Questionnaires reveal that the manager roles in the nominally inspired sub-structured teams, which are more central in communication and information flow, experience a greater cognitive and workload burden than their counterparts in the interacting sub-structured teams. Moreover, members in the nominally inspired sub-structured teams experience their teams as inferior on various dimensions, including communication and feedback effectiveness, yet their performance is superior. Overall, this work adds to the literature on nominal versus interacting problem-solving teams, extending the finding to larger, interdisciplinary teams.
An Investigation of the Impact of Combustion Chamber Geometry on Turbulent Burning Speeds in a Thermodynamic Model
Authors: Akın Kutlar Osman , Emre Doğan Hüseyin , Demirci Abdurrahman , Arslan Hikmet
Published: January 2023

Combustion is the main parameter that affects efficiency and exhaust gas emissions. Recently, different studies have been carried out to increase the combustion rates due to the increasing use of the alternative fuels and lean mixtures in spark ignition engines. In general, in the absence of systems such as an optical access engine or ionization probes, combustion process evaluation is done based on cylinder pressure. In this study, the effect of different combustion chamber geometries on the turbulent burning speeds was investigated experimentally and theoretically. A three-zone, quasi-dimensional thermodynamic model for a spark ignition engine was constructed. Measured cylinder pressure data were used to establish the transition between the zones of the model and determine turbulent burning speeds. Two different turbulent speeds were calculated in the model, these are flame propagation and consumption speeds. It was seen that combustion chamber geometry significantly affected turbulent burning speeds. In MAN-Ricardo shapes and cylindrical shapes, the turbulent burning speeds decreased after it reached a maximum value in the combustion period. In flat geometry, without any bowl, speed continuously decreased different from other two designs. By means of a quasi-dimensional thermodynamic model, mean values of the turbulent burning and the flame propagation speeds can be calculated without having any optical observation.
Numerical Studies of Bubbles in Swirling Channel Flows
Authors: Liu Wen , Lu Jiacai , Tryggvason Gretar
Published: January 2023

The motion of bubbles in upflow in a vertical rotating closed channel is examined numerically, using a front tracking/finite volume method. The flow is driven upward by a constant pressure gradient. The Reynolds number is low enough so that the flow remains laminar and the Eötvös number is sufficiently low so the bubbles remain nearly spherical. A bubble is placed between the centerline and the walls and for low rotation rate the bubble moves to a wall, due to the lift force and the fluid shear near the walls, but for higher rotation rate the bubble moves to the center of the channel, due to the radial pressure gradient established by the rotation. For intermediate rotation rates, we find bubbles where the lift force and the pressure gradient balance and the bubbles remain between the centerline and the walls. We also examine the collective motion of a few bubbles and show that their dynamics are similar to what is observed for a single bubble.
Automatic Clustering of Metocean Conditions on the Brazilian Coast
Authors: Moreno Felipe M. , Tannuri Eduardo A. , Cozman Fabio G.
Published: January 2023

This paper introduces a pipeline that assembles a dataset of metocean conditions consisting of wind, wave, and surface currents, and then clusters these data to find the characteristic environmental conditions of each region on the Brazilian coast and the associated Exclusive Economic Zone. Clustering uses the Partitioning Around Medoids algorithm with the silhouette coefficient. As examples, we first present an analysis of the whole Exclusive Economic Zone and then a focused analysis around the Santos port in Southeastern Brazil.
Improving the Power Output of a Partially Shaded Photovoltaic Array through a Hybrid Magic Square Configuration with Differential Evolution based Adaptive P&O MPPT Method
Authors: Muniyandi Vijay , Saravanan M. , Balasubramanian Ashok Kumar
Published: January 2023

A partially shaded photovoltaic (PV) array's characteristic curve is convoluted due to disparity in irradiance levels between shaded and unshaded PV panels, resulting in power mismatch losses. This work presents a new hybrid approach combining the Magic Square (MS) array configuration and Differential Evolution based adaptive perturb and observe (DEAPO) MPPT methodology to overcome the abovementioned problem. The proposed hybrid methodology is implemented in two steps: first, repositioning the PV panels as per the MS configuration to decrease the power losses of partial shading. In MS configuration, the concentrated shadow on a single row or column can spread over to the entire PV array equally without any physical or electrical switching of PV panels. Second, the DEAPO MPPT method is developed to find the global peak power point on the PV characteristic curve. PID controller coefficients are optimized by DE to enhance the tracking speed and convergence of the adaptive P&O MPPT. The simulation study of this work has been implemented using PV arrays in MATLAB/SIMULINK environment and the real-time validation is done through a 5 kW PV array. The proficiency of the proposed hybrid approach is tested by creating various non-uniform and uniform shading patterns on the PV array. The simulation and experimental results prove that the proposed hybrid approach increases the power output by 19% and 20% higher than the existing Total Cross Tie (TCT) configuration under non-uniform and uniform shading cases respectively.
An Innovative Design for a Solar Water Heating System Utilizing a Flat-Shaped Heat Pipe
Authors: Siritan Methida , Vafai Kambiz , Kammuang-Lue Niti , Terdtoon Pradit , Sakulchangsatjatai Phrut
Published: January 2023

In this work, an innovative design for a solar water heating system using a flat-shaped heat pipe as a heat transfer device is presented to pave the way for a substantial increase in the thermal performance of these systems. An analytical study is utilized to investigate the thermal performance of the solar water heating system. The analytical results of the flat-shaped heat pipe system are compared with the results of the evacuated tube solar water heating system with a U-tube, thermosyphon, and closed-loop pulsating heat pipe. It is found that the water temperature difference between the inlet and outlet of the flat-shaped heat pipe system is substantially higher than the U-tube, thermosyphon, and closed-loop pulsating heat pipe system by as much as 31.4, 22.5, and 18.5 °C, respectively, at a nominal 0.6 l/min mass flowrate. Furthermore, utilizing the flat-shaped heat pipe in the solar water heating system optimizes the thermal conductivity of the solar setup due to a reduction in the condenser section length. These reductions also lead to a large reduction in the weight and cost of the system.
Acoustic characterization of nanofibers for optimization with porous substrate
Authors: Chen Victor , Perez Pablos Ignacio , Chen Jer-Ming
Published: January 2023

Nanofiber-porous systems comprising a porous substrate overlaid with nanofiber weave offer the potential for higher acoustic absorption than the substrate alone with negligible increase in thickness. The characterization of nanofibers from acoustic measurements is investigated in this work, and a regression model for predicting their acoustic properties from a single physical parameter is proposed to enable the design of nanofiber-porous systems directly from fabrication parameters. Characterization as a resistive screen via Johnson–Champoux–Allard and lumped element models for transfer matrix computations of absorption coefficient for nanofiber-porous systems exhibited good agreement with the measured spectra. The lumped element model was chosen as it was defined by fewer parameters and did not require nanofiber layer thickness measurements, eliminating the associated uncertainty. A regression model for lumped element parameters vs areal density established a design tool based on a single, easily measured physical property for optimized absorption at target frequencies without prior acoustic characterization of the nanofiber layer, enabling the analysis of complex acoustic networks incorporating nanofiber-porous systems. Practical considerations of applying adhesives at the nanofiber-porous interface were studied to evaluate possible enhancement of acoustic performance. For comparison with prior work by others, flow resistances from physical measurement and acoustic characterization were compared.
Developmental Progression and Sex Differences in Agility During Continuous Two-Footed Jumping Among Children Aged 4–16 Years
Authors: Muro Ayane , Takatoku Nozomi , Ohtaka Chiaki , Fujiwara Motoko , Nakata Hiroki
Published: January 2023

We investigated performance levels on conducting continuous two-footed jumping of preschool children (4 years old) to high school students (16 years old) to clarify the developmental progression and sex differences in motor coordination and agility. In total, 450 children (boys: 227; girls: 223) participated in this study. We set 10 obstacles to jump over for continuous two-footed jumping and analyzed the movement time (MT), aerial time (AT), and contact time (CT), and variabilities in AT and CT in 7 year-based categories, using a high-speed camera. We also used multiple regression analysis to identify the predictors of MT. MT and CT shortened until 8 years, whereas AT continued to shorten after 8 years, suggesting that the jumping strategy differs between those younger/older than 8 years. MT, AT, and CT were significantly shorter among boys than girls from preschool children to high school students. In addition, when using multiple regression analysis, the main predictor of MT changed gradually from SD of CT to AT with increasing age. Our findings suggest that the motor control mechanisms related to continuous two-footed jumping differ depending on the age and sex and provide findings to advance understanding of the age-related motor coordination and agility in children.
Reconstruction of distinct vertebrate gastrulation modes via modulation of key cell behaviors in the chick embryo
Authors: Chuai Manli , Serrano Nájera Guillermo , Serra Mattia , Mahadevan Lakshminarayanan , Weijer Cornelis J.
Published: January 2023

The morphology of gastrulation driving the internalization of the mesoderm and endoderm differs markedly among vertebrate species. It ranges from involution of epithelial sheets of cells through a circular blastopore in amphibians to ingression of mesenchymal cells through a primitive streak in amniotes. By targeting signaling pathways controlling critical cell behaviors in the chick embryo, we generated crescent- and ring-shaped mesendoderm territories in which cells can or cannot ingress. These alterations subvert the formation of the chick primitive streak into the gastrulation modes seen in amphibians, reptiles, and teleost fish. Our experimental manipulations are supported by a theoretical framework linking cellular behaviors to self-organized multicellular flows outlined in detail in the accompanying paper. Together, this suggests that the evolution of gastrulation movements is largely determined by changes in a few critical cell behaviors in the mesendoderm territory across different species and controlled by a relatively small number of signaling pathways.
CLASP2 recognizes tubulins exposed at the microtubule plus-end in a nucleotide state–sensitive manner
Authors: Luo Wangxi , Demidov Vladimir , Shen Qi , Girão Hugo , Chakraborty Manas , Maiorov Aleksandr , Ataullakhanov Fazly I. , Lin Chenxiang , Maiato Helder , Grishchuk Ekaterina L.
Published: January 2023

CLASPs (cytoplasmic linker-associated proteins) are ubiquitous stabilizers of microtubule dynamics, but their molecular targets at the microtubule plus-end are not understood. Using DNA origami–based reconstructions, we show that clusters of human CLASP2 form a load-bearing bond with terminal non-GTP tubulins at the stabilized microtubule tip. This activity relies on the unconventional TOG2 domain of CLASP2, which releases its high-affinity bond with non-GTP dimers upon their conversion into polymerization-competent GTP-tubulins. The ability of CLASP2 to recognize nucleotide-specific tubulin conformation and stabilize the catastrophe-promoting non-GTP tubulins intertwines with the previously underappreciated exchange between GDP and GTP at terminal tubulins. We propose that TOG2-dependent stabilization of sporadically occurring non-GTP tubulins represents a distinct molecular mechanism to suppress catastrophe at the freely assembling microtubule ends and to promote persistent tubulin assembly at the load-bearing tethered ends, such as at the kinetochores in dividing cells.
A universal sequencing read interpreter
Authors: Kijima Yusuke , Evans-Yamamoto Daniel , Toyoshima Hiromi , Yachie Nozomu
Published: January 2023

Massively parallel DNA sequencing has led to the rapid growth of highly multiplexed experiments in biology. These experiments produce unique sequencing results that require specific analysis pipelines to decode highly structured reads. However, no versatile framework that interprets sequencing reads to extract their encoded information for downstream biological analysis has been developed. Here, we report INTERSTELLAR (interpretation, scalable transformation, and emulation of large-scale sequencing reads) that decodes data values encoded in theoretically any type of sequencing read and translates them into sequencing reads of another structure of choice. We demonstrated that INTERSTELLAR successfully extracted information from a range of short- and long-read sequencing reads and translated those of single-cell (sc)RNA-seq, scATAC-seq, and spatial transcriptomics to be analyzed by different software tools that have been developed for conceptually the same types of experiments. INTERSTELLAR will greatly facilitate the development of sequencing-based experiments and sharing of data analysis pipelines.
North Atlantic cooling triggered a zonal mode over the Indian Ocean during Heinrich Stadial 1
Authors: Du Xiaojing , Russell James M. , Liu Zhengyu , Otto-Bliesner Bette L. , Oppo Delia W. , Mohtadi Mahyar , Zhu Chenyu , Galy Valier V. , Schefuß Enno , Yan Yan , Rosenthal Yair , Dubois Nathalie , Arbuszewski Jennifer , Gao Yu
Published: January 2023

Abrupt changes in the Atlantic meridional overturning circulation (AMOC) are thought to affect tropical hydroclimate through adjustment of the latitudinal position of the intertropical convergence zone (ITCZ). Heinrich Stadial 1 (HS1) involves the largest AMOC reduction in recent geological time; however, over the tropical Indian Ocean (IO), proxy records suggest zonal anomalies featuring intense, widespread drought in tropical East Africa versus generally wet but heterogeneous conditions in the Maritime Continent. Here, we synthesize proxy data and an isotope-enabled transient deglacial simulation and show that the southward ITCZ shift over the eastern IO during HS1 strengthens IO Walker circulation, triggering an east-west precipitation dipole across the basin. This dipole reverses the zonal precipitation anomalies caused by the exposed Sunda and Sahul shelves due to glacial lower sea level. Our study illustrates how zonal modes of atmosphere-ocean circulation can amplify or reverse global climate anomalies, highlighting their importance for future climate change.
Compton scattering driven by intense quantum light
Authors: Khalaf Majed , Kaminer Ido
Published: January 2023

Compton scattering is a cornerstone of quantum physics, describing the fundamental electron-photon interaction. Inverse Compton scattering can create attosecond x-ray pulses by high-intensity lasers driving free electrons. So far, in all theory and experiments, the observables of Compton scattering and its generalizations could be described by treating the driving electromagnetic field classically. Motivated by advances in the generation of squeezed light with high intensity, we consider driving the Compton effect with nonclassical light. We develop a framework to describe the nonperturbative interaction of a charged particle with driving fields of an arbitrary quantum light state. We obtain analytical results for the Compton emission spectrum when driven by intense thermal and squeezed vacuum states, showing noticeably broader emission spectra relative to a classical drive, thus reaching higher emission frequencies for the same average intensity. We envision quantum light properties such as squeezing and entanglement as degrees of freedom to control various radiation phenomena.
Auxin promotes hypocotyl elongation by enhancing BZR1 nuclear accumulation in
Arabidopsis
Authors: Yu Zipeng , Ma Jinxin , Zhang Mengyue , Li Xiaoxuan , Sun Yi , Zhang Mengxin , Ding Zhaojun
Published: January 2023

Auxin and brassinosteroids (BRs) are two major growth-promoting phytohormones that shape hypocotyl elongation; however, the cross-talk between auxin and BR in this process is not fully understood. In this study, we found that auxin-induced hypocotyl elongation is dependent on brassinazole-resistant 1 (BZR1), a core BR signaling component. Auxin promotes BZR1 nuclear accumulation in hypocotyl cells, a process dependent on mitogen-activated protein kinase 3 (MPK3) and MPK6, which are both activated by auxin and whose encoding genes are highly expressed in hypocotyls. We determined that MPK3/MPK6 phosphorylate and reduce the protein stability of general regulatory factor 4 (GRF4), a member of the 14-3-3 family of proteins that retain BZR1 in the cytoplasm. In summary, this study reveals the molecular mechanism by which auxin promotes hypocotyl elongation by enhancing BZR1 nuclear accumulation via MPK3/MPK6-regulated GRF4 protein stability.
Spleen tyrosine kinase inhibition restores myeloid homeostasis in COVID-19
Authors: Wigerblad Gustaf , Warner Seth A. , Ramos-Benitez Marcos J. , Kardava Lela , Tian Xin , Miao Rui , Reger Robert , Chakraborty Mala , Wong Susan , Kanthi Yogendra , Suffredini Anthony F. , Dell’Orso Stefania , Brooks Stephen , King Christopher , Shlobin Oksana , Nathan Steven D. , Cohen Jonathan , Moir Susan , Childs Richard W. , Kaplan Mariana J. , Chertow Daniel S. , Strich Jeffrey R.
Published: January 2023

Spleen tyrosine kinase (SYK) is a previously unidentified therapeutic target that inhibits neutrophil and macrophage activation in coronavirus disease 2019 (COVID-19). Fostamatinib, a SYK inhibitor, was studied in a phase 2 placebo-controlled randomized clinical trial and was associated with improvements in many secondary end points related to efficacy. Here, we used a multiomic approach to evaluate cellular and soluble immune mediator responses of patients enrolled in this trial. We demonstrated that SYK inhibition was associated with reduced neutrophil activation, increased circulation of mature neutrophils (CD10
+
CD33
−
), and decreased circulation of low-density granulocytes and polymorphonuclear myeloid-derived suppressor cells (HLA-DR
−
CD33
+
CD11b
−
). SYK inhibition was also associated with normalization of transcriptional activity in circulating monocytes relative to healthy controls, an increase in frequency of circulating nonclassical and HLA-DR
hi
classical monocyte populations, and restoration of interferon responses. Together, these data suggest that SYK inhibition may mitigate proinflammatory myeloid cellular and soluble mediator responses thought to contribute to immunopathogenesis of severe COVID-19.
Vaccination with S
pan
, an antigen guided by SARS-CoV-2 S protein evolution, protects against challenge with viral variants in mice
Authors: Zhao Yongliang , Ni Wenjia , Liang Simeng , Dong Lianghui , Xiang Min , Cai Zeng , Niu Danping , Zhang Qiuhan , Wang Dehe , Zheng Yucheng , Zhang Zhen , Zhou Dan , Guo Wenhua , Pan Yongbing , Wu Xiaoli , Yang Yimin , Jing Zhaofei , Jiang Yongzhong , Chen Yu , Yan Huan , Zhou Yu , Xu Ke , Lan Ke
Published: January 2023

SARS-CoV-2 continues to accumulate mutations to evade immunity, leading to breakthrough infections after vaccination. How researchers can anticipate the evolutionary trajectory of the virus in advance in the design of next-generation vaccines requires investigation. Here, we performed a comprehensive study of 11,650,487 SARS-CoV-2 sequences, which revealed that the SARS-CoV-2 spike (S) protein evolved not randomly but into directional paths of either high infectivity plus low immune resistance or low infectivity plus high immune resistance. The viral infectivity and immune resistance of variants are generally incompatible, except for limited variants such as Beta and Kappa. The Omicron variant has the highest immune resistance but showed high infectivity in only one of the tested cell lines. To provide cross-clade immunity against variants that undergo diverse evolutionary pathways, we designed a new pan-vaccine antigen (S
pan
). S
pan
was designed by analyzing the homology of 2675 SARS-CoV-2 S protein sequences from the NCBI database before the Delta variant emerged. The refined S
pan
protein harbors high-frequency residues at given positions that reflect cross-clade generality in sequence evolution. Compared with a prototype wild-type (S
wt
) vaccine, which, when administered to mice, induced serum with decreased neutralization activity against emerging variants, S
pan
vaccination of mice elicited broad immunity to a wide range of variants, including those that emerged after our design. Moreover, vaccinating mice with a heterologous S
pan
booster conferred complete protection against lethal infection with the Omicron variant. Our results highlight the importance and feasibility of a universal vaccine to fight against SARS-CoV-2 antigenic drift.
Activation of MAP2K signaling by genetic engineering or HF-rTMS promotes corticospinal axon sprouting and functional regeneration
Authors: Boato Francesco , Guan Xiaofei , Zhu Yanjie , Ryu Youngjae , Voutounou Mariel , Rynne Christopher , Freschlin Chase R. , Zumbo Paul , Betel Doron , Matho Katie , Makarov Sergey N. , Wu Zhuhao , Son Young-Jin , Nummenmaa Aapo , Huang Josh Z. , Edwards Dylan J. , Zhong Jian
Published: January 2023

Facilitating axon regeneration in the injured central nervous system remains a challenging task. RAF-MAP2K signaling plays a key role in axon elongation during nervous system development. Here, we show that conditional expression of a constitutively kinase-activated BRAF in mature corticospinal neurons elicited the expression of a set of transcription factors previously implicated in the regeneration of zebrafish retinal ganglion cell axons and promoted regeneration and sprouting of corticospinal tract (CST) axons after spinal cord injury in mice. Newly sprouting axon collaterals formed synaptic connections with spinal interneurons, resulting in improved recovery of motor function. Noninvasive suprathreshold high-frequency repetitive transcranial magnetic stimulation (HF-rTMS) activated the BRAF canonical downstream effectors MAP2K1/2 and modulated the expression of a set of regeneration-related transcription factors in a pattern consistent with that induced by BRAF activation. HF-rTMS enabled CST axon regeneration and sprouting, which was abolished in MAP2K1/2 conditional null mice. These data collectively demonstrate a central role of MAP2K signaling in augmenting the growth capacity of mature corticospinal neurons and suggest that HF-rTMS might have potential for treating spinal cord injury by modulating MAP2K signaling.
Going Back in Time: Increasing Penicillin Susceptibility among Methicillin-Susceptible Staphylococcus aureus Osteoarticular Infections in Children
Authors: McNeil J. Chase , Sommer Lauren M. , Vallejo Jesus G. , Boyle Mary , Hulten Kristina G. , Kaplan Sheldon L. , Fritz Stephanie A.
Published: January 2023

In the late 1940s to 1950s,
Staphylococcus aureus
isolates first-gained resistance to penicillin. Recently, some centers have described an increase in the proportion of methicillin susceptible
S. aureus
(MSSA) which are also susceptible to penicillin (PSSA).
Mycobacterium smegmatis: The Vanguard of Mycobacterial Research
Authors: Sparks Ian L. , Derbyshire Keith M. , Jacobs William R. , Morita Yasu S.
Published: January 2023

The genus
Mycobacterium
contains several slow-growing human pathogens, including
Mycobacterium tuberculosis
,
Mycobacterium leprae
, and
Mycobacterium avium
.
Mycobacterium smegmatis
is a nonpathogenic and fast growing species within this genus. In 1990, a mutant of
M. smegmatis
, designated mc
2
155, that could be transformed with episomal plasmids was isolated, elevating
M. smegmatis
to model status as the ideal surrogate for mycobacterial research.
tRNAs Are Stable After All: Pitfalls in Quantification of tRNA from Starved Escherichia coli Cultures Exposed by Validation of RNA Purification Methods
Authors: Prossliner Thomas , Agrawal Shreya , Heidemann Ditte F. , Sørensen Michael A. , Svenningsen Sine L.
Published: January 2023

We show that
E. coli
tRNAs are remarkably stable during several days of nutrient starvation, although rRNA is degraded extensively under these conditions. The levels of these two major RNA classes are considered to be strongly coregulated at the level of transcription.
Metabolic Sensing of Extracytoplasmic Copper Availability via Translational Control by a Nascent Exported Protein
Authors: Öztürk Yavuz , Andrei Andreea , Blaby-Haas Crysten E. , Daum Noel , Daldal Fevzi , Koch Hans-Georg
Published: January 2023

Metabolite sensing is a fundamental biological process, and the perception of dynamic changes in the extracellular environment is of paramount importance for the survival of organisms. Bacteria usually adjust their metabolisms to changing environments via transcriptional regulation.
Helicobacter pylori Chronic Infection Selects for Effective Colonizers of Metaplastic Glands
Authors: O’Brien V. P. , Jackson L. K. , Frick J. P. , Rodriguez Martinez A. E. , Jones D. S. , Johnston C. D. , Salama N. R.
Published: January 2023

Chronic infection with
Helicobacter pylori
is the primary risk factor for developing stomach cancer. As disease progresses
H. pylori
must adapt to a changing host tissue environment that includes induction of new cell fates in the cells that line the stomach.
Draft Genome Sequences of 20 Clostridium botulinum Type A Isolates from Foodborne Botulism Outbreaks
Authors: Halpin Jessica L. , Gómez Gerardo A. , Dykes Janet K. , Lúquez Carolina
Published: January 2023

Here, we present 20 draft genome sequences of
Clostridium botulinum
type A isolates originating from foodborne outbreaks in the United States and Ethiopia. Publicly available genomes enhance our understanding of
C. botulinum
genomics and are an asset in bioterrorism preparedness.
Coding-Complete Genome Sequences of Two Atypical Porcine Pestivirus Strains from Anhui Province, China
Authors: Mou Chunxiao , Xie Sihan , Pan Shuonan , Chen Zhenhai
Published: January 2023

In 2021, two atypical porcine pestivirus (APPV) strains, AH06/2021 and AH22/2021, were identified from suckling piglets showing congenital tremor in Anhui Province, China. Genome sequence analysis indicated that the two strains shared 81.19% to 93.98% nucleotide identities with other APPV strains.
The Full Genome Sequences of Pseudomonas sp. Strain MM221 and
Pseudoarthrobacter
sp. Strain MM222, Isolated from a Meadow in Bielefeld, Germany
Authors: Eisenhut Marion , Hawrylo Marian , Trevlopoulou Katerina , Fingerhut Hannah , Niemann Sophia , Brokate Lukas , Kniekamp Niklas , Grenda Christian F. , Güttler Marina , Wobbe Lutz , Bräutigam Andrea , Frommer Bianca
Published: January 2023

The bacterial strains
Pseudomonas
sp. strain MM221 and
Pseudoarthrobacter
sp. strain MM222 were isolated from a sandy soil sample. Here, we report on their complete genome sequences, including a circular plasmid for MM221, which were assembled after sequencing with an Oxford Nanopore Technologies flow cell.
Unique Features of the Gut Microbiome Characterized in Animal Models of Angelman Syndrome
Authors: Beitnere Ulrika , Vilanova-Cuevas Brayan , Christian Sarah G. , Taylor Clint , Berg Elizabeth L. , Copping Nycole A. , Dindot Scott V. , Silverman Jill L. , Gareau Mélanie G. , Segal David J.
Published: January 2023

Angelman syndrome (AS)-associated gastrointestinal (GI) symptoms significantly impact quality of life in patients. In AS models in mouse, rat, and pig, AS animals showed impaired colonization of the gut microbiota compared to wild-type (healthy) control animals. Common changes in AS microbiomes across all three animal models may play a causal effect for GI symptoms and may help to identify ways to treat these comorbidities in patients in the future.
Mycobacterium tuberculosis Requires the Outer Membrane Lipid Phthiocerol Dimycocerosate for Starvation-Induced Antibiotic Tolerance
Authors: Block Alisha M. , Namugenyi Sarah B. , Palani Nagendra P. , Brokaw Alyssa M. , Zhang Leanne , Beckman Kenneth B. , Tischler Anna D.
Published: January 2023

Mycobacterium tuberculosis
causes 10 million cases of active TB disease and over 1 million deaths worldwide each year. TB treatment is complex, requiring at least 6 months of therapy with a combination of antibiotics.