bluuebunny/crossref_metadata_2025 huggingface dataset:
A Whole School, Whole Community, Whole Child Approach to Support Student Physical Activity and Nutrition: Introduction/Methods
Authors: Sliwa Sarah A. , Hawkins Georgianne Tiu , Lee Sarah M. , Hunt Holly
Published: September 2023

Background

We introduce the Whole School, Whole Community, Whole Child approach to supporting student and school staff physical activity and nutrition and describe the methods used to generate the evidence synthesized across the special issue articles.

Methods

A 2‐phase literature review search included a search of systematic reviews (2010‐2018) for individual qualifying articles (Phase 1) and a search for individual articles on topics not addressed by a review (2010‐2020) or that needed an update because they were in a review that was older (2010‐2016) or showed insufficient evidence (Phase 2). Research librarians developed search strategies. In each phase, pairs of subject matter experts applied criteria to review abstracts and full‐text articles and extracted data using standardized forms. We included 314 articles, describing 293 studies.

Findings

Most of the included studies looked at elementary or secondary school level interventions; 51% were rated poor quality, and few took place in a rural setting.

Implications for School Health Policy, Practice, and Equity

Most of the identified studies engaged majority minority or racially/ethnically diverse schools, suggesting that these interventions are feasible in a variety of settings.

Conclusions

This collection of 10 articles identifies evidence‐based interventions, gaps in research, and implications for health equity.
The School Environment and Physical and Social‐Emotional Well‐Being: Implications for Students and School Employees
Authors: Hawkins Georgianne Tiu , Chung Chloe S. , Hertz Marci F. , Antolin Noehealani
Published: September 2023

Background

The school environment, consisting of the physical environment and social‐emotional climate (SEC), plays a crucial role in both student and employee health; however, there is a lack of recent literature synthesizing school environment interventions in K‐12 settings. We describe updated evidence about school environment interventions to support K‐12 student and employee health in the United States.

Methods

A 2‐phase search included a review of reviews (2010‐2018), followed by a search for individual articles (2010‐2020) that targeted school physical environment and/or SEC to address physical activity (PA) and/or nutrition. We also investigated how nutrition and PA interventions with an SEC component improves social‐emotional and/or mental health outcomes. Because research on dietary and PA behaviors for school employees is limited; we included studies on other worksites (eg, hospitals and offices) to provide insight for school employees.

Findings

We identified 40 articles describing 40 unique studies and 45 interventions and grouped them by intervention type. Physical environment interventions demonstrated significant and positive nutrition and PA behavioral outcomes for students; outcomes among employees were mixed. Interventions with SEC components reported improvements in some mental health outcomes.

Implications

The school environment can affect dietary and PA behaviors as well as mental health for students and employees.

Conclusions

Establishing healthy school environments can support student and employee PA, dietary behaviors, and mental health.
Personal emergency response systems and people with intellectual and developmental disabilities in the United States
Authors: Friedman Carli
Published: September 2023

Personal Emergency Response Systems (PERS) are electronic medical alert devices that help people with intellectual and developmental disabilities (IDD) receive assistance in emergencies. According to research on older adults, PERS improve health outcomes, provide people with a sense of security and peace of mind, promote independence, and prevent institutionalization. The aim of this study was to examine if, and how, states provided PERS to people with IDD in their Medicaid Home and Community Based Services (HCBS) waiver programs in fiscal year (FY) 2021. To do so, we qualitatively and quantitatively analyzed HCBS data on participant services and cost‐neutrality demonstrations to examine thematic trends in how and why states offered PERS, as well as total unduplicated participants, total projected spending, projected spending per participant, reimbursement rates, and annual service provision per participant. In FY 2021, 42 waivers (39.25%) from 25 states and the District of Columbia (57.78%) projected spending $9.87 million on PERS services for 9538 people with IDD. PERS services included the installation of devices (77.78%), monthly service fees (73.61%), equipment maintenance (44.44%), and training of people with IDD or their caregivers about the equipment (41.67%). States said they provided PERS in order to prevent institutionalization (23.61%), promote independence (16.67%), and maximize mobility (11.11%). Given the potential benefits for independent living, independence, and reducing costs, as well as the disparities unearthed in this study, we believe states should expand how they provide PERS to people with IDD in HCBS and do so in a more consistent manner. This may be especially beneficial as PERS can be cost‐prohibitive for many people with IDD, who frequently live in poverty, and HCBS reimbursement for technology is the top barrier to implementing technology according to IDD providers.
Advancements and hurdles of deeper‐offshore aquaculture in China
Authors: Dong Shuang‐Lin , Dong Yun‐Wei , Huang Liu‐Yi , Zhou Yan‐Gen , Cao Ling , Tian Xiang‐Li , Han Li‐Min , Li Da‐Hai
Published: September 2023

Open offshore areas boast strong physical self‐purification capacity and abundant non‐fossil energy resources, such as wind, waves, and solar energy. Consequently, the global community anticipates nearshore aquaculture to transition towards offshore to help increase production, alleviate eutrophication, and reduce greenhouse gas emissions. To date, China has constructed over 40 sets of deeper‐offshore aquaculture (DOA) infrastructures, encompassing various types of pens, cages and closed containment systems. Although DOA holds vast potential to address food security and aquaculture sustainability in China, its current development trajectory struggles to meet those goals and primarily achieves profitability by focusing on high‐value species or products. For DOA to realize its potential, innovative production systems must tackle three key contradictions: enterprise profitability versus product affordability, clean energy‐based products versus carbon‐intensive products, and automated operation versus re‐employment of coastal fish farmers. Resolving these contradictions requires the development of a large‐scale, anti‐typhoon offshore enclosure that integrates mariculture with other industries, such as wind farming, food processing, and tourism. This approach will foster a sustainable balance between profitability, environmental impact, and employment opportunities in the sector.
Understanding the regulator–regulatee relationship for developing safety culture
Authors: Willis Sara , Holman David , Clarke Sharon , Hartwig Angelique
Published: September 2023

Regulatory authorities in safety‐critical industries typically seek to influence the safety culture of the organizations they oversee. However, we know little about how regulatory authorities achieve this influence (e.g., what roles are adopted, relationship characteristics) and, more generally, about how external actors shape an organization's safety culture. Using a qualitative design in the nuclear industry, we developed our conceptual and empirical understanding of the roles through which a regulator influences the safety culture of their regulated organizations and what characteristics within the regulator–regulatee relationship facilitate positive safety culture developments. Data were collected through interviews with inspectors from a nuclear regulator and employees of regulated nuclear organizations, and from an inspection of regulatory documents. The findings identified that the regulator was perceived to hold three complementary roles for safety culture development: being an enforcer, working as a partner (providing opportunities for licenseholders to improve beyond compliance), and acting as an advisor to regulated organizations. Analysis also showed that effective relationships in these roles, and which were central to influencing safety culture, were perceived to be characterized by professionalism, transparency, and balance between formal enforcement and informal exchange. Theoretical implications to advance conceptualizations of safety culture as well as practical implications for risk regulators are discussed.
Semiparametric recovery of central dimension reduction space with nonignorable nonresponse
Authors: Zheng Siming , Wan Alan T. K. , Zhou Yong
Published: September 2023

Sufficient dimension reduction (SDR) methods are effective tools for handling high dimensional data. Classical SDR methods are developed under the assumption that the data are completely observed. When the data are incomplete due to missing values, SDR has only been considered when the data are randomly missing, but not when they are nonignorably missing, which is arguably more difficult to handle due to the missing values' dependence on the reasons they are missing. The purpose of this paper is to fill this void. We propose an intuitive, easy‐to‐implement SDR estimator based on a semiparametric propensity score function for response data with non‐ignorable missing values. We refer to it as the dimension reduction‐based imputed estimator. We establish the theoretical properties of this estimator and examine its empirical performance via an extensive numerical study on real and simulated data. As well, we compare the performance of our proposed dimension reduction‐based imputed estimator with two competing estimators, including the fusion refined estimator and cumulative slicing estimator. A distinguishing feature of our method is that it requires no validation sample. The SDR theory developed in this paper is a non‐trivial extension of the existing literature, due to the technical challenges posed by nonignorable missingness. All the technical proofs of the theorems are given in the Appendix .
Archiving Archaeological Data: Understanding Current Practice through Case Studies from Established Repositories
Authors:   University of York, Evans Tim , Hollander Hella ,   DANS, Gilissen Valentijn ,   DANS, Jakobsson Ulf ,   SND, Wright Holly ,   University of York
Published: September 2023

The workflows examined are representative of operational workflows around data assessment and data removal that are common to all data repositories, as well as specific strategies of dealing with Microsoft Access Databases, a commonly deposited file format used by archaeologists for assessment and analysis. The paper will present each workflow as a succinct case study with an emphasis on why the decisions have been made to follow a certain method. This will be followed by a discussion on similarities and differences in approach and implementation so as to bring together core recommendations that can be used by others currently building or scoping the development of new digital repositories in the archaeological sector. The paper will link out to copies of the detailed workflows and policies to be deposited within COPTR, a finding aid for helping find tools to deal with practical data management issues.
The Deflection Limit of Slab-Like Topologically Interlocked Structures
Authors: Ullmann Silvan , Kammer David S. , Feldfogel Shai
Published: September 2023

Topologically interlocked structures (TIS) are structural assemblies that achieve stability and carrying capacity through the geometric arrangement of interlocking blocks, relying solely on contact and friction forces for load transfer. Unlike beam-like TIS, whose deflection never exceeds the height of the blocks, the deflection of slab-like TIS often does. Yet, the upper limit of deflection of slab-like TIS, a key parameter defining their loading energy capacity, remains unexplored. Here, we establish a theoretical upper bound for the deflection capacity of slab-like TIS and outline a systematic design strategy to approach this upper bound. This strategy is based on engineering the contact interfaces such that the non-central blocks are more engaged in the structural response, leading to a more global and holistic deformation mode with higher deflections. We demonstrate the application of this strategy in a numerical case study on a typical slab-like TIS and show that it leads to an increase in deflection by a factor of 3.5, yielding a value closer to the upper bound than previously reported in the literature. We find that the resulting deflection mode engages all the blocks equally, avoids localized sliding modes, and resembles that of monolithic equivalents. Lastly, we show that the strategy not only maximizes TIS’ deflection capacity but also their loading energy capacity.
Simulation analyses of carrier dynamics in npn-type GaN-heterojunction bipolar transistors with different hole-concentration p-base layers
Authors: Mase Akira , Iida Yusuke , Takimoto Masaya , Nikai Yutaka , Egawa Takashi , Miyoshi Makoto
Published: September 2023

In this study, the operation of npn-type GaN-based heterojunction bipolar transistors with different net acceptor concentrations in p-base regions was simulated. It was confirmed that there is a critical net acceptor concentration (NA-ND) depending on the thickness of the base region and that if the NA-ND is lower than the critical value, the collector current may anomalously increase, regardless of base current injection. This phenomenon is caused by the punch-through process via the depletion layer extending from the collector–base junction. The effect of the valence band energy offset at the emitter-base heterojunction (ΔEV) on the current gain (β) was also investigated, and the results showed that β peaks when ΔEV is 0.22–0.30 eV. This is determined by the balance between the hot-electron injection and thermal diffusion processes in the electron transport from the emitter to the base.
A single-channel virtual receiving array using a time-reversal chaotic cavity
Authors: Im Seonghun , Lee Jae-Wan , Han Taewoo , Ohm Won-Suk
Published: September 2023

Chaotic reverberation in a cavity, when coupled with time reversal acoustics, can be harnessed to build a perfect time-reversal mirror for transmitting and receiving highly focused sounds with a small number of transducers. In this article, a virtual receiving array, comprised of a single receiving transducer and a chaotic cavity, is developed based on time reversal processing of the reverberation inside the cavity. A prototype array, having 10 × 10 virtual receiving elements, is built and evaluated against a comparable physical array in terms of its localization and waveform reproduction capabilities. It turns out that the most crucial factor in the success of a virtual array is the ergodicity of its chaotic cavity, the exact mathematical expression for which is also derived. The virtual receiving array presented here may find some niche applications in reverberant environments, where a physical array turns out to be too costly or cumbersome to operate.
Social Supports and Barriers for Older Adults Not Participating in Group Physical Activity
Authors: Morrison Lindsay , McDonough Meghan H. , Hewson Jennifer , Toohey Ann , Din Cari , Kenny Sarah J.
Published: September 2023

Group physical activity can provide physical and social benefits; however, social barriers or a lack of social support may affect participation. This study examined social-support needs and barriers among older adults who were not participating in group physical activities. Using interpretive description, semistructured interviews were conducted with 38 older adults (M = 70.9 years; 81.6% women). Themes were grouped into two categories. Category 1, expectations and initial impressions, consisted of the following: (a) Groups cannot meet everyone’s expectations or interests, (b) groups are intimidating to join, and (c) the need for inclusive programming. Category 2, social processes within group physical activity, consisted of (a) modeling physical activity behaviors, (b) sharing information and suggestions about physical activity opportunities, and (c) encouragement and genuine interest. Outreach to this population should aim to address these barriers and utilize these supportive behaviors to reduce feelings of intimidation and promote participation among older adults.
Infection-experienced HSPCs protect against infections by generating neutrophils with enhanced mitochondrial bactericidal activity
Authors: Darroch Hannah , Keerthisinghe Pramuk , Sung Yih Jian , Rolland Leah , Prankerd-Gough Anneke , Crosier Philip S. , Astin Jonathan W. , Hall Christopher J.
Published: September 2023

Hematopoietic stem and progenitor cells (HSPCs) respond to infection by proliferating and generating in-demand neutrophils through a process called emergency granulopoiesis (EG). Recently, infection-induced changes in HSPCs have also been shown to underpin the longevity of trained immunity, where they generate innate immune cells with enhanced responses to subsequent microbial threats. Using larval zebrafish to live image neutrophils and HSPCs, we show that infection-experienced HSPCs generate neutrophils with enhanced bactericidal functions. Transcriptomic analysis of EG neutrophils uncovered a previously unknown function for mitochondrial reactive oxygen species in elevating neutrophil bactericidal activity. We also reveal that driving expression of zebrafish C/EBPβ within infection-naïve HSPCs is sufficient to generate neutrophils with similarly enhanced bactericidal capacity. Our work suggests that this demand-adapted source of neutrophils contributes to trained immunity by providing enhanced protection toward subsequent infections. Manipulating demand-driven granulopoiesis may provide a therapeutic strategy to boost neutrophil function and treat infectious disease.
Copper isotope evidence for sulfide fractionation and lower crustal foundering in making continental crust
Authors: Liu Sheng-Ao , Rudnick Roberta L. , Liu Wen-Ran , Teng Fang-Zhen , Wu Tian-Hao , Wang Ze-Zhou
Published: September 2023

The continental crust is strongly depleted in copper compared with its building blocks—primary arc magmas—and this depletion is intrinsically associated with continental crust formation. However, the process by which Cu removal occurs remains enigmatic. Here we show, using Cu isotopes, that subduction-zone processes and mantle melting produce limited fractionation of Cu isotopes in arc magmas, and, instead, the heterogeneous Cu isotopic compositions of lower crustal rocks, which negatively correlate with Cu contents, suggest segregation or accumulation of isotopically light sulfides during intracrustal differentiation of arc magmas. This is supported by the extremely light Cu isotopic compositions of lower crustal mafic cumulates and heavy Cu isotopic compositions of differentiated magmas in thick continental arcs. Intracrustal differentiation of mantle-derived magmas and subsequent foundering of sulfide-rich mafic cumulates preferentially removes isotopically light Cu, leaving a Cu-depleted and isotopically heavy continental crust.
High-density, spontaneous magnetic biskyrmions induced by negative thermal expansion in ferrimagnets
Authors: Song Yuzhu , Xu Tiankuo , Zhao Guoping , Xu Yuanji , Zhong Zhicheng , Zheng Xinqi , Shi Naike , Zhou Chang , Hao Yiqing , Huang Qingzhen , Xing Xianran , Zhang Ying , Chen Jun
Published: September 2023

Magnetic skyrmions are topologically protected quasiparticles that are promising for applications in spintronics. However, the low stability of most magnetic skyrmions leads to either a narrow temperature range in which they can exist, a low density of skyrmions, or the need for an external magnetic field, which greatly limits their wide application. In this study, high-density, spontaneous magnetic biskyrmions existing within a wide temperature range and without the need for a magnetic field were formed in ferrimagnets owing to the existence of a negative thermal expansion of the lattice. Moreover, a strong connection between the atomic-scale ferrimagnetic structure and nanoscale magnetic domains in Ho(Co,Fe)
3
was revealed via in situ neutron powder diffraction and Lorentz transmission electron microscopy measurements. The critical role of the negative thermal expansion in generating biskyrmions in HoCo
3
based on the magnetoelastic coupling effect is further demonstrated by comparing the behavior of HoCo
2.8
Fe
0.2
with a positive thermal expansion.
A critical role for CaMKII in behavioral timescale synaptic plasticity in hippocampal CA1 pyramidal neurons
Authors: Xiao Kuo , Li Yiding , Chitwood Raymond A. , Magee Jeffrey C.
Published: September 2023

Behavioral timescale synaptic plasticity (BTSP) is a type of non-Hebbian synaptic plasticity reported to underlie place field formation. Despite this important function, the molecular mechanisms underlying BTSP are poorly understood. The α-calcium-calmodulin-dependent protein kinase II (αCaMKII) is activated by synaptic transmission–mediated calcium influx, and its subsequent phosphorylation is central to synaptic plasticity. Because the activity of αCaMKII is known to outlast the event triggering phosphorylation, we hypothesized that it could mediate the extended timescale of BTSP. To examine the role of αCaMKII in BTSP, we performed whole-cell in vivo and in vitro recordings in CA1 pyramidal neurons from mice engineered with a point mutation at the autophosphorylation site (T286A) causing accelerated signaling kinetics. Here, we demonstrate a profound deficit in synaptic plasticity, strongly suggesting that αCaMKII signaling is required for BTSP. This study elucidates part of the molecular mechanism of BTSP and provides insight into the function of αCaMKII in place cell formation and ultimately learning and memory.
Digital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs
Authors: Tayyab Muhammad , Barrett Donal , van Riel Gijs , Liu Shujing , Reinius Björn , Scharfe Curt , Griffin Peter , Steinmetz Lars M. , Javanmard Mehdi , Pelechano Vicent
Published: September 2023

Fast and accurate detection of nucleic acids is key for pathogen identification. Methods for DNA detection generally rely on fluorescent or colorimetric readout. The development of label-free assays decreases costs and test complexity. We present a novel method combining a one-pot isothermal generation of DNA nanoballs with their detection by electrical impedance. We modified loop-mediated isothermal amplification by using compaction oligonucleotides that self-assemble the amplified target into nanoballs. Next, we use capillary-driven flow to passively pass these nanoballs through a microfluidic impedance cytometer, thus enabling a fully compact system with no moving parts. The movement of individual nanoballs is detected by a change in impedance providing a quantized readout. This approach is flexible for the detection of DNA/RNA of numerous targets (severe acute respiratory syndrome coronavirus 2, HIV, β-lactamase gene, etc.), and we anticipate that its integration into a standalone device would provide an inexpensive (<$5), sensitive (10 target copies), and rapid test (<1 hour).
Rewiring the pneumococcal capsule pathway for investigating glycosyltransferase specificity and genetic glycoengineering
Authors: Su Tong , Chua Wan-Zhen , Liu Yao , Fan Jingsong , Tan Si-Yin , Yang Dai-wen , Sham Lok-To
Published: September 2023

Virtually all living cells are covered with glycans. Their structures are primarily controlled by the specificities of glycosyltransferases (GTs). GTs typically adopt one of the three folds, namely, GT-A, GT-B, and GT-C. However, what defines their specificities remain poorly understood. Here, we developed a genetic glycoengineering platform by reprogramming the capsular polysaccharide pathways in
Streptococcus pneumoniae
to interrogate GT specificity and manipulate glycan structures. Our findings suggest that the central cleft of GT-B enzymes is important for determining acceptor specificity. The constraint of the glycoengineering platform was partially alleviated when the specificity of the precursor transporter was reduced, indicating that the transporter contributes to the overall fidelity of glycan synthesis. We also modified the pneumococcal capsule to produce several medically important mammalian glycans, as well as demonstrated the importance of regiochemistry in a glycosidic linkage on binding lung epithelial cells. Our work provided mechanistic insights into GT specificity and an approach for investigating glycan functions.
A protein panel in cerebrospinal fluid for diagnostic and predictive assessment of Alzheimer’s disease
Authors: Haque Rafi , Watson Caroline M. , Liu Jiaqi , Carter E. Kathleen , Duong Duc M. , Lah James J. , Wingo Aliza P. , Roberts Blaine R. , Johnson Erik C. B. , Saykin Andrew J. , Shaw Leslie M. , Seyfried Nicholas T. , Wingo Thomas S. , Levey Allan I.
Published: September 2023

Alzheimer’s disease (AD) is a neurodegenerative disease with heterogenous pathophysiological changes that develop years before the onset of clinical symptoms. These preclinical changes have generated considerable interest in identifying markers for the pathophysiological mechanisms linked to AD and AD-related disorders (ADRD). On the basis of our prior work integrating cerebrospinal fluid (CSF) and brain proteome networks, we developed a reliable and high-throughput mass spectrometry–selected reaction monitoring assay that targets 48 key proteins altered in CSF. To test the diagnostic utility of these proteins and compare them with existing AD biomarkers, CSF collected at baseline visits was assayed from 706 participants recruited from the Alzheimer’s Disease Neuroimaging Initiative. We found that the targeted CSF panel of 48 proteins (CSF 48 panel) performed at least as well as existing AD CSF biomarkers (Aβ
42
, tTau, and pTau
181
) for predicting clinical diagnosis, FDG PET, hippocampal volume, and measures of cognitive and dementia severity. In addition, for each of those outcomes, the CSF 48 panel plus the existing AD CSF biomarkers significantly improved diagnostic performance. Furthermore, the CSF 48 panel plus existing AD CSF biomarkers significantly improved predictions for changes in FDG PET, hippocampal volume, and measures of cognitive decline and dementia severity compared with either measure alone. A potential reason for these improvements is that the CSF 48 panel reflects a range of altered biology observed in AD/ADRD. In conclusion, we show that the CSF 48 panel complements existing AD CSF biomarkers to improve diagnosis and predict future cognitive decline and dementia severity.
Treatment pathways, switches, and inappropriate treatment during invasive pulmonary aspergillosis: real-world experiences from a global research network study
Authors: Henao-Martínez Andrés F. , Chastain Daniel B. , Thompson George R.
Published: September 2023

Despite advancements in diagnosing and treating invasive pulmonary aspergillosis (IPA), there is limited knowledge of real-world treatment pathways and medication switches. We queried the TrinetX global research network database and identified 5,410 patients diagnosed with IPA. The most common initial treatments were voriconazole (49%), fluconazole (11%), and posaconazole (7%). Most patients remained on voriconazole (80%) or isavuconazole (78%) throughout the treatment duration. Switches were more frequent for those initially treated with fluconazole, echinocandins, or posaconazole.
Single-cell mass distributions reveal simple rules for achieving steady-state growth
Authors: Roller Benjamin R. K. , Hellerschmied Cathrine , Wu Yanqi , Miettinen Teemu P. , Gomez Annika L. , Manalis Scott R. , Polz Martin F.
Published: September 2023

Optical density is a proxy of total biomass concentration and is commonly used for measuring the growth of bacterial cultures. However, there is a misconception that exponential optical density growth is equivalent to steady-state population growth. Many cells comprise a culture and individuals can differ from one another. Hallmarks of steady-state population growth are stable frequency distributions of cellular properties over time, something total biomass growth alone cannot quantify. Using single-cell mass sensors paired with optical density measurements, we explore when steady-state population growth prevails in typical batch cultures. We find the average cell mass of
Escherichia coli
and
Vibrio cyclitrophicus
growing in several media increases by 0.5–1 orders of magnitude within a few hours of inoculation, and that time-invariant mass distributions are only achieved for short periods when cultures are inoculated with low initial biomass concentrations from overnight cultures. These species achieve an effective steady-state after approximately 2.5–4 total biomass doublings in rich media, which can be decomposed to 1 doubling of cell number and 1.5–3 doublings of average cell mass. We also show that typical batch cultures in rich media depart steady-state early in their growth curves at low cell and biomass concentrations. Achieving steady-state population growth in batch culture is a delicate balancing act, so we provide general guidance for commonly used rich media. Quantifying single-cell mass outside of steady-state population growth is an important first step toward understanding how microbes grow in their natural context, where fluctuations pervade at the scale of individuals.

IMPORTANCE

Microbiologists have watched clear liquid turn cloudy for over 100 years. While the cloudiness of a culture is proportional to its total biomass, growth rates from optical density measurements are challenging to interpret when cells change size. Many bacteria adjust their size at different steady-state growth rates, but also when shifting between starvation and growth. Optical density cannot disentangle how mass is distributed among cells. Here, we use single-cell mass measurements to demonstrate that a population of cells in batch culture achieves a stable mass distribution for only a short period of time. Achieving steady-state growth in rich medium requires low initial biomass concentrations and enough time for individual cell mass accumulation and cell number increase via cell division to balance out. Steady-state growth is important for reliable cell mass distributions and experimental reproducibility. We discuss how mass variation outside of steady-state can impact physiology, ecology, and evolution experiments.
Complete genome sequences of cluster G1 and cluster K4
Mycobacterium smegmatis
phages omnicritical and Barkley26
Authors: Sali Ojas , Patel Dave M. , Ortega Michaelangelo C. , Han Sydnee , Esperanza Gonzales Hanford Gerille , Haneefzai Omar Sulaiman , Herrera Carlos , Kim Jireh , Knoles Brooke , Lopez Abigail , Richardson Justin Aaron , Roach David Andres , Vergonia-Fehlman Maxene , Vincent Jessica , Yim Sang Ho , Cutter Leo I. C. , Strong Christy , Tsourkas Philippos K. , Regner Kurt
Published: September 2023

We present the complete genome sequence of two Actinobacteriophages, OmniCritical and Barkley26, isolated in Clark County, NV. Over two semesters, The University of Nevada, Las Vegas (UNLV) students isolated and purified phages and manually annotated the genomes. The courses follow the HHMI Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Sciences (SEA-PHAGES) curricula.
A combined transcriptomic and physiological approach to understanding the adaptive mechanisms to cope with oxidative stress in
Fusarium graminearum
Authors: Park Jiyeun , Lee Hyun-Hee , Moon Heeji , Lee Nahyun , Kim Sieun , Kim Jung-Eun , Lee Yoonji , Min Kyunghun , Kim Hun , Choi Gyung Ja , Lee Yin-Won , Seo Young-Su , Son Hokyoung
Published: September 2023

In plant-pathogen interactions, oxidative bursts are crucial for plants to defend themselves against pathogen infections. Rapid production and accumulation of reactive oxygen species kill pathogens directly and cause local cell death, preventing pathogens from spreading to adjacent cells. Meanwhile, the pathogens have developed several mechanisms to tolerate oxidative stress and successfully colonize plant tissues. In this study, we investigated the mechanisms responsible for resistance to oxidative stress by analyzing the transcriptomes of six oxidative stress-sensitive strains of the plant pathogenic fungus
Fusarium graminearum
. Weighted gene co-expression network analysis identified several pathways related to oxidative stress responses, including the DNA repair system, autophagy, and ubiquitin-mediated proteolysis. We also identified hub genes with high intramodular connectivity in key modules and generated deletion or conditional suppression mutants. Phenotypic characterization of those mutants showed that the deletion of
FgHGG4
,
FgHGG10
, and
FgHGG13
caused sensitivity to oxidative stress, and further investigation on those genes revealed that transcriptional elongation and DNA damage responses play roles in oxidative stress response and pathogenicity. The suppression of
FgHGL7
also led to hypersensitivity to oxidative stress, and we demonstrated that
FgHGL7
plays a crucial role in heme biosynthesis and is essential for peroxidase activity. This study increases the understanding of the adaptive mechanisms to cope with oxidative stress in plant pathogenic fungi.

IMPORTANCE

Fungal pathogens have evolved various mechanisms to overcome host-derived stresses for successful infection. Oxidative stress is a representative defense system induced by the host plant, and fungi have complex response systems to cope with it.
Fusarium graminearum
is one of the devastating plant pathogenic fungi, and understanding its pathosystem is crucial for disease control. In this study, we investigated adaptive mechanisms for coping with oxidative stress at the transcriptome level using oxidative stress-sensitive strains. In addition, by introducing genetic modification technique such as CRISPR-Cas9 and the conditional gene expression system, we identified pathways/genes required for resistance to oxidative stress and also for virulence. Overall, this study advances the understanding of the oxidative stress response and related mechanisms in plant pathogenic fungi.
Lineage classification and antitubercular drug resistance surveillance of
Mycobacterium tuberculosis
by whole-genome sequencing in Southern India
Authors: Rao Mahadev , Wollenberg Kurt , Harris Michael , Kulavalli Shrivathsa , Thomas Levin , Chawla Kiran , Shenoy Vishnu Prasad , Varma Muralidhar , Saravu Kavitha , Hande H. Manjunatha , Shanthigrama Vasudeva Chidananda Sanju , Jeffrey Brendan , Gabrielian Andrei , Rosenthal Alex
Published: September 2023

Whole-genome sequencing has created a revolution in tuberculosis management by providing a comprehensive picture of the various genetic polymorphisms with unprecedented accuracy. Studies mapping genomic heterogeneity in clinical isolates of
Mycobacterium tuberculosis
using a whole-genome sequencing approach from high tuberculosis burden countries are underrepresented. We report whole-genome sequencing results of 242 clinical isolates of culture-confirmed
M. tuberculosis
isolates from tuberculosis patients referred to a tertiary care hospital in Southern India. Phylogenetic analysis revealed that the isolates in our study belonged to five different lineages, with Indo-Oceanic (lineage 1,
n
= 122) and East-African Indian (lineage 3,
n
= 80) being the most prevalent. We report several mutations in genes conferring resistance to first and second line antitubercular drugs including the genes
rpoB
,
katG
,
ahpC
,
inhA
,
fabG1
,
embB
,
pncA
,
rpsL
,
rrs
, and
gyrA
. The majority of these mutations were identified in relatively high proportions in lineage 1. Our study highlights the utility of whole-genome sequencing as a potential supplemental tool to the existing genotypic and phenotypic methods, in providing expedited comprehensive surveillance of mutations that may be associated with antitubercular drug resistance as well as lineage characterization of
M. tuberculosis
isolates. Further larger-scale whole-genome datasets with linked minimum inhibition concentration testing are imperative for resolving the discrepancies between whole-genome sequencing and phenotypic drug sensitivity testing results and quantifying the level of the resistance associated with the mutations for optimization of antitubercular drug and precise dose selection in clinics.

IMPORTANCE

Studies mapping genetic heterogeneity of clinical isolates of
M. tuberculosis
for determining their strain lineage and drug resistance by whole-genome sequencing are limited in high tuberculosis burden settings. We carried out whole-genome sequencing of 242
M. tuberculosis
isolates from drug-sensitive and drug-resistant tuberculosis patients, identified and collected as part of the TB Portals Program, to have a comprehensive insight into the genetic diversity of
M. tuberculosis
in Southern India. We report several genetic variations in
M. tuberculosis
that may confer resistance to antitubercular drugs. Further wide-scale efforts are required to fully characterize
M. tuberculosis
genetic diversity at a population level in high tuberculosis burden settings for providing precise tuberculosis treatment.
Supplemental Material: Svalbox Digital Model Database: A geoscientific window into the High Arctic
Authors: Betlem Peter , al. et
Published: September 2023

Table S1: Svalbox Digital Model Database digital outcrop models (DOMs) and identifiers. Table S2: Svalbox Digital Model Database metadata parameters, values, and descriptors. Table S3: Additional details for the framework schematic provided in Figure 3 and steps on how to recreate the Svalbox Digital Model Database elsewhere. 
Supplemental Material: Tracking multiple stages of serpentinization processes of the Yarlung Zangbo Suture Zone peridotites in southern Tibet: Implications for the tectonic evolution of the Neotethyan oceanic lithosphere
Authors: Zhao Qi , YAN Yi , et al.
Published: September 2023

Tables S1-S3.
Gastrointestinal mucormycosis following liver transplantation: lessons learnt
Authors: Zackariah Nafiya Muhammed , Rajakrishnan Haritha , Surendran Sudhindran , Paulose Roopa Rachel
Published: September 2023

Gastrointestinal mucormycosis (GIM) is an uncommonly encountered fungal infection following solid-organ transplantation. GIM is known to be associated with immunocompromised states, remains difficult to diagnose and often results in fatal outcomes. It is plausibly the delay in initiation of appropriate treatment strategies that leads to failure of response and patient demise. We report two cases of GIM following live donor liver transplantation, presenting with bleeding and perforation, respectively, highlighting the challenges in making a timely diagnosis of mucormycosis, particularly in immunocompromised patients.
Case of split notochord syndrome: a neonate with thoracic neuroenteric cyst, abdominal duodenal duplication cyst, malrotation and vertebral anomalies
Authors: Obeida Alaa , Mota Ana , Kayani Riaz , Agrawal Shruti , Aslam Adil
Published: September 2023

The authors describe a case of a male neonate with split notochord syndrome presenting with cervico-thoracic deformity, thoracic neuroenteric cyst, separate abdominal duodenal duplication cyst and concurrent intestinal malrotation. This combination of abnormalities is very rare. When these lesions are suspected, patients must be investigated carefully.

This case is presented not only to recount an infrequent combination of structural abnormalities but also to raise awareness of the signs that should point to clinical suspicion and prompt diagnosis.

Following surgical excision of the thoracic neuroenteric cyst, the patient has made a good recovery.
Oral cladribine treatment and idiosyncratic drug-induced liver injury in multiple sclerosis
Authors: Rakers Florian , Fritsch Almut , Herrmann Andreas , Tannapfel Andrea , Schwab Matthias
Published: September 2023

Background

Oral cladribine (OC) is approved for the treatment of highly active relapsing multiple sclerosis. Postmarketing safety assessments have reported rare, but occasionally severe cases of liver injury in temporal association with OC, with pathophysiologic mechanisms still unknown. In the only detailed case report on this topic, idiosyncratic drug-induced liver injury (iDILI) during OC treatment was well characterised for the first time, but occurred in the context of prior high-dose steroid exposure. Although high-dose steroids are known to induce iDILI in patients with multiple sclerosis with a delay of up to 12 weeks, OC was assumed to be the culprit agent for observed liver injury and the role of steroid exposure was not further investigated.

Case

Herein, we describe a case of a 35-year-old women treated with high-dose oral prednisolone during the first treatment cycle OC and subsequently developed iDILI. A causality assessment of the role of prednisolone and OC was performed using the updated Roussel Uclaf Causality Assessment Method which also included a negative re-exposure test for OC during the second OC treatment cycle 1 year later.

Conclusion

Our observations suggest that prednisolone or interactions between prednisolone and OC are more likely to foster development of iDILI rather than OC treatment itself.
Safety of influenza vaccination during pregnancy: a systematic review
Authors: Wolfe Dianna M , Fell Deshayne , Garritty Chantelle , Hamel Candyce , Butler Claire , Hersi Mona , Ahmadzai Nadera , Rice Danielle B , Esmaeilisaraji Leila , Michaud Alan , Soobiah Charlene , Ghassemi Marco , Khan Paul A , Sinilaite Angela , Skidmore Becky , Tricco Andrea C , Moher David , Hutton Brian
Published: September 2023

Objective

We conducted a systematic review to evaluate associations between influenza vaccination during pregnancy and adverse birth outcomes and maternal non-obstetric serious adverse events (SAEs), taking into consideration confounding and temporal biases.

Methods

Electronic databases (Ovid MEDLINE ALL, Embase Classic+Embase and the Cochrane Central Register of Controlled Trials) were searched to June 2021 for observational studies assessing associations between influenza vaccination during pregnancy and maternal non-obstetric SAEs and adverse birth outcomes, including preterm birth, spontaneous abortion, stillbirth, small-for-gestational-age birth and congenital anomalies. Studies of live attenuated vaccines, single-arm cohort studies and abstract-only publications were excluded. Records were screened using a liberal accelerated approach initially, followed by a dual independent approach for full-text screening, data extraction and risk of bias assessment. Pairwise meta-analyses were conducted, where two or more studies met methodological criteria for inclusion. The Grading of Recommendations, Assessment, Development and Evaluation approach was used to assess evidence certainty.

Results

Of 9443 records screened, 63 studies were included. Twenty-nine studies (24 cohort and 5 case–control) evaluated seasonal influenza vaccination (trivalent and/or quadrivalent) versus no vaccination and were the focus of our prioritised syntheses; 34 studies of pandemic vaccines (2009 A/H1N1 and others), combinations of pandemic and seasonal vaccines, and seasonal versus seasonal vaccines were also reviewed. Control for confounding and temporal biases was inconsistent across studies, limiting pooling of data. Meta-analyses for preterm birth, spontaneous abortion and small-for-gestational-age birth demonstrated no significant associations with seasonal influenza vaccination. Immortal time bias was observed in a sensitivity analysis of meta-analysing risk-based preterm birth data. In descriptive summaries for stillbirth, congenital anomalies and maternal non-obstetric SAEs, no significant association with increased risk was found in any studies. All evidence was of very low certainty.

Conclusions

Evidence of very low certainty suggests that seasonal influenza vaccination during pregnancy is not associated with adverse birth outcomes or maternal non-obstetric SAEs. Appropriate control of confounding and temporal biases in future studies would improve the evidence base.
Undernutrition in children aged 0–59 months by region and over time: secondary analysis of the Burkina Faso 2012–2018 National Nutrition Surveys
Authors: Boua Palwende Romuald , Rouamba Toussaint , Bambara Estelle , Kaboré Saidou , Compaore Ella W R , Ouedraogo Boureima , Tinto Halidou , Newell Marie-Louise , Ward Kate , Sorgho Hermann
Published: September 2023

The global burden of undernutrition remains high, responsible for significant under-five mortality in resource-limited settings. Numerous sustainable development goals (SDGs) are linked to nutrition, and nationally representative nutrition surveillance is a key activity to track progress towards SDGs and guide efficient programmes.

Objectives

The aim of this study is to look at spatial and temporal trends in undernutrition in children under 5 years age in Burkina Faso.

Setting

We used data from annual National Nutrition Surveys using Standardised Monitoring and Assessment of Relief and Transitions methodology (anthropometry, morbidity) over 7 years (2012–2018) in Burkina Faso.

Participants

Children of under 5 years from households selected through systemic sampling at countrywide level.

Main outcome measures

Prevalence of stunting (height-for-age z-score, <−2), underweight (weight-for-age z-score, <−2) and wasting (weight-for-height z-score, <−2) at regional and national. We used general linear mixed models, adjusted by age, survey year, sex, presence of fever and/or diarrhoea, and poverty index to quantify the risk of undernutrition over time and by region of residence.

Results

Between 2012 and 2018, decreases were observed overall in the prevalence of growth retardation (stunting) decreased from 33.0% (95% CI 32.3 to 33.8) in 2012 to 26.7% (95% CI 26.2 to 27.3) in 2018. Underweight reduced from 24.4% (95% CI 23.7 to 25.1) to 18.7% (95% CI 18.2 to 19.2) for the same period and wasting decreased from 10.8% (95% CI 10.3 to 11.3) in 2012 to 8.4% (95% CI 8.1 to 8.8) in 2018. However, there was substantial variation across the country, with increased risk of undernutrition in the regions of Sahel, East and Cascades primarily. High-risk regions were characterised by a lower poverty index and limited access to healthcare services.

Conclusions

Our findings could inform national policymakers in refining and optimising resource allocation based on the identification of high-risk areas.