bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlation of Escherichia coli inactivation with histotripsy bubble cloud size
Authors: Ambekar Pratik A. , Khokhlova Tatiana D. , Wang Yak-Nam , Rosnitskiy Pavel B. , Leotta Daniel , Thomas Gilles P. , Totten Stephanie , Piersonn Shelby , Bruce Matthew , Maxwell Adam D. , Chan Keith , Liles W. Conrad , Dellinger Evan P. , Adedipe Adeyinka , Monsky Wayne , Matula Thomas
Published: July 2024

Bacterial loads can be effectively reduced with cavitation-mediated focused ultrasound, or histotripsy. Our previous in vitro work with Escherichia coli (E. coli) established strong trends of bactericide with increasing peak negative pressure amplitude, pulse length, PRF, and treatment time. The current study correlates bactericide as a function of the histotripsy bubble cloud size produced for these treatment parameters at several frequencies. Histotripsy was applied to E. coli suspensions in 10-ml sample vials at 810 kHz, 1.2 MHz, or 3.25 MHz for 40 min. Separately, cavitation was recorded using a Photron Fastrax high-speed camera for acoustic parameters equivalent to those used in the E. coli studies. The images were used to quantify the maximum size of each bubble cloud, with the assumption that the cloud was axially symmetric around the propagation direction. A strong linear relationship exists between log kill versus cloud size (R2 = 0.96). Remarkably, across all variables studied, the log-reduction in viable bacteria exhibited a direct proportional relationship with the dimensions of the bubble cloud. This strong correlation between bacterial reduction and cavitation bubble cloud size could have significance for clinical applications where bacteria cannot easily be sampled. [Work supported by NIH R01AR080120 and R01EB023910.]
Understanding pickleball noise at the source: The vibroacoustics of the pickleball paddle and ball
Authors: Russell Daniel A.
Published: July 2024

Pickleball continues to be America's fastest-growing sport, growing by roughly 150% every year with 48.3 million US adults (19% of the adult population) having played at least one game in 2023. This immense popularity and growth is accompanied by a similar increase in the number and voracity of complaints from the residential communities surrounding pickleball courts. This paper aims to explain the source of the pickleball noise—a short duration impulse with a strong tonal component near 1250 Hz—due to the impact of the pickleball ball and paddle, with a specific focus on the vibrational modes of the paddle that contribute most strongly to the tonal nature of the sound. Experimental modal analysis was performed on several paddles (wood, aluminum, composite, and carbon fiber) as well as the first paddle to meet the new USA Pickleball Quiet Category requirements. Spectral analysis of the impact identifies the offending tonal component near 1250 Hz to be a strongly radiating “membrane-type” mode of the paddle surface. Paddles for which this mode shape has a significantly higher or lower in frequency and amplitude result in a much less annoying impact sound. The role of vibrational modes in the ball will also be considered.
Slow dynamics and the role of moisture
Authors: Yoritomo John
Published: July 2024

The elastic behavior of rocks and other composite materials cannot be entirely captured by the traditional theory of nonlinear elasticity, where the stress field is related to powers of the strain field. Rather, these materials display non-classical nonlinear elastic behavior, such as hysteresis, end-point memory, fast dynamics, and slow dynamics. Slow dynamics (SD) is characterized by a drop in material stiffness due to a minor mechanical conditioning, followed by a slow recovery back to the original macroscopic elastic state. SD has drawn particular attention because the recovery, often logarithmic in time, has been observed in a wide variety of materials, on lengths scales from the laboratory to the seismic, and on time scales from milliseconds to years. The universal character suggests a simple, fundamental mechanism for the SD recovery. This talk will present recent experiments that seek to test proposed SD mechanisms. In particular, the role of moisture will be investigated. The main experimental venue is the simplified structure introduced in previous work—a single bead confined between two slabs of a similar material. The main benefit of this structure over more commonly studied SD materials (sandstones and concrete) is the ability to control the environment around the contact points.
Forces on a singing wineglass rim
Authors: Orzolek Megan F. , Mertz Alexander M. , Jonson Michael L.
Published: July 2024

The characterization of friction is a multiscale problem involving a balance between asperity contacts and fluid film forces, most commonly modeled with a velocity-dependent coefficient of friction. Periodic stick–slip phenomena are often associated with the friction force that causes mechanical vibration. This type of vibration can cause noise to radiate via structural modes of a system. Notable examples include journal bearings, brake squeal, turkey calls, and wineglasses. Singing wineglasses have been used for centuries as musical instruments, so musical acousticians have studied the structural vibrations and acoustic output. However, the tri-axial force applied to the rim has not been measured. A test rig was designed to measure the vertical, tangential, and radial dynamic forces applied to the spinning glass rim and simultaneously capture the radiated noise. The sound radiated from the wineglass was observed to depend on the relative velocity at the rim and applied vertical load, so a stability region for a clear sound was determined. Additionally, the strongest radiating modes and harmonics in the pressure were found in the concurrently measured nonlinear force. This work may be extended to confirm the force measurement by existing friction models, a water medium, and more complicated systems.
Analysis, design, and installation of vibration isolation for lightweight helipads
Authors: Rodrigues Alfredo , Dias Ashwin , Saddik Freddy
Published: July 2024

This case study discusses the design and manufacturing steps for the installation of a vibration isolation solution for two lightweight helidecks installed on the rooftop of an existing medical center building. The design stage involved the analysis of the relevant information, involving several specialties, such as Acoustics (for sources of vibration and acoustic performance requirements), Heliport Design[AR1] (for the type of aircraft, MTOW, number of supports, static and dynamic loads), and Structural (for the types of connections to the existing building structure). A collaborative effort between CDM Stravitec and the helideck supplier led the design through a progressive and iterative process where a final design that responded to the strong acoustical requirements and the complex nature of a fully functional and integrated lightweight helideck. Along the design, compromises where made ensure that requirements are met for both acoustic and structural performance. The solution delivered was a prefabricated box, which could easily be installed on site, comprised the necessary components, such as springs and uplift restraints to deal with the challenging aspects of the isolation of lightweight helidecks. The paper also discusses the challenges and best practices encountered during the production and installation of the system.
Control parameters for coordinative structures in speech production
Authors: Masapollo Matthew , Nittrouer Susan
Published: July 2024

In skilled speech production, sets of articulators work cooperatively to achieve task-specific movement goals, despite rampant contextual variation. Efforts to understand these functional units, termed coordinative structures, have focused on identifying the essential control parameters responsible for allowing articulators to achieve these goals, with some research focusing on temporal parameters (relative timing of movements) and other research focusing on spatiotemporal parameters (phase angle of movement onset for one articulator, relative to another). Here, we compared findings across three recent studies where both types of control parameters were investigated, using electromagnetic articulography recordings. In each study, talkers produced VCV utterances, with alternative V (/ɑ/−/ɛ/) and C (/t/−/d/ or /p/−/ b/), across variation in rate (fast–slow) and stress (first syllable stressed–unstressed). Two measures were obtained: (i) the timing of tongue-tip or lower-lip raising onset for intervocalic C, relative to jaw opening–closing cycles, and (ii) the angle of tongue-tip or lower-lip raising onset, relative to the jaw phase plane. All three studies showed that the correlations of tongue-tip/lower-lip movement onset latencies and jaw opening-closing cycle durations were stronger and more reliable than the correlations of tongue-tip/lower-lip phase angles and jaw opening-closing cycle durations, demonstrating that timing is the critical control parameter.
PrEgg: A free and open source Praat script for electroglottography measurements
Authors: Chan May Pik Yu , Kuang Jianjing
Published: July 2024

Electroglottography is a popular method of phonation analysis due to its non-invasive nature. In order to ease the extraction of systematic EGG measures, we wrote PrEgg, an open source Praat script designed to extract Contact Quotient (CQ), Skew Quotient (SQ) and Peak Increase in Contact (PIC) values. The script offers two measures for CQ and SQ, calculated using the EGG threshold method developed by Rothenberg (1988) and the DEGG method from Henrich et al. (2004), and PIC is further calculated from the DEGG signal. To test the validity of the script, we ran the Praat script on EGG data on Yi provided in the “Production and Perception of Linguistic Voice Quality” project at UCLA. We compared our results on CQ measurements using both the threshold method and the DEGG method with the provided CQ and CQPM measurements extracted from EggWorks, a UCLA software. Overall results are comparable between PrEgg and EggWorks. PrEgg is accompanied by a manual and available at https://github.com/maypychan/praat-egg.
Real-time magnetic resonance imaging of velopharyngeal port posture during long pauses in naturalistic speech
Authors: Diebel Joshua O. , Gick Bryan , Islam Jahurul , Weinstein Jade
Published: July 2024

Velum’s behavior as a postural substrate in naturalistic speech is not well understood and is largely based on studies of inter-utterance velopharyngeal port posture (VPP). While existing literature [e.g., Gick et al., 2004 Phonetica, 61(4); Ramanarayanan, 2013 JASA, 134(1)] describes posture variations based on rest positions, ready positions, and inter-speech pauses, a less explored aspect is the behavior of the velum during extended pauses in naturalistic speech. Addressing this gap, the present study analyzes velum posture during naturalistic speech to characterize VPP during prolonged pauses. This study draws from a corpus of real-time magnetic resonance imaging (rtMRI) videos of L1 English speakers including those engaging in unstructured speech tasks. Results based on sequences corresponding to long pauses in naturalistic speech will be reported, outlining VPP characteristics, and quantifying findings in terms of time spent in and shifts between velum positions. Implications for motor control differences in naturalistic and elicited speech data will be discussed.
Broad and fine acoustic categories in bod, bond, bald, and bard: A step toward acoustic phonology
Authors: Kelley Matthew C.
Published: July 2024

Acoustics is central to the study of speech communication, but it is conspicuously under-represented in abstract representations of speech. Many flavors of phonological analysis tend toward articulatory descriptions, and transcriptions focus on strings of articulatory actions. All this is despite acoustics being easier to measure than articulation with current technology. The present study explores basic concepts for an acoustic phonology, with two types of postulated categories: broad and fine. Resonant, turbulent, transient, and occludent types of sounds comprise the broad categories, as general methods of filtering the speech source. Fine categories are conceptualized as specific types of acoustic actions within a broad category. These acoustic actions are goal-oriented, as for achieving a particular acoustic effect like the presence of antiformants or a lowered F2 or F3. However, these actions are not explicitly restricted to manipulating traditional phonetic features like formants. By default, fine categories are assumed to be produced in parallel when possible, yielding overlap effects like anticipatory nasalization, lateralization, and rhotacization. These concepts are explored in a microanalysis of bod, bond, bald, and bard from the speaker in the Massive Auditory Lexical Decision data set, with an eye to seeding the ground for a future acoustic phonology.
Custom lens design for ultrasonic inspection of immersed anisotropic parts
Authors: Katch Lauren , Arguelles Andrea P.
Published: July 2024

Inspection of anisotropic parts using immersion ultrasonic waves poses resolution challenges caused by directionally dependent wave properties. Currently, focused lenses with spherical or cylindrical geometries are the standard method for creating convergent, small cross-section, and high amplitude beams within solids. These lenses form a conical beam that uniformly refracts at the fluid-solid interface of the immersed part when the solid is isotropic, producing the desired focusing behavior. However, for anisotropic solids, refraction becomes directionally dependent, which distorts the beam and causes non-uniform focal profiles and, in some cases, multiple foci. In this work, the forward wave propagation for an immersed anisotropic solid is modeled and exploited to develop custom lens geometries. These custom lenses utilize inverted slowness profiles to produce conical beams within the anisotropic solid. By incorporating these lenses, the focused beam behavior is improved and becomes more circular, higher in amplitude, and smaller in the cross-sectional area. These lenses have the potential to improve inspection resolution in anisotropic solids, an effort beneficial to the additive, aerospace, and electronics industries.
Effects of increasing orbital number on the field transformation in focused vortex beams
Authors: Gokani Chirag A. , Haberman Michael R. , Hamilton Mark F.
Published: July 2024

Acoustic vortex beams possess helical wavefronts characterized by an orbital number n. In the presence of focusing, the toroidal vortex ring for n = 1 moves out of the focal plane z = d and toward the source with increasing n, accompanied by a departure from its toroidal shape. In this talk, ray theory is developed to explain this field transformation. An expression is derived for the radius and cross-sectional area of the annular channel formed by the family of rays emanating from a thin circular ring centered at the origin in the source plane z = 0. This expression leads to explicit results for the field amplitude and caustic coordinates due to a focused vortex source with an arbitrary axisymmetric amplitude distribution. Comparison with field calculations in which diffraction is included demonstrate that the caustics describe the redistribution of the global maximum and its shift toward the source plane with increasing n. For moderate focusing gains (of order 10 or 20), a toroidal vortex ring for n = 1 transforms with increasing n into a spheroidal surface in the prefocal region 0 < z < d having volume nλd 2/6, where λ is the wavelength, inside of which exists a shadow zone. [C.A.G. was supported by the ARL:UT McKinney Fellowship in Acoustics.]
Derivations of transfer functions for estimating ship underwater radiated noise from onboard vibrations
Authors: Cintosun Esen
Published: July 2024

The adverse impacts of underwater radiated noise (URN) from marine vessels on marine life are increasingly recognized. URN estimation and subsequent monitoring could be used to track URN and take measures to reduce it in sensitive environments (e.g., a marine life protected area). Two common analytical radiated noise power approximations and two empirical methods are assessed for URN estimation. The assessments were carried out by testing the methods on data from acoustic range measurements of an ORCA-class training vessel of the Royal Canadian Navy, named Patrol Craft Training (PCT) Moose and a DAMEN Combi Freighter 3850, named Heinz G. The analytical approximations are called equivalent radiated power and power from volume velocity; both are used to estimate URN directly from the onboard ship vibration measurements. The empirical methods are based on the correlations of onboard vibrations with measured URN, from which the derived transfer functions. The analytical and empirical transfer functions are compared. A statistical energy analysis model of PCT Moose is also used to estimate onboard vibrations from the ship’s engine, generator, and propeller specifications for URN estimation at the design stage.
Great Lakes fisheries vessels and uncrewed surface vessels: A publicly available dataset
Authors: Senczyszyn Steven , Barnard Andrew , Kocher Erik , Evans Thomas M. , Rudstam Lars G. , Sethi Suresh A. , Yule Daniel L. , Warner David M. , Farha Steven A. , Dufour Mark R. , O'Brien Timothy P. , Dieter Patricia M. , Roberts James J. , Watkins James M. , Esselman Peter
Published: July 2024

For decades, fish abundance surveys have been performed by large, crewed fisheries vessels using echosounders or trawling. However, the estimates obtained by these traditional methods may be biased due to the propagated noise generated by these vessels. A three-year collaborative effort has been conducted to measure the radiated acoustic signature of 17 fisheries vessels operating across all five of the Great Lakes under several operating conditions. This was done using a mobile ship noise measurement system developed specifically for this purpose. Additionally, with the recent advent of uncrewed surface vessels (USVs, “Saildrone”), an alternative “quiet” method of performing these abundance surveys is now possible. A detailed acoustic characterization was conducted for a USV to provide a comparison between traditional “loud” fisheries vessels and these “quiet” surface vessels. This talk will detail the acoustic signatures of all 18 vessels, compare the “loud” and “quiet” vessels, and provide a detailed description of the vessel measurement profiles which are now available as a public dataset. This dataset includes the time domain acoustic measurements, sound speed profiles, and GPS tracks of the measured vessels.
Identification of intracellular bacteria from multiple single-cell RNA-seq platforms using CSI-Microbes
Authors: Robinson Welles , Stone Joshua K. , Schischlik Fiorella , Gasmi Billel , Kelly Michael C. , Seibert Charlie , Dadkhah Kimia , Gertz E. Michael , Lee Joo Sang , Zhu Kaiyuan , Ma Lichun , Wang Xin Wei , Sahinalp S. Cenk , Patro Rob , Leiserson Mark D. M. , Harris Curtis C. , Schäffer Alejandro A. , Ruppin Eytan
Published: July 2024

The study of the tumor microbiome has been garnering increased attention. We developed a computational pipeline (CSI-Microbes) for identifying microbial reads from single-cell RNA sequencing (scRNA-seq) data and for analyzing differential abundance of taxa. Using a series of controlled experiments and analyses, we performed the first systematic evaluation of the efficacy of recovering microbial unique molecular identifiers by multiple scRNA-seq technologies, which identified the newer 10x chemistries (3′ v3 and 5′) as the best suited approach. We analyzed patient esophageal and colorectal carcinomas and found that reads from distinct genera tend to co-occur in the same host cells, testifying to possible intracellular polymicrobial interactions. Microbial reads are disproportionately abundant within myeloid cells that up-regulate proinflammatory cytokines like
IL1
Β and
CXCL8
, while infected tumor cells up-regulate antigen processing and presentation pathways. These results show that myeloid cells with bacteria engulfed are a major source of bacterial RNA within the tumor microenvironment (TME) and may inflame the TME and influence immunotherapy response.
Carbon-phosphorus cycle models overestimate CO
2
enrichment response in a mature
Eucalyptus
forest
Authors: Jiang Mingkai , Medlyn Belinda E. , Wårlind David , Knauer Jürgen , Fleischer Katrin , Goll Daniel S. , Olin Stefan , Yang Xiaojuan , Yu Lin , Zaehle Sönke , Zhang Haicheng , Lv He , Crous Kristine Y. , Carrillo Yolima , Macdonald Catriona , Anderson Ian , Boer Matthias M. , Farrell Mark , Gherlenda Andrew , Castañeda-Gómez Laura , Hasegawa Shun , Jarosch Klaus , Milham Paul , Ochoa-Hueso Raúl , Pathare Varsha , Pihlblad Johanna , Nevado Juan Piñeiro , Powell Jeff , Power Sally A. , Reich Peter , Riegler Markus , Ellsworth David S. , Smith Benjamin
Published: July 2024

The importance of phosphorus (P) in regulating ecosystem responses to climate change has fostered P-cycle implementation in land surface models, but their CO
2
effects predictions have not been evaluated against measurements. Here, we perform a data-driven model evaluation where simulations of eight widely used P-enabled models were confronted with observations from a long-term free-air CO
2
enrichment experiment in a mature, P-limited
Eucalyptus
forest. We show that most models predicted the correct sign and magnitude of the CO
2
effect on ecosystem carbon (C) sequestration, but they generally overestimated the effects on plant C uptake and growth. We identify leaf-to-canopy scaling of photosynthesis, plant tissue stoichiometry, plant belowground C allocation, and the subsequent consequences for plant-microbial interaction as key areas in which models of ecosystem C-P interaction can be improved. Together, this data-model intercomparison reveals data-driven insights into the performance and functionality of P-enabled models and adds to the existing evidence that the global CO
2
-driven carbon sink is overestimated by models.
ZBTB21 suppresses CRE-mediated transcription to impair synaptic function in Down syndrome
Authors: Qiao Muzhen , Huang Qianwen , Wang Xin , Han Jiahuai
Published: July 2024

Down syndrome (DS) is the most common chromosomal disorder and a major cause of intellectual disability. The genetic etiology of DS is the extra copy of chromosome 21 (HSA21)–encoded genes; however, the contribution of specific HSA21 genes to DS pathogenesis remains largely unknown. Here, we identified ZBTB21, an HSA21-encoded zinc-finger protein, as a transcriptional repressor in the regulation of synaptic function. We found that normalization of the
Zbtb21
gene copy number in DS mice corrected deficits in cognitive performance, synaptic function, and gene expression. Moreover, we demonstrated that ZBTB21 binds to canonical cAMP-response element (CRE) DNA and that its binding to CRE could be competitive with CRE-binding factors such as CREB. ZBTB21 represses CRE-dependent gene expression and results in the negative regulation of synaptic plasticity, learning and memory. Together, our results identify ZBTB21 as a CRE-binding protein and repressor in cAMP-dependent gene regulation, contributing to cognitive defects in DS.
nucMACC: An MNase-seq pipeline to identify structurally altered nucleosomes in the genome
Authors: Wernig-Zorc Sara , Kugler Fabian , Schmutterer Leo , Räß Patrick , Hausmann Clemens , Holzinger Simon , Längst Gernot , Schwartz Uwe
Published: July 2024

Micrococcal nuclease sequencing is the state-of-the-art method for determining chromatin structure and nucleosome positioning. Data analysis is complex due to the AT-dependent sequence bias of the endonuclease and the requirement for high sequencing depth. Here, we present the nucleosome-based MNase accessibility (nucMACC) pipeline unveiling the regulatory chromatin landscape by measuring nucleosome accessibility and stability. The nucMACC pipeline represents a systematic and genome-wide approach for detecting unstable (“fragile”) nucleosomes. We have characterized the regulatory nucleosome landscape in
Drosophila melanogaster
,
Saccharomyces cerevisiae
, and mammals. Two functionally distinct sets of promoters were characterized, one associated with an unstable nucleosome and the other being nucleosome depleted. We show that unstable nucleosomes present intermediate states of nucleosome remodeling, preparing inducible genes for transcriptional activation in response to stimuli or stress. The presence of unstable nucleosomes correlates with RNA polymerase II proximal pausing. The nucMACC pipeline offers unparalleled precision and depth in nucleosome research and is a valuable tool for future nucleosome studies.
Integrating hydrogels manipulate ECM deposition after spinal cord injury for specific neural reconnections via neuronal relays
Authors: Tan Zan , Xiao Longyou , Ma Junwu , Shi Kaixi , Liu Jialin , Feng Feng , Xie Pengfei , Dai Yu , Yuan Qiuju , Wu Wutian , Rong Limin , He Liumin
Published: July 2024

A bioinspired hydrogel composed of hyaluronic acid-
graft
-dopamine (HADA) and a designer peptide HGF-(RADA)
4
-DGDRGDS (HRR) was presented to enhance tissue integration following spinal cord injury (SCI). The HADA/HRR hydrogel manipulated the infiltration of PDGFRβ
+
cells in a parallel pattern, transforming dense scars into an aligned fibrous substrate that guided axonal regrowth. Further incorporation of NT3 and curcumin promoted axonal regrowth and survival of interneurons at lesion borders, which served as relays for establishing heterogeneous axon connections in a target-specific manner. Notable improvements in motor, sensory, and bladder functions resulted in rats with complete spinal cord transection. The HADA/HRR + NT3/Cur hydrogel promoted V2a neuron accumulation in ventral spinal cord, facilitating the recovery of locomotor function. Meanwhile, the establishment of heterogeneous neural connections across the hemisected lesion of canines was documented in a target-specific manner via neuronal relays, significantly improving motor functions. Therefore, biomaterials can inspire beneficial biological activities for SCI repair.
PI3Kγ inhibition circumvents inflammation and vascular leak in SARS-CoV-2 and other infections
Authors: Shepard Ryan M. , Ghebremedhin Anghesom , Pratumchai Isaraphorn , Robinson Sally R. , Betts Courtney , Hu Jingjing , Sasik Roman , Fisch Kathleen M. , Zak Jaroslav , Chen Hui , Paradise Marc , Rivera Jason , Amjad Mohammad , Uchiyama Satoshi , Seo Hideya , Campos Alejandro D. , Dayao Denise Ann , Tzipori Saul , Piedra-Mora Cesar , Das Soumita , Hasteh Farnaz , Russo Hana , Sun Xin , Xu Le , E. Alexander Laura Crotty , Duran Jason M. , Odish Mazen , Pretorius Victor , Kirchberger Nell C. , Chin Shao-ming , Von Schalscha Tami , Cheresh David , Morrey John D. , Alargova Rossitza , O’Connell Brenda , Martinot Theodore A. , Patel Sandip P. , Nizet Victor , Martinot Amanda J. , Coussens Lisa M. , Teijaro John R. , Varner Judith A.
Published: July 2024

Virulent infectious agents such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and methicillin-resistant
Staphylococcus aureus
(MRSA) induce tissue damage that recruits neutrophils, monocyte, and macrophages, leading to T cell exhaustion, fibrosis, vascular leak, epithelial cell depletion, and fatal organ damage. Neutrophils, monocytes, and macrophages recruited to pathogen-infected lungs, including SARS-CoV-2–infected lungs, express phosphatidylinositol 3-kinase gamma (PI3Kγ), a signaling protein that coordinates both granulocyte and monocyte trafficking to diseased tissues and immune-suppressive, profibrotic transcription in myeloid cells. PI3Kγ deletion and inhibition with the clinical PI3Kγ inhibitor eganelisib promoted survival in models of infectious diseases, including SARS-CoV-2 and MRSA, by suppressing inflammation, vascular leak, organ damage, and cytokine storm. These results demonstrate essential roles for PI3Kγ in inflammatory lung disease and support the potential use of PI3Kγ inhibitors to suppress inflammation in severe infectious diseases.
The Genome Explorer genome browser
Authors: Herson James , Krummenacker Markus , Spaulding Aaron , O'Maille Paul , Karp Peter D.
Published: July 2024

Are two adjacent genes in the same operon? What are the order and spacing between several transcription factor binding sites? Genome browsers are software data visualization and exploration tools that enable biologists to answer questions such as these. In this paper, we report on a major update to our browser, Genome Explorer, that provides nearly instantaneous scaling and traversing of a genome, enabling users to quickly and easily zoom into an area of interest. The user can rapidly move between scales that depict the entire genome, individual genes, and the sequence; Genome Explorer presents the most relevant detail and context for each scale. By downloading the data for the entire genome to the user’s web browser and dynamically generating visualizations locally, we enable ﬁne control of zoom and pan functions and real-time redrawing of the visualization, resulting in smoother and more intuitive exploration of a genome than is possible with other browsers. Further, genome features are presented together, in-line, using familiar graphical depictions. In contrast, many other browsers depict genome features using data tracks, which have low information density and can visually obscure the relative positions of features. Genome Explorer diagrams have a high information density that provides larger amounts of genome context and sequence information to be presented in a given-sized monitor than for tracks-based browsers. Genome Explorer provides optional data tracks for the analysis of large-scale data sets and a unique comparative mode that aligns genomes at orthologous genes with synchronized zooming.

IMPORTANCE

Genome browsers provide graphical depictions of genome information to speed the uptake of complex genome data by scientists. They provide search operations to help scientists find information and zoom operations to enable scientists to view genome features at different resolutions. We introduce the Genome Explorer browser, which provides extremely fast zooming and panning of genome visualizations and displays with high information density.
Jejunal ischaemia following inferior mesenteric artery angioembolisation for type 2 endoleak
Authors: Lacey Hester , Gill Roger , Joshi Dhiraj , Caruana Mario
Published: July 2024

We present a rare case of short-segment jejunal infarction following inferior mesenteric artery embolisation for type 2 endoleak in a patient who previously underwent endovascular repair of abdominal aortic aneurysm. Potential causes for the event might include thromboembolism or traumatic thrombosis of a jejunal branch of the superior mesenteric artery (SMA) caused by a buddy guide wire used to maintain the position of the long vascular sheath in the SMA hiatus. The condition was recognised on CT and treated with resection of the infarcted segment of the small bowel followed by primary anastomosis.
Changes in sick notes associated with COVID-19 from 2020 to 2022: a cohort study in 24 million primary care patients in OpenSAFELY-TPP
Authors: Schaffer Andrea L , Park Robin Y , Tazare John , Bhaskaran Krishnan , MacKenna Brian , Denaxas Spiros , Dillingham Iain , Bacon Sebastian C J , Mehrkar Amir , Bates Christopher , Goldacre Ben , Greaves Felix , Macleod John ,   The OpenSAFELY Collaborative,   National Core Studies Collaborative, Tomlinson Laurie A , Walker Alex
Published: July 2024

Objectives

Long-term sickness absence from employment has negative consequences for the economy and can lead to widened health inequalities. Sick notes (also called ‘fit notes’) are issued by general practitioners when a person cannot work for health reasons for more than 7 days. We quantified the sick note rate in people with evidence of COVID-19 in 2020, 2021 and 2022, as an indication of the burden for people recovering from COVID-19.

Design

Cohort study.

Setting

With National Health Service (NHS) England approval, we used routine clinical data (primary care, hospital and COVID-19 testing records) within the OpenSAFELY-TPP database.

Participants

People 18–64 years with a recorded positive test or diagnosis of COVID-19 in 2020 (n=365 421), 2021 (n=1 206 555) or 2022 (n=1 321 313); general population matched in age, sex and region in 2019 (n=3 140 326), 2020 (n=3 439 534), 2021 (n=4 571 469) and 2022 (n=4 818 870); people hospitalised with pneumonia in 2019 (n=29 673).

Primary outcome measure

Receipt of a sick note in primary care.

Results

Among people with a positive SARS-CoV-2 test or COVID-19 diagnosis, the sick note rate was 4.88 per 100 person-months (95% CI 4.83 to 4.93) in 2020, 2.66 (95% CI 2.64 to 2.67) in 2021 and 1.73 (95% CI 1.72 to 1.73) in 2022. Compared with the age, sex and region-matched general population, the adjusted HR for receipt of a sick note over the entire follow-up period (up to 10 months) was 4.07 (95% CI 4.02 to 4.12) in 2020 decreasing to 1.57 (95% CI 1.56 to 1.58) in 2022. The HR was highest in the first 30 days postdiagnosis in all years. Among people hospitalised with COVID-19, after adjustment, the sick note rate was lower than in people hospitalised with pneumonia.

Conclusions

Given the under-recording of postacute COVID-19-related symptoms, these findings contribute a valuable perspective on the long-term effects of COVID-19. Despite likely underestimation of the sick note rate, sick notes were issued more frequently to people with COVID-19 compared with those without, even in an era when most people are vaccinated. Most sick notes occurred in the first 30 days postdiagnosis, but the increased risk several months postdiagnosis may provide further evidence of the long-term impact.
Menstrual Practice Needs Scale short form (MPNS-SF) and rapid (MPNS-R):
development in Khulna, Bangladesh, and validation in cross-sectional surveys
from Bangladesh and Uganda
Authors: Hennegan Julie , Hasan Md Tanvir , Jalil Tasfiyah , Hunter Erin C , Head Alexandra , Jabbar Abdul , Mohosin Arifa Bente , Zoha Nigar Sultana , Alam Muhammad Khairul , Dunstan Laura , Akter Sabina , Zaman Afreen , Kaiser Adrita , Smith Calum , Bagala Lillian , Azzopardi Peter S
Published: July 2024

Objectives

Develop and validate short and rapid forms of the 36-item Menstrual
Practice Needs Scale (MPNS-36).

Design

Item reduction prioritised content validity and was informed by
cognitive interviews with schoolgirls in Bangladesh, performance of
scale items in past research and stakeholder feedback. The original
MPNS-36 was revalidated, and short and rapid forms tested in a
cross-sectional survey. This was followed by further tests of
dimensionality, internal consistency and validity in multiple
cross-sectional surveys.

Setting and participants

Short form (MPNS-SF) and rapid form (MPNS-R) measures were developed
in a survey of 313 menstruating girls (mean age=13.51) in Khulna,
Bangladesh. They were further tested in the baseline survey of the
Adolescent Menstrual Experiences and Health Cohort, in Khulna,
Bangladesh (891 menstruating girls, mean age=12.40); and the dataset
from the MPNS-36 development in Soroti, Uganda (538 menstruating girls,
mean age=14.49).

Results

The 18-item short form reflects the six original subscales, with the
four core subscales demonstrating good fit in all three samples (Khulna
pilot: root mean square error of approximation (RMSEA)=0.064, 90% CI
0.043 to 0.084, Comparative Fit Index (CFI)=0.94, Tucker-Lewis Index
(TLI)=0.92. Cohort baseline: RMSEA=0.050, 90% CI 0.039 to 0.062,
CFI=0.96, TLI=0.95. Uganda: RMSEA=0.039, 90% CI 0.028 to 0.050,
CFI=0.95, TLI=0.94). The 9-item rapid form captures diverse needs. A
two-factor structure was the most appropriate but fell short of adequate
fit (Khulna pilot: RMSEA=0.092, 90% CI 0.000 to 0.158, CFI=0.93,
TLI=0.89). Hypothesised associations between the MPNS scores and other
constructs were comparable between the MPNS-36 and MPNS-SF in all
populations, and replicated, with attenuation, in the MPNS-R. Internal
consistency remained acceptable.

Conclusions

The MPNS-SF offers a reliable and valid measure of adolescent girls’
menstrual hygiene experience while reducing participant burden, to
support implementation and improve measurement in menstrual health
research. The MPNS-R provides a brief measure with poorer structural
validity, suited to short surveys and including menstrual health within
broader research topics.
Healing the Past by Nurturing the Future: trauma-aware, healing-informed care to improve support for Aboriginal and Torres Strait Islander families – implementation and evaluation study protocol
Authors: Jones Kimberley Ann , Henderson Helen , Bright Tess , Segal Leonie , Mauerhofer Olivia , Lake Katherine Jane , Julian Rebekah , Duncan Jhodie , Raymond Anita , Jones Amanda , Cameron Danielle , Fergie Doseena , Andrews Shawana , Stewart Skye , Atkinson Caroline , Elliot Alison , Crawford Belinda , Mohammed Janine , Bundle Gina , Hirvonen Tanja , Gnanamanickam Emmanuel , Davis Elise , Gee Graham , Herrman Helen , McLachlan Helen , Fisher Jane , Lovett Raymond , Campbell Sandy , Forster Della Anne , Clark Yvonne , Atkinson Judith , Marriott Rhonda , Chamberlain Catherine
Published: July 2024

Introduction

Complex trauma can have serious impacts on the health and well-being of Aboriginal and Torres Strait Islander families. The perinatal period represents a ‘critical window’ for recovery and transforming cycles of trauma into cycles of healing. The Healing the Past by Nurturing the Future (HPNF) project aims to implement and evaluate a programme of strategies to improve support for Aboriginal and Torres Strait islander families experiencing complex trauma.

Method

The HPNF programme was codesigned over 4 years to improve awareness, support, recognition and assessment of trauma. Components include (1) a trauma-aware, healing-informed training and resource package for service providers; (2) trauma-awareness resources for parents; (3) organisational readiness assessment; (4) a database for parents and service providers to identify accessible and appropriate additional support and (5) piloting safe recognition and assessment processes. The programme will be implemented in a large rural health service in Victoria, Australia, over 12 months. Evaluation using a mixed-methods approach will assess feasibility, acceptability, cost, effectiveness and sustainability. This will include service user and provider interviews; service usage and cost auditing; and an administrative linked data study of parent and infant outcomes.

Analysis

Qualitative data will be analysed using reflexive thematic analysis. Quantitative and service usage outcomes will be described as counts and proportions. Evaluation of health outcomes will use interrupted time series analyses. Triangulation of data will be conducted and mapped to the Consolidated Framework for Implementation Research and Reach, Effectiveness, Adoption, Implementation and Maintenance frameworks to understand factors influencing feasibility, acceptability, effectiveness, cost and sustainability.

Ethics and dissemination

Approval granted from St Vincent’s Melbourne Ethics Committee (approval no. 239/22). Data will be disseminated according to the strategy outlined in the codesign study protocol, in-line with the National Health and Medical Research Council Aboriginal and Torres Strait Islander Research Excellence criteria.
Impact of defocus incorporated multiple segments (DIMS) spectacle lenses for myopia control on quality of life of the children: a qualitative study
Authors: Fatimah Mobashir , Agarkar Sumita , Narayanan Anuradha
Published: July 2024

Objective

To assess the impact of DIMS (defocus incorporated multiple segments) spectacle lenses on the quality of life of children using it.

Methods

Separate in-depth interviews were conducted with children using DIMS as a myopia control strategy for at least 1 month and their parents based on prepared guides. The recorded audio of the interviews was transcribed, and the significant data points were coded using a hybrid approach, that is, both the inductive and deductive coding methods were used to identify themes. The generated codes were further grouped, categorised and finally fitted as per relevance into the subdomains of the four domains of the WHO Quality of Life—Brief framework, namely the domains of social relationships, physical, psychological and environmental health.

Results

A total of 29 interviews were conducted, 15 with children (mean age: 12.47±2.13 years) and 14 with parents. Thematic analysis was done and a total of 63 codes were generated with 2, 16, 17 and 28 codes aligning to the domains of social relationships, environmental, psychological and physical health, respectively. Most parents did not notice any change in their child’s visual behaviour, yet children did experience symptoms such as peripheral blurred vision, eyestrain, headache, haloes and more during the adaptation period. High-cost, scratch-prone nature and difficulty in procurement were a few concerns raised by parents.

Conclusions

Participants were satisfied with most of the facets of social relationships, physical and psychological health domains. However, a few facets such as quality, accessibility and finance of the environmental health domain need improvement.
Deodorant pad for ulcerated breast cancer: safety and efficacy
Authors: Ishiba Toshiyuki , Ishida Hirohiko , Inoue Michiaki , Tazoe Yuki , Sakai Mami , Fujita Yuki , Kida Hiroko , Kosaka Taijiro , Ishihara Sakiko , Nara Miyako , Adachi Mio , Saita Chiaki , Goto Risa , Iwamoto Naoko , Nakatsugawa Noriko , Toi Masakazu , Aruga Tomoyuki
Published: July 2024

Objectives

APOLLO study, ‘efficacy and safety of the deodorAnt Pad against Odour and uLceration for LOcally advanced breast cancer’, aimed to assess the safety and efficacy of wearing a deodorant pad in patients with locally advanced breast cancer (LABC) with an ulceration.

Methods

Komagome Pads were previously developed by Juntendo University and Kao Corporation. In test A, a conventional pad consisting of gauze, a commercially available diaper, pad, etc and the Komagome Pad were compared over 3 days to assess their efficacy and possible improvements for short-term use. In test B, the Komagome Pad was used continuously for 1 month to evaluate its safety during long-term use.

Results

This study included 14 patients in test A and nine in test B. In odour evaluation using sensory testing in test A, nine patients reported more significant efficacy in odour suppression with the Komagome Pad. The odour intensity of the Komagome Pad was lower on the gas chromatography-mass spectrometry. The group with a high level of exudation reported significantly higher satisfaction with the Komagome Pad. In test B, no adverse events were observed.

Conclusions

A new deodorant pad for LABC demonstrated high safety and deodorant efficacy.
TEMPORAL EVOLUTION OF PERMEABILITY FOR POROUS ROCK DURING MINERAL DISSOLUTION AND PRECIPITATION PROCESS BASED ON FRACTAL THEORY
Authors: CHEN AIMIN , MIAO TONGJUN , SHEN XIAOMENG , YU BOMING
Published: July 2024

Mineral dissolution and precipitation reactions occur in a variety of porous rocks due to the deviations from a geochemical equilibrium between solid matrix and flow fluid, resulting in the alteration of the petrophysical properties of rocks. A physically-based theoretical model is proposed based on fractal theory for quantitatively assessing the temporal evolution of permeability for porous rocks undergoing mineral dissolution and precipitation reactions. The proposed model is associated with pore structure parameters, such as initial porosity [Formula: see text], the tortuosity fractal dimensions [Formula: see text], the initial fractal dimension [Formula: see text], and the overall dissolution rate [Formula: see text] considering the precipitation reactions in porous rocks. The proposed model provides a better prediction of the time dependence of permeability compared with the available experimental data. The essential effects of the overall dissolution rate and pore structural parameters of porous rocks on the dimensionless time-dependent permeabilities are investigated in detail. It is found that the overall dissolution rate has obvious effects on the dimensionless time dependence of permeabilities. The present model may provide useful insights into the understanding of permeability change during mineral dissolution and precipitation reactions in porous rocks.
Exploration of Nanomedicine-Based Dry Powder Inhalation Formulation Co-Loaded with Erlotinib and Curcumin for Treatment of Non-Small Cell Lung Cancer
Authors: Rahman Mohammad Akhlaquer
Published: July 2024

Erlotinib is used as first-line chemotherapy for the treatment of non-small cell lung cancer (NSCLC), which accounts for approximately 85% of lung cancers. Curcumin has potential antitumor effects in different types of cancer including NSCLS with additional chemopreventive and radioprotective effects. The aim of the study was to develop erlotinib and curcumin co-loaded dry powder inhalation (EC-DPI) formulation using nanoprecipitation technique with a goal of achieving a stronger cytotoxic effect against A549 cancer cells. The optimized DPI formulation resulted in suitable particle size (313.28 ± 26.19 nm), polydispersity index (0.156 ± 0.016) and zeta potential (29.4 ± 1.22 mV). Carr’s index (6.62 ± 1.43) and Hausner ratio (1.058 ± 0.03) demonstrated excellent flowability of the powder. The fine particle fraction (64.7 ± 7.8%) and mass median aerodynamic diameter (2.98 ± 0.04 [Formula: see text]m) of the optimized formulation revealed good aerosol performance and its suitability for direct delivery to the lungs. In-vitro cytotoxic potential of EC-DPI was determined against A549 cancer cells and compared with curcumin-loaded DPI formulation (C-DPI) and erlotinib-loaded DPI formulation (E-DPI). The IC[Formula: see text] values for E-DPI and C-DPI were found to be 36.6 ± 2.4 [Formula: see text]M and 24.4 ± 2.7 [Formula: see text]M, respectively. The IC[Formula: see text] value for EC-DPI was 20.5 ± 2.1 [Formula: see text]M confirming the synergistic effect of both drugs against A549 cancer cells. The internalization of the drug inside A549 cells was detected by a cellular uptake study. The EC-DPI demonstrated the highest cellular uptake (0.07 ± 0.006 ng/[Formula: see text]g) followed by the formulation containing curcumin (0.05 ± 0.003 ng/[Formula: see text]g) and erlotinib (0.03 ± 0.004 ng/[Formula: see text]g) alone at the end of 6 h. Hence, the developed DPI formulation can be considered as a potential therapeutic approach for the direct delivery of erlotinib and curcumin to treat NSCLC.
DMTM: Fast Obstacle Detection and Tracking for Motion Planning
Authors: Analooee Ali , Nikoobin Amin
Published: July 2024

This paper presents an obstacle detection and tracking framework for mobile robots and autonomous vehicles equipped with LiDAR (Light Detecting and Range finding) sensors. The framework contains a detection module (DM) for clustering the point cloud and modeling the obstacles, and a tracking module (TM) for recognizing the obstacles and estimating their velocities. In order to detect the obstacles, DM segments the point cloud by finding the gaps in it. Detected obstacles are modeled by one or two line segments depending on their geometry. TM gets the line segments returned by DM as the obstacles to track. To this end, first, the obstacles are labeled and their features are stored. Thereafter, a set of equations are solved to recognize the labeled obstacles. Finally, the Kalman filter is used to calculate the translational and rotational velocities of the obstacles. The framework is evaluated in experiments on a robot platform and using the KITTI dataset. The results indicate satisfactory performance in terms of effectiveness and quickness and confirm that DM and TM are qualified enough to perform in real time as ancillary modules of mobile robots and autonomous vehicles. Especially, because of robust and accurate obstacle modeling, the velocity diagrams are smooth and coherent, a point which is not seen in similar researches.