bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Development of an Adherence Measure for Pediatric Failure to Thrive/Faltering Growth
Authors: David Jennie G. , Kiely Jenna R. , Kersten Hans B. , Bennett David S. 
Published: December 2022

Objective: Failure to thrive/faltering growth (FTT/FG) is often multiply determined and involves caregiver adherence to various recommendations to optimize child weight gain. The current study at an interdisciplinary FTT/FG clinic (a) documented the taxonomy of treatment recommendations made for children with FTT/FG (Study 1) and (b) developed an adherence measure, which was used by trained clinicians to examine the relationship between adherence and weight gain (Study 2). Methods: In Study 1, all treatment recommendations made to caregivers of 102 children with FTT/FG were recorded and categorized into domains. Based on domains identified in Study 1, a seven-domain adherence measure was developed. Using a new sample in Study 2 ( n = 131, aged 1 to 10 years), clinicians assessed caregiver adherence to recommendations made at the prior clinic visit and examined the association between adherence and weight gain. Results: From Study 1, clinic recommendations fell within seven domains, including the following four that were expected to be associated with weight gain: liquids, food, behavior, and meal structure. Study 2 found that caregiver adherence, overall, was generally high ( M = 3.0, SD = .80, rated on a 0 to 4 scale). Greater overall adherence was associated with greater weight gain ( r = .253, p = .02). Examining specific recommendations, adherence to using high-calorie add-ons and limiting long mealtimes were associated with greater weight gain. Conclusions: The adherence measure developed in this study can be used to assist clinicians in the management of FTT/FG. Future research is needed to further identify specific treatment recommendations whose adherence is most closely associated with children’s weight gain. Implications for Impact Statement Failure to thrive/faltering growth (FTT/FG), is complex as clinical presentations may vary depending on the child, with a universal goal of increasing weight and growth. Understanding the role of caregiver adherence to recommendations from interdisciplinary providers for FTT/FG has not been explored in the extant literature, and this study developed an adherence measure for this population in an interdisciplinary clinic setting. Overall adherence and adherence to several specific recommendations were significantly associated with greater weight gain, demonstrating a novel application of adherence assessment for children with FTT/FG.
Clinical Application of a Peer Coaching Intervention to Enhance Self-Management for Adolescents and Young Adults With Inflammatory Bowel Disease
Authors: Pollock McLean D. , Brotkin Samuel M. , Denio Erin , Dave Sneha , Fisher Edwin B. , Docherty Sharron L. , Maslow Gary R. 
Published: December 2022

Objective: The purpose of this article is to characterize the current evidence base related to peer support interventions for adolescents and young adults (AYAs) with inflammatory bowel disease (IBD) and to describe a peer support program to enhance self-management for AYAs with IBD through a case study. There is strong theory and compelling evidence suggesting that AYAs with IBD could benefit from and are interested in receiving peer support to enhance self-management; however, literature on peer support interventions for AYAs with IBD is lacking. Methods: This study (a) presents a topical review describing qualitative factors AYAs with IBD would seek in a peer support program as well as existing peer support programs for this population, (b) presents an innovative one-to-one peer support program targeting self-management through a case study, and (c) discusses clinical implications and directions for future research. Results: Peer support offers a promising approach for AYAs with IBD that is feasible and acceptable to patient populations. However, results from the present topical review identified only two studies that examined peer support interventions for AYAs with IBD. The case study demonstrates how a theoretically driven program uses peer support to promote self-management and adaptive behavioral change. Conclusions: The paucity of literature in this area reveals a critical opportunity for future research and clinical programming to improve existing practices by leveraging peer support. We present the application of an innovative mobile-based peer coaching intervention that has the potential to support AYAs with IBD in their self-management. Implications for Impact Statement The purpose of this article is to present the current evidence base related to peer support for adolescents and young adults (AYAs) with inflammatory bowel disease (IBD) and to describe a peer support program to enhance self-management for AYAs with IBD through a case study. Peer support, such as the one-to-one peer coaching model presented in this article, offers a promising approach for AYAs with IBD that is feasible, developmentally appropriate, and acceptable to patient populations. Given the nascent nature of the literature on peer support interventions for AYAs with IBD, further research is needed to develop this area and inform clinical practice, which should consider opportunities to intentionally leverage peer support in settings in which AYAs with IBD currently engage.
U-IMPACT: a universal 3D microfluidic cell culture platform
Authors: Lee Seung-Ryeol , Kim Youngtaek , Kim Suryong , Kim Jiho , Park Seonghyuk , Rhee Stephen , Park Dohyun , Lee Byungjun , Baek Kyusuk , Kim Ho-Young , Jeon Noo Li 
Published: December 2022

AbstractThe development of organs-on-a-chip has resulted in advances in the reconstruction of 3D cellular microenvironments. However, there remain limitations regarding applicability and manufacturability. Here, we present an injection-molded plastic array 3D universal culture platform (U-IMPACT) for various biological applications in a single platform, such as cocultures of various cell types, and spheroids (e.g., tumor spheroids, neurospheres) and tissues (e.g., microvessels). The U-IMPACT consists of three channels and a spheroid zone with a 96-well plate form factor. Specifically, organoids or spheroids (~500 μm) can be located in designated areas, while cell suspensions or cell-laden hydrogels can be selectively placed in three channels. For stable multichannel patterning, we developed a new patterning method based on capillary action, utilizing capillary channels and the native contact angle of the materials without any modification. We derived the optimal material hydrophilicity (contact angle of the body, 45–90°; substrate, <30°) for robust patterning through experiments and theoretical calculations. We demonstrated that the U-IMPACT can implement 3D tumor microenvironments for angiogenesis, vascularization, and tumor cell migration. Furthermore, we cultured neurospheres from induced neural stem cells. The U-IMPACT can serve as a multifunctional organ-on-a-chip platform for high-content and high-throughput screening.
Many-body quantum chaos and space-time translational invariance
Authors: Chan Amos , Shivam Saumya , Huse David A. , De Luca Andrea 
Published: December 2022

AbstractWe study the consequences of having translational invariance in space and time in many-body quantum chaotic systems. We consider ensembles of random quantum circuits as minimal models of translational invariant many-body quantum chaotic systems. We evaluate the spectral form factor as a sum over many-body Feynman diagrams in the limit of large local Hilbert space dimension q. At sufficiently large t, diagrams corresponding to rigid translations dominate, reproducing the random matrix theory (RMT) behaviour. At finite t, we show that translational invariance introduces additional mechanisms via two novel Feynman diagrams which delay the emergence of RMT. Our analytics suggests the existence of exact scaling forms which describe the approach to RMT behavior in the scaling limit where both t and L are large while the ratio between L and LTh(t), the many-body Thouless length, is fixed. We numerically demonstrate, with simulations of two distinct circuit models, that the resulting scaling functions are universal in the scaling limit.
Self-assembling nanofibrous bacteriophage microgels as sprayable antimicrobials targeting multidrug-resistant bacteria
Authors: Tian Lei , He Leon , Jackson Kyle , Saif Ahmed , Khan Shadman , Wan Zeqi , Didar Tohid F. , Hosseinidoust Zeinab 
Published: December 2022

AbstractNanofilamentous bacteriophages (bacterial viruses) are biofunctional, self-propagating, and monodisperse natural building blocks for virus-built materials. Minifying phage-built materials to microscale offers the promise of expanding the range function for these biomaterials to sprays and colloidal bioassays/biosensors. Here, we crosslink half a million self-organized phages as the sole structural component to construct each soft microgel. Through an in-house developed, biologics-friendly, high-throughput template method, over 35,000 phage-built microgels are produced from every square centimetre of a peelable microporous film template, constituting a 13-billion phage community. The phage-exclusive microgels exhibit a self-organized, highly-aligned nanofibrous texture and tunable auto-fluorescence. Further preservation of antimicrobial activity was achieved by making hybrid protein-phage microgels. When loaded with potent virulent phages, these microgels effectively reduce heavy loads of multidrug-resistant Escherichia coli O157:H7 on food products, leading to up to 6 logs reduction in 9 hours and rendering food contaminant free.
High-fidelity qutrit entangling gates for superconducting circuits
Authors: Goss Noah , Morvan Alexis , Marinelli Brian , Mitchell Bradley K. , Nguyen Long B. , Naik Ravi K. , Chen Larry , Jünger Christian , Kreikebaum John Mark , Santiago David I. , Wallman Joel J. , Siddiqi Irfan 
Published: December 2022

AbstractTernary quantum information processing in superconducting devices poses a promising alternative to its more popular binary counterpart through larger, more connected computational spaces and proposed advantages in quantum simulation and error correction. Although generally operated as qubits, transmons have readily addressable higher levels, making them natural candidates for operation as quantum three-level systems (qutrits). Recent works in transmon devices have realized high fidelity single qutrit operation. Nonetheless, effectively engineering a high-fidelity two-qutrit entanglement remains a central challenge for realizing qutrit processing in a transmon device. In this work, we apply the differential AC Stark shift to implement a flexible, microwave-activated, and dynamic cross-Kerr entanglement between two fixed-frequency transmon qutrits, expanding on work performed for the ZZ interaction with transmon qubits. We then use this interaction to engineer efficient, high-fidelity qutrit CZ† and CZ gates, with estimated process fidelities of 97.3(1)% and 95.2(3)% respectively, a significant step forward for operating qutrits on a multi-transmon device.
Single-shot self-supervised object detection in microscopy
Authors: Midtvedt Benjamin , Pineda Jesús , Skärberg Fredrik , Olsén Erik , Bachimanchi Harshith , Wesén Emelie , Esbjörner Elin K. , Selander Erik , Höök Fredrik , Midtvedt Daniel , Volpe Giovanni 
Published: December 2022

AbstractObject detection is a fundamental task in digital microscopy, where machine learning has made great strides in overcoming the limitations of classical approaches. The training of state-of-the-art machine-learning methods almost universally relies on vast amounts of labeled experimental data or the ability to numerically simulate realistic datasets. However, experimental data are often challenging to label and cannot be easily reproduced numerically. Here, we propose a deep-learning method, named LodeSTAR (Localization and detection from Symmetries, Translations And Rotations), that learns to detect microscopic objects with sub-pixel accuracy from a single unlabeled experimental image by exploiting the inherent roto-translational symmetries of this task. We demonstrate that LodeSTAR outperforms traditional methods in terms of accuracy, also when analyzing challenging experimental data containing densely packed cells or noisy backgrounds. Furthermore, by exploiting additional symmetries we show that LodeSTAR can measure other properties, e.g., vertical position and polarizability in holographic microscopy.
Predicting European cities’ climate mitigation performance using machine learning
Authors: Hsu Angel , Wang Xuewei , Tan Jonas , Toh Wayne , Goyal Nihit 
Published: December 2022

AbstractAlthough cities have risen to prominence as climate actors, emissions’ data scarcity has been the primary challenge to evaluating their performance. Here we develop a scalable, replicable machine learning approach for evaluating the mitigation performance for nearly all local administrative areas in Europe from 2001-2018. By combining publicly available, spatially explicit environmental and socio-economic data with self-reported emissions data from European cities, we predict annual carbon dioxide emissions to explore trends in city-scale mitigation performance. We find that European cities participating in transnational climate initiatives have likely decreased emissions since 2001, with slightly more than half likely to have achieved their 2020 emissions reduction target. Cities who report emissions data are more likely to have achieved greater reductions than those who fail to report any data. Despite its limitations, our model provides a replicable, scalable starting point for understanding city-level climate emissions mitigation performance.
Cannabinoid non-cannabidiol site modulation of TRPV2 structure and function
Authors: Zhang Liying , Simonsen Charlotte , Zimova Lucie , Wang Kaituo , Moparthi Lavanya , Gaudet Rachelle , Ekoff Maria , Nilsson Gunnar , Hellmich Ute A. , Vlachova Viktorie , Gourdon Pontus , Zygmunt Peter M. 
Published: December 2022

AbstractTRPV2 is a ligand-operated temperature sensor with poorly defined pharmacology. Here, we combine calcium imaging and patch-clamp electrophysiology with cryo-electron microscopy (cryo-EM) to explore how TRPV2 activity is modulated by the phytocannabinoid Δ9-tetrahydrocannabiorcol (C16) and by probenecid. C16 and probenecid act in concert to stimulate TRPV2 responses including histamine release from rat and human mast cells. Each ligand causes distinct conformational changes in TRPV2 as revealed by cryo-EM. Although the binding for probenecid remains elusive, C16 associates within the vanilloid pocket. As such, the C16 binding location is distinct from that of cannabidiol, partially overlapping with the binding site of the TRPV2 inhibitor piperlongumine. Taken together, we discover a new cannabinoid binding site in TRPV2 that is under the influence of allosteric control by probenecid. This molecular insight into ligand modulation enhances our understanding of TRPV2 in normal and pathophysiology.
Structural basis of sequence-specific RNA recognition by the antiviral factor APOBEC3G
Authors: Yang Hanjing , Kim Kyumin , Li Shuxing , Pacheco Josue , Chen Xiaojiang S. 
Published: December 2022

AbstractAn essential step in restricting HIV infectivity by the antiviral factor APOBEC3G is its incorporation into progeny virions via binding to HIV RNA. However, the mechanism of APOBEC3G capturing viral RNA is unknown. Here, we report crystal structures of a primate APOBEC3G bound to different types of RNAs, revealing that APOBEC3G specifically recognizes unpaired 5’-AA-3’ dinucleotides, and to a lesser extent, 5’-GA-3’ dinucleotides. APOBEC3G binds to the common 3’A in the AA/GA motifs using an aromatic/hydrophobic pocket in the non-catalytic domain. It binds to the 5’A or 5’G in the AA/GA motifs using an aromatic/hydrophobic groove conformed between the non-catalytic and catalytic domains. APOBEC3G RNA binding property is distinct from that of the HIV nucleocapsid protein recognizing unpaired guanosines. Our findings suggest that the sequence-specific RNA recognition is critical for APOBEC3G virion packaging and restricting HIV infectivity.
Tissue and liquid biopsy profiling reveal convergent tumor evolution and therapy evasion in breast cancer
Authors: Sivakumar Smruthy , Jin Dexter X. , Tukachinsky Hanna , Murugesan Karthikeyan , McGregor Kimberly , Danziger Natalie , Pavlick Dean , Gjoerup Ole , Ross Jeffrey S. , Harmon Robert , Chung Jon , Decker Brennan , Dennis Lucas , Frampton Garrett M. , Molinero Luciana , Oesterreich Steffi , Venstrom Jeffrey M. , Oxnard Geoffrey R. , Hegde Priti S. , Sokol Ethan S. 
Published: December 2022

AbstractPathological and genomic profiling have transformed breast cancer care by matching patients to targeted treatments. However, tumors evolve and evade therapeutic interventions often through the acquisition of genomic mutations. Here we examine patients profiled with tissue (TBx) and liquid biopsy (LBx) as part of routine clinical care, to characterize the tumor evolutionary landscape and identify potential vulnerabilities in the relapsed setting. Real-world evidence demonstrates that LBx is utilized later in care and identifies associations with intervening therapy. While driver events are frequently shared, acquired LBx alterations are detected in a majority of patients, with the highest frequency in ER+ disease and in patients with longer biopsy intervals. Acquired mutations are often polyclonal and present at lower allelic fractions, suggesting multi-clonal convergent evolution. In addition to well-characterized resistance mutations (e.g.,ESR1,NF1,RB1,ERBB2), we observe a diversity of rarer but potentially targetable mutations (e.g.,PIK3CA, HRAS/NRAS/KRAS,FGFR1/2/3,BRAF) and fusions (e.g.,FGFR1/2,ERBB2,RET), as well asBRCA1/2reversions through a variety of mechanisms, including splice alterations and structural deletions. This study provides insights on treatment and selection-driven tumor evolution and identifies potential combinatorial treatment options in advanced breast cancer.
Targeting endogenous kidney regeneration using anti-IL11 therapy in acute and chronic models of kidney disease
Authors: Widjaja Anissa A. , Viswanathan Sivakumar , Shekeran Shamini G. , Adami Eleonora , Lim Wei-Wen , Chothani Sonia , Tan Jessie , Goh Joyce Wei Ting , Chen Hui Mei , Lim Sze Yun , Boustany-Kari Carine M. , Hawkins Julie , Petretto Enrico , Hübner Norbert , Schafer Sebastian , Coffman Thomas M. , Cook Stuart A. 
Published: December 2022

AbstractThe kidney has large regenerative capacity, but this is compromised when kidney damage is excessive and renal tubular epithelial cells (TECs) undergo SNAI1-driven growth arrest. Here we investigate the role of IL11 in TECs, kidney injury and renal repair. IL11 stimulation of TECs induces ERK- and p90RSK-mediated GSK3β inactivation, SNAI1 upregulation and pro-inflammatory gene expression. Mice with acute kidney injury upregulate IL11 in TECs leading to SNAI1 expression and kidney dysfunction, which is not seen inIl11deleted mice or in mice administered a neutralizing IL11 antibody in either preemptive or treatment modes. In acute kidney injury, anti-TGFβ reduces renal fibrosis but exacerbates inflammation and tubule damage whereas anti-IL11 reduces all pathologies. Mice with TEC-specific deletion ofIl11ra1have reduced pathogenic signaling and are protected from renal injury-induced inflammation, fibrosis, and failure. In a model of chronic kidney disease, anti-IL11 therapy promotes TEC proliferation and parenchymal regeneration, reverses fibroinflammation and restores renal mass and function. These data highlight IL11-induced mesenchymal transition of injured TECs as an important renal pathology and suggest IL11 as a therapeutic target for restoring stalled endogenous regeneration in the diseased kidney.
Local striatal volume and motor reserve in drug-naïve Parkinson’s disease
Authors: Jeong Seong Ho , Lee Eun-Chong , Chung Seok Jong , Lee Hye Sun , Jung Jin Ho , Sohn Young H. , Seong Joon-Kyung , Lee Phil Hyu 
Published: December 2022

AbstractMotor reserve (MR) may explain why individuals with similar pathological changes show marked differences in motor deficits in Parkinson’s disease (PD). In this study, we investigated whether estimated individual MR was linked to local striatal volume (LSV) in PD. We analyzed data obtained from 333 patients with drug naïve PD who underwent dopamine transporter scans and high-resolution 3-tesla T1-weighted structural magnetic resonance images. Using a residual model, we estimated individual MRs on the basis of initial UPDRS-III score and striatal dopamine depletion. We performed a correlation analysis between MR estimates and LSV. Furthermore, we assessed the effect of LSV, which is correlated with MR estimates, on the longitudinal increase in the levodopa-equivalent dose (LED) during the 4-year follow-up period using a linear mixed model. After controlling for intracranial volume, there was a significant positive correlation between LSV and MR estimates in the bilateral caudate, anterior putamen, and ventro-posterior putamen. The linear mixed model showed that the large local volume of anterior and ventro-posterior putamen was associated with the low requirement of LED initially and accelerated LED increment thereafter. The present study demonstrated that LSV is crucial to MR in early-stage PD, suggesting LSV as a neural correlate of MR in PD.
A library of base editors for the precise ablation of all protein-coding genes in the mouse mitochondrial genome
Authors: Silva-Pinheiro Pedro , Mutti Christian D. , Van Haute Lindsey , Powell Christopher A. , Nash Pavel A. , Turner Keira , Minczuk Michal 
Published: December 2022

AbstractThe development of curative treatments for mitochondrial diseases, which are often caused by mutations in mitochondrial DNA (mtDNA) that impair energy metabolism and other aspects of cellular homoeostasis, is hindered by an incomplete understanding of the underlying biology and a scarcity of cellular and animal models. Here we report the design and application of a library of double-stranded-DNA deaminase-derived cytosine base editors optimized for the precise ablation of every mtDNA protein-coding gene in the mouse mitochondrial genome. We used the library, which we named MitoKO, to produce near-homoplasmic knockout cells in vitro and to generate a mouse knockout with high heteroplasmy levels and no off-target edits. MitoKO should facilitate systematic and comprehensive investigations of mtDNA-related pathways and their impact on organismal homoeostasis, and aid the generation of clinically meaningful in vivo models of mtDNA dysfunction.
Mechanical Unloading of Engineered Human Meniscus Models Under Simulated Microgravity: A Transcriptomic Study
Authors: Ma Zhiyao , Li David Xinzheyang , Chee Ryan K. W. , Kunze Melanie , Mulet-Sierra Aillette , Sommerfeldt Mark , Westover Lindsey , Graf Daniel , Adesida Adetola B. 
Published: December 2022

AbstractOsteoarthritis (OA) primarily affects mechanical load-bearing joints, with the knee being the most common. The prevalence, burden and severity of knee osteoarthritis (KOA) are disproportionately higher in females, but hormonal differences alone do not explain the disproportionate incidence of KOA in females. Mechanical unloading by spaceflight microgravity has been implicated in OA development in cartilaginous tissues. However, the mechanisms and sex-dependent differences in OA-like development are not well explored. In this study, engineered meniscus constructs were generated from healthy human meniscus fibrochondrocytes (MFC) seeded onto type I collagen scaffolds and cultured under normal gravity and simulated microgravity conditions. We report the whole-genome sequences of constructs from 4 female and 4 male donors, along with the evaluation of their phenotypic characteristics. The collected data could be used as valuable resources to further explore the mechanism of KOA development in response to mechanical unloading, and to investigate the molecular basis of the observed sex differences in KOA.