bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Use of Methylphenidate During Inpatient Rehabilitation After Pediatric Traumatic Brain Injury: Population Characteristics and Prescribing Patterns
Authors: Caliendo Eric , Lowder Ryan , McLaughlin Matthew J. , Watson William D. , Baum Katherine T. , Blackwell Laura S. , Koterba Christine H. , Hoskinson Kristen R. , Tlustos Sarah J. , Shah Sudhin A. , Suskauer Stacy J. , Kurowski Brad G. 
Published: August 2023

Objective:
To understand how methylphenidate (MPH) is used in youth with traumatic brain injury (TBI) during inpatient pediatric rehabilitation.

Setting:
Inpatient pediatric rehabilitation.

Participants:
In total, 234 children with TBI; 62 of whom received MPH and 172 who did not. Patients were on average 11.6 years of age (range, 2 months to 21 years); 88 of 234 were female; the most common mechanism of injury was motor vehicle collision (49%); median (IQR) acute hospital length of stay (LOS) and inpatient rehabilitation LOS were 16 (10-29) and 23 (14-39), respectively; 51 of 234 were in a disorder of consciousness cognitive state at time of inpatient rehabilitation admission.

Design:
Multicenter, retrospective medical record review.

Main Measure(s):
Patient demographic data, time to inpatient pediatric rehabilitation admission (TTA), cognitive state, MPH dosing (mg/kg/day).

Results:
Patients who received MPH were older (P = .011); TTA was significantly longer in patients who received MPH than those who did not (P =.002). The lowest recorded dose range by weight was 0.05 to 0.89 mg/kg/d, representing an 18-fold difference; the weight-based range for the maximum dose was 0.11 to 0.97 mg/kg/d, a 9-fold difference. Patients in lower cognitive states at admission (P = .001) and at discharge (P = .030) were more likely to receive MPH. Five patients had side effects known to be associated with MPH; no serious adverse events were reported.

Conclusion:
This multicenter study indicates that there is variable use of MPH during acute inpatient rehabilitation for children with TBI. Children who receive MPH tend to be older with lower cognitive states. Dosing practices are likely consistent with underdosing. Clinical indications for MPH use during inpatient pediatric rehabilitation should be better defined. The use of MPH, as well as its combination with other medications and treatments, during inpatient rehabilitation needs to be further explored.
The Role of Children in the Transmission of SARS-CoV-2, a Shifting Paradigm
Authors: Arguedas Adriano , Swerdlow David L. , Curcio Daniel 
Published: August 2023

AbstractPediatric populations contribute to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission through a combination of exposure, susceptibility, and transmissibility. In this narrative review, SARS-CoV-2 infection in children is assessed to ascertain their role in transmission, by considering the characteristics of pediatric populations regarding their exposure and susceptibility to SARS-CoV-2 infection and COVID-19, and their transmission of the virus. A series of PubMed searches were conducted between November 2020 and February 2023 to identify articles describing SARS-CoV-2 transmission in children. The literature suggests that schools are key areas of exposure of children and adolescents to SARS-CoV-2, which contributed to school closures to mitigate spread and break transmission chains. However, the effectiveness of these measures is debated. Although SARS-CoV-2 appeared to infect children and adolescents less frequently than adults early in the pandemic, infection rates have risen considerably among the pediatric population with the emergence of variants of concern. Compared with adults and populations at high risk, children generally have a milder course of disease. The predominant role of children in transmission of SARS-CoV-2 is thought to involve household and school settings, although the relative contribution of each to transmission is questioned. Through their exposure, susceptibility, and transmissibility of SARS-CoV-2, children and adolescents are a key population contributing to the transmission of the virus. Our continued and evolving understanding of the role of children in transmission of SARS-CoV-2 has important implications to define appropriate preventive and therapeutic strategies for the pediatric population and the wider community.
Ray-tracing–guided myopic LASIK: real-world clinical outcomes
Authors: He George , Bala Chandra 
Published: August 2023

Purpose:To assess effectiveness of individualized ray-trace based laser in situ keratomileusis (LASIK) for correction of myopia in everyday clinical practice.Setting:Single-site private practice.Design:Retrospective nonrandomised unmasked chart review.Methods:Consecutive, myopic eyes (range ≤−8.25 diopters [D] sphere; astigmatism 0 to −4.25 D) treated with ray-trace based LASIK were included. Patients underwent wavefront, tomography, and biometry assessment using the InnovEyes Sightmap diagnostic device. The ray-trace based algorithm (InnovEyes algorithm) then generated an individualized 3D eye model and calculated a customized LASIK ablation profile. Postoperative visual acuity, refractive error and whole eye higher-order aberrations (HOAs) were evaluated over 3 months.Results:The procedure was performed on 400 eyes (200 patients). Mean preoperative manifest refraction spherical equivalent was −3.39 ± 1.58 D (right eye −3.84 ± 1.63 D, left eye −3.98 ± 1.75 D). At month 3, uncorrected distance visual acuity (UDVA) was ≥20/20 in all eyes, ≥20/16 in 89% (right eye 90%, left eye 89%), ≥20/12 in 51% (54% right eye; 47% left eye), and 20/10 in 8% (right eye 8%; left eye 9%) of eyes respectively. UDVA was within 1 line of preoperative corrected distance visual acuity in 98% of eyes (right eye 98.5%; left eye 98%) and 39% of eyes (right eye 38%; left eye 39%) gained 1 line improvement. There was a statistically but not clinically significant increase in total HOAs (right eye 0.06 ± 0.133 μm; left eye 0.057 ± 0.125 μm;P< .001). The spherical aberration decreased (right eye −0.047 ± 0.095 μm,P< .001; left eye −0.051 ± 0.091 μm,P< .001).Conclusions:Ray-trace based LASIK was safe and effective for correction of myopia with and without astigmatism. Approximately, half the eyes achieved ≥20/12.5 UDVA and 8% achieved 20/10. There was no clinically significant increase in total whole eye HOAs.
Dose Changes for Long-term Opioid Patients Following a State Opioid Prescribing Policy
Authors: Qiu Sijia , Liu Yan , Adetunji Doyinsola O. , Hartzell Sarah , Larson Madalyn , Friedman Sarah 
Published: August 2023

Background:
In 2018, Nevada implemented opioid prescribing legislation (AB474) to support the uptake of CDC pain care guidelines. We studied the law’s association with doses over threshold levels of morphine milligram equivalents (MMEs) and with time to dose increases and decreases, among long-term opioid patients.

Methods:
A difference-in-difference study examined dosing changes across opioid prescription episodes (ie, prescriptions within 30 day and within the same dosing threshold). Patients with at least 120 days supply over 6 months in Nevada and Colorado Medicaid pharmacy claims were included. Using a logistic regression model, we compare the predicted probabilities that opioid episodes exceeded 50 MME before and after implementation of the law, in both states. Adjusted hazard ratios (aHR) from a gap time survival model estimated time to escalate above 50 MME among low-dose episodes (<50 MME), and time to de-escalate below 50 MME among high-dose episodes (≥50 MME).

Results:
Among 453,577 episodes (74,292 patients), the Nevada law was associated with a 2.9% reduction in prescriptions over 50 MME (95% CI: −3.5, −2.3) compared with Colorado. While the law was also associated with slower escalation (Nevada: aHR = 0.75; 95% CI: 0.72, 0.77, Colorado: aHR = 1.04; 95% CI: 1.01, 1.06), it was also associated with slower de-escalation (Nevada: aHR = 0.87; 95% CI: 0.84, 0.89, Colorado: aHR = 0.97; 95% CI: 0.96, 0.99).

Conclusions:
Slower dose escalations, rather than faster dose de-escalation, likely explain post-law reductions in doses over 50 MME. Slower dose de-escalations may be due to longer days supply post-policy.
Lack of Follow-Up for Celiac Disease During Childhood Not Associated With Poor Health Outcomes: A Regional Swedish Cohort Study
Authors: Ulnes Maria , Albrektsson Henrik , Størdal Ketil , Saalman Robert , Ludvigsson Jonas F. , Mårild Karl 
Published: August 2023

Objectives:
The objective of the study is to examine the association between the lack of follow-up for celiac disease (CD) during childhood and dietary adherence, disease remission, and health-related quality of life (HRQoL).

Methods:
We invited 243 randomly selected children diagnosed with CD in 2013–2018 in Gothenburg, Sweden, and 162 consented to participate (67%). We retrieved information on clinical follow-up and current wellbeing using medical and laboratory records data, as well as validated questionnaires on symptoms of CD, dietary adherence, and HRQoL. We analyzed tissue-transglutaminase antibodies (tTGA) as a measure of disease remission. We defined lack of follow-up as no CD-related physician/dietician-led visit or measurement of tTGA over the past 24 months of study enrollment.

Results:
The mean age at study enrolment was 12.7 (range 7.8–18.2) years. Out of 162 children with an average disease duration of 5.3 (range 2.3–8.8) years, 23 (14%) lacked follow-up. tTGA had normalized in 94% [95% confidence interval (CI) = 71%–100%] of children without follow-up versus 91% (95% CI: 85%–95%) of children with continued follow-up. Of children without follow-up, 65% (95% CI: 38%–86%) reported a dietary adherence score indicating very good adherence, versus 72% (95% CI: 63%–80%) of those with continued follow-up. Also, lack of follow-up was not significantly associated with growth, symptom scores, or HRQoL.

Conclusions:
In this regional cohort study of mostly older children and adolescents, lack of follow-up for CD was not significantly linked to dietary adherence, disease remission, or HRQoL. How these results hold in larger, unselected samples with longer follow-up, including transition to adult care, warrants further study.
Prediction of Biliary Complications After Human Liver Transplantation Using Hyperspectral Imaging and Convolutional Neural Networks: A Proof-of-concept Study
Authors: Fodor Margot , Zelger Philipp , Pallua Johannes D. , Huck Christian W. , Hofmann Julia , Otarashvili Giorgi , Pühringer Marlene , Zelger Bettina , Hermann Martin , Resch Thomas , Cardini Benno , Oberhuber Rupert , Öfner Dietmar , Sucher Robert , Hautz Theresa , Schneeberger Stefan 
Published: August 2023

Background.
Biliary complications (BCs) negatively impact the outcome after liver transplantation. We herein tested whether hyperspectral imaging (HSI) generated data from bile ducts (BD) on reperfusion and machine learning techniques for data readout may serve as a novel approach for predicting BC.

Methods.
Tissue-specific data from 136 HSI liver images were integrated into a convolutional neural network (CNN). Fourteen patients undergoing liver transplantation after normothermic machine preservation served as a validation cohort. Assessment of oxygen saturation, organ hemoglobin, and tissue water levels through HSI was performed after completing the biliary anastomosis. Resected BD segments were analyzed by immunohistochemistry and real-time confocal microscopy.

Results.
Immunohistochemistry and real-time confocal microscopy revealed mild (grade I: 1%–40%) BD damage in 8 patients and moderate (grade II: 40%–80%) injury in 1 patient. Donor and recipient data alone had no predictive capacity toward BC. Deep learning-based analysis of HSI data resulted in >90% accuracy of automated detection of BD. The CNN-based analysis yielded a correct classification in 72% and 69% for BC/no BC. The combination of HSI with donor and recipient factors showed 94% accuracy in predicting BC.

Conclusions.
Deep learning-based modeling using CNN of HSI-based tissue property data represents a noninvasive technique for predicting postoperative BC.
Lateral gating mechanism and plasticity of the BAM complex in micelles andE. coli
Authors: Gopinath Aathira , Rath Tobias , Morgner Nina , Joseph Benesh 
Published: August 2023

AbstractThe β-barrel assembly machinery (BAM) mediates folding and insertion of the majority of OMPs in Gram-negative bacteria. BAM is a penta-heterooligomeric complex consisting of the central β-barrel BamA and four interacting lipoproteins BamB, C, D, and E. The conformational switching of BamA between inward-open (IO) and lateral-open (LO) conformations is required for substrate recognition and folding. However, the mechanism for the lateral gating or how the structural details observedin vitrocorrespond with the cellular environment remains elusive. Here we addressed these questions by characterizing the conformational heterogeneity of BamAB, BamACDE and BamABCDE complexes in detergent micelles and orE. coliusing pulsed dipolar electron spin resonance spectroscopy (PDS). We show that the binding of BamB does not induce any visible changes in BamA and the BamAB complex exists in the IO conformation. The BamCDE complex induces an IO to LO transition through a coordinated movement along the BamA barrel. However, the extracellular loop (L6) is unaffected by the presence of lipoproteins and exhibits a large segmental dynamics extending to the exit pore. PDS experiments with BamABCDE complex in intactE. coliconfirmed the dynamic behavior of both the lateral gate and the L6 in the native environment. Our results demonstrate that the BamCDE complex plays a key role for the function by regulating lateral gating in BamA.
A platform for dissecting force sensitivity and multivalency in actin networks
Authors: Levin Joseph T. , Pan Ariel , Barrett Michael T. , Alushin Gregory M. 
Published: August 2023

AbstractThe physical structure and dynamics of cells are supported by micron-scale actin networks with diverse geometries, protein compositions, and mechanical properties. These networks are composed of actin filaments and numerous actin binding proteins (ABPs), many of which engage multiple filaments simultaneously to crosslink them into specific functional architectures. Mechanical force has been shown to modulate the interactions between several ABPs and individual actin filaments, but it is unclear how this phenomenon contributes to the emergent force-responsive functional dynamics of actin networks. Here, we engineer filament linker complexes and combine them with photo-micropatterning of myosin motor proteins to produce anin vitroreconstitution platform for examining how force impacts the behavior of ABPs within multi-filament assemblies. Our system enables the monitoring of dozens of actin networks with varying architectures simultaneously using total internal reflection fluorescence microscopy, facilitating detailed dissection of the interplay between force-modulated ABP binding and network geometry. We apply our system to study a dimeric form of the critical cell-cell adhesion protein α-catenin, a model force-sensitive ABP. We find that myosin forces increase α-catenin’s engagement of small filament bundles embedded within networks. This activity is absent in a force-sensing deficient mutant, whose binding scales linearly with bundle size in both the presence and absence of force. These data are consistent with filaments in smaller bundles bearing greater per-filament loads that enhance α-catenin binding, a mechanism that could equalize α-catenin’s distribution across actin-myosin networks of varying sizes in cells to regularize their stability and composition.
Virological characteristics of the SARS-CoV-2 XBB.1.5 variant
Authors: Tamura Tomokazu , Irie Takashi , Deguchi Sayaka , Yajima Hisano , Tsuda Masumi , Nasser Hesham , Mizuma Keita , Plianchaisuk Arnon , Suzuki Saori , Uriu Keiya , Begum MST Monira , Shimizu Ryo , Jonathan Michael , Suzuki Rigel , Kondo Takeshi , Ito Hayato , Kamiyama Akifumi , Yoshimatsu Kumiko , Shofa Maya , Hashimoto Rina , Anraku Yuki , Kimura Kanako Terakado , Kita Shunsuke , Sasaki Jiei , Sasaki-Tabata Kaori , Maenaka Katsumi , Nao Naganori , Wang Lei , Oda Yoshitaka ,   The Genotype to Phenotype Japan (G2P-Japan) Consortium, Ikeda Terumasa , Saito Akatsuki , Matsuno Keita , Ito Jumpei , Tanaka Shinya , Sato Kei , Hashiguchi Takao , Takayama Kazuo , Fukuhara Takasuke 
Published: August 2023

SummaryCirculation of SARS-CoV-2 Omicron XBB has resulted in the emergence of XBB.1.5, a new Variant of Interest. Our phylogenetic analysis suggests that XBB.1.5 evolved from XBB.1 by acquiring the F486P spike (S) mutation, subsequent to the acquisition of a nonsense mutation in ORF8. Neutralization assays showed similar abilities of immune escape between XBB.1.5 and XBB.1. We determined the structural basis for the interaction between human ACE2 and the S protein of XBB.1.5, showing similar overall structures between the S proteins of XBB.1 and XBB.1.5. The intrinsic pathogenicity of XBB.1.5 in hamsters is lower than that of XBB.1. Importantly, we found that the ORF8 nonsense mutation of XBB.1.5 resulted in impairment of MHC expression.In vivoexperiments using recombinant viruses revealed that the XBB.1.5 mutations are involved with reduced virulence of XBB.1.5. Together, these data suggest that the mutations in ORF8 and S could enhance spreading of XBB.1.5 in humans.
Evolution ofE. coliin a mouse model of inflammatory bowel disease leads to a disease-specific bacterial genotype and trade-offs with clinical relevance
Authors: Unni Rahul , Andreani Nadia Andrea , Vallier Marie , Heinzmann Silke S. , Taubenheim Jan , Guggeis Martina A. , Tran Florian , Vogler Olga , Künzel Sven , Hövener Jan-Bernd , Rosenstiel Philip , Kaleta Christoph , Dempfle Astrid , Unterweger Daniel , Baines John F. 
Published: August 2023

AbstractInflammatory bowel disease (IBD) is a persistent inflammatory condition that affects the gastrointestinal tract and presents significant challenges in its management and treatment. Despite the knowledge that within-host bacterial evolution occurs in the intestine, the disease has rarely been studied from an evolutionary perspective. In this study, we aimed to investigate the evolution of resident bacteria during intestinal inflammation and whether- and how disease-related bacterial genetic changes may present trade-offs with potential therapeutic importance. Here, we perform anin vivoevolution experiment ofE. coliin a gnotobiotic mouse model of IBD, followed by multiomic analyses to identify disease-specific genetic and phenotypic changes in bacteria that evolved in an inflamed versus a non-inflamed control environment. Our results demonstrate distinct evolutionary changes inE. colispecific to inflammation, including a single nucleotide variant that independently reached high frequency in all inflamed mice. Usingex vivofitness assays, we find that these changes are associated with a higher fitness in an inflamed environment compared to isolates derived from non-inflamed mice. Further, using large-scale phenotypic assays, we show that bacterial adaptation to inflammation results in clinically relevant phenotypes, which intriguingly include collateral sensitivity to antibiotics. Bacterial evolution in an inflamed gut yields specific genetic and phenotypic signatures. These results may serve as a basis for developing novel evolution-informed treatment approaches for patients with intestinal inflammation.
WITHDRAWN: Identification and functional analysis of extrachromosomal circular DNA in plasma extracellular vesicles of liver failure patients
Authors: Xiang Xi , Hong Xiaoning , Yu Yang , Li Jing , Yu Jiaying , Xiao Wenjun , Chen Chen , Huang Defa , Zhong Tianyu , Li Jiang , Qian Yongbing , Li Zhigang 
Published: August 2023

Withdrawal statementThe authors have withdrawn their manuscript owing to having identified certain issues with the current representation of the data in the manuscript after performing further analyses of the bioinformatics data from their eccDNA sequencing results. Therefore, the authors do not wish this work to be cited as reference for the project. A revised and corrected version will be submitted in the future. If you have any questions, please contact the corresponding authors.
The non-structural proteins NS3 and NS5A of Hepatitis C Virus (HCV) are degraded by two host proteolysis systems
Authors: Mohamed Sara , Soppa Jörg 
Published: August 2023

AbstractEach lifecycle of the Hepatitis C virus (HCV) produces structural and non-structural (NS) proteins in equimolar. Structural proteins were either assembled or degraded by host proteolysis systems, while NS proteins remain inside the host cells and don’t accumulate. Therefore, they must be degraded. Here, NS3 and NS5A half-lives were quantified in the presence of autolysosome and proteasome different modulators. Inhibitors of both systems increased the half-life, while inducers decreased the half-life. Furthermore, polyubiquitination of NS3 and NS5A was observed. Additionally, their intracellular co-localization with autolysosome (LAMP2) and proteasome (PSMB5) was observed, and inhibitors of both systems increased the degree of co-localization. A better understanding of NS protein degradation might help to improve medical interventions during HCV infections in the future.