bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Age and Severe Acute Respiratory Syndrome Coronavirus 2 Breakthrough Infection on Humoral Immune Responses After Three Doses of Coronavirus Disease 2019 mRNA Vaccine
Authors: Mwimanzi Francis , Lapointe Hope R , Cheung Peter K , Sang Yurou , Yaseen Fatima , Kalikawe Rebecca , Datwani Sneha , Burns Laura , Young Landon , Leung Victor , Ennis Siobhan , Brumme Chanson J , Montaner Julio S G , Dong Winnie , Prystajecky Natalie , Lowe Christopher F , DeMarco Mari L , Holmes Daniel T , Simons Janet , Niikura Masahiro , Romney Marc G , Brumme Zabrina L , Brockman Mark A 
Published: February 2023

AbstractBackgroundLonger-term immune response data after 3 doses of coronavirus disease 2019 (COVID-19) mRNA vaccine remain limited, particularly among older adults and after Omicron breakthrough infection.MethodsWe quantified wild-type- and Omicron-specific serum immunoglobulin (Ig)G levels, angiotensin-converting enzyme 2 displacement activities, and live virus neutralization up to 6 months after third dose in 116 adults aged 24–98 years who remained COVID-19 naive or experienced their first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection during this time.ResultsAmong the 78 participants who remained COVID-19 naive throughout follow up, wild-type- and Omicron-BA.1-specific IgG concentrations were comparable between younger and older adults, although BA.1-specific responses were consistently significantly lower than wild-type-specific responses in both groups. Wild-type- and BA.1-specific IgG concentrations declined at similar rates in COVID-19-naive younger and older adults, with median half-lives ranging from 69 to 78 days. Antiviral antibody functions declined substantially over time in COVID-19-naive individuals, particularly in older adults: by 6 months, BA.1-specific neutralization was undetectable in 96% of older adults, versus 56% of younger adults. Severe acute respiratory syndrome coronavirus 2 infection, experienced by 38 participants, boosted IgG levels and neutralization above those induced by vaccination alone. Nevertheless, BA.1-specific neutralization remained significantly lower than wild-type, with BA.5-specific neutralization lower still. Higher Omicron BA.1-specific neutralization 1 month after third dose was an independent correlate of lower SARS-CoV-2 infection risk.ConclusionsResults underscore the immune benefits of the third COVID-19 mRNA vaccine dose in adults of all ages and identify vaccine-induced Omicron-specific neutralization as a correlate of protective immunity. Systemic antibody responses and functions however, particularly Omicron-specific neutralization, decline rapidly in COVID-19-naive individuals, particularly in older adults, supporting the need for additional booster doses.
The entropy of galaxy spectra: how much information is encoded?
Authors: Ferreras Ignacio , Lahav Ofer , Somerville Rachel S , Silk Joseph 
Published: February 2023

Abstract
The inverse problem of extracting the stellar population content of galaxy spectra is analysed here from a basic standpoint based on information theory. By interpreting spectra as probability distribution functions, we find that galaxy spectra have high entropy, thus leading to a rather low effective information content. The highest variation in entropy is unsurprisingly found in regions that have been well studied for decades with the conventional approach. We target a set of six spectral regions that show the highest variation in entropy – the 4000 Å break being the most informative one. As a test case with real data, we measure the entropy of a set of high-quality spectra from the Sloan Digital Sky Survey, and contrast entropy-based results with the traditional method based on line strengths. The data are classified into star-forming (SF), quiescent (Q), and active galactic nucleus (AGN) galaxies, and show – independently of any physical model – that AGN spectra can be interpreted as a transition between SF and Q galaxies, with SF galaxies featuring a more diverse variation in entropy. The high level of entanglement complicates the determination of population parameters in a robust, unbiased way, and affects traditional methods that compare models with observations, as well as machine learning (especially deep learning) algorithms that rely on the statistical properties of the data to assess the variations among spectra. Entropy provides a new avenue to improve population synthesis models so that they give a more faithful representation of real galaxy spectra.
Long-term weight changes are associated with initial weight changes after nonalcoholic fatty liver disease diagnosis
Authors: DiBattista Jacob V. , Lok Anna S. , Chen Vincent L. 
Published: February 2023

Objectives:
Weight loss is the mainstay of treatment of NAFLD, but longitudinal data on weight changes and their impact on liver disease are limited. We aimed to characterize weight trajectory up to 5 years of follow-up, effects of weight loss on liver enzyme levels, and predictors of weight loss in NAFLD.

Methods:
This was a single-center retrospective study of consecutive patients with hepatic steatosis diagnosed on imaging, liver biopsy, or transient elastography between 2010 and 2020. The primary outcome was ≥5% weight change at 1–2 years. Secondary outcomes were weight change at 4–5 years and alanine aminotransferase level at 1–2 and 4–5 years. We conducted multivariable logistic regression to identify predictors of ≥5% weight loss at 1–2 years.

Results:
We included 11,559 patients with NAFLD. At year 1–2, 27% had ≥5% weight loss, whereas 26% had ≥5% weight gain. Total 59% and 68% of patients with weight loss and gain, respectively, sustained their weight change by year 4–5. Patients with weight loss at year 1–2 had lower alanine aminotransferase levels at year 1–2 and 4–5. Predictors of ≥5% weight loss included female sex, severe obesity, diabetes, and consultation with a dietitian or pharmacist.

Conclusions:
Over half of patients with NAFLD had ≥5% weight loss or gain within 1–2 years, and these changes were usually sustained at 4–5 years. Intensive intervention early after NAFLD diagnosis may result in long-term weight loss and decreased NAFLD disease activity.
Long-Term Outcomes After Autologous Intestinal Reconstructive Surgery in Children With Short Bowel Syndrome
Authors: Pajunen Sanni , Mutanen Annika , Kivisaari Reeta , Merras-Salmio Laura , Pakarinen Mikko P. 
Published: February 2023

Objectives:
Autologous intestinal reconstructive (AIR) surgery is frequently utilized in the management of pediatric short bowel syndrome (SBS). However, little is known about the long-term sequela of these procedures.

Methods:
We undertook a retrospective follow-up study addressing parenteral nutrition (PN) dependence, nutritional status, intestinal morbidity, and related complications in SBS patients having undergone AIR surgery (SBS-AIR, n = 19). We compared results with conservatively treated control SBS patients (SBS-C, n = 45). Eligible patients were identified from our institutional intestinal failure registry during 1985–2019.

Results:
After median 11.4 follow-up years, 42% of SBS-AIR patients received PN in relation to 36% in SBS-C group (P = 0.6210), and overall PN duration was significantly longer (35.4 vs 10 months, P = 0.0004) in SBS-AIR group. Although symptoms of intestinal dysfunction improved in majority (62%) of patients after AIR surgery, their symptoms remained more frequent and severe at latest follow-up compared to SBS-C group (39% vs 5%, P = 0.0015). Although bacterial overgrowth was more frequent in SBS-AIR group (53% vs 24%, P = 0.0416), latest endoscopy findings and fecal calprotectin levels as well as occurrence of anastomotic/staple line ulcerations were comparable between groups. Histological liver steatosis (50% vs 18%, P = 0.042) and impaired bone health (26% vs 6.7%, P = 0.042) were more frequent in SBS-AIR patients.

Conclusions:
While AIR surgery improved gastrointestinal symptoms and transition to enteral autonomy in majority of patients, a noteworthy proportion of them continued to suffer from clinically significant intestinal dysfunction and related complications. Close long-term follow-up of pediatric AIR surgery patients is mandatory.
Clinical Course of Very Early-Onset Inflammatory Bowel Disease
Authors: Cucinotta Ugo , Arrigo Serena , Dipasquale Valeria , Gramaglia Simone Maria Calogero , Laganà Francesca , Romano Claudio , Gandullia Paolo 
Published: February 2023

Objectives:
Data on the phenotypes and disease outcomes of very early-onset inflammatory bowel disease (VEO-IBD) are limited. The aims of this study were to describe the clinical features, outcomes, and treatment response of VEO-IBD patients and to compare them with later-onset pediatric inflammatory bowel disease (P-IBD) patients.

Methods:
All consecutive patients aged 0–6 years who were diagnosed with Crohn disease (CD), ulcerative colitis, or IBD unclassified (IBD-U) at 2 academic hospitals from 2010 to March 2021 were included. They were compared to sex-matched IBD patients aged 6–17 years.

Results:
Two hundred thirty-two patients were included, 78 (34%) with VEO-IBD and 154 (66%) with P-IBD. IBD-U was the most common diagnosis in the VEO-IBD group compared to P-IBD (28% vs 3%, P < 0.001), while CD was predominant in older children (27% vs 52%, P < 0.001). The VEO-IBD group showed lower rates of clinical remission after induction with steroids compared to older children (82% vs 93%, P = 0.01), higher rates of steroid resistance (14% vs 5%, P = 0.02), and steroid dependence (27% vs 8%, P < 0.001). The number of patients who started anti-tumor necrosis factor (TNF)-α agents was similar between the groups. Anti-TNF-α retention was lower in the VEO-IBD group at 1 and 2 years (59% vs 85%, P = 0.003; 16% vs 55%, P < 0.001, respectively). Surgical risk appeared to be higher for VEO-IBD (32% vs 14%, P < 0.001).

Conclusions:
When compared to P-IBD patients, patients with VEO-IBD may have a more severe disease course, a poorer response to steroids and anti-TNF-α agents, and require more frequent surgical procedures.
Assessing the performance of ChatGPT in answering questions regarding cirrhosis and hepatocellular carcinoma
Authors: Yeo Yee Hui , Samaan Jamil S. , Ng Wee Han , Ting Peng-Sheng , Trivedi Hirsh , Vipani Aarshi , Ayoub Walid , Yang Ju Dong , Liran Omer , Spiegel Brennan , Kuo Alexander 
Published: February 2023

AbstractBackgroundPatients with cirrhosis and hepatocellular carcinoma (HCC) require extensive and personalized care to improve outcomes. ChatGPT (Generative Pre-trained Transformer), a natural language processing model, holds potential to provide professional yet patient-friendly support.AimExamining the accuracy and reproducibility of ChatGPT in answering questions regarding knowledge, management, and emotional support for cirrhosis and HCC.MethodChatGPT’s responses to 164 questions were independently graded by two transplant hepatologists and resolved by a third reviewer. The performance of ChatGPT was compared to physicians or trainees in two validated questionnaires. ChatGPT’s knowledge on cirrhosis care was tested using 26 quality measures of cirrhosis management. Finally, its emotional support capacity was tested.ResultsChatGPT regurgitated extensive knowledge of cirrhosis and HCC, but for questions with correct responses, only a small proportion was labelled as comprehensive. The performance was better in basic knowledge, lifestyle, and treatment than in the domains of diagnosis and preventive medicine. For the quality measures, the model answered 76.9% of questions correctly but failed to specify decision-making cut-offs and treatment durations. Compared to physicians/trainees, ChatGPT lacked knowledge of regional guidelines variations, such as HCC screening criteria. However, it provided practical and multifaceted advice to patients and caregivers regarding the next steps and adjusting to a new diagnosis.ConclusionIn summary, we analyzed the areas of robustness and limitations of ChatGPT’s responses on the management of cirrhosis and HCC and relevant emotional support. ChatGPT may have a role as an adjunct informational tool for patients and physicians to improve outcomes.Conflict of Interest DisclosuresNone declared.Funding/SupportNoneEthics ApprovalSince all responses from ChatGPT were publicly available, approval from the institutional review board was not sought.Guarantors of article:Dr. Kuo and SpiegelAuthor ContributionsConcept and design: Yeo, Samaan, Spiegel, KuoAcquisition of data: Yeo, Samaan, Ng, VipaniData review: Ting, Trivedi, KuoStatistical analysis: YeoDrafting of the manuscript: Yeo, Samaan, NgCritical revision of the manuscript: All authors
A unifying model for discordant and concordant results in human neuroimaging studies of facial viewpoint selectivity
Authors: Revsine Cambria , Gonzalez-Castillo Javier , Merriam Elisha P , Bandettini Peter A , Ramírez Fernando M 
Published: February 2023

AbstractOur ability to recognize faces regardless of viewpoint is a key property of the primate visual system. Traditional theories hold that facial viewpoint is represented by view-selective mechanisms at early visual processing stages and that representations become increasingly tolerant to viewpoint changes in higher-level visual areas. Newer theories, based on single-neuron monkey electrophysiological recordings, suggest an additional intermediate processing stage invariant to mirror-symmetric face views. Consistent with traditional theories, human studies combining neuroimaging and multivariate pattern analysis (MVPA) methods have provided evidence of view-selectivity in early visual cortex. However, contradictory results have been reported in higher-level visual areas concerning the existence in humans of mirror-symmetrically tuned representations. We believe these results reflect low-level stimulus confounds and data analysis choices. To probe for low-level confounds, we analyzed images from two popular face databases. Analyses of mean image luminance and contrast revealed biases across face views described by even polynomials—i.e., mirror-symmetric. To explain major trends across human neuroimaging studies of viewpoint selectivity, we constructed a network model that incorporates three biological constraints: cortical magnification, convergent feedforward projections, and interhemispheric connections. Given the identified low-level biases, we show that a gradual increase of interhemispheric connections across network layers is sufficient to replicate findings of mirror-symmetry in high-level processing stages, as well as view-tuning in early processing stages. Data analysis decisions—pattern dissimilarity measure and data recentering—accounted for the variable observation of mirror-symmetry in late processing stages. The model provides a unifying explanation of MVPA studies of viewpoint selectivity. We also show how common analysis choices can lead to erroneous conclusions.
Force generation in the coiling tendrils ofPassiflora caerulea
Authors: Klimm Frederike , Speck Thomas , Thielen Marc 
Published: February 2023

AbstractTendrils of climbing plants coil along their length and thus form a striking helical spring and generate tensional forces. We have found that, for tendrils of the passion flowerPassiflora caerulea, the generated force lies in the range of 6-140 mN, which is sufficient to lash the plant tightly to its substrate. Further, we revealed that the generated force strongly correlates with the water status of the plant. By combining force measurements with anatomical investigations and dehydration-rehydration experiments on both entire tendril segments and isolated lignified tissues, we are able to propose a two-phasic principle of spring formation: First, during the free coiling phase, the tendril coiling is based on the active contraction of a fiber ribbon in interaction with the surrounding parenchyma as resistance layer. Second, in a stabilization phase, the entire center of the coiled tendril lignifies, stiffening the spring and securing its function independent of hydration status.
Inversely regulated immune-related processes mediate anxiety-obesity links in zebrafish
Authors: Yehuda Hila , Madrer Nimrod , Goldberg Doron , Soreq Hermona , Meerson Ari 
Published: February 2023

AbstractAnxiety disorders often associate with metabolic impairments, but the underlying developmental and molecular mechanisms are yet unknown. To seek RNAs that may link anxiety and obesity, we subjected RNA from zebrafish larvae of a caffeine-induced anxiety model and a high fat diet (HFD)-induced obesity model to RNA-sequencing. We found differentially expressed genes in the larval anxiety and obesity models, including long noncoding RNAs and transfer fragment RNAs. Surprisingly, they were inversely regulated and comprised overrepresentation of immune system pathways, e.g., interleukin signaling and inflammation. Similarly, inverse regulation persisted in adulthood, but with different overrepresented immune system processes, e.g., T cell activation, leukocyte cell-cell adhesion and antigen processing and presentation. Furthermore, unlike the known link in adult zebrafish, obesity in zebrafish larvae was not accompanied by anxiety-like behavior. These results may reflect an antagonistic pleiotropic phenomenon involving re-adjusted modulation of the anxiety-metabolic links with the immune system. Furthermore, the HFD potential to normalize the anxiety-upregulated immune-related genes may explain previously reported protective roles of high fat diet in rodent anxiety and Alzheimer’s disease models.
Palmitoyl transferase ZDHHC20 promotes pancreatic cancer metastasis
Authors: Tomić Goran , Sheridan Clare , Refermat Alice Y. , Baggelaar Marc P. , Sipthorp James , Sudarshan Bhuvana , Ocasio Cory A. , Suárez-Bonnet Alejandro , Priestnall Simon L. , Herbert Eleanor , Tate Edward W. , Downward Julian 
Published: February 2023

AbstractMetastasis is one of the defining features of pancreatic ductal adenocarcinoma (PDAC) that contributes to poor prognosis. In this study, the palmitoyl transferase ZDHHC20 was identified in anin vivoshRNA screen as critical for metastatic outgrowth, with no effect on proliferation and migrationin vitro, or primary PDAC growth in mice. This phenotype is abrogated in immunocompromised animals, and in animals with depleted natural killer (NK) cells, indicating that ZDHHC20 affects the interaction of tumour cells and the innate immune system. Using a chemical genetics platform for ZDHHC20-specific substrate profiling, a number of novel substrates of this enzyme were identified. These results describe a role for palmitoylation in enabling distant metastasis that could not have been detected usingin vitroscreening approaches and identify potential effectors through which ZDHHC20 promotes metastasis of PDAC.
Aquaporin-4 mediated aggregation of Alzheimer’s amyloid β-peptide
Authors: Maroli Nikhil 
Published: February 2023

AbstractClearance of Alzheimer’s amyloid oligomers from the brain is crucial for preventing cell toxicity. Dementia complications arise as a result of apoptosis, which is caused by peptide plaques on the lipid surface of cells. Here, we employed all-atom and coarse-grained molecular dynamics simulations to investigate the aggregation of amyloid peptides at the lipid surface and the role of the Aquaporin-4 (AQP4) in facilitating peptide clearance from astrocytes. The network of protein-protein interactions through text mining revealed that the expression of AQP4 and amyloid aggregation were strongly correlated. It has also been revealed that the role of aquaporins in the etiology of Alzheimer’s involves several interconnected proteins and pathways. The nature of aggregation at the surface of the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer was revealed by the interaction of amyloid oligomers. The membrane-bound pore region of AQP4 interacts with the peptide and slows its aggregation. This interaction maintains the helical content of the peptide while lowering its toxicity at the lipid surface. The hydrophobicity of the peptide also decreased because of these interactions, which may help in the removal of the peptide from astrocytes. Long-term coarse-grained MD simulations demonstrated different features of oligomer aggregation at the surface and strong oligomer attraction to AQP4, which inhibited aggregation. Additionally, the water dynamics of aquaporins demonstrate how the selectivity filter is broken to disrupt water flow. Our findings also provide insight into the physiological alterations in brain tissue associated with Alzheimer’s disease, including water retention and increased water flow in the CSF. Furthermore, in vitro thioflavin fluorescence spectroscopy revealed a slower aggregation of the peptide in the presence of AQP4.
Lower-limb Nonparametric Functional Muscle Network: Test-retest Reliability Analysis
Authors: O’Keeffe Rory , Yang Jinghui , Mehrdad Sarmad , Rao Smita , Atashzar S. Farokh 
Published: February 2023

AbstractObjectiveFunctional muscle network analysis has attracted a great deal of interest in recent years, promising high sensitivity to changes of intermuscular synchronicity, studied mostly for healthy subjects and recently for patients living with neurological conditions (e.g., those caused by stroke). Despite the promising results, the between- and within-session reliability of the functional muscle network measures are yet to be established. Here, for the first time, we question and evaluate the test-retest reliability of non-parametric lower-limb functional muscle networks for controlled and lightly-controlled tasks, i.e., sit-to-stand, and over-the-ground walking, respectively, in healthy subjects.MethodFifteen subjects (eight females) were included over two sessions on two different days. The muscle activity was recorded using 14 surface electromyography (sEMG) sensors. The intraclass correlation coefficient (ICC) of the within-session and between-session trials was quantified for the various network metrics, including degree and weighted clustering coefficient. In order to compare with common classical sEMG measures, the reliabilities of the root mean square (RMS) of sEMG and the median frequency (MDF) of sEMG were also calculated.ResultsThe ICC analysis revealed superior between-session reliability for muscle networks, with statistically significant differences when compared to classic measures.Conclusion and SignificanceThis paper proposed that the topographical metrics generated from functional muscle network can be reliably used for multi-session observations securing high reliability for quantifying the distribution of synergistic intermuscular synchronicities of both controlled and lightly controlled lower limb tasks. In addition, the low number of sessions required by the topographical network metrics to reach reliable measurements indicates the potential as biomarkers during rehabilitation.