bluuebunny/crossref_metadata_2025_split huggingface dataset:
Health‐Related Quality of Life in Pediatric Inflammatory Bowel Disease During COVID‐19 Pandemic
Authors: Fedele Flora , Martinelli Massimo , Strisciuglio Caterina , Dolce Pasquale , Giugliano Francesca Paola , Scarpato Elena , Staiano Annamaria , Miele Erasmo 
Published: July 2022

Objectives:The aims of our study were to evaluate health‐related quality of life (HRQoL) in children affected by inflammatory bowel disease (IBD) during the first wave of Coronavirus disease 2019 (COVID‐19) pandemic and after 12 months.Methods:This was a single‐center, prospective, observational study conducted between April 2020 and April 2021. Children from 10 to 18 years with a confirmed diagnosis of IBD were enrolled during the first COVID‐19–related national quarantine. The following information was collected at the baseline and after 12 months: IBD subtype, location and phenotype, disease activity, current and previous therapies. Patients were asked to complete the PROMIS Anxiety and IMPACT III questionnaires.Results:One hundred and eighteen patients were enrolled, of whom 54 (46%) were affected by Crohn disease (CD) and 64 (54%) with ulcerative colitis (UC; median age: 15.5 years, range 10.3–18; M/F: 68/50). Median HRQoL was significantly decreased after 12 months compared with the beginning of COVID‐19–related quarantine (T1: 76.7 vs T2: 72.8; P < 0.001). At 12 months, a higher number of children were reported to be in active disease when compared with the enrollment [T2: 22/108 (20.4%) vs T1: 12/118 (10%); P = 0.02]. Multivariate analysis showed a significant influence on HRQoL of quarantine period (P < 0.001), female sex (P = 0.016), biologic therapy (P = 0.011), and active disease (P < 0.001).Conclusions:A deterioration of HRQoL after 12 months from COVID‐19–related quarantine was observed. Additionally, the higher number of children with active disease at 12 months compared with enrollment may suggest detrimental consequences of the reduced disease control, contributing to decreased HRQoL.
Intensive Outpatient Treatment of Pediatric Rumination Syndrome in the Era of Telemedicine
Authors: Hawa Kathryn , Lu Peter L. , Holzmacher Meghan , Wall Jody , Bali Neetu , Vaz Karla , Yacob Desale , Di Lorenzo Carlo , Van Diest Ashley Kroon 
Published: July 2022

Objectives:We have had success treating children with severe rumination syndrome using a multidisciplinary intensive outpatient program (IOP) involving multiple treatment sessions daily. During the coronavirus disease 2019 (COVID‐19) pandemic, we temporarily transitioned care to telemedicine. The objective of this study is to compare outcomes of patients with rumination syndrome who completed IOP treatment in person versus by telemedicine.Methods:We performed a retrospective review of patients diagnosed with rumination syndrome who participated in IOP treatment from 2018 to 2020. Similar treatment sessions were performed involving medical and behavioral techniques provided by a multidisciplinary team during telemedicine visits. Families/patients were asked to complete a survey outlining their child’s current rumination symptom severity and review the IOP.Results:We included 34 patients (79% F, median age 15 years, range 7–19 years) who completed IOP treatment. Twenty‐six patients (76%) were treated in person and 8 patients (24%) by telemedicine. For patients treated in person, 76% (19/25) had improvement in symptoms while 16% (4/25) had complete resolution of symptoms. For patients treated by telemedicine, 88% (7/8) had improvement in their symptoms. There were no significant differences between groups in likelihood of improvement. Overall, 78% (18/23) preferred in person therapy while 17% (4/23) did not have a preference. All 18 of the in‐person cohort who completed follow‐up surveys preferred in‐person management.Conclusions:Multidisciplinary intensive outpatient treatment for children and adolescents with severe rumination syndrome is effective. Although telemedicine may be an alternative to in person therapy, majority of families prefer in person visits.
Titers and capacity of neutralizing antibodies against SARS-CoV-2 variants after heterologous booster vaccination in health care workers primed with two doses of ChAdOx1 nCov-19: a single-blinded, randomized clinical trial
Authors: Chuang Chih-Hsien , Huang Chung-Guei , Huang Ching-Tai , Chen Yi-Ching , Kung Yu-An , Chen Chih-Jung , Chuang Tzu-Chun , Liu Ching-Chi , Huang Po-Wei , Yang Shu-Li , Gu Po-Wen , Shih Shin-Ru , Chiu Cheng-Hsun 
Published: July 2022

AbstractBackgroundBooster vaccination is important because of waning immunity and variant immune evasion. We conducted a single-blinded, randomized trial to evaluate the safety, reactogenicity, and immunogenicity of heterologous booster vaccination in health care workers (HCW) who had received two doses of ChAdOx1 nCov-19.Methods and findingsHCW at least 90 days after the second dose were enrolled to receive one of the four vaccines: BNT162b2, half-dose mRNA-1273, mRNA-1273, and MVC-COV1901. The primary outcomes were humoral and cellular immunogenicity and the secondary outcomes safety and reactogenicity 28 days post-booster. 340 HCW were enrolled: 83 received BNT162b2 (2 excluded), 85 half-dose mRNA-1273, 85 mRNA-1273, and 85 MVC-COV1901. mRNA vaccines had more reactogenicity than protein vaccine.Anti-spike IgG increased by a fold of 8.4 for MCV-COV1901, 32.2 for BNT162b2, 47.6 for half-dose mRNA-1273 and 63.2 for mRNA1273. The live virus microneutralization assay (LVMNA) against the wild type, alpha and delta variants were consistent with anti-spike IgG for all booster vaccines. The LVMNA in the four groups against omicron variant were 6.4 to 13.5 times lower than those against the wild type. Serum neutralizing antibody against omicron variant was undetectable in 60% of the participants who received MCV-COV1901 as a booster by LVMNA. By using pseudovirus neutralizing assay, we found that neutralization activity in the four groups against omicron variant were 4.6 to 5.2 times lower than that against the D614G. All booster vaccines induced comparable T cell response.ConclusionsThird dose booster not only increases neutralizing antibody titer but also enhances antibody capacity against SARS-CoV-2 variants. mRNA vaccines are preferred booster vaccines for those after primary series of ChAdOx1 nCov-19.Trial registrationClinicalTrials.govNCT05132855
Virtual wards: A rapid evidence synthesis and implications for the care of older people
Authors: Norman Gill , Bennett Paula , Vardy Emma R.L.C. 
Published: July 2022

AbstractVirtual wards are an area of rapid development within the National Health Service in the UK, and frailty has been selected as one of the first clinical pathways to be developed. This is in the context of existing longstanding hospital at home services in some areas. A rapid evidence synthesis was completed to guide the local healthcare system in the North West of England. This is a rapid approach to synthesising existing research which focuses on existing evidence synthesis where possible. Questions were addressed on clinical-effectivness, cost-effectiveness, barriers and facilitators, models of care and use in practice, and staff and patient and carer experience. We found that whilst there was a significant evidence base for hospital at home, there was less evidence for virtual wards. There is lack of guidance for key aspects of virtual wards including team characteristics, outcome selection and data protection. We recommend that research and evaluation is integrated into development of virtual ward models of care. Of particular relevance for older people cared for on virtual wards is the issue of carer strain, an area which may be frequently overlooked.
The Art of Pain: A Quantitative Colour Analysis of the Self-Portraits of Frida Kahlo
Authors: Turkheimer Federico E. , Liu Jingyi , Fagerholm Erik D. , Dazzan Paola , Loggia Marco L. , Bettelheim Eric 
Published: July 2022

ABSTRACTFrida Kahlo (1907-1954) was a Mexican artist who is remembered for her self-portraits, pain and passion, and bold, vibrant colours. This work aims to use her life story and her artistic production in a longitudinal study to examine with quantitative tools the effects of physical and emotional pain (rage) on artistic expression.Kahlo suffered from polio as a child, was involved in a bus accident as a teenager where she suffered multiple fractures of her spine and had 30 operations throughout her lifetime. She also had a tempestuous relationship with her painter husband, Diego Rivera. Her physical and personal troubles however became the texture of her vivid visual vocabulary — usually expressed through the depiction of Mexican and indigenous culture or the female experience and form.We applied colour analysis to a series of Frida’s self-portraits and revealed a very strong association of physical pain and emotional rage with low wavelength colours (red and yellow), indicating that the expression of her ailments was, consciously or not, achieved by increasing the perceived luminance of the canvas. Further quantitative analysis that used the fractal dimension identified “The broken column” as the portrait with higher compositional complexity, which matches previous critical acclaim of this portrait as the climax of her art. These results confirm the ability of colour analysis to extract emotional and cognitive features from artistic work. We suggest that these tools could be used as markers to support artistic and creative interventions in mental health.
Integrating Isoniazid Preventive Therapy into the Fast-Track HIV Treatment Model in Urban Zambia: A Proof-of -Concept Pilot Project
Authors: Mukumbwa-Mwenechanya Mpande , Mubiana Muhau , Somwe Paul , Zyambo Khozya , Simwenda Maureen , Zongwe Nancy , Kalunkumya Estella , Mwango Linah Kampilimba , Rabkin Miriam , Mpesela Felton , Chungu Fred , Mwanza Felix , Preko Peter , Bolton-Moore Carolyn , Bosomprah Samuel , Sharma Anjali , Morton Khunga , Kasonde Prisca , Mulenga Lloyd , Lingu Patrick , Mulenga Priscilla Lumano 
Published: July 2022

AbstractIntroductionMost people living with HIV (PLHIV) who are established on treatment in Zambia receive multi-month prescribing and dispensing (MMSD) of antiretroviral therapy (ART) and are enrolled in less-intensive differentiated service delivery (DSD) models, such as Fast Track (FT), in which clients pick up ART every 3-6 months and make clinical visits to health facilities every 6 months. In 2019, Zambia introduced Isoniazid Preventive Therapy (IPT) with scheduled visits at 2 weeks and 1, 3, and 6 months. The asynchronous IPT and HIV appointment schedules were inconvenient and not client centered. In response, we piloted integrated MMSD/IPT in the FT HIV treatment model.MethodsWe implemented and evaluated a proof-of-concept pilot project at one purposively selected high-volume facility in Lusaka, Zambia between July 2019 and May 2020. We sensitized stakeholders, adapted training materials and standard operating procedures, and screened adults in FT for TB as per national guidelines. Participants received structured TB/IPT education, a 6-month supply of isoniazid and ART, an aligned 6th month IPT/MMSD clinic appointment, and phone appointments at 2 weeks and months 1-5 following IPT initiation. We used descriptive statistics to characterize IPT completion rates, phone appointment keeping, side effect frequency and Fisher’s exact test to determine if these varied by participant characteristics. Notes from monthly meetings and discussions were used to synthesize key lessons learned.Results1,167 clients were screened for eligibility and 818 (70.1%) were enrolled. Two thirds (66%) were female, median age was 42 years, and 56.6% had been on ART for ≥ 5 years. 738 (90.2%) completed a 6-month course of IPT and 66 (8.1%) reported IPT-related side effects. 539 clients (65.9%) attended all 7 telephone appointments. There were no significant differences in these outcomes by age, sex, or time on ART. Lessons learnt include the value of promoting project ownership, client empowerment, securing supply chain, adapting existing processes, and cultivating a collaborative structured learning environment.ConclusionsIntegrating multi-month dispensing and telephone follow up of IPT into the FT HIV treatment model is a promising approach to scaling-up TB preventive treatment among PLHIV, although limited by barriers to consistent phone access.
MetaGeneMark-2: Improved Gene Prediction in Metagenomes
Authors: Gemayel Karl , Lomsadze Alexandre , Borodovsky Mark 
Published: July 2022

AbstractAccurate prediction of protein-coding genes in metagenomic contigs presents a well-known challenge. Particularly difficult is to identify short and incomplete genes as well as positions of translation initiation sites. It is frequently assumed that initiation of translation in prokaryotes is controlled by a ribosome binding site (RBS), a sequence with the Shine-Dalgarno (SD) consensus situated in the 5’ UTR. However, ∼30% of the 5,007 genomes, representing the RefSeq collection of prokaryotic genomes, have either non-SD RBS sequences or no RBS site due to physical absence of the 5’ UTR (the case of leaderless transcription). Predictions of the gene 3’ ends are much more accurate; still, errors could occur due to the use of incorrect genetic code. Hence, an effective gene finding algorithm would identify true genetic code in a process of the sequence analysis. In this work prediction of gene starts was improved by inferring the GC content dependent generating functions for RBS sequences as well as for promoter sequences involved in leaderless transcription. An additional feature of the algorithm was the ability to identify alternative genetic code defined by a reassignment of the TGA stop codon (the only stop codon reassignment type known in prokaryotes). It was demonstrated that MetaGeneMark-2 made more accurate gene predictions in metagenomic sequences than several existing state-of-the-art tools.
Leptospira interrogans prevents macrophage cell death and pyroptotic IL1β release through its atypical lipopolysaccharide
Authors: Bonhomme Delphine , Hernandez-Trejo Veronica , Papadopoulos Stylianos , Pigache Rémi , d’Andon Martine Fanton , Outlioua Ahmed , Boneca Ivo G. , Werts Catherine 
Published: July 2022

AbstractLeptospira interrogans are bacteria that can infect all vertebrates and are responsible for leptospirosis, a neglected zoonosis. Some hosts are susceptible to leptospirosis whereas mice are resistant and get chronically colonized. Although leptospires escape recognition by some immune receptors, they activate NLRP3-inflammasome and trigger IL1β secretion. Classically, IL1β secretion is associated with lytic inflammatory cell death called pyroptosis, resulting from cytosolic LPS binding to inflammatory caspases. Interestingly, we showed that L. interrogans do not trigger cell death in either murine, human, hamster, or bovine macrophages, escaping both pyroptosis and apoptosis. Strikingly, we also revealed in murine cells, a potent antagonistic effect of leptospires and their atypical LPS on spontaneous and E. coli LPS-induced cell death. The leptospiral LPS efficiently prevents caspase 11 dimerization and subsequent gasdermin D cleavage. Finally, we showed that pyroptosis escape by leptospires prevents massive IL1 β release, and we consistently found no major role of IL1-Receptor in controlling experimental leptospirosis in vivo. Overall, our findings described a novel mechanism by which leptospires dampen inflammation, thus potentially contributing to their stealthiness.Graphical abstract
Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets
Authors: Zhang Shilu , Pyne Saptarshi , Pietrzak Stefan , Halberg Spencer , McCalla Sunnie Grace , Siahpirani Alireza Fotuhi , Sridharan Rupa , Roy Sushmita 
Published: July 2022

AbstractCell type-specific gene expression patterns are outputs of transcriptional gene regulatory networks (GRNs) that connect transcription factors and signaling proteins to target genes. Single-cell technologies such as single cell RNA-sequencing (scRNA-seq) and single cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq), can examine cell-type specific gene regulation at unprecedented detail. However, current approaches to infer cell type-specific GRNs are limited in their ability to integrate scRNA-seq and scATAC-seq measurements and to model network dynamics on a cell lineage. To address this challenge, we have developed single-cell Multi-Task Network Inference (scMTNI), a multi-task learning framework to infer the GRN for each cell type on a lineage from scRNA-seq and scATAC-seq data. Using simulated and real datasets, we show that scMTNI is a broadly applicable framework for linear and branching lineages that accurately infers GRN dynamics and identifies key regulators of fate transitions for diverse processes such as cellular reprogramming and differentiation.
Coevolution-based prediction of key allosteric residues for protein function regulation
Authors: Xie Juan , Zhang Weilin , Zhu Xiaolei , Deng Minghua , Lai Luhua 
Published: July 2022

AbstractAllostery is fundamental to many biological processes. Due to the distant regulation nature, how allosteric mutations, modifications and effector binding impact protein function is difficult to forecast. In protein engineering, remote mutations cannot be rationally designed without large scale experimental screen. Allosteric drugs have raised much attention due to their high specificity and possibility of overcoming existing drug-resistant mutations. However, optimization of allosteric compounds remains challenging. Here, we developed a novel computational method KeyAlloSite to predict allosteric site and to identify key allosteric residues (allo-residues) based on the evolutionary coupling model. We found that protein allosteric sites are strongly coupled to orthosteric site compared to non-functional sites. We further inferred key allo-residues by pairwise comparing the difference of evolutionary coupling scores of each residue in the allosteric pocket with the functional site. Our predicted key allo-residues are in accordance with previous experimental studies for typical allosteric proteins like BCR-ABL1, Tar and PDZ3, as well as key cancer mutations. We also showed that KeyAlloSite can be used to predict key allosteric residues distant from the catalytic site that are important for enzyme catalysis. Our study demonstrates that weak coevolutionary couplings contain important information of protein allosteric regulation function. KeyAlloSite can be applied in studying the evolution of protein allosteric regulation, designing and optimizing allosteric drugs, performing functional protein design and enzyme engineering.
LLPSWise - fast and accurate prediction of LLPS constituents
Authors: Pu Mengchen , Fu Biao , Zhang Yingsheng J. 
Published: July 2022

AbstractThe recent discovery of different types of biological liquid-liquid phase separation (LLPS) systems presents enormous opportunities to uncover underlying biological mechanisms from a single-molecule level to mesoscopic scales and beyond. While progress has been made on the front of computational prediction of LLPS propensity of proteins, the constituent identification of LLPS systems continues to be a pertinent issue that has yet to be addressed. Compiled evidence indicates that the biological mechanism of LLPS involves the employment of different biomolecules into their liquid-liquid separation phase. Since constituent identification relies on experimental approaches, the process is arduous and inefficient. Here, we propose a sequence based LLPS propensity prediction method and scan the human proteome and biochemical pathways to establish a systematic biological view of LLPS. Additionally, we present a fast, accurate method for identifying the constituents of LLPS systems. The source code for our method is available via https://github.com/promethiume/LLPSWise
Fully Desktop Fabricated Flexible Graphene Electrocorticography (ECoG) Arrays
Authors: Hu Jia , Hossain Ridwan Fayaz , Navabi Zahra S. , Tillery Alana , Laroque Michael , Donaldson Preston D. , Swisher Sarah L. , Kodandaramaiah Suhasa B. 
Published: July 2022

ABSTRACTFlexible Electrocorticography (ECoG) electrode arrays that conform to the cortical surface and record surface field potentials from multiple brain regions provide unique insights into how computations occurring in distributed brain regions mediate behavior. Current flexible ECoG devices require highly specialized microfabrication methods, precluding the ability to fabricate customizable and low-cost flexible ECoG devices easily. Here we present a fully desktop fabricated flexible graphene ECoG array. First, we synthesized a stable, conductive ink via liquid exfoliation of Graphene in Cyrene. Next, we have established a stencil-printing process for patterning the graphene ink via laser-cut stencils on flexible polyimide substrates. Benchtop tests indicate that the graphene electrodes have good conductivity of ∼ 1.1 × 103 S·cm-1, flexibility to maintain their electrical connection under static bending, and electrochemical stability in a 15-day accelerated corrosion test. Chronically implanted graphene ECoG devices remain fully functional for up to 180 days, with average in vivo impedances of 24.72 ± 95.23 k Ω at 1 kHz. The ECoG device can measure spontaneous surface field potentials from mice under awake and anesthetized states and sensory stimulus-evoked responses. The stencil-printing fabrication process can be used to create Graphene ECoG devices with customized electrode layouts within 24 hours using commonly available laboratory equipment.
Readiness to retrieve memories of different ages: An ERP dissociation of orienting and difficulty
Authors: Leiker Emily K. , Johnson Jeffrey D. 
Published: July 2022

ABSTRACTA well-established finding in episodic memory research is that the likelihood of successful retrieval is affected by the ‘age’ of the targeted memory (i.e. based on the duration of the encoding-retrieval interval). Although such findings are usually interpreted in terms of the memory trace changing in quality or accessibility over time, there is growing evidence that memory performance also depends on preparatory attention and strategic orienting at the time of retrieval. Here, we investigated such readiness to retrieve, as indexed by event-related brain potentials (ERPs), when memory retrieval was aimed toward candidate traces of different ages. As retrieving remote versus recent memories is associated with increased difficulty, the current study was designed to dissociate difficulty from the memory age effects. Subjects encoded two lists of pictures separated by one week, with the items in each list presented once or four times. A series of memory tests targeting pictures from only one week-by-repetition condition at a time were then completed, while new pictures and those from the other conditions were rejected. Consistent with previous results, new-item ERPs were more positive over posterior scalp when recent compared to remote lists were targeted. Importantly, this difference remained when difficulty was matched, and the ERP correlates of difficulty were distinct in both timing and polarity from those of orienting. Together, these findings provide further support for the idea that the age of a targeted memory alone places different demands on readiness and can lead to the differential adoption of retrieval orienting strategies.