bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Characteristics and Etiology of Community-acquired Pneumonia in US Children, 2015–2018
Authors: Yun Ki Wook , Wallihan Rebecca , Desai Ankita , Alter Sherman , Ambroggio Lilliam , Cohen Daniel M. , El-Assal Ossama , Marzec Sarah , Florin Todd A. , Keaton Meghan , Shah Samir S. , Ruddy Richard M. , Sharpe Samantha , Leber Amy L. , Everhart Kathy , Mejias Asuncion , Ramilo Octavio ,   on behalf of the Children’s Hospitals Initiative for Research in Pneumonia
Published: February 2022

Background:
Pneumonia has a major impact on childhood health and health care costs. This study was designed to obtain contemporary information on the clinical characteristics and etiology of community-acquired pneumonia (CAP) in children from both inpatient and outpatient settings in the USA.

Methods:
We conducted a prospective, multicenter, observational study of CAP among previously healthy children 2 months to 18 years of age in 6 children’s hospitals in Ohio from 2015 to 2018. For pathogen detection, nasopharyngeal swabs were collected from all subjects. Blood and pleural fluid cultures were available per standard of care.

Results:
We enrolled a convenience sample of 441 patients: 380 hospitalized and 61 outpatients. Tachypnea and radiologic findings of consolidation and pleural effusion were more frequent among inpatients than outpatients. A pathogen was detected in 64.6% of patients: viruses in 55.6%, atypical bacteria in 8.8% and pyogenic bacteria in 4.3%. Eighteen (4.1%) patients had both viruses and bacteria detected. Rhinovirus/enterovirus (RV; 18.6%) and respiratory syncytial virus (RSV; 16.8%) were the viruses most frequently detected, and Mycoplasma pneumoniae (8.2%) and Streptococcus pneumoniae (2.3%) were the most common bacteria. Except for S. pneumoniae, which was identified more frequently in inpatients, there were no significant differences between inpatients and outpatients in the proportions of children with specific pathogens detected.

Conclusions:
Rhinovirus/enterovirus and RSV among viruses and M. pneumoniae and S. pneumoniae among bacteria were the most common pathogens detected in children with CAP. Tachypnea and chest radiographs with consolidation and/or pleural effusion were associated with hospitalization.
Childhood-onset Takayasu arteritis
Authors: Millan Pamela , Gavcovich Tara B. , Abitbol Carolyn 
Published: February 2022

Purpose of review
Takayasu arteritis is a rare chronic granulomatous large vessel vasculitis that predominantly affects the aorta and its branches. The purpose of this review is to unite the current knowledge regarding the pathophysiology, cause, and epidemiology as well as diagnosis, prognosis, and treatment of this condition in children.

Recent findings
Although the etiopathogenesis is not fully understood, studies suggest an autoimmune basis for the disease as well as a genetic predisposition. It is a disease primarily affecting young women with up to a third of cases with onset in childhood. There are distinct features of childhood-onset Takayasu arteritis (cTA) that merit this separate review. Diagnostic criteria and clinical manifestations are unique in pediatric patients with renovascular hypertension being the most prevalent presentation. Traditional treatments involving high-dose corticosteroids and cytotoxic agents are being reconsidered for less toxic contemporary biologic agents. Current algorithms for treatment include early introduction of corticosteroid-sparing agents, such as methotrexate or mycophenolate as well as tumor necrosis factor-alpha (TNF-α) inhibitor (infliximab, adalimumab) and/or interleukin-6 (IL-6) receptor inhibitor (tocilizumab).

Summary
Early diagnosis of cTA with goals to develop effective and well tolerated treatment paradigms are essential to improve the long-term prognosis of this rare and devastating disease.
Incidence and risk factors for recurrent sexually transmitted infections among MSM on HIV pre-exposure prophylaxis
Authors: Zeggagh Jérémy , Bauer Rebecca , Delaugerre Constance , Carette Diane , Fressard Lisa , Charreau Isabelle , Chidiac Christian , Pialoux Gilles , Tremblay Cécile , Cua Eric , Robineau Olivier , Raffi François , Capitant Catherine , Spire Bruno , Meyer Laurence , Molina Jean Michel ,   and the Ipergay Study Group
Published: February 2022

Objective:
High rates of sexually transmitted infections (STIs) have been reported among pre-exposure prophylaxis (PrEP) users. We wished to assess the incidence and risk factors for recurrent STIs.

Design:
The ANRS IPERGAY trial was a prospective study investigating PrEP among MSM and transgender women in outpatient clinics in France and Canada. In all, 429 participants were enrolled, offered up to 4 years of PrEP and screened for bacterial STIs (syphilis, chlamydia and gonorrhea) at baseline and every 6 months.

Methods:
STIs incidence was calculated yearly. Cox proportional hazards model regression was used to explore associations between participants characteristics at baseline and recurrent STI during follow-up.

Results:
Over a median follow-up of 23 months, bacterial STI incidence was 75, 33, 13, 32 and 30 per 100 person-years for all STIs, rectal STIs, syphilis, gonorrhea and chlamydia, respectively. STI incidence significantly increased from the first year to the fourth year of the study (55 vs. 90 per 100 person-years, P < 0.001). During the study period, 167 participants (39%) presented with more than one bacterial STIs which accounted for 86% of all STIs. Baseline risk factors associated with recurrent STIs in a multivariate analysis were an STI at baseline [hazards ratio: 1.48 (95% confidence interval (CI): 1.06–2.07), P = 0.02], more than eight sexual partners in prior 2 months [hazards ratio: 1.72 (95% CI: 1.21–2.43), P = 0.002] and the use of gamma-hydroxybutyrate [hazards ratio: 1.66 (95% CI: 1.16–2.38), P = 0.005].

Conclusion:
STI incidence was high and increased over time. Most STIs were concentrated in a high-risk group that should be targeted for future interventions.
Synchronous Reconstruction of the Jaw Using a “One and a Half”-Barrel Fibular Bone Graft for Ossifying Fibroma Patients
Authors: Liu Tong , Zhou Qian , Ding Zhangfan , Xuan Ming , Wang Xiaoyi , Xie Huixu 
Published: February 2022

Background:
Ossifying fibroma is one of the common benign tumors that affect the appearance and functions of the jaw. Ossifying fibroma may exhibit a wide range of biological behaviors, leading to deformities involving the jaw and other secondary facial deformities. Hence, to improve the function of the jaw and the patient’s general facial appearance (bearing in mind each patient’s facial shape and, or appearance), the authors thus, however, used a ‘‘one and a half”-barrel fibular bone graft to achieve the ideal height and radian of the bone graft.

Case Presentation:
Between July 2017 and January 2021, the authors retrospectively collected and analyzed clinical and surgical data from 39 patients who had undergone operations in our hospital. Twenty patients were operated on using our new surgical method, whereas 19 patients received conventional or debulking operation. Clinical factors associated with the operation were assessed, including classification of the jaw defects, perioperative complications, and postoperative outcomes.

Results:
All the flaps ultimately survived. According to the postoperative satisfaction survey, patients who underwent reconstruction were satisfied with their postoperative facial appearance, with an average of 8.5 out of 10. Based on the preoperative clinical data, 26 patients had suitable bone grafts for dentures to improve their oral function.

Conclusions:
A ‘‘one and a half’’-barrel fibular bone graft effectively improves the facial appearance of patients and as well as provides an appropriate height and radian for the bone graft.
A new immunocompetent rectal cancer model to study radiation therapy
Authors: Kim Jin K. , Wu Chao , Del Latto Michael , Gao Yajing , Choi Seo-Hyun , Kierstead Maria , Sauvé Charles-Etienne Gabriel , Firat Canan , Perez Almudena Chaves , Sillanpaa Jussi , Chen Chin-Tung , Lawrence Kayla E. , Paty Philip B. , Barriga Francisco M , Shia Jinru , Sawyers Charles L. , Lowe Scott W. , García-Aguilar Julio , Romesser Paul B. , Smith J. Joshua 
Published: February 2022

AbstractWe describe a new mouse model of rectal cancer (RC) involving rapid tumor organoid engraftment via orthotopic transplantation; the resulting RC tumors invaded inward from the mucosal surface and metastasized to distant organs. Histologically the tumors closely resemble human RC and mirror remodeling of the tumor microenvirnoment (TME) in response to radiation. This murine RC model thus recapitulates the pathogenesis of human RC, thereby fulfilling the need for a physiologically accurate model for preclinical efficacy studies.
Biosynthesis and apoplast accumulation of the apocarotenoid pigment azafrin in parasitizing roots of Escobedia grandiflora
Authors: Cardona-Medina Edison , Santos Marisa , Nodari Rubens , Hornero-Méndez Damaso , Peris Arnau , Wong Darren C. J. , Matus José Tomás , Rodríguez-Concepción Manuel 
Published: February 2022

SummaryThe herbaceous hemiparasite Escobedia grandiflora (Orobanchaceae) is used in traditional medicine in the Andean region. Their roots accumulate an orange pigment with a significant relevance as a cooking dye that exhibits antioxidant and cardioprotective properties.The present work combined metabolic and cytological analyses with de novo transcriptome assembly, gene expression studies, and phylogenetic analyses to confirm the chemical identity of the pigment and investigate its biosynthesis and function in Escobedia roots.The pigment was conclusively shown to be azafrin, an apocarotenoid likely derived from the cleavage of β-carotene. Candidate genes for the production of azafrin in Escobedia roots are proposed based on RNA-seq supported by RT-qPCR and phylogeny reconstruction analyses. In particular, our data suggest that azafrin production relies a carotenoid cleavage dioxygenase (CCD) different from CCD7 and similar to CCD4 enzymes. We also show that azafrin is delivered to the root apoplast and that it accumulates in the area where the Escobedia haustorium contacts the host’s root, suggesting a role of azafrin in the parasitization process.Altogether, our work represents an unprecedented step forward in our understanding of the Escobedia parasitization system, but it also provides vital information towards the eventual domestication of this valuable medicinal plant.
Superparamagnetic iron oxide enclosed hollow gold nanostructure with tunable surface plasmon resonances to promote near-infrared photothermal conversion
Authors: Yuan Muzhaozi , Feng Xuhui , Yan Tian-Hao , Chen Jingfan , Ma Xuezhi , Cunha Preston , Lan Shoufeng , Li Ying , Zhou Hong-Cai , Wang Ya 
Published: February 2022

AbstractIn this study, to enhance deep tissue penetration by near-infrared (NIR) light, a novel superparamagnetic iron oxide enclosed hollow gold nanoshell (SPIO-HGNS) structure with tunable size and surface plasmon resonance (SPR) in the NIR range was designed and synthesized through a 2-step template-enabled galvanic replacement reaction. Here, Ag coated SPIO (SPIO-Ag) was prepared as a template with tunable outer diameters by way of adjusting the Ag content. SPIO-HGNS with variable hollow gold inner diameters can then be synthesized based on the determined outer diameter of the SPIO-Ag template through a galvanic replacement reaction between HAuCl3 and Ag coating on the SPIO surface. With incrementing amounts of Ag, three SPIO-HGNS structures were synthesized with comparable shell thicknesses around 6.7 nm and an average inner diameter of 38.7, 39.4, and 40.7 nm, respectively, evidenced by TEM and ICP results. The structure of SPIO-HGNS was confirmed by identifying Au111 lattice and the elemental mapping of Fe and Au using energy-dispersive X-ray spectroscopy. The Ultraviolet-Visible-NIR absorption spectra showed red-shifted SPR peaks (820, 855, and 945 nm) with the increasing inner diameters of SPIO-HGNS, which was also supported by an absorption cross-section simulation. The photothermal results showed that the three SPIO-HGNS structures, when exposed to ~30 s of 400 mW laser irradiation, exhibited photothermal temperature rises of 5.9, 4.6, and 2.9 °C, respectively. This study explored the tuning of SPR properties in NIR-responsive magneto-plasmonic nanoparticles through a facile preparation procedure, paving the way for potential applications in photothermal therapies.
Ingestion of microplastic fibres, but not microplastic beads, impacts growth rates in the tropical house cricket Gryllodes sigillatus
Authors: Fudlosid Serita , Ritchie Marshall W. , Muzzatti Matthew J. , Allison Jane E. , Provencher Jennifer , MacMillan Heath A. 
Published: February 2022

AbstractMicroplastic is a growing concern as an environmental contaminant as it is ubiquitous in our ecosystems. Microplastics are present in terrestrial environments, yet the majority of studies have focused on the adverse effects of microplastics on aquatic biota. We hypothesized that microplastic ingestion by a terrestrial insect would have localized effects on gut health and nutrient absorption, such that prolonged dietary microplastic exposure would impact growth rate and adult body size. We further hypothesized that plastic form (fibres vs. beads) would influence these effects because of the nature of gut-plastic interactions. Freshly hatched tropical house crickets (Gryllodes sigillatus) were fed a standard diet containing different concentrations of either fluorescent polyethylene microplastic beads (75-105 μm), or untreated polyethylene terephthalate microfibers (<5 mm) until they died or reached adulthood (approximately 8 weeks). Weight and body length were measured weekly and microplastic ingestion was confirmed through fluorescence microscopy and visual inspection of the frass. While, to our surprise, we found no effect of polyethylene bead ingestion on growth rate or final body size of G. sigillatus, females experienced a reduction in size and weight when fed high concentrations of polyethylene terephthalate microfibers. These results suggest that high concentrations of polyethylene beads of the 100 μm size range can pass through the cricket gut without a substantial negative effect on their growth and development time, but high concentrations of polyethylene terephthalate microfibers cannot. Although we report the negative effects of microplastic ingestion on the growth of G. sigillatus, it remains uncertain what threats microplastics pose to terrestrial insects.
Estimation of COVID-19 cases prevented by vaccination in California
Authors: Tan Sophia , Park Hailey , Rodríguez-Barraquer Isabel , Rutherford George W. , Bibbins-Domingo Kirsten , Lo Nathan C. 
Published: February 2022

AbstractImportanceDespite widespread vaccination against COVID-19 in the United States, there are limited empirical data quantifying the public health impact in the population.ObjectiveTo estimate the number of cases of COVID-19 averted due to COVID-19 vaccinationDesign, Setting, and ParticipantsThe California Department of Public Health (CDPH) provided person-level data on COVID-19 cases and COVID-19 vaccine administration. To estimate the number of COVID-19 cases that would have occurred in the vaccine era in absence of vaccination, we applied a statistical model that estimated the relationship of COVID-19 cases in the pre-vaccine era between the unvaccinated age group (<12 years) and vaccine-eligible groups (≥12 years) to COVID-19 case data after the start of vaccination. The primary study outcome was the difference between predicted number of COVID-19 cases in absence of vaccination and observed COVID-19 cases with vaccination. As a sensitivity analysis, we developed a second independent model that estimated the number of vaccine-averted COVID-19 cases by applying published data on vaccine effectiveness to data on COVID-19 vaccine administration and estimated risk of COVID-19 over time.InterventionCOVID-19 vaccinationMain Outcomes and MeasuresCOVID-19 casesResultsThere were 4,585,248 confirmed COVID-19 cases in California from January 1, 2020 to October 16, 2021, during which 27,164,680 vaccine-eligible individuals ≥12 years were reported to have received at least 1 dose of a COVID-19 vaccine in the vaccine era (79.5% of the eligible population). We estimated that 1,523,500 [95% prediction interval (976,800-2,230,800)] COVID-19 cases were averted and there was a 34% [95% prediction interval (25-43)] reduction in cases due to vaccination in the primary model. Approximately 66% of total cases averted occurred after the delta variant became the dominant strain of SARS-CoV-2 circulating in California. Our alternative model identified comparable findings.Conclusions and RelevanceThis study provides robust evidence on the public health impact of COVID-19 vaccination in the United States and further supports the urgency for continued vaccination.Key PointsQuestionHow many COVID-19 cases have been prevented by COVID-19 vaccination in California?FindingsIn this empirical analysis of California using data from the Department of Public Health, we estimated that COVID-19 vaccination has prevented over 1.5 million COVID-19 cases from the introduction of vaccination through October 16, 2021.MeaningThese findings support that COVID-19 vaccination had a large public health impact in California in terms of averted cases of COVID-19 and can be generalized across the United States.
Comparative transcriptomics unveil distinctive metabolic pathway of phosphonate utilization by diatom Phaeodactylum tricornutum
Authors: Shu Huilin , You Yanchun , Wang Hongwei , Wang Jingtian , Li Ling , Lin Xin , Ma Jian 
Published: February 2022

AbstractPhosphonates are important constituents of marine organic phosphorus, however, the bioavailability and catabolism of phosphonates by eukaryotic phytoplankton remain enigmatic. Here, we use diatom Phaeodactylum tricornutum to investigate the bioavailability of phosphonates and elaborate the underlying molecular mechanism. Our results showed that 2-aminoethylphosphonic (2-AEP) can be utilized as alternative phosphorus source. Comparative transcriptomics unveil the 2-AEP utilization comprising two steps, molecular uptake through clathrin-mediated endocytosis and incorporation into the membrane phospholipids in the form of diacylglyceryl-2-AEP (DAG-2-AEP). In the global ocean, we found the prevalence of key genes responsible for vesicle formation (CLTC, AP-2) and DAG-AEP synthesis (PCYT2 and EPT1) in diatom assemblage. In accordance with the observation of elevated transcript abundance in cold waters, our culture experiments showed that cells grown in 2-AEP are more active at lower temperature. This study elucidated a distinctive mechanism of phosphonate utilization by diatom and inspected the ecological implications in adaptive mechanism.
An intergeneric recombinant geminivirus causes soybean stay-green disease
Authors: Cheng Ruixiang , Mei Ruoxin , Yan Rong , Chen Hongyu , Miao Dan , Cai Lina , Fan Jiayi , Li Gairu , Xu Ran , Lu Weiguo , Gao Yu , Ye Wenwu , Su Shuo , Han Tianfu , Gai Junyi , Wang Yuanchao , Tao Xiaorong , Xu Yi 
Published: February 2022

AbstractSoybean is one of the most valuable legume crops in the world with high nutritional value. Recently, the outbreak of soybean stay-green syndrome has swept the soybean production in the Huang-Huai-Hai region of China, resulting in huge yield losses, which has become an epidemic and prominent problem in soybean production. However, the cause of the stay-green syndrome remains obscure. Here, we report a novel intergeneric recombinant geminivirus which causes soybean stay-green symptoms. Viral small RNA-based screening identified a new recombinant geminvirus from field soybean stay-green samples. The complete genome sequence of the virus contains 2762 nucleotide (nt) and appears to be an intergeneric recombinant virus in which protein coding for coat protein (V1) is similar to member of genus Mastrevirus, whereas proteins coding for V2, C2, C3 are most similar to those of viruses in the Maldovirus genus, and C1 and C4 are most similar to virus in genus Begomovirus. Inoculation of the infectious clone of the recombinant geminivirus through Agrobacterium rhizogenes causes typical soybean stay-green syndrome which resembles field symptoms including delayed leaf senescence, flat pods and abnormal seeds. The recombinant geminivirus can be detected in seed coat but not in cotyledon and embryo, thus failing to be transmitted by seeds. Moreover, the genome variation and epidemiological dynamic analysis were also carried out to help the continuous epidemiological surveillance of this emerging geminivirus. Collectively, this new geminivirus is tentatively named soybean stay-green associated virus (SoSGV). Our determination of the causal agent of soybean stay-green disease will bolster efforts to develop effective management strategies to control this prevalent disease in the field.
Flavobacterium johnsoniae Tyrosine Ammonia Lyase (FjTAL) in-silico Structure Prediction and Molecular Docking to L-Tyrosine, p-Coumaric Acid (pHCA) and Caffeic Acid
Authors: Majd Seyyed Amirreza Mousavi 
Published: February 2022

AbstractResponsible for the conversion of L-tyrosine to p-coumaric acid in Flavobacterium johnsoniae, FjTAL has drawn the attention of many biochemical engineers who wish to carry out a sustainable biosynthetic scheme for the production of aromatic compounds. In this study, with the aid of various computational tools, the secondary and tertiary structures of FjTAL have been predicted. The results suggest that FjTAL forms a homo-tetramer when active as a cytosolic enzyme and it is mostly consisted of alpha helices. With the aid of molecular docking, one can hypothesize that FjTAL is likely to bind to L-tyrosine, p-coumaric acid, and caffeic acid with a similar molecular mechanism and thus, p-coumaric acid and caffeic acid may exhibit a negative feedback response toward the enzyme and inhibit its activity competitively. Two distinct binding pockets have been discovered, one of which contains highly conserved residues among several species. The residues which form the prosthetic group 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) also emerge in the evolutionary conserved binding pocket. The other discovered cavity, could either be a second binding site for the ligands or simply an artifact of the molecular docking task.
Pancreas resident macrophage-induced fibrosis has divergent roles in pancreas inflammatory injury and PDAC
Authors: Baer John M. , Zuo Chong , Kang Liang-I , Alarcon de la Lastra Angela , Borcherding Nicholas C. , Knolhoff Brett L. , Bogner Savannah J. , Zhu Yu , Lewis Mark A. , Zhang Nan , Kim Ki-Wook , Fields Ryan C. , Mills Jason C. , Ding Li , Randolph Gwendalyn J. , DeNardo David G. 
Published: February 2022

SummaryTissue-resident macrophages (TRMs) are long-lived cells that maintain locally and can be phenotypically distinct from monocyte-derived macrophages (MDMs). However, whether TRMs and MDMs have functional distinction under differing pathologies is not understood. Here, we show a significant portion of macrophages that accumulated during pancreatitis and pancreatic cancer were expanded from TRMs. We further established that pancreas TRMs have a distinct extracellular matrix remodeling phenotype that was critical for maintaining tissue homeostasis during inflammation. Loss of TRMs led to exacerbation of severe pancreatitis and animal death, due to impaired acinar cell survival and recovery. In pancreatitis, TRMs elicited protective effects by triggering the accumulation and activation of fibroblasts, which was necessary for initiating fibrosis as a wound healing response. The same TRM-driven fibrosis, however, drove pancreas cancer pathogenesis and progression. Together, these findings indicate that TRMs play divergent roles in the pathogenesis of pancreatitis and cancer through regulation of stromagenesis.