bluuebunny/crossref_metadata_2025_split huggingface dataset:
The US Coronavirus Disease 2019 (COVID-19) Surveillance Environment: An Ecological Analysis of the Relationship of Testing Adequacy in the Context of Vaccination
Authors: Choi Daesung , Nielsen Jannie , Waller Lance A , Patel Shivani A 
Published: June 2022

Abstract

Background
Coronavirus disease 2019 (COVID-19) testing is a critical component of public health surveillance and pandemic control, especially among the unvaccinated, as the nation resumes in-person activities. This study examined the relationships between COVID-19 testing rates, testing positivity rates, and vaccination coverage across US counties.

Methods
Data from the Health and Human Services’ Community Profile Report and 2016–2020 American Community Survey 5-Year Estimates were used. A total of 3114 US counties were analyzed from January through September 2021. Associations among the testing metrics and vaccination coverage were estimated using multiple linear regression models with fixed effects for states and adjusted for county demographics. COVID-19 testing rates (polymerase chain reaction [PCR] testing per 1000), testing positivity (percentage of all PCR tests that were positive), and vaccination coverage (percentage of county population that was fully vaccinated) were determined.

Results
Nationally, median daily COVID-19 testing rates were highest in January and September (35.5 and 34.6 tests per capita, respectively) and lowest in July (13.2 tests per capita). Monthly testing positivity was between 0.03 and 0.12 percentage points lower for each percentage points of vaccination coverage, and monthly testing rates were between 0.08 and 0.22 tests per capita higher for each percentage point of vaccination coverage.

Conclusions
The quantity of COVID-19 testing was associated with vaccination coverage, implying counties having populations with relatively lower protection against the virus are conducting less testing than counties with relatively more protection. Monitoring testing practices in relation to vaccination coverage may be used to monitor the sufficiency of COVID-19 testing based on population susceptibility to the virus.
Antibiotic Use and Stewardship Practices in a Pediatric Community-based Cohort Study in Peru: Shorter Would be Sweeter
Authors: Schiaffino Francesca , Colston Josh M , Paredes Olortegui Maribel , Rengifo Pinedo Silvia , Zamora Babilonia Marcelo , Ramal Asayag Cesar , Peñataro Yori Pablo , Kosek Margaret N 
Published: June 2022

Abstract

Background
There is a need to evaluate antibiotic use, duration of therapy, and stewardship in low- and middle-income countries to guide the development of appropriate stewardship programs that are global in scope and effectively decrease unnecessary antibiotic use.

Methods
We prospectively collected information on illness occurrence and antibiotic use from a cohort of 303 children. We evaluated the incidence, duration of therapy, and appropriateness of antibiotic prescriptions by 5 main antibiotic prescribers (physicians and nurses, pharmacists, nursing assistants, self-prescriptions, and neighbors or family members).

Results
Ninety percent of children received an antibiotic during follow-up, and on average, by the end of follow-up a child had spent 4.3% of their first 5 years of life on antibiotics. The most frequent prescribers were physicians/nurses (79.4%), followed by pharmacists (8.1%), self-prescriptions (6.8%), nursing assistants (3.7%), and family or neighbors (1.9%). Of the 3702 courses of antibiotics prescribed, 30.9% were done so for the occurrence of fever, 25.3% for diarrhea, 2.8% for acute lower respiratory disease, 2.7% for dysentery, and 38.2% for an undetermined illness. Courses exceeding the recommended duration were common for the principal diseases for which treatment was initiated, with 27.3% of courses exceeding the recommended length duration, representing a potential reduction in 13.2% of days on which this cohort spent on antibiotics.

Conclusions
Stewardship programs should target medical personnel for a primary care stewardship program even in a context in which antibiotics are available to the public with little or no restrictions and appropriate duration should be emphasized in this training.
Doubly robust identification for causal panel data models
Authors: Arkhangelsky Dmitry , Imbens Guido W 
Published: June 2022

SummaryWe study identification and estimation of causal effects in settings with panel data. Traditionally, researchers follow model-based identification strategies relying on assumptions governing the relation between the potential outcomes and the observed and unobserved confounders. We focus on a different, complementary approach to identification, where assumptions are made about the connection between the treatment assignment and the unobserved confounders. Such strategies are common in cross-section settings, but rarely used with panel data. We introduce different sets of assumptions that follow the two paths to identification and develop a double robust approach. We propose estimation methods that build on these identification strategies.
Microbial biodiversity contributes to soil carbon release: a case study on fire disturbed boreal forests
Authors: Zhou Xuan , Sun Hui , Heinonsalo Jussi , Pumpanen Jukka , Berninger Frank 
Published: June 2022

AbstractMicrobial communities often possess enormous diversity, raising questions about whether this diversity drives ecosystem functioning, especially the influence of diversity on soil decomposition and respiration. Although functional redundancy is widely observed in soil microorganisms, evidence that species occupy distinct metabolic niches has also emerged. In this paper, we found that apart from the environmental variables, increases in microbial diversity, notably bacterial diversity, lead to an increase in soil C emissions. This was demonstrated using structural equation modelling (SEM), linking soil respiration with naturally differing levels of soil physio-chemical properties, vegetation coverage, and microbial diversity after fire disturbance. Our SEMs also revealed that models including bacterial diversity explained more variation of soil CO2 emissions (about 45%) than fungal diversity (about 38%). A possible explanation of this discrepancy is that fungi are more multifunctional than bacteria and, therefore, an increase in fungal diversity does not necessarily change soil respiration. Further analysis on functional gene structure suggested that bacterial and fungal diversities mainly explain the potential decomposition of recalcitrant C compare with that of labile C. Overall, by incorporating microbial diversity and the environmental variables, the predictive power of models on soil C emission was significantly improved, indicating microbial diversity is crucial for predicting ecosystem functions.
Glyphosate-based herbicide exposure: effects on gill microbiota of rainbow trout (Oncorhynchus mykiss) and the aquatic bacterial ecosystem
Authors: Bellec Laure , Le Du-Carré Jessy , Almeras Fabrice , Durand Lucile , Cambon-Bonavita Marie-Anne , Danion Morgane , Morin Thierry 
Published: June 2022

AbstractThe herbicide glyphosate has been widely used in the past 40 years, under the assumption that side effects were minimal. In recent years, its impact on microbial compositions and potential indirect effects on plant, animal and human health have been strongly suspected. Glyphosate and co-formulates have been detected in various water sources, but our understanding of their potential effects on aquatic animals is still in its infancy compared with mammals. In this study, we investigated the effect of chronic exposure to an environmentally relevant concentration of glyphosate on bacterial communities of rainbow trout (Oncorhynchus mykiss). Gills, gut contents and gut epithelia were then analyzed by metabarcoding targeting the 16S rRNA gene. Our results revealed that rainbow trout has its own bacterial communities that differ from their surrounding habitats and possess microbiomes specific to these three compartments. The glyphosate-based herbicide treatment significantly affected the gill microbiome, with a decrease in diversity. Glyphosate treatments disrupted microbial taxonomic composition and some bacteria seem to be sensitive to this environmental pollutant. Lastly, co-occurrence networks showed that microbial interactions in gills tended to decrease with chemical exposure. These results demonstrate that glyphosate could affect microbiota associated with aquaculture fish.
Using champion-oriented mindset to overcome the challenges of graduate school: impact of workshop for graduate school skills on underrepresented minority retention
Authors: Marshall Andrea G , Palavicino-Maggio Caroline B , Neikirk Kit , Vue Zer , Beasley Heather K , Garza-Lopez Edgar , Murray Sandra A , Martinez Denise , Crabtree Amber , Conley Zachary C , Vang Larry , Davis Jamaine S , Powell-Roach Keesha L , Campbell Susan , Dal Angyth B , Shao Bryanna , Alexander Stefanie , Vang Nancy , Vue Neng , Vue Mein , Shuler Haysetta D , Spencer Elsie C , Morton Derrick J , Hinton Antentor 
Published: June 2022

Abstract
Despite efforts to increase diversity, a glaring underrepresentation of minorities (URM) persists in the fields of science, technology, engineering, and mathematics (STEM). Graduate school can be a stressful step in the STEM pipeline, especially for students previously unaware of the structure and challenges of postgraduate education. To promote successful minority participation in STEM and prepare prospective students for the impending challenges of applying for and attending graduate school, we developed a workshop based on the mentoring and fostering of a champion-oriented mindset entitled, “The Trials and Tribulations of Graduate School: How Do You Make an Impact?.” Students from the HBCU Winston-Salem State University attended the workshop, and a pre/post—a 10-point Likert scale-based survey was administered. The questions used in this seminar were newly designed by the authors as program evaluations. The results suggest that the workshop was well-received by the students and provided information that they considered helpful to help navigate the graduate school process.
Schindler's legacy: from eutrophic lakes to the phosphorus utilization strategies of cyanobacteria
Authors: Xiao Man , Burford Michele A , Wood Susanna A , Aubriot Luis , Ibelings Bas W , Prentice Matthew J , Galvanese Elena F , Harris Ted D , Hamilton David P 
Published: June 2022

AbstractDavid Schindler and his colleagues pioneered studies in the 1970s on the role of phosphorus in stimulating cyanobacterial blooms in North American lakes. Our understanding of the nuances of phosphorus utilization by cyanobacteria has evolved since that time. We review the phosphorus utilization strategies used by cyanobacteria, such as use of organic forms, alternation between passive and active uptake, and luxury storage. While many aspects of physiological responses to phosphorus of cyanobacteria have been measured, our understanding of the critical processes that drive species diversity, adaptation and competition remains limited. We identify persistent critical knowledge gaps, particularly on the adaptation of cyanobacteria to low nutrient concentrations. We propose that traditional discipline-specific studies be adapted and expanded to encompass innovative new methodologies and take advantage of interdisciplinary opportunities among physiologists, molecular biologists, and modellers, to advance our understanding and prediction of toxic cyanobacteria, and ultimately to mitigate the occurrence of blooms.
Genomics and pathotypes of the many faces ofEscherichia coli
Authors: Geurtsen Jeroen , de Been Mark , Weerdenburg Eveline , Zomer Aldert , McNally Alan , Poolman Jan 
Published: June 2022

AbstractEscherichia coli is the most researched microbial organism in the world. Its varied impact on human health, consisting of commensalism, gastrointestinal disease, or extraintestinal pathologies, has generated a separation of the species into at least eleven pathotypes (also known as pathovars). These are broadly split into two groups, intestinal pathogenic E. coli (InPEC) and extraintestinal pathogenic E. coli (ExPEC). However, components of E. coli’s infinite open accessory genome are horizontally transferred with substantial frequency, creating pathogenic hybrid strains that defy a clear pathotype designation. Here, we take a birds-eye view of the E. coli species, characterizing it from historical, clinical, and genetic perspectives. We examine the wide spectrum of human disease caused by E. coli, the genome content of the bacterium, and its propensity to acquire, exchange, and maintain antibiotic resistance genes and virulence traits. Our portrayal of the species also discusses elements that have shaped its overall population structure and summarizes the current state of vaccine development targeted at the most frequent E. coli pathovars. In our conclusions, we advocate streamlining efforts for clinical reporting of ExPEC, and emphasize the pathogenic potential that exists throughout the entire species.
Intraoperative conversion from video-assisted thoracoscopic lobectomy to thoracotomy for non-small-cell lung cancer: Does it have an impact on long-term survival?
Authors: Ren Zhi-Zhen , Deng Han-Yu , Huang Weijia , Zhou Qinghua 
Published: June 2022

Summary
A best evidence topic in thoracic surgery was written according to a structured protocol. The question addressed was whether intraoperative conversions to thoracotomy have an impact on long-term survival for patients with non-small-cell lung cancer who underwent video-assisted thoracoscopic lobectomy initially. A total of 461 papers were found using the reported search, of which 6 retrospective cohort studies represented the best evidence to answer the clinical question. The authors, date of publication, journal, country of the authors, patient group, study type, relevant outcomes and results of these papers were tabulated. Five cohort studies clarified that conversion did not compromise long-term survival, whereas 1 cohort study reported worse long-term outcomes after conversion to thoracotomy. However, the limited samples, different characteristics between groups and selection bias due to inherent design made it difficult to make a conclusion. Based on the current evidence, we concluded that intraoperative conversion from video-assisted thoracoscopic surgery (VATS) to thoracotomy for non-small-cell lung cancer might not impact long-term survival compared to a successful VATS lobectomy. In-hospital mortality might not be prejudiced, whereas longer hospitalizations were observed. However, whether conversion would adversely affect postoperative complication rates remained unclear because of the conflicting results. Moreover, 3 studies reported no statistical differences in short- and long-term survival between emergency and non-emergency conversions. Therefore, we suggest that thoracic surgeons should not hesitate to convert VATS into thoracotomy in the case of blood vessel injury or difficult hilum.
Single-stage repair for ascending aortic aneurysm, artery stenosis and occlusion of neck vessels caused by Takayasu arteritis
Authors: Nakai Yosuke , Nishikawa Yusuke , Saito Takayuki , Suda Hisao 
Published: June 2022

Abstract
Takayasu arteritis results in a variety of vascular symptoms, and there are some cases in which progressive vascular lesions require surgical intervention. We present a case with ascending aortic aneurysm, right common carotid artery stenosis, left common carotid artery occlusion and left subclavian artery stenosis caused by Takayasu arteritis that was successfully treated with total arch replacement and ascending aorta to right internal carotid artery bypass.
Alpha-2 Adrenoreceptor Antagonist Yohimbine Potentiates Consolidation of Conditioned Fear
Authors: Sperl Matthias F J , Panitz Christian , Skoluda Nadine , Nater Urs M , Pizzagalli Diego A , Hermann Christiane , Mueller Erik M 
Published: June 2022

AbstractBackgroundHyperconsolidation of aversive associations and poor extinction learning have been hypothesized to be crucial in the acquisition of pathological fear. Previous animal and human research points to the potential role of the catecholaminergic system, particularly noradrenaline and dopamine, in acquiring emotional memories. Here, we investigated in a between-participants design with 3 groups whether the noradrenergic alpha-2 adrenoreceptor antagonist yohimbine and the dopaminergic D2-receptor antagonist sulpiride modulate long-term fear conditioning and extinction in humans.MethodsFifty-five healthy male students were recruited. The final sample consisted of n = 51 participants who were explicitly aware of the contingencies between conditioned stimuli (CS) and unconditioned stimuli after fear acquisition. The participants were then randomly assigned to 1 of the 3 groups and received either yohimbine (10 mg, n = 17), sulpiride (200 mg, n = 16), or placebo (n = 18) between fear acquisition and extinction. Recall of conditioned (non-extinguished CS+ vs CS−) and extinguished fear (extinguished CS+ vs CS−) was assessed 1 day later, and a 64-channel electroencephalogram was recorded.ResultsThe yohimbine group showed increased salivary alpha-amylase activity, confirming a successful manipulation of central noradrenergic release. Elevated fear-conditioned bradycardia and larger differential amplitudes of the N170 and late positive potential components in the event-related brain potential indicated that yohimbine treatment (compared with a placebo and sulpiride) enhanced fear recall during day 2.ConclusionsThese results suggest that yohimbine potentiates cardiac and central electrophysiological signatures of fear memory consolidation. They thereby elucidate the key role of noradrenaline in strengthening the consolidation of conditioned fear associations, which may be a key mechanism in the etiology of fear-related disorders.
Invasive Meningococcal Disease Among People Experiencing Homelessness—United States, 2016–2019
Authors: Rudmann Keegan C , Brown Nicole E , Rubis Amy B , Burns Meagan , Ramsey April , De Las Nueces Denise , Martin Tasha , Barnes Meghan , Davizon Emily Spence , Retchless Adam C , Potts Caelin , Wang Xin , Hariri Susan , McNamara Lucy A 
Published: June 2022

Abstract

Background
Recently, several invasive meningococcal disease (IMD) outbreaks caused by Neisseria meningitidis have occurred among people experiencing homelessness (PEH). However, overall IMD risk among PEH is not well described. We compared incidence and characteristics of IMD among PEH and persons not known to be experiencing homelessness (non-PEH) in the United States.

Methods
We analyzed 2016–2019 IMD data from the National Notifiable Diseases Surveillance System and enhanced meningococcal disease surveillance. Incidence was calculated using US census data and point-in-time counts from the US Department of Housing and Urban Development.

Results
Of cases from states participating in enhanced surveillance during 2016–2019 (n = 1409), 45 cases (3.2%) occurred among PEH. Annual incidence was higher among PEH (2.12 cases/100 000) than non-PEH (0.11 cases/100 000; relative risk, 19.8; 95% confidence interval [CI], 14.8–26.7). Excluding outbreak-associated cases (PEH n = 18, 40%; non-PEH n = 98, 7.2%), incidence among PEH remained elevated compared to incidence in non-PEH (relative risk, 12.8; 95% CI, 8.8–18.8). Serogroup C was identified in 68.2% of PEH cases compared to 26.4% in non-PEH (P &lt; .0001).

Conclusions
PEH are at increased risk for IMD. Further assessment is needed to determine the feasibility and potential impact of meningococcal vaccination for PEH in the United States.
Risk of Severe Coronavirus Disease 2019 Disease in Individuals With Down Syndrome: A Matched Cohort Study From a Large, Integrated Health Care System
Authors: Ku Jennifer H , Levin Myron J , Luo Yi , Florea Ana , Lin I Chun , Tian Yun , Tseng Hung Fu 
Published: June 2022

Abstract

Background
Down syndrome (DS) is associated with an increased risk of infections attributed to immune defects. Whether individuals with DS are at an increased risk of severe coronavirus disease 2019 (COVID-19) remains unclear.

Methods
In a matched cohort study, we evaluated the risk of COVID-19 infection and severe COVID-19 disease in individuals with DS and their matched counterparts in a pre-COVID-19 vaccination period at Kaiser Permanente Southern California. Multivariable Cox proportion hazard regression was used to investigate associations between DS and risk of COVID-19 infection and severe COVID-19 disease.

Results
Our cohort included 2541 individuals with DS and 10 164 without DS matched on age, sex, and race/ethnicity (51.6% female, 53.3% Hispanic, median age 25 years [interquartile range, 14–38]). Although the rate of COVID-19 infection in individuals with DS was 32% lower than their matched counterparts (adjusted hazard ratio [aHR], 0.68; 95% confidence interval [CI], .56–.83), the rate of severe COVID-19 disease was 6-fold higher (aHR, 6.14; 95% CI, 1.87–20.16).

Conclusions
Although the risk of COVID-19 infection is lower, the risk of severe disease is higher in individuals with DS compared with their matched counterparts. Better infection monitoring, early treatment, and promotion of vaccine for COVID-19 are warranted for DS populations.
The Clinical and Genomic Epidemiology of Rhinovirus in Homeless Shelters—King County, Washington
Authors: Chow Eric J , Casto Amanda M , Roychoudhury Pavitra , Han Peter D , Xie Hong , Pfau Brian , Nguyen Tien V , Sereewit Jaydee , Rogers Julia H , Cox Sarah N , Wolf Caitlin R , Rolfes Melissa A , Mosites Emily , Uyeki Timothy M , Greninger Alexander L , Hughes James P , Shim M Mia , Sugg Nancy , Duchin Jeffrey S , Starita Lea M , Englund Janet A , Chu Helen Y 
Published: June 2022

Abstract

Background
Rhinovirus (RV) is a common cause of respiratory illness in all people, including those experiencing homelessness. RV epidemiology in homeless shelters is unknown.

Methods
We analyzed data from a cross-sectional homeless shelter study in King County, Washington, October 2019–May 2021. Shelter residents or guardians aged ≥3 months reporting acute respiratory illness completed questionnaires and submitted nasal swabs. After 1 April 2020, enrollment expanded to residents and staff regardless of symptoms. Samples were tested by multiplex RT-PCR for respiratory viruses. A subset of RV-positive samples was sequenced.

Results
There were 1066 RV-positive samples with RV present every month of the study period. RV was the most common virus before and during the coronavirus disease 2019 (COVID-19) pandemic (43% and 77% of virus-positive samples, respectively). Participants from family shelters had the highest prevalence of RV. Among 131 sequenced samples, 33 RV serotypes were identified with each serotype detected for ≤4 months.

Conclusions
RV infections persisted through community mitigation measures and were most prevalent in shelters housing families. Sequencing showed a diversity of circulating RV serotypes, each detected over short periods of time. Community-based surveillance in congregate settings is important to characterize respiratory viral infections during and after the COVID-19 pandemic.

Clinical Trials Registration
NCT04141917.