bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seeking Good Work in the COVID-19 Recovery
Authors: Griffiths Melda Lois , Gray Benjamin J. , Kyle Richard G. , Davies Alisha R. 
Published: September 2022

Objective
Disruption to working lives spurred by the COVID-19 pandemic may shape people’s preferences for future employment. We aimed to identify the components of work prioritized by a UK sample and the employment changes they had considered since the start of the COVID-19 pandemic.

Methods
A nationally representative longitudinal household survey was conducted in Wales at two time points between 2020 and 2021.

Results
Those in poorer health prioritized flexibility and were more likely to consider retiring. Those with limiting preexisting conditions or low mental well-being were more likely to consider becoming self-employed. Those experiencing financial insecurity (including those with high wage precarity or those furloughed) were more likely to consider retraining, becoming self-employed, or securing permanent employment.

Conclusions
Ensuring flexible, secure, and autonomous work is accessible for individuals facing greater employment-related insecurity may be key.
Molecular Analysis of HPV-independent Primary Endometrial Squamous Cell Carcinoma Reveals TP53 and CDKN2A Comutations
Authors: Hopkins Mark R. , Palsgrove Doreen N. , Ronnett Brigitte M. , Vang Russell , Lin Jeffrey , Murdock Tricia A. 
Published: September 2022

Human papillomavirus (HPV)-independent primary endometrial squamous cell carcinoma (PESCC) is a rare but aggressive subtype of endometrial carcinoma for which little is known about the genomic characteristics. Traditional criteria have restricted the diagnosis of PESCC to cases without any cervical involvement. However, given that modern ancillary techniques can detect HPV and characteristic genetic alterations that should identify the more common mimics in the differential diagnosis, including endometrial endometrioid carcinoma with extensive squamous differentiation and HPV-associated primary cervical squamous cell carcinoma, those criteria may benefit from revision. To further characterize PESCC, we identified 5 cases of pure squamous cell carcinoma dominantly involving the endometrium that had the potential to be PESCC: 1 case involving only the endometrium and 4 cases with some involvement of the cervix. Clinicopathologic features were assessed and immunohistochemical analysis (p16, estrogen receptor, progesterone receptor, and p53), HPV RNA in situ hybridization (high-risk and low-risk cocktails and targeted probes for 16 and 18), and molecular studies were performed. All tumors showed aberrant/mutation-type p53 expression, were negative for estrogen receptor, progesterone receptor, and p16, and had no detectable HPV. Per whole-exome sequencing, 4 of the 5 tumors demonstrated comutations in TP53 and CDKN2A (p16). Four patients died of disease within 20 months (range, 1 to 20 mo; mean, 9 mo), and 1 patient had no evidence of disease at 38 months. PESCC represents a unique, clinically aggressive subtype of endometrial cancer with TP53 and CDKN2A comutations. This characteristic profile, which is similar to HPV-independent squamous cell carcinoma of the vulva, is distinct from endometrioid carcinoma with extensive squamous differentiation and HPV-associated primary cervical squamous cell carcinoma and can be used to distinguish PESCC from those mimics even when cervical involvement is present. Diagnostic criteria for PESCC should be relaxed to allow for cervical involvement when other pathologic features are consistent with, and ancillary techniques are supportive of classification as such.
Targeted Private Well Outreach Following a Change in Drinking Water Standard: Arsenic and the New Jersey Private Well Testing Act
Authors: O'Neill Heidi S. , Flanagan Sara V. , Gleason Jessie A. , Spayd Steven E. , Schwartz Rebecca I. , Procopio Nicholas A. 
Published: September 2022

Context:
When the New Jersey Private Well Testing Act (PWTA) became effective in 2002, the maximum contaminant level (MCL) for arsenic in the United States was 50 μg/L. In 2006, the federal and New Jersey MCLs were lowered to 10 μg/L and 5 μg/L, respectively.

Objective:
To notify and provide free arsenic water testing for homeowners who had a PWTA arsenic result that passed for the MCL in 2006 or earlier but would exceed under the more health protective MCL enacted in 2006, which is still in effect as of this publication date.

Design:
About 1200 homeowners with PWTA arsenic results between 5 μg/L and 50 μg/L were offered free arsenic water testing. More than 400 homeowners requested tests and 292 returned samples.

Setting:
New Jersey, United States.

Participants:
Homeowners with a passing PWTA arsenic result before 2006 that would have failed under the New Jersey arsenic MCL enacted in 2006.

Main Outcome Measures:
Return rate of testing kits; number of tests exceeding arsenic MCL; and participant survey results.

Results:
Untreated well water samples (n = 279) were collected and 62.4% exceeded the New Jersey MCL. Treated well water samples (n = 102) were collected and 11.8% exceeded the current New Jersey MCL. In all, about 40% of drinking water samples from the tap, including those with or with no arsenic treatment, exceeded the New Jersey MCL. A survey of participants (n = 69) found that although many (67%) respondents reported that they at least had some idea that wells in their area are vulnerable to naturally occurring contaminants, such as arsenic, many (68%) reported that they had little or no idea that the New Jersey arsenic MCL had been lowered from 50 μg/L to 5 μg/L in 2006.

Conclusions:
This effort further illuminates the necessity and significance of public health outreach for private well water users, especially after drinking water standards change.
“I Have to Ask”: A Mixed-Methods Study on the Collection of Sexual Orientation and Gender Identity Data Within the San Francisco County COVID-19 Case Investigation and Contact Tracing Program
Authors: Gutierrez-Mock Luis , Burgess Hailey , Pardo Seth , Persson Maceo , Gagliano Jayne , Ho Y. Xian , Reid Michael J. A. 
Published: September 2022

Objective:
To understand how the San Francisco (SF) COVID-19 case investigation and contact tracing (CICT) workforce documented sexual orientation and gender identity (SOGI) data, as well as a qualitative assessment of the workforce's capacity to successfully collect that data.

Methods:
This mixed-methods project analyzed data from 2 sources: SOGI item completeness among adult completed/partially completed interviews in the SF digital CICT COVID-19 database, and a secondary data analysis of qualitative data from 16 semistructured 90-minute virtual interviews with the SF CICT workforce, between November 14, 2020, and April 14, 2021.

Results:
Among 15 416 COVID-19 cases and 7836 close contacts, sexual orientation data are missing from 20% of cases and 17% of contacts. The proportion of transgender/nonbinary individuals was 0.32% and 0.5%, respectively. The SF CICTs participants discussed challenges in collecting SOGI data, not understanding SOGI measure rationale, and feeling uncomfortable asking the questions.

Conclusion:
Qualitative interviews with the COVID-19 CICT workforce and quantitative data on SOGI parameters in COVID-19 surveillance suggest that these data may have been underreported. Our results strongly suggest that comprehensive training is crucial in the collection of SOGI data among COVID-19 cases and their close contacts. If SOGI data are not collected accurately, the true impact of COVID-19 among lesbian, gay, bisexual, transgender, and queer populations remains unknown, preventing data-driven allocation of COVID-19 funds to lesbian, gay, bisexual, transgender, and queer communities.
Factors Influencing the Results of COVID-19 Case Outreach—Results From a California Case Investigation/Contact Tracing Program
Authors: Barnes-Josiah Debora , Kundeti Hemanth , Cramer Daniel 
Published: September 2022

Context:
Considerable research has examined impacts of case investigation and contact tracing (CI/CT) programs on the spread of infectious diseases such as COVID-19, but there are few reports on factors affecting the ability of these programs to obtain interviews and acquire key information.

Objective:
To investigate programmatic and case-specific factors associated with CI outcomes using data from the Public Health Institute's Tracing Health CI/CT program. Analyses were designed to detect variability in predictors of whether interviews and key information were obtained rather than quantify specific relationships.

Design:
Logistic regression models examined variability in the predictive value of interview timeliness and respondent characteristics on outreach outcomes and interview results.

Setting and Participants:
Participants were members of a large California health care network with a positive laboratory test for COVID-19 and outreach from January 1 to July 31, 2021.

Main Outcome Measures:
The primary outcome was the result of outreach attempts: completed interview, refused interview, or failure to reach the infected person. Secondary outcomes considered whether respondents provided information on symptom onset, employment, and contact information or a reason for declining to provide information, and whether resource support was requested or accepted.

Results:
Of 9391 eligible records, 65.6% were for completed interviews, 6.0% were refusals, and 28.3% were failed outreach. One-third of respondents (36.7%) provided information on contacts (mean = 0.97 contacts per respondent, 2.6 for those naming at least 1). Privacy concerns were the most common reasons for not providing contact information. Among respondent characteristics and interview timeliness, only race and number of symptoms showed statistically significant effects in all adjusted analyses.

Conclusions:
Significant variation existed in outreach outcomes by subject characteristics and interview timeliness. CI/CT programs carefully focused to characteristics and needs of specific communities will likely have the greatest impact on the spread of COVID-19 and other communicable diseases.
High Uptake and Series Completion of COVID-19 Vaccine at Community-Based Vaccination for Latinos With Limited English Proficiency
Authors: Bigelow Benjamin F. , Saxton Ronald E. , Martínez Diego A. , Flores-Miller Alejandra , Shin Jong M. , Parent Cassandra , Williams Samantha , Phillips Katherine Hartman , Yang Cui , Page Kathleen Raquel 
Published: September 2022

Background:
Despite the disproportionate impact of COVID-19 on Latinos, there were disparities in vaccination, especially during the early phase of COVID-19 immunization rollout.

Methods:
Leveraging a community-academic partnership established to expand access to SARS-CoV2 testing, we implemented community vaccination clinics with multifaceted outreach strategies and flexible appointments for limited English proficiency Latinos.

Results:
Between February 26 and May 7 2021, 2250 individuals received the first dose of COVID-19 vaccination during 18 free community events. Among them, 92.4% (95% confidence interval [CI], 91.2%-93.4%) self-identified as Hispanic, 88.7% (95% CI, 87.2%-89.9%) were limited English proficiency Spanish speakers, 23.1% (95% CI, 20.9%-25.2%) reported prior COVID-19 infection, 19.4% (95% CI, 16.9%-22.25%) had a body mass index of more than 35, 35.0% (95% CI, 32.2%-37.8%) had cardiovascular disease, and 21.6% (95% CI, 19.2%-24.0%) had diabetes. The timely second-dose completion rate was high (98.7%; 95% CI, 97.6%-99.2%) and did not vary by outreach method.

Conclusion:
A free community-based vaccination initiative expanded access for Latinos with limited English proficiency at high risk for COVID-19 during the early phase of the immunization program in the US.
Deep Learning-Based Automatic Detection and Grading of Motion-Related Artifacts on Gadoxetic Acid-Enhanced Liver MRI
Authors: Park Taeyong , Kim Dong Wook , Choi Sang Hyun , Khang Seungwoo , Huh Jimi , Hong Seung Baek , Lee Tae Young , Ko Yousun , Kim Kyung Won , Lee Seung Soo 
Published: September 2022

Objectives
The aim of this study was to develop and validate a deep learning-based algorithm (DLA) for automatic detection and grading of motion-related artifacts on arterial phase liver magnetic resonance imaging (MRI).

Materials and Methods
Multistep DLA for detection and grading of motion-related artifacts, based on the modified ResNet-101 and U-net, were trained using 336 arterial phase images of gadoxetic acid-enhanced liver MRI examinations obtained in 2017 (training dataset; mean age, 68.6 years [range, 18–95]; 254 men). Motion-related artifacts were evaluated in 4 different MRI slices using a 3-tier grading system. In the validation dataset, 313 images from the same institution obtained in 2018 (internal validation dataset; mean age, 67.2 years [range, 21–87]; 228 men) and 329 from 3 different institutions (external validation dataset; mean age, 64.0 years [range, 23–90]; 214 men) were included, and the per-slice and per-examination performances for the detection of motion-related artifacts were evaluated.

Results
The per-slice sensitivity and specificity of the DLA for detecting grade 3 motion-related artifacts were 91.5% (97/106) and 96.8% (1134/1172) in the internal validation dataset and 93.3% (265/284) and 91.6% (948/1035) in the external validation dataset. The per-examination sensitivity and specificity were 92.0% (23/25) and 99.7% (287/288) in the internal validation dataset and 90.0% (72/80) and 96.0% (239/249) in the external validation dataset, respectively. The processing time of the DLA for automatic grading of motion-related artifacts was from 4.11 to 4.22 seconds per MRI examination.

Conclusions
The DLA enabled automatic and instant detection and grading of motion-related artifacts on arterial phase gadoxetic acid-enhanced liver MRI.
Guillain-Barré syndrome in an era of global infections and 21st century vaccination
Authors: Lunn Michael P. 
Published: September 2022

Purpose of review
Guillain-Barre syndrome is sometimes a severe and disabling postinfectious neuromuscular paralysis that is causally associated with a number of well defined infections, and occasionally with immunization. The severe acute respiratory syndrome coronavirus 2 (Sars-CoV-2) pandemic and the worldwide immunization programme provoked fears of an epidemic of coronavirus disease 2019 (COVID-19) related disease. As we emerge from the pandemic this review summarises some of the huge volume of publications about Guillain-Barre syndrome (GBS), COVID-19 and immunisation against it.

Recent findings
In the early months of COVID-19, there were concerns of significant numbers of cases of GBS resulting from SARS-CoV-2 infection. Large epidemiological studies have provided reassurance that the association of GBS with COVID-19 is small or absent. Despite considerable efforts, plausible pathogenic mechanisms aligned with our understanding of GBS causation have not been identified. Reliable data from national surveillance of COVID-19 vaccinations have shown GBS to occur at about 5.8 cases per million first doses of adenovirus vectored COVID-19 vaccines, otherwise not distinguishable from incident naturally occurring cases. However, this risk is far outweighed by the protective benefits of vaccination in the at-risk older deciles of age.

Summary
With no obvious link of GBS to COVID-19 epitopes, in particular the spike (S-)protein, but a clearly demonstrable causation in some susceptible individuals from the global rollout of novel adenovirus vectored vaccine technologies, adenoviruses are of significant interest in the pathogenesis of GBS as well as vectors in their many expanding pharmaceutical applications.
Inclusion body myositis: evolving concepts
Authors: Perez-Rosendahl Mari , Mozaffar Tahseen 
Published: September 2022

Purpose of review
To discuss recent developments in our understanding of epidemiology, diagnostics, biomarkers, pathology, pathogenesis, outcome measures, and therapeutics in inclusion body myositis (IBM).

Recent findings
Recent epidemiology data confirms a relatively higher prevalence in the population aged above 50 years and the reduced life expectancy. Association with cancer and other systemic disorders is better defined. The role of magnetic resonance imaging (MRI) and ultrasound in diagnosis as well as in following disease progression has been elucidated. There are new blood and imaging biomarkers that show tremendous promise for diagnosis and as outcome measures in therapeutic trials. Improved understanding of the pathogenesis of the disease will lead to better therapeutic interventions, but also highlights the importance to have sensitive and responsive outcome measures that accurately quantitate change.

Summary
There are exciting new developments in our understanding of IBM which should lead to improved management and therapeutic options.
A multi-population-based genomic analysis uncovers unique haplotype variants and crucial mutant genes in SARS-CoV-2
Authors: Sheikh Afzal , Huang He , Parvin Sultana , Badruzzaman Mohammad , Ahmed Tofayel , Hossain Ekhtear , Baran Iri Sato , Saud Zahangir Alam 
Published: September 2022

AbstractBackgroundCOVID-19 is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Rigorous detection and treatment strategies against SARS-CoV-2 have become very challenging due to continuous evolutions to the viral genome. Therefore, careful genomic analysis is sorely needed to understand transmission, the cellular mechanism of pathogenicity, and the development of vaccines or drugs.ObjectiveIn this study, we intended to identify SARS-CoV-2 genome variants that may help understand the cellular and molecular foundation of coronavirus infections required to develop effective intervention strategies.MethodsSARS-CoV-2 genome sequences were downloaded from an open-source public database, processed, and analyzed for variants in target detection sites and genes.ResultsWe have identified six unique variants, G---AAC, T---AAC---T; AAC---T; C----C; C-------C; and C--------T at the nucleocapsid region and eleven major hotspot mutant genes: nsp3, surface glycoprotein, nucleocapsid phosphoprotein, ORF8, nsp6, nsp2, nsp4, helicase, membrane glycoprotein, 3’-5’ exonuclease, and 2’-O-ribose methyltransferases. In addition, we have identified eleven major mutant genes that may have a crucial role in SARS-CoV-2 pathogenesis.ConclusionStudying haplotype variants and 11 major mutant genes to understand the mechanism of action of fatal pathogenicity and inter-individual variations in immune responses is inevitable for managing target patient groups with identified variants and developing effective anti-viral drugs and vaccines.
Expanding growers’ choice of disease management options can promote suboptimal social outcomes
Authors: Murray-Watson Rachel E. , Cunniffe Nik J. 
Published: September 2022

1AbstractPrevious models of growers’ decision-making during epidemics have unrealistically limited disease management choices to just two options. Here, we expand previous game-theoretic models of grower decision-making to include three control options: crop that is either tolerant, resistant, or susceptible to disease. Using Tomato Yellow Leaf Curl Virus (TYLCV) as a case study, we investigate how growers can be incentivised to use different control options to achieve socially-optimal outcomes. To do this, we consider the efforts of a “social planner” who moderates the price of crops. We find that subsidising tolerant crop costs the social planner more in subsidies, as its use encourages selfishness and widespread adoption. Subsidising resistant crop, however, provides widespread benefits by reducing the prevalence of disease across the community of growers, including those that do not control, reducing the number of subsidies required from the social planner. We then use Gini coefficients to measure equitability of each subsidisation scheme. This study highlights how grower behaviour can be altered using crop subsidies to promote socially-optimal outcomes during epidemics.
Immune dynamics at single cell protein level after delta/omicron infection in COVID-19 vaccinated convalescent individuals
Authors: Bajaj Rimpi , Yang Zhiqi , Hammer Vincent , Pöschel Simone , Bieber Kristin , Salker Madhuri S , Casadei Nicolas , Ossowski Stephan , Riess Olaf , Singh Yogesh 
Published: September 2022

AbstractBoth COVID-19 mRNA or recombinant Adenovirus vector (rAdVV) based vaccines have shown a great efficacy in generating humoral and cellular immune responses. Two doses of the COVID-19 vaccines generate enough antibodies and generate spike-specific T cell responses. However, after 6-8 months there is a decline in antibody production and T cell responses. Due to the rise of new SARS-CoV-2 variants of concern, a third or even fourth dose of vaccine was recommended for the elderly, immune comprised and frontline medical health care workers. However, despite additional booster doses given, those who were infected with either delta or omicron (during December 2021 – March 2022) had symptoms of illness. By what means these COVID-19 vaccines provide immunity against the SARS-CoV-2 virus at the molecular level is not explored extensively yet and, it is an emerging research field as to how the SARS-CoV-2 virus is able to evade the host immunity. Most of the infected people had mild symptoms whilst some were asymptomatic. Many of the people had developed nucleocapsid antibodies against the SARS-CoV-2 delta/omicron variants confirming a humoral immune response against viral infection. Furthermore, cellular analysis shows that post-vaccinated recovered COVID-19 individuals have significantly reduced NK cells and increased T naïve CD4+, TEM CD8+ and B cells. This decrease in cellular immunity corresponds to individuals who recovered from alpha variants infection and had mild symptoms. Our results highlight that booster doses clearly reduce the severity of infection against delta/omicron infection. Furthermore, our cellular and humoral immune system is trained by vaccines and ready to deal with breakthrough infections in the future.
Resistance of SARS-CoV-2 Omicron Subvariant BA.4.6 to Antibody Neutralization
Authors: Wang Qian , Li Zhiteng , Ho Jerren , Guo Yicheng , Yeh Andre Yanchen , Liu Michael , Wang Maple , Yu Jian , Sheng Zizhang , Huang Yaoxing , Liu Lihong , Ho David D. 
Published: September 2022

AbstractSARS-CoV-2 Omicron subvariants BA.4.6, BA.4.7, and BA.5.9 have recently emerged, and BA.4.6 appears to be expanding even in the presence of BA.5 that is globally dominant. Compared to BA.5, these new subvariants harbor a mutation at R346 residue in the spike glycoprotein, raising concerns for further antibody evasion. We compared the viral receptor binding affinity of the new Omicron subvariants with BA.5 by surface plasmon resonance. We also performed VSV-based pseudovirus neutralization assays to evaluate their antigenic properties using sera from individuals who received three doses of a COVID-19 mRNA vaccine (boosted) and patients with BA.1 or BA.2 breakthrough infection, as well as using a panel of 23 monoclonal antibodies (mAbs). Compared to the BA.5 subvariant, BA.4.6, BA.4.7, and BA.5.9 showed similar binding affinities to hACE2 and exhibited similar resistance profiles to boosted and BA.1 breakthrough sera, but BA.4.6 was slightly but significantly more resistant than BA.5 to BA.2 breakthrough sera. Moreover, BA.4.6, BA.4.7, and BA.5.9 showed heightened resistance over to a class of mAbs due to R346T/S/I mutation. Notably, the authorized combination of tixagevimab and cilgavimab completely lost neutralizing activity against these three subvariants. The loss of activity of tixagevimab and cilgavimab against BA.4.6 leaves us with bebtelovimab as the only therapeutic mAb that has retained potent activity against all circulating forms of SARS-CoV-2. As the virus continues to evolve, our arsenal of authorized mAbs may soon be depleted, thereby jeopardizing the wellbeing of millions of immunocompromised persons who cannot robustly respond to COVID-19 vaccines.