bluuebunny/crossref_metadata_2025 huggingface dataset:
Advancing Small Business Inclusion in Public Procurement: Evidence From U.S. Federal Government R&D Contracts
Authors: Roy Dwaipayan , Mishra Anant , Sinha Kingshuk K
Published: August 2024

To encourage small business inclusion in public procurement, the U.S. federal government has established the set-aside program that mandates government agencies to award a portion of their contracts to small businesses. We study whether and to what extent the performance of R&D contracts awarded through this program differs from those awarded through open competition. Analyzing a large dataset of federal R&D contracts, we find that despite restricting competition to small businesses, set-aside R&D contracts experience lower schedule and cost overrun than R&D contracts awarded through open competition. Furthermore, although set-aside R&D contracts experience lower schedule and cost overrun when they are awarded to more experienced contractor firms, this benefit arises primarily from a contractor firm's experience in executing R&D contracts across different agencies compared to the firm's experience with the same agency. Finally, set-aside R&D contracts awarded early in a fiscal year experience lower schedule and cost overrun than those awarded later. Post-hoc analysis examining the underlying dimensions of different-agency experience highlights the asymmetric effects of related-agency experience and unrelated-agency experience of contractor firms on the performance of set-aside R&D contracts awarded by the Department of Defense. While related-agency experience improves contract performance, unrelated-agency experience has a detrimental effect on contract performance. These findings demonstrate that small business inclusion policies may not necessarily compromise contract performance. Importantly, they emphasize the need for federal agencies and contracting officers to consider the underlying dimensions of contractor firm experience and contract award timing to improve contract performance and taxpayer money utilization.
Incidence and Pitfalls of Adipose Tissue Encountered in Prostatic Transurethral Resections and Related Specimens
Authors: Wu Douglas Jian-Xian , Brooks James D. , Rizkalla Carol , Sangoi Ankur R.
Published: August 2024

While the presence of adipose tissue and its involvement by prostatic cancer (extraprostatic extension) is well-recognized in prostate biopsies, adipose tissue in transurethral resections of the prostate (TURP) is largely unexplored. Herein, 200 consecutive TURPs and related specimens were reviewed, including a separate 3-year analysis of specimens containing prostatic cancer, with the following data collected: presence of fat, presence of cancer within fat, and quantity of fat. For specimens with both fat and prostatic cancer, specimen weight and tumor volume were recorded. Within the 200 consecutive TURPs and related specimens, adipose tissue was identified in 20%; 55% had 2.5 mm of adipose tissue; the number of fragments with adipose tissue ranged from 1 to 14. No correlation between specimen weight and measured extent of adipose tissue or number of fragments with adipose tissue was identified. Of all the specimens with prostatic cancer, 15/56 (27%) involved adipose tissue, with two specimens with large cancer volume (>90%) demonstrating extensive involvement of adipose tissue. Adipose tissue is frequently present within TURP and related specimens with variability in extent. The etiology behind encountering adipose tissue is uncertain, and it could represent resection into peri-prostatic fat, intraprostatic fat, or bladder neck fat sampling. Although encountering adipose tissue involved by cancer in TURP and related specimens may imply extraprostatic extension (pT3a), further studies are needed to corroborate these findings as well as to determine if these should be included in reported synoptics.
Incidence of hand-foot syndrome with protein kinase inhibitors in advanced hepatocellular carcinoma patients who received atezolizumab-bevacizumab combination
Authors: Perrier Marine , Zuccaro Emma , Carlier Claire , Brugel Mathias , Slimano Florian , Bouché Olivier
Published: August 2024

Introduction

Treatment of advanced HepatoCellular Carcinoma (HCC) is based on first-line (L1) combination of atezolizumab and high-dose (HD) bevacizumab while second-line (L2) refers one antiangiogenic protein kinase inhibitors (aaPKI). This prolonged antiangiogenic pressure let us to observe an increasing occurrence of Hand-Foot Syndromes (HFS) in patients receiving aaPKI after HD bevacizumab combination. This study reports observations and discussions about the evidence and hypothesis that could be made.

Methods

Patients who received the L1 combination from September 1st 2020 to December 31st 2022 to identify L2 aaPKI. Demographic, biological, oncological data and occurrence of HFS were collected. In addition were collected the number of L1 combination cycles, type of aaPKI, and delay between last L1 cycle and L2 initiation. This study had a purely exploratory purpose, so no statistical analysis was planned.

Results

17 patients received an aaPKI after the L1 HD bevacizumab combination with a median time of 26 days from last L1 cycle to L2 start. Five patients experienced HFS including grade 3 ( n = 2) with sorafenib and cabozantinib. The HFS occurred with a median delay of 23 days (IQR: 21–28) from aaPKI start. Three patients experienced aaPKI-related dose-limiting toxicity.

Conclusions

Proportion of patients experienced HFS in our cohort did not differ from pivotal trials data and the sample size do not allow to conclude. Hypotheses include timing of aaPKI start in HCC treatment, vascular toxicity at aaPKI start after HD bevacizumab discontinuation instead combination, patient-related outcome for a better understanding of these aaPKI-related HFS post HD bevacizumab.
Antihistamine and COVID-19 outcomes in outpatients
Authors: Samimi Soodabeh , Nimrouzi Majid , Sousani Malihe , Vazani Yasaman
Published: August 2024

The World Health Organization declared the coronavirus disease 2019 (COVID-19) pandemic on March 11, 2020. Since then, researchers have been investigating the efficacy and side effects of its medication, up until now. From the viewpoint of Persian medicine, some medications such as antihistamines may cause retention of secretions and lead to exacerbation and spread of the disease in the body. There are studies with conflicting results regarding the effectiveness of antihistamines in COVID-19. Systematic reviews found a lack of data on beneficial effect of antihistamine-decongestant-analgesic combinations for the common cold and a limited short-term effect of antihistamines on severity of overall symptoms. This prospective cohort study was designed to investigate the relationship between the use of antihistamines and the severity of COVID-19 symptoms. Three hundred patients with a diagnosis of COVID-19 participated in the study in Shiraz, Iran from December 4, 2021 until January 24, 2022. The interviews were conducted via phone call by a single interviewer. Patients were followed weekly for 4 weeks. We collected information by using a data collection form, containing demographic information, underlying disease, COVID-19 symptoms, treatment methods, medications, and a list of antihistamines and herbs that might have been used. Generalized estimating equations were applied to assess the relationship between the severity of COVID-19 and the use of antihistamines, taking into account potential confounding factors such as time and herbal consumption. The difference in the severity of COVID-19 disease in antihistamine users compared to nonusers was not significant in 4 weeks despite the higher baseline severity in nonusers. The comparison of two groups of antihistamine users and nonusers showed that there was a significant difference (p = 0.001) regarding the use of herbal medicines.
Malaria Vectors Tend to Avoid the Indoor-Based Vector Control Tools in Wonji Sugar Estate, Oromia, Ethiopia
Authors: Lelisa Kidane , Golassa Lemu , Woldehawariat Yitbarek , Dugassa Sisay
Published: August 2024

Background:

There is a paucity of data regarding resting habits and comparison of the physiological states of Anopheles mosquito populations from indoor and outdoor collection venues in Ethiopia. Therefore, this study aims to investigate resting behavior and age structure of the malaria vectors in Wonji Sugar Estate.

Methods:

Longitudinal entomological study was conducted at Wonji Sugar Estate from July 2018 to June 2020. Pyrethrum spray catches (PSC), Pit Shelter (PIT), and Oral Aspirators were used to collect adult Anopheles species from various resting sites. Mosquitoes were identified to the species using morphological keys. Finally, the resting behavior of Anopheles mosquitoes were determined using standard protocol.

Results:

A total of 1406 mosquitoes were collected from indoor and outdoor resting venues, with the outdoor resting population being significantly higher ( F = 8.296, P = .04). The number of half-gravid/gravid Anopheles species collected from outdoors was higher than that from indoor resting venues ( F = 35.612, P = .00). Eight two percent of the indoor sampled Anopheles species left the indoor venue before completing their gonotrophic cycle. Anopheles pharoensis and An. coustani cx. exhibited exophily rate of 83.4% and 100%, respectively. The overall parity rate of Anopheles gambiae s.l. was 45.7%. The highest parity rate, daily survival rate, and longevity of Anopheles gambiae s.l. was 66.7%, 0.874, and 7.399 days, respectively. Anopheles gambiae s.l. reached the infective stages for Plasmodium falciparum and P. vivax in February 2019.

Conlusion:

Anopheles mosquitoes, including the major malaria vector Anopheles gambiae s.l., showed predominantly exophilic habits, underscoring the need for outdoor vector control strategies in addition to indoor-based interventions. The increase in the nulliparous population indicates a higher risk of vector-human contact. Meanwhile, the extended lifespan of Anopheles gambiae s.l. observed during the dry season could increase the risk of infectious bites.
Revisiting ‘think aloud’ in language learner strategy research
Authors: Cohen Andrew D. , Wang Isobel Kai-Hui
Published: August 2024

This article revisits the use of the term ‘think aloud protocols’ (TAP) as used in second language (L2) research studies as a means for collecting verbal report (VR) data dealing with language learner strategies (LLS). Given that there continue to appear L2 studies that use TAP without differentiating the actual type of VR that is involved, this study investigated the extent to which it makes a difference if the researchers fine-tune the types of VR responsible for yielding the given cognitive processing data. The study was conducted at the university level as part of an effort to investigate the dynamics of vocabulary strategy instruction (VSI) from different angles. Non-native-English-speaking developing teachers generated VR about the strategies that they selected when assuming the role of both tutor and student in one of six dyads. The VSI was focused on fine-tuning the students’ comprehension of vocabulary used in academic writing. The findings highlighted how different types of VR not only helped elicit strategies but also clarified participants’ verbalized thoughts, facilitated self-evaluations of strategies, and prompted reflection about areas for improvement. This study suggested that there is value in utilizing different types of VR in order to obtain a more robust measure of the cognitive processes involved in strategizing about word meanings, while at the same time calling attention to the complexities of strategy dynamics. The article ends with suggestions for future research and with pedagogical implications, such as that of enlisting different types of VR as a means by which teachers can demonstrate to learners the multifaceted nature of VSI.
Lingering longer: Performance, queer of color joy, and Baltimore’s VERSION
Authors: Tristano Michael
Published: August 2024

This essay moves through the nuances and complications of queer of color joy’s potentiality. Mobilized through performance, queer of color joy is theorized as containing possibilities “to explore the limits of human curiosity; renegotiate what relationships can look, feel, sound, and smell like; and use desire to propel us through the social world where we refuse colonial futures and expand decolonial options” (Tristano, 2022: 279). Through a performance ethnography of VERSION, a dance party for queer and trans people of color which takes place monthly in Baltimore, MD, USA, I detail how queer of color joy circulates through complex modes of power. I move to theorize queer of color joy further by exploring how queer of color joy lingers. Gesturing towards after the party (Chambers-Letson, 2018), I detail how queer of color joy is performed outside of VERSION; after 2:00 a.m., on the sidewalk, and through clouds of smoke. Lingering, I argue, further animates queer of color joy’s radical potential through queer relationality to nourish queer and trans of color lifeworlds.
Hannah Arendt, an anthropologist's ally? Relational subjects, political action, and anti-racism in the twenty-first century
Authors: Feldman Gregory
Published: August 2024

Hannah Arendt has never held a significant place in anthropology. Perhaps her focus on mid-twentieth-century Europe and the USA, where she misunderstood Black struggles, outdates her for a twenty-first-century global discipline. However, this article argues that core aspects of Arendt's oeuvre can advance debates on relational subjectivity and political action because her efforts to think past the scourge of totalitarianism in Europe parallel the discipline's own efforts to think past colonialism everywhere else in the world. These two intertwined phenomena require the same undoing of “modern” Western political discourse, particularly its emphasis on bounded entities like individuals, nations, and states. The article synthesizes Arendt's work on subjectivity and action to unite the anthropology of personhood, existential-phenomenological anthropology, and political anthropology for the sake of an ontology of subjectivity supporting progressive politics. It, firstly, presents Arendt's tripartite division of human existence—labor, work, and action—to convey her unique understanding of political life. Secondly, it presents the relational subject as composed of an inner plurality but appearing as a singularity requiring recognition from a plurality of other such subjects. Thirdly, it argues that Arendt's view of council-style politics exemplifies a generic polity allowing relational subjects to simultaneously reconstitute themselves and their polity through joint action. Fourthly, it examines her argument that racism marks the end of humanity so we can align her work with decolonial anthropology. This tricky task requires us to unpack Arendt's Conradian representations of the colonized to understand how imperialism abroad pre-conditioned the destruction of political life in Europe through totalitarianism.
Music Instruction at the California Labor School, 1942–1957
Authors: Hash Phillip M.
Published: August 2024

The purpose of this study was to examine music instruction at the California Labor School (CLS), located in San Francisco, California. This institution existed from 1942 to 1957 as a center for adult education affiliated with the Communist Party. Although the curriculum focused on Marxism and labor, the institution also offered classes in general subjects, vocational training, life skills, and the arts to enrich the lives of the immigrants, industrial workers, and people of color that it served. The music program included courses in music fundamentals, appreciation, and songwriting; group and individual instruction in voice, guitar, and piano; and ensembles for singers and instrumentalists. Many people studied music at the CLS for personal growth and enjoyment. Others, however, developed skills useful in promoting the agenda of the Communist Party and the American labor movement. This research focused on music teaching and learning at the CLS in relation to organization, administration, curriculum, ensembles, faculty, and political perspectives. The history of this institution as an agent of social change revealed ethical considerations for music education in modern PK–16 institutions. In addition, the CLS music program aligned with current recommendations for undergraduate study and could serve as an example for curriculum reform today.
Impact of Leadership on Unethical Pro-Organizational Behavior: A Systematic Literature Review and Future Research Directions
Authors: Ahmad Rahatulaain , Nejati Mehran , Farr-Wharton Ben , Bentley Tim
Published: August 2024

Unethical pro-organizational behavior (UPB) has received growing attention from organizational scholars in recent years. As leadership is a key predictor of employee behavior in organizations, research focusing on leadership and UPB holds great potential for theoretical and practical advancements. The current paper presents a comprehensive systematic review of published research exploring leadership and UPB since 2010. The review not only situates the concept of UPB within the relevant literature, but also incorporates various analyses, including context, theoretical perspective, and research design. It also identifies the leadership-based independent variables, mediators, and moderators that impact UPB, which can help advance future theorizing in the field. Lastly, the paper offers suggestions for future research that can help in repositioning the field in order to build more reliable and valuable theoretical and practical policy recommendations.
The Healthy Timing and Spacing of Pregnancies (HTSP) project: improving family planning in Siaya County, Kenya
Authors: Otchere Susan A. , Moraa Isabellah , Rotich Vincent , Omunyidde Stephen , Jillson Kimberly Q.
Published: August 2024

Background:

Religious leaders are influential and can impact the uptake of family planning (FP). In this study of the Healthy Timing and Spacing of Pregnancies (HTSP) project, led in Siaya County, Kenya, from September 2017 to June 2019, we present findings from the project’s evaluation, to determine changes in knowledge of the key HTSP messages; changes in the proportion of community members who correctly identify at least three methods of contraception; changes in knowledge of healthy child spacing; and changes in modern contraceptive prevalence rate.

Methods:

This is a two-staged ( baseline and endline) cross-sectional study, designed to assess the knowledge, practice, and coverage of HTSP/FP services. Primary data was collected using a questionnaire adapted from the United States Agency for International Development. Focus group discussion participants included men, women, representatives of community groups, faith leaders, and community heath volunteers. Frequencies were calculated from the ODK platform. Bivariate analytics (paired t test) were performed.

Results:

At baseline, women respondents aged 20–29 years constituted 66.3% of the women participants, dropping to 60.9% at endline. Women aged 30–34 years constituted 11.9% and 22% of the entire women respondents, at baseline and endline, respectively. Men aged 20–29 constituted 45.2% of all men respondents at baseline, and 35.4% at endline. There were statistically significant increases in the knowledge of modern contraceptives among women ( p = 0.0342), faith leaders ( p = 0.0464), and the entire population ( p = 0.0097), from baseline to endline.

Conclusion:

The HTSP model identifies success factors for FP interventions in Kenya and other low- and middle-income countries where faith leaders and community stakeholders are influential, and that women and faith leaders are much more easily impacted positively with these efforts, as measured by increased knowledge and awareness of modern contraceptive methods, compared with men.
Explosion mitigation by grids in combination with a water curtain
Authors: Schunck Thérèse , Eckenfels Dominique
Published: August 2024

The protection of people and structures against the effects of blast waves from terrorist attacks or industrial hazards is of great interest. Protective barriers are an effective means of reducing blast loads and mitigating the adverse effects. In this paper, solid protective barriers consisting of perforated plates and water film have been investigated. Two types of metal grids were tested, the first being a metal plate with small round holes and the second being a chain mail of steel rings. Open air blast tests were carried out to evaluate the protection solution under real conditions. Explosion tests were carried out with homogeneous spheres of composition B and configurations with two grids were studied. The addition of a water film to the first grid was also tested. A PCB sensor was used to evaluate the effect of the grids, or the grids covered with a film of water, on the reflected pressure on a wall behind the grids. It was observed that the overpressure and the impulse measured on the wall behind the grids with small round holes were reduced. The addition of a water film on the first grid resulted in greater attenuation. When two chains were used, the reflected overpressure on the wall was not reduced. However, the initial overpressure was reduced when a film of water flowed over the first mesh. A numerical simulation model is being developed. This will be a sizing tool to optimize the effectiveness of this explosion protection solution. This will make it possible to study the effects of different parameters (porosity, grid spacing, grid-to-wall distance…) on the reflected overpressure and impulse in a less time-consuming and costly way. Such a barrier could reduce the load on a building behind it in an advantageous and aesthetic way.
Multimodality and appraisal choices in Nigerian coronavirus-related WhatsApp memes
Authors: Oyebode Oluwabunmi O , Unuabonah Foluke Olayinka
Published: August 2024

This article explores coronavirus-related internet memes in the Nigerian WhatsApp space, to examine how multimodal elements are used for evaluation and intersubjective positioning. The theory utilises Kress and van Leeuwen’s visual grammar and Martin and White’s appraisal theory. The data, which comprise 147 purposively selected internet memes, were analysed qualitatively. The findings indicate that the meme producers employ verbal and non-verbal elements that show negative affect, judgement and appreciation of things. Using multimodal concepts, the represented participants are able to engage with the public through resources of disclaimers, entertainment, pronouncement and attribution. The study concludes that meme producers engage their addressees through appraisal resources to achieve their communicative goals of complaining about the negative effects of the pandemic on the people, evaluating the behaviour of different agents during the pandemic as well as providing support for people.
Metastatic Non–Small-Cell Lung Cancer Presenting as Renal Failure From IgA Nephropathy
Authors: Yassin Samer , Athota Sruthi , Khan Afnan , Patel Vraj , Williams James , Dwivedi Suyash
Published: August 2024

Studies have highlighted a potential link between malignancies and immunoglobulin A nephropathy (IgAN). In such studies, the treatment of malignancy improved the symptoms of IgAN. Here, we report a patient case involving a history of hypertension, tobacco use disorder, and chronic kidney disease (CKD) presenting with hematuria with acute renal failure secondary to IgAN per renal biopsy. Prompted by this association, a malignancy workup was performed including computed tomography (CT) body imaging and biopsies of mediastinal and cervical lymph nodes which revealed a metastatic adenocarcinoma. Current knowledge includes a general mechanism behind the development of IgAN that points toward glomerular deposition of tumor-specific immunoglobulin A (IgA) immunoglobulins. However, the association of IgAN and malignancy has no definitive management guidelines. This clinical case serves as an important contribution in the hopes of future development of guidelines regarding the surveillance and management of IgAN in the setting of malignancy.
Can Conversational Receptiveness Build Trust in the Media?
Authors: Tulan Dilan , Dorison Charles A. , Gibbs Nancy , Minson Julia A.
Published: August 2024

Trust in nonpartisan news is essential to civil society—but is declining in the United States. However, language that demonstrates active engagement with opposing views may build trust. One way to demonstrate such active engagement is conversational receptiveness: the use of linguistic features such as agreement, acknowledgment, subjectivity, and positive emotion, among others. A review of prior work on conversational receptiveness suggests its usefulness in interpersonal conflict. This toolkit might effectively apply also to the challenge of restoring trust in nonpartisan media. A demonstration study illustrates proof of concept: In 600 opinion articles from prominent news sources, more receptive language was associated with reader trust. Pending programmatic research will address limitations, feasibility constraints, open questions, and future empirical directions—including causal tests in applied settings. At a minimum, extrapolating conversational receptivity from its role in interpersonal conflict suggests a role in building trust in nonpartisan media. Conversational receptiveness might present a cost-effective, scalable approach for media producers to bridge political divides and rebuild trust—without alienating existing audiences.
Utility of pan-bacterial and pan-fungal PCR in endophthalmitis: case report and review of the literature
Authors: Ercanbrack Carson W. , Rahal Dania A. , Chauhan Muhammad Z. , Jabbehdari Sayena , Uwaydat Sami H.
Published: August 2024

Background

Endophthalmitis is a clinical diagnosis but identification of the disease-causing agent or agents allows for a more tailored treatment. This is routinely done through intraocular fluid cultures and staining. However, culture-negative endophthalmitis is a relatively common occurrence, and a causative organism cannot be identified. Thus, further diagnostic testing, such as pan-bacterial and pan-fungal polymerase chain reactions (PCRs), may be required.

Body

There are now newer, other testing modalities, specifically pan-bacterial and pan-fungal PCRs, that may allow ophthalmologists to isolate a causative agent when quantitative PCRs and cultures remain negative. We present a case report in which pan-fungal PCR was the only test, amongst quantitative PCRs, cultures, and biopsies, that was able to identify a pathogen in endophthalmitis. Pan-PCR has unique advantages over quantitative PCR in that it does not have a propensity for false-positive results due to contamination. Conversely, pan-PCR has drawbacks, including its inability to detect viruses and parasites and its increased turnaround time and cost. Based on two large retrospective studies, pan-PCR was determined not to be recommended in routine cases of systemic infection as it does not typically add value to the diagnostic workup and does not change the treatment course in most cases. However, in cases like the one presented, pan-bacterial and pan-fungal PCRs may be considered if empiric treatment fails or if the infective organism cannot be isolated. If pan-PCR remains negative or endophthalmitis continues to persist, an even newer form of testing, next-generation sequencing, may aid in the diagnostic workup of culture-negative endophthalmitis.

Conclusion

Pan-bacterial and pan-fungal PCR testing is a relatively new diagnostic tool with unique advantages and drawbacks compared to traditional culturing and PCR methods. Similar to the tests’ use in non-ophthalmic systemic infections, pan-bacterial and pan-fungal PCRs are unlikely to become the initial diagnosis test and completely replace culture methods. However, they can provide useful diagnostic information if an infectious agent is unable to be identified with traditional methods or if empiric treatment of endophthalmitis continues to fail.
RNA-DNA differences in variant calls from cattle tissues result in erroneous eQTLs
Authors: Leonard Alexander S. , Mapel Xena M. , Pausch Hubert
Published: August 2024

Background

Association testing between molecular phenotypes and genomic variants can help to understand how genotype affects phenotype. RNA sequencing provides access to molecular phenotypes such as gene expression and alternative splicing while DNA sequencing or microarray genotyping are the prevailing options to obtain genomic variants.

Results

We genotype variants for 74 male Braunvieh cattle from both DNA (~ 13-fold coverage) and deep total RNA sequencing from testis, vas deferens, and epididymis tissue (~ 250 million reads per tissue). We show that RNA sequencing can be used to identify approximately 40% of variants (7–10 million) called from DNA sequencing, with over 80% precision. Within highly expressed coding regions, over 92% of expected variants were called with nearly 98% precision. Allele-specific expression and putative post-transcriptional modifications negatively impact variant genotyping accuracy from RNA sequencing and contribute to RNA-DNA differences. Variants called from RNA sequencing detect roughly 75% of eGenes identified using variants called from DNA sequencing, demonstrating a nearly 2-fold enrichment of eQTL variants. We observe a moderate-to-strong correlation in nominal association p-values (Spearman ρ2 ~ 0.6), although only 9% of eGenes have the same top associated variant.

Conclusions

We find hundreds of thousands of RNA-DNA differences in variants called from RNA and DNA sequencing on the same individuals. We identify several highly significant eQTL when using RNA sequencing variant genotypes which are not found with DNA sequencing variant genotypes, suggesting that using RNA sequencing variant genotypes for association testing results in an increased number of false positives. Our findings demonstrate that caution must be exercised beyond filtering for variant quality or imputation accuracy when analysing or imputing variants called from RNA sequencing.
Association mapping with a diverse population of Puccinia graminis f. sp. tritici identified avirulence loci interacting with the barley Rpg1 stem rust resistance gene
Authors: Upadhaya Arjun , Upadhaya Sudha G. C. , Brueggeman Robert
Published: August 2024

Background

Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is an important disease of barley and wheat. A diverse sexual Pgt population from the Pacific Northwest (PNW) region of the US contains a high proportion of individuals with virulence on the barley stem rust resistance (R) gene, Rpg1. However, the evolutionary mechanisms of this virulence on Rpg1 are mysterious considering that Rpg1 had not been deployed in the region and the gene had remained remarkably durable in the Midwestern US and prairie provinces of Canada.

Methods and results

To identify AvrRpg1 effectors, genome wide association studies (GWAS) were performed using 113 Pgt isolates collected from the PNW (n = 89 isolates) and Midwest (n = 24 isolates) regions of the US. Disease phenotype data were generated on two barley lines Morex and the Golden Promise transgenic (H228.2c) that carry the Rpg1 gene. Genotype data was generated by whole genome sequencing (WGS) of 96 isolates (PNW = 89 isolates and Midwest = 7 isolates) and RNA sequencing (RNAseq) data from 17 Midwestern isolates. Utilizing ~1.2 million SNPs generated from WGS and phenotype data (n = 96 isolates) on the transgenic line H228.2c, 53 marker trait associations (MTAs) were identified. Utilizing ~140 K common SNPs generated from combined analysis of WGS and RNAseq data, two significant MTAs were identified using the cv Morex phenotyping data. The 55 MTAs defined two distinct avirulence loci, on supercontig 2.30 and supercontig 2.11 of the Pgt reference genome of Pgt isolate CRL 75-36-700-3. The major avirulence locus designated AvrRpg1A was identified with the GWAS using both barley lines and was delimited to a 35 kb interval on supercontig 2.30 containing four candidate genes (PGTG_10878, PGTG_10884, PGTG_10885, and PGTG_10886). The minor avirulence locus designated AvrRpg1B identified with cv Morex contained a single candidate gene (PGTG_05433). AvrRpg1A haplotype analysis provided strong evidence that a dominant avirulence gene underlies the locus.

Conclusions

The association analysis identified strong candidate AvrRpg1 genes. Further analysis to validate the AvrRpg1 genes will fill knowledge gaps in our understanding of rust effector biology and the evolution and mechanism/s of Pgt virulence on Rpg1.
Microbial carbohydrate active enzyme (CAZyme) genes and diversity from Menagesha Suba natural forest soils of Ethiopia as revealed by shotgun metagenomic sequencing
Authors: Sime Amsale Melkamu , Kifle Bezayit Amare , Woldesemayat Adugna Abdi , Gemeda Mesfin Tafesse
Published: August 2024

Background

The global over-reliance on non-renewable fossil fuels has led to the emission of greenhouse gases, creating a critical global environmental challenge. There is an urgent need for alternative solutions like biofuels. Advanced biofuel is a renewable sustainable energy generated from lignocellulosic plant materials, which can significantly contribute to mitigating CO2 emissions. Microbial Carbohydrate Active Enzymes (CAZymes) are the most crucial enzymes for the generation of sustainable biofuel energy. The present study designed shotgun metagenomics approaches to assemble, predict, and annotate, aiming to gain an insight into the taxonomic diversity, annotate CAZymes, and identify carbohydrate hydrolyzing CAZymes from microbiomes in Menagesha suba forest soil for the first time.

Results

The microbial diversity based on small subunit (SSU) rRNA analysis revealed the dominance of the bacterial domain representing 81.82% and 92.31% in the studied samples. Furthermore, the phylum composition result indicated the dominance of the phyla Proteobacteria (23.08%, 27.27%), Actinobacteria (11.36%, 20.51%), and Acidobacteria (10.26%, 15.91%). The study also identified unassigned bacteria which might have a unique potential for biopolymer hydrolysis. The metagenomic study revealed that 100,244 and 65,356 genes were predicted from the two distinct samples. A total number of 1806 CAZyme genes were identified, among annotated CAZymes, 758 had a known enzyme assigned to CAZymes. Glycoside hydrolases (GHs) CAZyme family contained most of the CAZyme genes with known enzymes such as β-glucosidase, endo-β-1,4-mannanase, exo-β-1,4-glucanase, α-L-arabinofuranosidase and oligoxyloglucan reducing end-specific cellobiohydrolase. On the other hand, 1048 of the identified CAZyme genes were putative CAZyme genes with unknown enzymatical activity and the majority of which belong to the GHs family.

Conclusions

In general, the identified putative CAZymes genes open up an opportunity for the discovery of new enzymes responsible for hydrolyzing biopolymers utilized for biofuel energy generation. This finding is used as a first-hand piece of evidence to serve as a benchmark for further and comprehensive studies to unveil novel classes of bio-economically valuable genes and their encoded products.
Person-centered care for common mental disorders in Ontario’s primary care patient-centered medical homes: a qualitative study of provider perspectives
Authors: Menear Matthew , Ashcroft Rachelle , Dahrouge Simone , Silveira Jose , Booton Jocelyn , Emode Monica , McKenzie Kwame
Published: August 2024

Background

For more than a decade, the Patient-Centered Medical Home model has been a guiding vision for the modernization of primary care systems. In Canada, Ontario’s Family Health Teams (FHTs) were designed in the mid-2000s with the medical home model in mind. These primary care clinics aim to provide accessible, comprehensive, and person-centered primary care services to communities across Ontario. Their services typically include mental health care for people experiencing common mental disorders, such as depression and anxiety disorders. It remains unclear, however, whether the mental health care delivered within FHTs is consistent with person-centered care approaches. In the current study, we aimed to explore the perspectives of FHT providers on the care delivered to people with common mental disorders to determine whether, and to what extent, they believed this care was person-centered.

Methods

We conducted a qualitative grounded theory study involving interviews with 65 health professionals and administrators from 18 FHTs across Ontario. Transcripts were coded using a three-step process of initial, focused, and axial coding that mixed inductive and deductive approaches informed by sensitizing concepts on person-centeredness.

Results

Practices and challenges associated with the delivery of mental health care in a person-centered way were captured by several themes regrouped into five domains: (1) patient as unique person, (2) patient-provider relationship, (3) sharing power and responsibility, (4) connecting to family and community, and (5) creating person-centered care environments. FHT providers perceived that they delivered person-centered care by delivering mental health care that was responsive, flexible, and consistent with biopsychosocial approaches. They emphasized the importance of creating long-lasting relationships with patients grounded in empathy and trust. Their challenges included being able to ensure continuity of care, adequately prioritizing patients’ mental health issues, and meaningfully engaging patients and families as partners in care.

Conclusions

Our findings suggest that FHT providers have adopted a range of person-centered practices for people with common mental disorders. However, greater attention to practices such as shared decision making, supporting self-management, and involving families in care would strengthen person-centeredness and bring teams closer to the Patient-Centered Medical Home vision.
Development of a self-assessment tool to address the functioning of community-dwelling older adults in general practice: a validation study of the EFA23 questionnaire
Authors: Rink Laura , Floto Caroline , Apel Katharina , Weiss Maren , Stegmeier Elmar , Kühlein Thomas , Sebastião Maria
Published: August 2024

Background

Multimorbidity is increasingly prevalent among ageing patients, leading to reduced daily functioning. To address the challenges posed by multimorbidity in older adults, a person- and context-centred approach is needed. This study aimed to develop a questionnaire as a self-assessment tool for older adults focusing on functioning in general practice based on the International Classification of Functioning, Disability and Health (ICF).

Methods

A mixed-methods approach was employed in the development and validation of the German EFA23 (Erfassung Funktionaler Gesundheit im Alter – 23 Fragen; Assessing Functional Health in Old Age – 23 questions) questionnaire. Based on an ICF subset developed in a preparatory phase and consensus study, questionnaire items were formulated and tested in a qualitative pretest, followed by a validation study. A workshop with general practitioners (GPs) was held to develop a supplementary manual for GPs on how to interpret the questionnaire results and discuss them with the patients.

Results

A total of 69 items were developed and tested in the qualitative pretest with 15 respondents, resulting in 37 items for the validation study. The validation study, involving 237 older adults, showed the presence of one significant principal component. It demonstrated good internal consistency (Cronbach’s alpha = 0.967) and construct validity, showing positive correlations with established assessment tools. Descriptive statistics showed differences between the means of self-assessment by patients and an external GP assessment. The final EFA23 questionnaire consists of 23 items assessing limitations in functioning.

Conclusions

The EFA23 questionnaire can be used as a valid self-assessment instrument to measure functioning in older adults, supporting a person- and context-centred approach in general practice.
COVID-19 infection and 2-year mortality in nursing home residents who survived the first wave of the pandemic
Authors: Sanchez Manuel , Courtois-Amiot Pauline , Herrault Vincent , Allart Hélène , Eischen Philippe , Chetaille Fabienne , Lepineux Denise , de Cathelineau Castille , Raynaud-Simon Agathe
Published: August 2024

Background

During the first COVID-19 pandemic wave (1st CoPW), nursing homes (NHs) experienced a high rate of COVID-19 infection and death. Residents who survived the COVID-19 infection may have become frailer. This study aimed to determine the predictive value of having a COVID-19 infection during the 1st CoPW for 2-year mortality in NH residents.

Methods

This was a retrospective study conducted in three NHs. Residents who had survived the 1st CoPW (March to May 2020) were included. The diagnosis of COVID-19 was based on the results of a positive reverse transcriptase-polymerase chain reaction test. The collected data also included age, sex, length of residence in the NH, disability status, legal guardianship status, nutritional status, need for texture-modified food, hospitalization or Emergency Department visits during lockdown and SARS-COV2 vaccination status during the follow-up. Non-adjusted and adjusted Cox models were used to analyse factors associated with 2-year post-1st CoPW mortality.

Results

Among the 315 CoPW1 survivors (72% female, mean age 88 years, 48% with severe disability), 35% presented with COVID-19. Having a history of COVID-19 was not associated with 2-year mortality: hazard ratio (HR) [95% confidence interval] = 0.96 [0.81–1.13], p = 0.62. The factors independently associated with 2-year mortality were older age (for each additional year, HR = 1.05 [1.03–1.08], p < 0.01), severe disability vs. moderate or no disability (HR = 1.35 [1.12–1.63], p < 0.01) and severe malnutrition vs. no malnutrition (HR = 1.29 [1.04–1.60], p = 0.02). Considering that vaccination campaign started during the follow-up, mortality was associated with severe malnutrition before and severe disability after the start of the campaign. Vaccination was independently associated with better survival (HR 0.71 [0.55–0.93], p = 0.02).

Conclusions

Having survived a COVID-19 infection during the 1st CoPW did not affect subsequent 2-year survival in older adults living in NHs. Severe malnutrition and disability remained strong predictor of mortality in this population, whereas vaccination was associated to better survival.
Factors associated with self-reports of limitations in activities of daily living among Medicare Fee-for-Service recipients
Authors: Hays Ron D. , Haas Ann , Haviland Amelia M. , Martino Steven C. , Orr Nate , Binion Joy , Elliott Marc N.
Published: August 2024

Background

Physical function is an important indicator of physical health and predicts mortality. This study identified characteristics associated with limitations in Medicare recipients' activities of daily living.

Methods

2019 Consumer Assessment of Healthcare Providers and Systems Fee-for-Service Medicare Survey data: 79,725 respondents (34% response rate) who were 65 and older and 53% female; 7% Black, 5% Hispanic, 4% Asian American, Native Hawaiian, or other Pacific Islander, 2% Multiracial, 1% American Indian/Alaskan Native; 35% with high school education or less. Walking, getting in and out of chairs, bathing, dressing, toileting, and eating (scored as having no difficulty versus being able to do with difficulty or unable to do) and a scale of these items were regressed on patient characteristics.

Results

After adjustment for all characteristics, function limitations were found for those who smoked (effect sizes of significant associations range .04-.13), had chronic health conditions (.02-.33), were 85 years or older (.09-.46), needed assistance completing the survey (.32–1.29), were female (.05-.07), and had low income and assets (.15-.47).

Conclusions

These nationally representative U.S. estimates of physical function characteristics are useful for interventions for vulnerable population subgroups.
Mortality and associated factors among patients with TB-HIV co-infection in Ethiopia: a systematic review and meta-analysis
Authors: Moges Sisay , Lajore Bereket Abrham
Published: August 2024

Background

Tuberculosis (TB) and human immunodeficiency virus (HIV) co-infection is a major public health problem in Ethiopia. Patients with TB-HIV co-infection have significantly higher mortality rates compared to those with TB or HIV mono-infection. This systematic review and meta-analysis aim to summarize the evidence on mortality and associated factors among patients with TB-HIV co-infection in Ethiopia.

Methods

Comprehensive searches were conducted in multiple electronic databases (PubMed/MEDLINE, Embase, CINAHL, Web of Science) for observational studies published between January 2000 and present, reporting mortality rates among TB/HIV co-infected individuals. Two reviewers performed study selection, data extraction, and quality assessment independently. Random-effects meta-analysis was used to pool mortality estimates, and heterogeneity was assessed using I² statistics. Subgroup analyses and meta-regression were performed to explore potential sources of heterogeneity.

Results

185 articles were retrieved with 20 studies included in the final analysis involving 8,113 participants. The pooled mortality prevalence was 16.65% (95% CI 12.57%-19.65%) with I2 : 95.98% & p-value < 0.00. Factors significantly associated with increased mortality included: older age above 44 years (HR: 1.82; 95% CI: 1.31–2.52), ambulatory(HR: 1.64; 95% CI: 1.23–2.18) and bedridden functional status(HR: 2.75; 95% CI: 2.01–3.75), extra-pulmonary Tuberculosis (ETB) (HR: 2.34; 95% CI: 1.76–3.10), advanced WHO stage III (HR: 1.76; 95% CI: 1.22–2.38) and WHO stage IV (HR: 2.17; 95% CI:1.41–3.34), opportunistic infections (HR: 1.75; 95% CI: 1.30–2.34), low CD4 count of < 50 cells/mm3 (HR: 3.37; 95% CI: 2.18–5.22) and lack of co-trimoxazole prophylaxis (HR: 2.15; 95% CI: 1.73–2.65).

Conclusions

TB/HIV co-infected patients in Ethiopia experience unacceptably high mortality, driven by clinical markers of advanced immunosuppression. Early screening, timely treatment initiation, optimizing preventive therapies, and comprehensive management of comorbidities are imperative to improve outcomes in this vulnerable population.