bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating microbial and environmental drivers of nitrification in alkaline forest soil
Authors: Poghosyan Lianna , Lehtovirta-Morley Laura E 
Published: July 2024

Abstract
Ammonia oxidation is a key step in the biogeochemical cycling of nitrogen, and soils are important ecosystems for nitrogen flux globally. Approximately 25% of the world’s soils are alkaline. While nitrification has been studied more extensively in agricultural alkaline soils, less is known about natural, unfertilized alkaline soils. In this study, microorganisms responsible for ammonia oxidation and several environmental factors (season, temperature, ammonia concentration, and moisture content) known to affect nitrification were studied in an alkaline forest soil with a pH ranging from 8.36 to 8.77. Ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea, and comammox were present, and AOB belonging to genera Nitrosospira and Nitrosomonas, originally comprising &lt;0.01% of the total bacterial community, responded rapidly to ammonia addition to the soil. No significant difference was observed in nitrification rates between seasons, but there was a significant difference between in situ field nitrification rates and rates in laboratory microcosms. Surprisingly, nitrification took place under many of the tested conditions, but there was no detectable increase in the abundance of any recognizable group of ammonia oxidizers. This study raises questions about the role of low-abundance microorganisms in microbial processes and of situations where zero or very low microbial growth coincides with metabolic activity. In addition, this study provides insights into nitrification in unfertilized alkaline soil and supports previous studies, which found that AOB play an important role in alkaline soils supplemented with ammonia, including agricultural ecosystems.
Proteomes of native and non-native symbionts reveal responses underpinning host-symbiont specificity in the cnidarian–dinoflagellate symbiosis
Authors: Mashini Amir , Oakley Clinton A , Peng Lifeng , Grossman Arthur R , Weis Virginia M , Davy Simon K 
Published: July 2024

Abstract
Cellular mechanisms responsible for the regulation of nutrient exchange, immune responses, and symbiont population growth in the cnidarian–dinoflagellate symbiosis are poorly resolved, particularly with respect to the dinoflagellate symbiont. Here, we characterized proteomic changes in the native symbiont Breviolum minutum during colonization of its host sea anemone Exaiptasia diaphana (“Aiptasia”). We also compared the proteome of this native symbiont in the established symbiotic state with that of a non-native symbiont, Durusdinium trenchii. The onset of symbiosis between Aiptasia and Breviolum minutum increased the accumulation of symbiont proteins associated with the acquisition of inorganic carbon and photosynthesis, nitrogen metabolism, micro- and macronutrient starvation, suppression of host immune responses, tolerance to low pH, and management of oxidative stress. Such responses are consistent with a functional, persistent symbiosis. In contrast, D. trenchii predominantly showed elevated levels of immunosuppressive proteins, consistent with the view that this symbiont is an opportunist that forms a less beneficial, less well-integrated symbiosis with this model anemone. By adding symbiont analysis to the already known responses of the host proteome, our results provide a more holistic view of cellular processes that determine host-symbiont specificity and how differences in symbiont partners (i.e. native versus non-native symbionts) may impact the fitness of the cnidarian–dinoflagellate symbiosis.
Social media use and mental health among older adults with multimorbidity: the role of self-care efficacy
Authors: Nie Zuoting , Gao Shiying , Chen Long , Yang Rumei , Edelman Linda S , Sward Katherine A , Jiang Yun , Demiris George 
Published: July 2024

Abstract

Objectives
To describe the prevalence and trends in the use of social media over time and explore whether social media use is related to better self-care efficacy and thus related to better mental health among United States older adults with multimorbidity.

Materials and Methods
Respondents aged 65 years+ and having 2 or more chronic conditions from the 2017-2020 Health Information National Trends Survey were analyzed (N = 3341) using weighted descriptive and logistic regression analyses.

Results
Overall, 48% (n = 1674) of older adults with multimorbidity used social media and there was a linear trend in use over time, increasing from 41.1% in 2017 to 46.5% in 2018, and then further up to 51.7% in 2019, and 54.0% in 2020. Users were often younger, married/partnered, and non-Hispanic White with high education and income. Social media use was associated with better self-care efficacy that was further related to better mental health, indicating a significant mediation effect of self-care efficacy in the relationship between social media use and mental health.

Discussion
Although older adults with multimorbidity are a fast-growing population using social media for health, significant demographic disparities exist. While social media use is promising in improving self-care efficacy and thus mental health, relying on social media for the management of multimorbidity might be potentially harmful to those who are not only affected by multimorbidity but also socially disadvantaged (eg, non-White with lower education).

Conclusion
Great effort is needed to address the demographic disparity and ensure health equity when using social media for patient care.
The action of coenzyme B12-dependent diol dehydratase on 3,3,3-trifluoro-1,2-propanediol results in elimination of all the fluorides with formation of acetaldehyde
Authors: Mori Koichi , Golding Bernard T , Toraya Tetsuo 
Published: July 2024

Abstract
3,3,3-Trifluoro-1,2-propanediol undergoes complete defluorination in two distinct steps: first, the conversion into 3,3,3-trifluoropropionaldehyde catalyzed by adenosylcobalamin (coenzyme B12)-dependent diol dehydratase; second, non-enzymatic elimination of all three fluorides from this aldehyde to afford malonic semialdehyde (3-oxopropanoic acid), which is decarboxylated to acetaldehyde. Diol dehydratase accepts 3,3,3-trifluoro-1,2-propanediol as a relatively poor substrate, albeit without significant mechanism-based inactivation of the enzyme during catalysis. Optical and electron paramagnetic resonance (EPR) spectra revealed the steady-state formation of cob(II)alamin and a substrate-derived intermediate organic radical (3,3,3-trifluoro-1,2-dihydroxyprop-1-yl). The coenzyme undergoes Co–C bond homolysis initiating a sequence of reaction by the generally accepted pathway via intermediate radicals. However, the greater steric size of trifluoromethyl and especially its negative impact on the stability of an adjacent radical centre compared to a methyl group has implications for the mechanism of the diol dehydratase reaction. Nevertheless, 3,3,3-trifluoropropionaldehyde is formed by the normal diol dehydratase pathway, but then undergoes non-enzymatic conversion into acetaldehyde, probably via 3,3-difluoropropenal and malonic semialdehyde.
Hypophosphatemic rickets and short stature
Authors: Davis Kelli , Imel Erik A , Kelley Jennifer 
Published: July 2024

Vignette
An 18-month-old male presented with gross motor delay and poor growth (weight z-score −2.21, length z-score −4.26). Radiographs showed metaphyseal irregularities suggesting metaphyseal dysplasia and sagittal craniosynostosis. Biochemical evaluation supported hypophosphatemic rickets [serum phosphorus 2.3 mg/dL (reference range (RR) 4.3–6.8), alkaline phosphatase 754 unit/L (RR 156–369)] due to renal phosphate wasting (TmP/GFR 4.3 mg/dL, normal for age 4.3-6.8), with C-terminal fibroblast growth factor 23 (FGF23) 125 RU/mL (&gt;90 during hypophosphatemia suggests FGF23-mediated hypophosphatemia). Treatment was initiated with calcitriol and phosphate. Genetic analysis showed a pathogenic variant of FGF23: c.527G &gt; A (p.Arg176Gln) indicative of autosomal dominant hypophosphatemic rickets (ADHR). Consistent with reports linking iron deficiency with the ADHR phenotype, low ferritin was detected. Following normalization of ferritin level (41 ng/mL) with oral ferrous sulfate replacement, biochemical improvement was demonstrated (FGF23 69 RU/mL, phosphorus 5.0 mg/dL and alkaline phosphatase 228 unit/L). Calcitriol and phosphate were discontinued. Three years later, the patient demonstrated improved developmental milestones, linear growth (length Z-score −2.01), radiographic normalization of metaphyses, and stabilization of craniosynostosis. While the most common cause of hypophosphatemic rickets is X-linked hypophosphatemia, other etiologies should be considered as treatment differs. In ADHR, normalization of iron leads to biochemical and clinical improvement.
Public Bioethics Amidst a Pluralist People: A Project of Presumption, Despair, or Hope?
Authors: Parviz Benjamin 
Published: July 2024

AbstractMichael Lamb’s recent book A Commonwealth of Hope presents an opportunity for bioethicists to engage in critical self-evaluation in order to consider anew why and how to engage difficult bioethical problems and questions with those who maintain diverse moral and metaphysical perspectives. Drawing on an account of the virtue of hope from Augustine of Hippo, Lamb develops a political theory in which hope provides common ground for political cooperation between diverse citizens of a commonwealth. The purpose of this introduction is to sketch out a framework by which to assess and evaluate whether bioethics demonstrates hope. This article provides a summary description of Lamb’s presentation of Augustine’s virtue of hope and his concept of politics. Then it considers implications of Lamb’s politics of hope for bioethics, identifying three features of hopeful bioethics, with which bioethicists can engage in self-reflection and evaluation.
Assessment of efficacy of chrysin in diabetes-associated cardiac complications in chick embryo and murine model
Authors: Das Joyani , Roy Sarkar Suparna , Das Ankita , Barui Ananya , Mitra Mazumder Papiya 
Published: July 2024

Abstract

Objectives
Patients with type 2 diabetes or prolonged diabetic condition are webbed into cardiac complications. This study aimed to ascertain the utility of chick embryo as an alternative to the mammalian model for type 2 diabetes-induced cardiac complications and chrysin as a protective agent.

Methods
Diabetes was activated in ovo model (chick embryo) using glucose along with β-hydroxybutyric acid. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, Alamar, and Kenacid blue assay were used to compare with chrysin-administered group. Blood glucose level, total cholesterol, triglyceride, and high-density lipoprotein were considered as endpoints. Diabetes was induced in Wistar albino rats by administering a high-fat diet and a subdued dose of streptozotocin (35 mg/kg, b.w). Percentage of glycated hemoglobin, creatinine kinase-MB, tumor necrosis factor-α, and C-reactive protein were evaluated and compared with chrysin administered group.

Key findings
Chrysin treatment improved elevated blood glucose levels and dyslipidemia in a diabetic group of whole embryos. Condensed cellular growth and protein content as well as enhanced cytotoxicity in ovo were shielded by chrysin. Chrysin reduced cardiac and inflammatory markers in diabetic rats and provided cellular protection to damage the heart of diabetic rats.

Conclusion
The protective action of chrysin in ovo model induced a secondary complication associated with diabetes, evidenced that the ovo model is an effective alternative in curtailing higher animal use in scientific research.
Successful management of locally advanced cervical cancer via total pelvic exenteration following neoadjuvant chemotherapy
Authors: Endo Yuta , Soeda Shu , Yoshimoto Yuki , Todate Yukitoshi , Hashimoto Tatsuru , Furukawa Shigenori , Teranishi Yasushi , Fujimori Keiya 
Published: July 2024

Abstract
Stage IVA cervical cancer is a tumor that invades the mucosa of the bladder or rectum without distant metastasis and is difficult to treat, and concurrent chemoradiotherapy is recommended. Although radical surgery following neoadjuvant chemotherapy is a treatment option for stage IVA cervical cancer, the evidence is limited. A 51-year-old woman with bulky cervical cancer and rectal invasion was referred to our hospital. Paclitaxel and cisplatin were administered as neoadjuvant chemotherapies. After two cycles of chemotherapy, the tumor size decreased markedly. Total pelvic exenteration was performed, and a complete resection was achieved. Four cycles of paclitaxel and cisplatin were administered postoperatively. Thirty-three months after the completion of adjuvant chemotherapy, the patient was alive and free of disease. Radical surgery after neoadjuvant chemotherapy may be a treatment option for stage IVA cervical cancer with bulky tumors.
Rosai–Dorfman disease differentiated from a posterior mediastinal tumour: a case report
Authors: Hirai Yoshimitsu , Takahashi Yuichi , Kaki Takahiro , Shima Aya , Kanai Kuninobu , Iwamoto Ryuta , Hirai Issei 
Published: July 2024

Abstract
Rosai–Dorfman disease presenting solely with intrathoracic lesions is exceptionally rare. Herein, we report the case of a 53-year-old man presenting with a posterior mediastinal tumour. Computed tomography revealed a 7-cm soft tissue shadow in the posterior mediastinum. Positron emission tomography-computed tomography demonstrated a high maximum standardized uptake value of 10.35 in the tumour, with no evidence of lymph node or other organ involvement. Serum marker levels were within the normal range. Thoracoscopic surgery was performed to obtain a biopsy for a definitive diagnosis and treatment planning. Postoperative histological findings revealed a diffuse infiltration of eosinophilic histiocytes, lymphocytes, and plasma cells. Immunohistochemical analysis indicated positivity for S-100 protein, oct-2, and cyclin D1 in these histiocytes. Consequently, the patient was diagnosed with Rosai–Dorfman disease and is currently asymptomatic, undergoing regular monitoring without treatment as an outpatient. The absence of characteristic findings, such as bilateral cervical lymphadenopathy, posed challenges in preoperative diagnosis.
tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development
Authors: Rappol Tom , Waldl Maria , Chugunova Anastasia , Hofacker Ivo L , Pauli Andrea , Vilardo Elisa 
Published: July 2024

Abstract
tRNA genes exist in multiple copies in the genome of all organisms across the three domains of life. Besides the sequence differences across tRNA copies, extensive post-transcriptional modification adds a further layer to tRNA diversification. Whilst the crucial role of tRNAs as adapter molecules in protein translation is well established, whether all tRNAs are actually expressed, and whether the differences across isodecoders play any regulatory role is only recently being uncovered. Here we built upon recent developments in the use of NGS-based methods for RNA modification detection and developed tRAM-seq, an experimental protocol and in silico analysis pipeline to investigate tRNA expression and modification. Using tRAM-seq, we analysed the full ensemble of nucleo-cytoplasmic and mitochondrial tRNAs during embryonic development of the model vertebrate zebrafish. We show that the repertoire of tRNAs changes during development, with an apparent major switch in tRNA isodecoder expression and modification profile taking place around the start of gastrulation. Taken together, our findings suggest the existence of a general reprogramming of the expressed tRNA pool, possibly gearing the translational machinery for distinct stages of the delicate and crucial process of embryo development.
Molecular basis for cA6 synthesis by a type III-A CRISPR–Cas enzyme and its conversion to cA4 production
Authors: Goswami Hemant N , Ahmadizadeh Fozieh , Wang Bing , Addo-Yobo Doreen , Zhao Yu , Whittington A Carl , He Huan , Terns Michael P , Li Hong 
Published: July 2024

Abstract
The type III-A (Csm) CRISPR–Cas systems are multi-subunit and multipronged prokaryotic enzymes in guarding the hosts against viral invaders. Beyond cleaving activator RNA transcripts, Csm confers two additional activities: shredding single-stranded DNA and synthesizing cyclic oligoadenylates (cOAs) by the Cas10 subunit. Known Cas10 enzymes exhibit a fascinating diversity in cOA production. Three major forms—cA3, cA4 and cA6have been identified, each with the potential to trigger unique downstream effects. Whereas the mechanism for cOA-dependent activation is well characterized, the molecular basis for synthesizing different cOA isoforms remains unclear. Here, we present structural characterization of a cA6-producing Csm complex during its activation by an activator RNA. Analysis of the captured intermediates of cA6 synthesis suggests a 3′-to-5′ nucleotidyl transferring process. Three primary adenine binding sites can be identified along the chain elongation path, including a unique tyrosine–threonine dyad found only in the cA6-producing Cas10. Consistently, disrupting the tyrosine–threonine dyad specifically impaired cA6 production while promoting cA4 production. These findings suggest that Cas10 utilizes a unique enzymatic mechanism for forming the phosphodiester bond and has evolved distinct strategies to regulate the cOA chain length.
High Prevalence of Highly Pathogenic Avian Influenza: A Virus in Vietnam's Live Bird Markets
Authors: Dao Duy Tung , Coleman Kristen K , Bui Vuong N , Bui Anh N , Tran Long H , Nguyen Quy D , Than Son , Pulscher Laura A , Marushchak Lyudmyla V , Robie Emily R , Nguyen-Viet Hung , Pham Phuc Duc , Christy Nathaniel C , Brooks John S , Nguyen Huy C , Rubrum Adam M , Webby Richard J , Gray Gregory C 
Published: July 2024

Abstract

Background
In recent years, Vietnam has suffered multiple epizootics of influenza in poultry.

Methods
From 10 January 2019 to 26 April 2021, we employed a One Health influenza surveillance approach at live bird markets (LBMs) and swine farms in Northern Vietnam. When the COVID-19 pandemic permitted, each month, field teams collected oral secretion samples from poultry and pigs, animal facility bioaerosol and fecal samples, and animal worker nasal washes at 4 LBMs and 5 swine farms across 5 sites. Initially samples were screened with molecular assays followed by culture in embryonated eggs (poultry swabs) or Madin-Darby canine kidney cells (human or swine swabs).

Results
Many of the 3493 samples collected had either molecular or culture evidence for influenza A virus, including 314 (37.5%) of the 837 poultry oropharyngeal swabs, 144 (25.1%) of the 574 bioaerosol samples, 438 (34.9%) of the 1257 poultry fecal swab samples, and 16 (1.9%) of the 828 human nasal washes. Culturing poultry samples yielded 454 influenza A isolates, 83 of which were H5, and 70 (84.3%) of these were highly pathogenic. Additionally, a positive human sample had a H9N2 avian-like PB1 gene. In contrast, the prevalence of influenza A in the swine farms was much lower with only 6 (0.4%) of the 1700 total swine farm samples studied, having molecular evidence for influenza A virus.

Conclusions
This study suggests that Vietnam's LBMs continue to harbor high prevalences of avian influenza A viruses, including many highly pathogenic H5N6 strains, which will continue to threaten poultry and humans.
Nab-paclitaxel plus S-1 versus nab-paclitaxel plus gemcitabine in patients with advanced pancreatic cancer: a multicenter, randomized, phase II study
Authors: Jin Min , Liu Hong-Li , Xue Jun , Ma Hong , Liu Jun-Li , Lin Zhen-Yu , Wang Jing , Bao Le-Qun , Luo Zhi-Guo , Yu Xiong-Jie , Li Shuang , Hu Jian-Li , Zhang Tao 
Published: July 2024

Abstract

Background
Encouraging antitumor activity of nab-paclitaxel plus S-1 (AS) has been shown in several small-scale studies. This study compared the efficacy and safety of AS versus standard-of-care nab-paclitaxel plus gemcitabine (AG) as a first-line treatment for advanced pancreatic cancer (PC).

Methods
In this multicenter, randomized, phase II trial, eligible patients with unresectable, locally advanced, or metastatic PC were recruited and randomly assigned (1:1) to receive AS (nab-paclitaxel 125 mg/m2 on days 1 and 8; S-1 twice daily on days 1 through 14) or AG (nab-paclitaxel 125 mg/m2 on days 1 and 8; gemcitabine 1000 mg/m2 on days 1 and 8) for 6 cycles. The primary endpoint was progression-free survival (PFS).

Results
Between July 16, 2019, and September 9, 2022, 62 patients (AS, n = 32; AG, n = 30) were treated and evaluated. With a median follow-up of 8.36 months at preplanned interim analysis (data cutoff, March 24, 2023), the median PFS (8.48 vs 4.47 months; hazard ratio [HR], 0.402; P = .002) and overall survival (OS; 13.73 vs 9.59 months; HR, 0.226; P &lt; .001) in the AS group were significantly longer compared to the AG group. More patients had objective response in the AS group than AG group (37.50% vs 6.67%; P = .005). The most common grade 3-4 adverse events were neutropenia and leucopenia in both groups, and gamma glutamyl transferase increase was observed only in the AG group.

Conclusion
The first-line AS regimen significantly extended both PFS and OS of Chinese patients with advanced PC when compared with the AG regimen, with a comparable safety profile. (ClinicalTrials.gov Identifier: NCT03636308).
A Community Development Approach in Physical Therapist Education
Authors: Varnado Kimberly , Mejia-Downs Anne , Scharmann Alexander , Richardson Shannon 
Published: July 2024

Abstract

Physical therapists should be able to screen patients for social determinants that impact health and refer to community resources as appropriate. To make appropriate referrals, physical therapists must equip themselves with skills to connect patients and clients to community resources outside the walls of their respective institutions, starting with developing these practices in physical therapist education programs. Experienced community builders recommend a community development approach where residents initiate and agree upon decisions, and outside stakeholders work as partners to elevate the community. The community should be supported to determine the desired outcomes in ways that enhance equity, inclusion, and social justice. Communities play a substantial role in health outcomes. Studies indicate that 85% of one’s health is connected to community and economic resources, while only 15% is affected by medical interventions. Connected communities are potent tools to enhance health. Connected communities are places where residents nurture neighborhood relationships that enable them to work together to create a good life supporting their collective well-being. The community-builder approach recenters people and their communities as fundamental health leaders; institutions can use their resources to elevate communities by relocating authority back to communities. Communities have assets and resources largely unrecognized, disconnected, and not mobilized by residents. Institutions are positioned to support citizens and their associations in discovering, connecting, and mobilizing these assets. This asset-based community development approach focuses on 5 principles: place-based, citizen-led, relationship-oriented, asset-based, and inclusion-focused. This perspective paper will describe ways institutions can elevate communities; the benefits of community development practices in physical therapist education programs; and explore examples of community partnerships and best practices to develop equitable alliances with residents in the community.

Impact
A large part of one’s health is directly related to where one lives. Physical therapists and physical therapist assistants can play a vital role in improving the health of society by engaging in their local communities through community development. Community development is a practice where community members and outside stakeholders, such as physical therapists, come together to meet the needs of a community.