bluuebunny/crossref_metadata_2025 huggingface dataset:
Relationship Between Sleep Quality and Constipation Severity in Patients With Parkinson Disease: A Cross-sectional Study
Authors: Doi Tomoko , Honda Ikumi , Nakajima Maki , Tamaoki Miharu , Hirayama Masaaki
Published: November 2023

BACKGROUND: Constipation in patients with Parkinson disease (PD) adversely affects motor symptoms, making defecation management critical. Sleep disturbance is another common complaint in patients with PD (PWP). Associations between sleep disturbances and constipation have been reported in recent studies on PD. If improving sleep quality is useful for managing constipation in PWP, it might serve as a new method of constipation management that is less physically and mentally distressing than laxatives. This study aimed to examine the relationship between sleep quality and constipation severity in PWP. METHODS: We administered a questionnaire on sleep and constipation to 1048 PWP. Constipation severity was assessed using Constipation Assessment Scale Japanese version 2 (CAS). General sleep quality was estimated using the Japanese versions of the Pittsburgh Sleep Quality Index (PSQI) and Athens Insomnia Scale. Sleep quality due to PD-specific nighttime problems was estimated using the Parkinson's Disease Sleep Scale-2 Japanese version (PDSS-2). We conducted a multiple regression analysis using the forced entry method to identify the variables that influenced CAS. RESULTS: We analyzed 350 PWP. Overall, 94.9% of PWP had constipation symptoms. The percentages of PWP with poor sleep were as follows: PSQI, 74.7%; Athens Insomnia Scale, 69.8%; and PDSS-2, 73.8%. Furthermore, 17.6% of the patients with constipation and 35.3% with sleep problems did not consult a healthcare provider. Multivariate analysis revealed that CAS was significantly associated only with PDSS-2 (standardized partial regression coefficient, 0.217; 95% confidence interval, 0.030-0.111). CONCLUSION: Poor sleep quality, related to PD-specific nighttime problems, was found be associated with worsening constipation severity. Nursing activities that help PWP with PD-specific nighttime problems have a more comfortable night's sleep would be key to alleviating constipation severity.
Infantile B-cell acute lymphoblastic leukaemia with the highest recorded count of white blood cells in the literature: case report and literature review
Authors: Asees Mohammad Y. , Shrateh Oadi N. , Assi Ayuob S. , Habbabeh Maysaa , Shiha Haneen Omar , Shakhsheer Shurouq
Published: November 2023

Introduction:

Infantile leukaemia is an uncommon haematological cancer that manifests within the first year of life. This malignancy is highly aggressive and possesses distinctive immunophenotypic, cytogenetic, and molecular attributes. It can originate from either myeloid or lymphoid cells. It often exhibits a higher incidence among females.

Case presentation:

A 1-month-old male infant, initially seemingly healthy, presented with irritability and feeding difficulties. Born without complications, routine neonatal assessments appeared normal, and physical examination revealed no abnormalities. However, laboratory tests indicated an extremely high white blood cell count, low platelets, and elevated haemoglobin. Further examinations showed a white blood cell count of 1450 × 106/l with a blood film revealing significant leukocytosis dominated by blast cells. Abdominal ultrasound confirmed hepatosplenomegaly which was not present during pregnancy. Subsequent bone marrow analysis and flow cytometry established a diagnosis of B-cell acute lymphoblastic leukaemia (B-ALL).

Clinical discussion:

It is rare for infantile ALL to manifest within the first month after birth. In most cases, the diagnosis is established before birth. When characteristic signs such as hepatosplenomegaly, leukaemia cutis, or infiltrative involvement of the extramedullary and central nervous systems are present, postnatal diagnoses are relatively straightforward. However, there are instances where children present with non-specific and ambiguous symptoms that resemble other medical conditions.

Conclusion:

This case underscores the importance of paediatricians being vigilant and attuned to the subtle indicators that differentiate common illnesses from serious conditions such as infantile ALL.
Neglected ureteral stent in a patient with chronic kidney disease and solitary functioning kidney: case report and review of literature
Authors: Sakr Mohamed , Badran Merhan , Pokhrel Prakriti , Asfeen Ummul Z. , Badran Nadin Nouh , Badran Maram Wahed
Published: November 2023

Introduction:

A ureteral stent is crucial for managing urinary flow obstruction, ureteral reconstructive surgeries, and iatrogenic ureteral injuries. The authors aim to report a case of forgotten double-J stent for 17 years, the longest time reported in literature in a patient with solitary kidney and no typical long-term complications as stones formation and encrustation.

Case presentation:

A 58-year-old male with chronic kidney disease and solitary left kidney presented with left loin pain. With creatinine higher than baseline (6.2 mg/dl), he reported a neglected double-J stent placed 17 years ago in a different hospital. In addition, non-contrast computed tomography and cystoscopy revealed hydronephrosis, cystitis, and an element of infra-vesical obstruction, evident by high bladder neck. Treatment included left percutaneous nephrostomy, but he was readmitted few weeks later for cystoscopy, ureteroscopy, and a new double-J insertion. Due to worsening renal function, he was readmitted four weeks later for cystoscopic removal of the new double-J stent and Transurethral Resection of the Prostate, after which creatinine returned to baseline.

Discussion:

Double-J stents are vital in urological procedures, but neglecting their presence can lead to severe complications like encrustations, stone formation, stent fractures, hydronephrosis, infections, and renal function loss. Treatment of long-term complications is difficult and should consider many factors, including the type and severity of associated complications and the patient’s preoperative status.

Conclusion:

Preventing complications from neglected or forgotten double-J stents through patient education and follow-up is crucial, especially in those with solitary functioning kidneys due to the imminent loss of renal function.
Exercise-induced rhabdomyolysis manifestations and complications: a case report
Authors: Alharbi Kholoud F. , Alfahmi Manal Z.
Published: November 2023

Introduction:

Rhabdomyolysis is a medical condition that results from damage to striated muscles that causes the release of their components into the bloodstream. Laboratory indications include high levels of creatinine kinase and myoglobin in the serum.

Importance:

This case report emphasizes the importance of having professional trainers in gyms and training centers who respect trainees’ limitations and physical capabilities and ensure that physical exercise programs are being conducted safely and effectively.

Case presentation:

A 39-year-old female healthcare provider presented to the emergency department at a tertiary/quaternary hospital in Saudi Arabia, with progressive right arm pain, swelling, weakness, and dark urine 2 days after an unaccustomed heavy physical exercise session with her personal trainer following a long pause from physical training.

Clinical discussion:

Levels of serum creatinine kinase, aspartate aminotransferase, and alanine transaminase were moderately elevated. There was no evidence of renal impairment, electrolyte disturbance, or coagulopathy. The patient was treated with analgesics, received hydration, and was discharged home under close observation and with a follow-up clinic visit scheduled to check for complications. Data were collected from the hospital’s electronic medical records, including clinical notes and laboratory investigations.

Conclusion:

Awareness campaigns need to be conducted to educate the public about healthy ways to exercise, such as gradually increasing the intensity of physical activity, warming up before exercising, cooling down after each workout, and staying hydrated. It is important that healthcare providers, trainees and trainers are able to recognize the signs of muscular injury following vigorous exercise in order to reduce the incidences of complications that could be deadly if they are not caught and managed early.
Use of Perioperative Advanced Practice Providers to Reduce Cost and Readmission in the Postoperative Hepatopancreatobiliary Population: Results of a Simulation Study
Authors: Smith Savannah R , Blair Catherine M , Lovasik Brendan P , Little Lori A , Sweeney John F , Sarmiento Juan M
Published: November 2023

BACKGROUND:

Postoperative healthcare use and readmissions are common among the hepatopancreatobiliary (HPB) population. We evaluated the surgical volume required to sustain advanced practice providers (APPs) in the perioperative setting for cost reduction.

STUDY DESIGN:

Using decision analysis modeling, we evaluated costs of employing dedicated perioperative APP navigators compared with no APPs navigators. Simulated subjects could: (1) present to an emergency department, with or without readmission, (2) present for direct readmission, (3) require additional office visits, or (4) require no additional care. We informed our model using the most current available published data and performed sensitivity analyses to evaluate thresholds under which dedicated perioperative APP navigators are beneficial.

RESULTS:

Subjects within the APP navigator cohort accumulated $1,270 and a readmission rate of 6.9%, compared with $2,170 and 13.5% with no APP navigators, yielding a cost savings of $905 and 48% relative reduction in readmission. Based on these estimated cost savings and national salary ranges, a perioperative APPs become financially self-sustaining with 113 to 139 annual HPB cases, equating to 2 to 3 HPB cases weekly. Sensitivity analyses revealed that perioperative APP navigators were no longer cost saving when direct readmission rates exceeded 8.9% (base case 3.7%).

CONCLUSIONS:

We show that readmissions are reduced by nearly 50% with an associated cost savings of $900 when employing dedicated perioperative APPs. This position becomes financially self-sufficient with an annual HPB case load of 113 to 139 cases. High-volume HPB centers could benefit from postdischarge APP navigators to optimize outcomes, minimize high-value resource use, and ultimately save costs.
Modelling of surface reactions and diffusion mediated by bulk diffusion
Authors: Duda Fernando P. , Forte Neto Francisco S. , Fried Eliot
Published: November 2023

We develop a continuum framework applicable to solid-state hydrogen storage, cell biology and other scenarios where the diffusion of a single constituent within a bulk region is coupled via adsorption/desorption to reactions and diffusion on the boundary of the region. We formulate content balances for all relevant constituents and develop thermodynamically consistent constitutive equations. The latter encompass two classes of kinetics for adsorption/desorption and chemical reactions—fast and Marcelin–De Donder, and the second class includes mass action kinetics as a special case. We apply the framework to derive a system consisting of the standard diffusion equation in bulk and FitzHugh–Nagumo type surface reaction–diffusion system of equations on the boundary. We also study the linear stability of a homogeneous steady state in a spherical region and establish sufficient conditions for the occurrence of instabilities driven by surface diffusion. These findings are verified through numerical simulations which reveal that instabilities driven by diffusion lead to the emergence of steady-state spatial patterns from random initial conditions and that bulk diffusion can suppress spatial patterns, in which case temporal oscillations can ensue. We include an extension of our framework that accounts for mechanochemical coupling when the bulk region is occupied by a deformable solid.

This article is part of the theme issue ‘Foundational issues, analysis and geometry in continuum mechanics’.
Loss of pseudo-momentum, energy-release rate and the effective mass of a moving dislocation
Authors: Markenscoff Xanthippi
Published: November 2023

In a seminal paper in the Philosophical Transactions of the Royal Society (A244, 87–112). Eshelby (Eshelby 1951
Phil. Trans. R. Soc. Lond. A
244, 87–112. (
doi:10.1098/rsta.1951.0016
)) introduced the concept of ‘the force on an elastic singularity’ and suggested that the extensions to dynamics include the application of the momentum flux. In this direction, it is shown that, in the non-uniformly motion of a dislocation there is a loss in quasi-momentum (or pseudo-momentum) across the scales ε to ε
2
, which induces an effective mass of the dislocation, and a loss in kinetic energy across the scales. It is shown through Noether's theorem that the rate of change of quasi-momentum in the volume enclosing the dislocation is equal to the flux of it through the surface minus a quasi-force, which is the dynamic
J
integral. The connection between the variation in the Hamiltonian and in the Lagrangian relates the quasi-force to the energy-release rate, yielding the same effective mass, while providing physical meaning both through momentum and energy. The effective mass of a dislocation is important in relating the energetics of defects from the micro to the macro scales, and the loss of quasi-momentum can have wider applications in continua.

This article is part of the theme issue 'Foundational issues, analysis and geometry in continuum mechanics'.
Candidatus Kirkpatrickella diaphorinae gen. nov., sp. nov., an uncultured endosymbiont identified in a population of Diaphorina citri from Hawaii
Authors: Henry Elizabeth , Carlson Curtis R. , Kuo Yen-Wen
Published: November 2023

Diaphorina citri is the hemipteran pest and vector of a devastating bacterial pathogen of citrus worldwide. In addition to the two core bacterial endosymbionts of D. citri, Candidatus Carsonella ruddii and Candidatus Profftella armatura, the genome of a novel endosymbiont and as of yet undescribed microbe was discovered in a Hawaiian D. citri population through deep sequencing of multiple D. citri populations. Found to be closely related to the genus

Asaia

in the family

Acetobacteraceae

by 16S rRNA gene sequence analysis, it forms a sister clade along with other insect-associated 16S rRNA gene sequences from uncultured bacterium found associated with Aedes koreicus and Sogatella furcifera. Multilocus sequence analysis confirmed the phylogenetic placement sister to the

Asaia

clade. Despite the culturable

Asaia

clade being the closest phylogenetic neighbour, attempts to culture this newly identified bacterial endosymbiont were unsuccessful. On the basis of these distinct genetic differences, the novel endosymbiont is proposed to be classified into a candidate genus and species ‘Candidatus Kirkpatrickella diaphorinae’. The full genome was deposited in GenBank (accession number CP107052; prokaryotic 16S rRNA OP600170).
Longitudinal stability of individual brain plasticity patterns in blindness
Authors: Amaral Lénia , Thomas Peyton , Amedi Amir , Striem-Amit Ella
Published: November 2023

The primary visual cortex (V1) in individuals born blind is engaged in a wide spectrum of tasks and sensory modalities, including audition, touch, language, and memory. This widespread involvement raises questions regarding the constancy of its role and whether it might exhibit flexibility in its function over time, connecting to diverse network functions in response to task-specific demands. This would suggest that reorganized V1 takes on a role similar to cognitive multiple-demand system regions. Alternatively, it is possible that the varying patterns of plasticity observed in the blind V1 can be attributed to individual factors, whereby different blind individuals recruit V1 for different functions, highlighting the immense idiosyncrasy of plasticity. In support of this second account, we have recently shown that V1 functional connectivity varies greatly across blind individuals. But do these represent stable individual patterns of plasticity or merely instantaneous changes, for a multiple-demand system now inhabiting V1? Here we tested if individual connectivity patterns from the visual cortex of blind individuals are stable over time. We show that over two years, fMRI functional connectivity from the primary visual cortex is unique and highly stable in a small sample of repeatedly sampled congenitally blind individuals. Further, using multivoxel pattern analysis, we demonstrate that the unique reorganization patterns of these individuals allow decoding of participant identity. Together with recent evidence for substantial individual differences in visual cortex connectivity, this indicates there may be a consistent role for the visual cortex in blindness, which may differ for each individual. Further, it suggests that the variability in visual reorganization in blindness across individuals could be used to seek stable neuromarkers for sight rehabilitation and assistive approaches.
Family, community, institutional and policy factors on COVID-19 vaccine perceptions among urban poor adolescents in seven countries: qualitative cross-site analysis
Authors: Ramaiya Astha , Mmari Kristin , Luiza Borges Ana , Cabral Cristiane , Mafuta Eric , Lulebo Aimee , Yu Chunyan , Pinandari Anggriyani Wahyu , Wilopo Siswanto Agus , Chipeta Effie , Hunersen Kara
Published: November 2023

Purpose

The number of studies examining family, community, institutional and policy factors on COVID-19 vaccine perceptions is limited, with most concentrating on high-income countries and using predominantly quantitative methods. To address this gap, the goal of this manuscript is to qualitatively explore these factors and how they shape adolescents’ perspectives on COVID-19 vaccines across seven countries.

Methods

Focus group discussions (FGDs) were conducted among urban poor adolescent populations (13 - 18 years) across seven countries: Ghent, Belgium; Sao Paulo, Brazil, Shanghai; China, Kinshasa, Democratic Republic of Congo (DRC); Semarang and Denpasar, Indonesia; Blantyre, Malawi and New Orleans, United States of America (USA). An inductive thematic analytical approach was used to understand the emerging themes across the different countries based on the study’s objectives.

Results

The study found that all influences were inter-connected and contributed towards vaccine perceptions among adolescents, which were largely positive except in the two African countries and to an extent in the USA. Family and community influences played a large role in vaccine perceptions, however, this differed by context. Our findings suggest adolescents’ perceptions about vaccines were more positive in countries with higher vaccination rates, i.e. China and Indonesia versus countries with lower vaccination rates i.e. Malawi and DRC. Vaccine mandates within schools, offices, and public places were also discussed with varying perceptions based on government trust.

Conclusion

Adolescents’ perceptions of the Covid-19 vaccine are based on a variety of elements, such as families, community, institutions, and policies. Prioritizing one or another path may not be sufficient to improve vaccine adherence during future pandemics, as we experienced with Covid-19. Strategies to make vaccine perceptions more positive among urban poor adolescents should address both family and community perceptions. However, policies and robust programs around immunization are still needed.
Unveiling the Hidden Viromes Across the Animal Tree of Life: Insights from a Taxonomic Classification Pipeline Applied to Invertebrates of 31 Metazoan Phyla
Authors: Alfonso Pau , Butković Anamarija , Fernández Rosa , Riesgo Ana , Elena Santiago F.
Published: November 2023

Invertebrates constitute the majority of animal species on Earth, including most disease-causing agents or vectors, with more diverse viromes when compared to vertebrates. Recent advancements in high-throughput sequencing have significantly expanded our understanding of invertebrate viruses, yet this knowledge remains biased toward a few well-studied animal lineages. In this study, we analyze invertebrate DNA and RNA viromes for 31 phyla using 417 publicly available RNA-Seq datasets from diverse environments in the marine-terrestrial and marine-freshwater gradients. This study aims to (i) estimate virome compositions at the family level for the first time across the Animal Tree of Life, including the first exploration of the virome in several phyla, (ii) quantify the diversity of invertebrate viromes and characterize the structure of invertebrate-virus interaction networks, and (iii) investigate host phylum and habitat influence on virome differences. Results showed that a set of few viral families of eukaryotes, comprisingRetroviridae,Flaviviridaeand several families of giant DNA viruses, were ubiquitous and highly abundant. Nevertheless, some differences emerged between phyla, revealing for instance a less diverse virome in Ctenophora compared to the other animal phyla. Compositional analysis of the viromes showed that the host phylum explained over five times more variance in composition than its habitat. Moreover, significant similarities were observed between the viromes of some phylogenetically related phyla, which could highlight the influence of co-evolution in shaping invertebrate viromes.

Importance

This study significantly enhances our understanding of the global animal virome by characterizing the viromes of previously unexamined invertebrate lineages from a large number of animal phyla. It showcases the great diversity of viromes within each phylum and investigates the role of habitat shaping animal viral communities. Furthermore, our research identifies dominant virus families in invertebrates and distinguishes phyla with analogous viromes. This study sets the road towards a deeper understanding of the virome across the Animal Tree of Life.
The highly abundant mRNA m1A modification: a new layer of gene regulation in dinoflagellates
Authors: Li Chongping , Li Ying , Guo Jia , Wang Yuci , Shi Xiaoyan , Zhang Yangyi , Liang Nan , Yuan Jie , Xu Jiawei , Chen Hao
Published: November 2023

The N1-methyladenosine (m1A) is a positively charged RNA modification known to disrupt base pairing and influence RNA stability. Despite its limited presence in the mRNA of various organism models, including yeast, mouse, and human, the exact processes of m1A biosynthesis, distribution, regulation, and function remain controversial. Dinoflagellates are a major group of single-celled eukaryotic phytoplankton having peculiar crystalline chromosomes. Their genes are arranged in unidirectional gene clusters along the chromosomes and only have minimal transcriptional regulation, implying the involvement of other critical regulatory mechanisms in gene expression. Here, we found that m1A rather than m6A is the most prevalent mRNA modification in dinoflagellates and asymmetrically distributed along mature transcripts. Utilizing the dinoflagellate speciesAmphidinium carteraeas a study model, we identified 13481 m1A peaks characterized by a non-tRNA T-loop-like sequence motif within the transcripts of 10794 genes, many of which are involved in carbon and nitrogen metabolism. With enrichment around stop codon region and 3’ UTR, dinoflagellate mRNA m1A exhibits negative correlation with translation efficiency. Notably, nitrogen depletion (N-depletion) treatment led to significant global decrease of mRNA m1A amount, causing dramatic variation in translation rates with minimal changes in transcription. Additionally, our analysis uncovered distinctive methylation patterns of m1A modification that appears to post-transcriptionally modulate gene expression through regulating translation efficiency. Thus, our findings provide the first comprehensive m1A map of dinoflagellate mRNA, shedding light on its crucial role as a post-transcriptional regulatory layer to compensate the degeneration of transcriptional regulation in dinoflagellate. This study also sets the stage for further investigation into the biogenesis and functional significance of mRNA m1A in eukaryotes.
NASTRA: Accurate analysis of short tandem repeat markers by nanopore sequencing with repeat-structure-aware algorithm
Authors: Ren Zilin , Zhang Jiarong , Zhang Yixiang , Yang Tingting , Sun Pingping , Xue Jiguo , Bo Xiaochen , Zhou Bo , Yan Jiangwei , Ni Ming
Published: November 2023

Forensic short-tandem repeats (STR) genetic markers are multi-allelic and widely utilized for individual identification, kinship testing, and cell-line authentication. Nanopore sequencing, known for its portability, is emerging as a promising approach for STR typing, facilitating real-time and in-field testing. However, its efficacy is often hampered by sequencing noise. Previous methods rely on alignment-based genotyping, necessitating known alleles, which limits their applicability to unknown alleles. Here, we introduced NASTRA, an innovative allele reference-free tool for precise germline analysis of STR genetic markers. NASTRA incorporates a recursive algorithm to infer repeat structures of allele sequences using only known repeat motifs. Our tests, conducted on 80 individual samples and 8 DNA standards, have demonstrated NASTRA’s exceptional 100% accuracy in genotyping nearly all diploid STRs across various multiplex kits and flow cells. It surpasses alignment-based methods in accuracy and speed. In a paternity testing case study, NASTRA accurately identified three relationships among six individuals within an 18-minute sequencing duration. These results underscore NASTRA’s ability to perform STR analysis on both NGS and nanopore sequencing platforms, significantly enhancing the utility of nanopore sequencing in relevant applications.

GRAPHICAL ABSTRACT
The effect of D-cycloserine on brain connectivity over a course of pulmonary rehabilitation
Authors: Finnegan Sarah L. , Harrison Olivia K. , Ezra Martyn , Harmer Catherine J. , Nichols Thomas E. , Rahman Najib M. , Reinecke Andrea , Pattinson Kyle T.S.
Published: November 2023

Rationale

Combining traditional therapies such as pulmonary rehabilitation with brain- targeted drugs may offer new therapeutic opportunities for the treatment of chronic breathlessness. Recent work has shown that D-cycloserine, a partial NMDA-receptor agonist which has been shown to enhance cognitive behavioural therapies, modifies the relationship between breathlessness related brain activity and breathlessness anxiety over pulmonary rehabilitation. However, whether these changes are supported by alterations to underlying brain structure remains unknown. Here we examine the effect of D-cycloserine over a course of pulmonary rehabilitation on regional brain volume and connectivity.

Methods

72 participants with mild-to-moderate COPD took part in a longitudinal study in parallel to their pulmonary rehabilitation course. Diffusion tensor brain imaging, self-report questionnaires and clinical measures of respiratory function were collected at three time points (before, during and after pulmonary rehabilitation). Participants were assigned to 250mg of D-cycloserine or placebo, which they were administered with on four occasions in a randomised, double-blind procedure.

Results

Following four sessions of pulmonary rehabilitation, improvements in breathlessness anxiety were linked with increased insula-hippocampal structural connectivity in the D-cycloserine group. No group differences were found following the completion of pulmonary rehabilitation, or in the integrity of structural connectivity.

Conclusions

The action of D-cycloserine on brain connectivity appears to be restricted to within a short time-window of its administration. This temporary boost of the brain connectivity of two key regions associated with the evaluation of unpleasantness may support the re-evaluation of breathlessness cues, illustrated improvements in breathlessness anxiety. This work highlights the relevance of targeting breathlessness expectation in pulmonary rehabilitation.
Social Network Strategies to Distribute HIV Self-testing Kits: A Global Systematic Review and Network Meta-analysis
Authors: Hu Siyue , Jing Fengshi , Fan Chengxin , Dai Yifan , Xie Yewei , Zhou Yi , Lv Hang , He Xi , Wu Dan , Tucker Joseph D. , Tang Weiming
Published: November 2023

Introduction

Social network strategies, in which social networks are utilized to influence individuals or communities, are increasingly being used to deliver human immunodeficiency virus (HIV) interventions to key populations. We summarized and critically assessed existing research on the effectiveness of social network strategies in promoting HIV self-testing (HIVST).

Methods

Using search terms related to social network interventions and HIVST, we searched five databases for trials published between January 1st, 2010, and June 30th, 2023. Outcomes included uptake of HIV testing, HIV seroconversion, and linkage to antiretroviral therapy (ART) or HIV Care. We used network meta-analysis to assess the uptake of HIV testing through social network strategies compared with control methods. A pairwise meta-analysis of studies with a comparison arm that reported outcomes was performed to assess relative risks (RR) and their corresponding 95% confidence intervals (CI).

Results and discussion

Among the 3,745 manuscripts identified, 33 studies fulfilled the inclusion criteria, including one quasi-experimental study, 17 RCTs and 15 observational studies. Networks HIVST testing was organized by peers (distributed to known peers, 15 studies), partners (distributed to their sexual partners, 10 studies), and peer educators (distributed to unknown peers, 8 studies). The results showed that all of the three social network distribution strategies enhanced the uptake of HIV testing compared to standard facility-based testing. Among social networks, peer distribution had the highest uptake of HIV testing (79% probability, SUCRA 0.92), followed by partner distribution (72% probability, SUCRA 0.71), and peer educator distribution (66% probability, SUCRA 0.29). Pairwise meta-analysis showed that peer distribution (RR 2.29, 95% CI 1.54-3.39, 5 studies) and partner distribution (RR 1.45, 95% CI 1.05-2.02, 7 studies) also increased the probability of detecting HIV reactivity during testing within the key population when compared to the control. Linkage to ART or HIV Care remained comparable to facility-based testing across the three HIVST distribution strategies.

Conclusions

Network-based HIVST distribution is considered effective in augmenting HIV testing rates and reaching marginalized populations compared to facility-based testing. These strategies can be integrated with the existing HIV care services, to fill the testing gap among key populations globally.

PROSPERO Number: CRD42022361782
Polymer Implantable Electrode Foundry: A shared resource for manufacturing polymer-based microelectrodes for neural interfaces
Authors: Scholten Kee , Xu Huijing , Lu Zhouxiao , Jiang Wenxuan , Ortigoza-Diaz Jessica , Petrossians Artin , Orler Steven , Gallonio Rachael , Liu Xin , Song Dong , Meng Ellis
Published: November 2023

Large scale monitoring of neural activity at the single unit level can be achieved via electrophysiological recording using implanted microelectrodes. While neuroscience researchers have widely employed chronically implanted electrode-based interfaces for this purpose, a commonly encountered limitation is loss of highly resolved signals arising from immunological response over time. Next generation electrode-based interfaces improve longitudinal signal quality using the strategy of stabilizing the device-tissue interface with microelectrode arrays constructed from soft and flexible polymer materials. The limited availability of such polymer microelectrode arrays has restricted access to a small number of researchers able to build their own custom devices or who have developed specific collaborations with engineering researchers who can produce them. Here, a new technology resource model is introduced that seeks to widely increase access to polymer microelectrode arrays by the neuroscience research community. The Polymer Implantable Electrode (PIE) Foundry provides custom and standardized polymer microelectrode arrays as well as training and guidance on best-practices for implantation and chronic experiments.
Acinetobacter guillouiaestrain isolated from sludge capable of partially degrade polyethylene terephthalate: genomic and biochemical insights
Authors: Akhtar Naheed , Najjari Afef , Tullberg Cecilia , Awan Muhammad Siddique , Majeed Zahid , Grey Carl , Zhang Baozhong , Linares-Pastén Javier A.
Published: November 2023

The escalating accumulation of plastic waste in terrestrial and aquatic ecosystems profoundly threatens environmental health and biodiversity while impacting human well-being. Recently, many microorganisms capable of degrading polyethylene terephthalate (PET) have been reported, primarily sourced from terrestrial soils and marine environments. Notably, the challenge of PET pollution in aquatic environments has remained a persistent research concern. In this study, we present the isolation and characterization ofAcinetobacter guillouiaestrain I-MWF, obtained from a wastewater treatment plant in Makri, AJK, Pakistan, using molecular phylogenetic analysis based on genome sequencing. Results revealed that this strain exhibits the ability for PET powder degradation, as confirmed by HPLC/LCMS analysis. Furthermore, we conducted whole-genome sequencing using Illumina technology and bioinformatically explored this strain’s potential repertoire of lipase and esterase enzymes. Under optimized conditions of 23°C and pH 7 in mineral salt media with PET powder as the sole organic substrate,A. guillouiaeI-MWF could degrade partially. Extracellular enzymes yielded PET depolymerization products identified as mono(2- hydroxyethyl) terephthalic acid and terephthalic acid. The sequenced genome of this strain spans 4.61 Mb with a mean G + C content of 38.2%, containing 4,178 coding genes, 71 tRNA, and six rRNA genes. Although no cutinase-like enzymes were identified, our analysis unveiled a diverse array of putative lipases and three esterases, all sharing the typical α/β hydrolase fold. Additionally, comprehensive molecular modelling analysis suggested that some of the 18 identified extracellular hydrolases may be involved in polyester enzymatic depolymerization processes.
Total-evidence phylogenetic analysis resolves the evolutionary timescale of mantis shrimps (Stomatopoda) and provides insights into their molecular and morphological evolutionary rates
Authors: Van Der Wal Cara , Ahyong Shane T. , Adams Maxim W.D. , Lo Nathan , Ho Simon Y.W.
Published: November 2023

The crustacean order Stomatopoda comprises approximately 500 species of mantis shrimps. These marine predators, common in tropical and subtropical waters, possess sophisticated visual systems and specialized hunting appendages. In this study, we infer the evolutionary relationships within Stomatopoda using a combined data set of 77 morphological characters, whole mitochondrial genomes, and three nuclear markers. Our data set includes representatives from all seven stomatopod superfamilies, including the first sequence data from Erythrosquilloidea. Using a Bayesian relaxed molecular clock with fossil-based calibration priors, we estimate that crown-group unipeltatan stomatopods appeared ∼140 (95% credible interval 201–102) million years ago in the Mesozoic. Additionally, our results support the hypothesis that specialized smashing and spearing appendages appeared early in the evolutionary history of Unipeltata. We found no evidence of a correlation between rates of morphological and molecular evolution across the phylogeny, but identified very high levels of among-lineage rate variation in the morphological characters. Our total-evidence analysis recovered evolutionary signals from both molecular and morphological data sets, demonstrating the merit in combining these sources of information for phylogenetic inference and evolutionary analysis.
A WIDESPREAD PICORNAVIRUS AFFECTS THE HAEMOCYTES OF THE NOBLE PEN SHELL (PINNA NOBILIS) LEADING TO IMMUNOSUPPRESSION
Authors: Carella Francesca , Prado Patricia , Vico Gionata De , Palić Dušan , Villari Grazia , García-March José Rafael , Tena-Medialdea José , Melendreras Emilio Cortés , Casalduero Francisca Giménez- , Sigovini Marco , Aceto Serena
Published: November 2023

The widespread mass mortality of the noble pen shell (Pinna nobilis) has occurred in several Mediterranean countries in the past seven years. Single-stranded RNA virus affecting immune cells and leading to immune disfunction have been widely reported in human and animal species. Here we present data linkingP. nobilismass mortality events (MMEs) to haemocyte picornavirus (PV) infection. This study was performed on 30 specimens, from wild and captive populations. We sampledP. nobilisfrom two regions of Spain, Catalonia [24 animals] and Murcia [two animals]), and one region in Italy (Venice [four animals]). The low number of analyzed specimens was due to the scarcity of remaining individuals in the Mediterranean Sea. In 100% of our samples, ultrastructure revealed the presence of a virus (20nm diameter), capable of replicating within granulocytes and hyalinocytes, leading to the accumulation of complex vesicles of different dimensions within the cytoplasm. As the PV infection progressed, dead haemocytes, infectious exosomes, and budding of extracellular vesicles were visible, along with endocytic vesicles entering other cells. The THC (total haemocyte count) values observed in both captive (eight animals) (3.5 x 104- 1.60 x105ml-1cells) and wild animals (14 samples) (1.90 - 2.42 x105ml-1cells) were lower than those reported before MMEs. Sequencing ofP. nobilis(six animals) haemocyte cDNA libraries revealed the presence of two main sequences ofPicornavirales, familyMarnaviridae. The highest number of reads belonged to animals that exhibited active replication phases and abundant viral particles from Trasmission Electron Microscopy (TEM) observations. These sequences correspond to the genusSogarnavirus- a picornavirus identified in the marine diatomChaetoceros tenuissimus(namedC. tenuissimusRNA virus type II). Real time PCR performed on the two most abundant RNA viruses previously identified byin silicoanalysis revealed positive results only for the sequences similar toC. tenuissimusRNA virus. These results may not be considered conclusive of picornavirus identification in noble pen shell haemocytes, and require further studies. Our findings suggest that picornavirus infection likely causes immunosuppression, making individuals prone to opportunistic infections which is a potential cause for the MMEs observed in the Mediterranean.
Phenogenomic resources immortalized in a panel of wild-derived strains of five species of house mice
Authors: Piálek Jaroslav , Ďureje Ľudovít , Hiadlovská Zuzana , Kreisinger Jakub , Aghová Tatiana , Bryjová Anna , Čížková Dagmar , Goüy de Bellocq Joëlle , Hejlová Helena , Janotová Kateřina , Martincová Iva , Orth Annie , Piálková Jana , Pospíšilová Iva , Rousková Ludmila , Bímová Barbora Vošlajerová , Bonhomme François , Forejt Jiří , Macholán Miloš , Klusáčková Pavla
Published: November 2023

The house mouse,Mus musculus, is a widely used animal model in biomedical research, with classical laboratory strains (CLS) being the most frequently employed. However, the limited genetic variability in CLS hinders their applicability in evolutionary studies. Wild-derived strains (WDS), on the other hand, provide a suitable resource for such investigations. This study quantifies genetic and phenotypic data of 101 WDS representing 5 species, 3 subspecies, and 8 natural Y consomic strains and compares them with CLS. Genetic variability was estimated using whole mtDNA sequences, thePrdm9gene, and copy number variation at two sex chromosome-linked genes. WDS exhibit a large natural variation with up to 2173 polymorphic sites in mitogenomes, whereas CLS display 92 sites. Moreover, while CLS have twoPrdm9alleles, WDS harbour 46 different alleles. Although CLS resembleM. m. domesticusandM. m. musculusWDS, they differ from them in 8 and 11 out of 15 phenotypic traits, respectively. The results suggest that WDS can be a useful tool in evolutionary studies and have great potential for medical applications.
COMPARATIVE TRANSCRIPTOMICS REVEALS THE MOLECULAR MECHANISMS OF MAIZE IN RESPONSE TO DOWNY MILDEW CAUSED BYPeronosclerospora philippinensis(WESTON) SHAW
Authors: Fernandez Edward Cedrick J. , Simon-Ada Eliza Vie M. , Mendoza Jay-Vee S. , Manohar Anand Noel C. , Gardoce Roanne R. , Laude Tonette P. , Dela Cueva Fe M. , Lantican Darlon V.
Published: November 2023

Maize is the Philippines’ second most valuable staple crop based on overall value and total area planted. Yellow maize, which is the most important type, is utilized as feed for poultry and swine. Still, local maize production is hampered by the Philippine downy mildew (DM) disease caused by the pathogenPeronosclerospora philippinensis(Weston) Shaw, causing substantial losses in maize production annually. To comprehend the underlying resistance mechanisms upon the presence of the disease, we performed an RNA-Seq comparative transcriptomics approach between mock-inoculated and DM-inoculated susceptible and resistant yellow maize inbred lines. Among the identified differentially expressed genes (DEGs), we detected 43 DEGs shared in both genotypes which may play roles in the basal defense response of maize upon DM infection. We also identified 68 DEGs exclusive to the susceptible genotype, providing insights into the molecular responses underlying successful DM disease progression in maize. Further, we detected 651 DEGs unique to the resistant genotype. This set of genes revealed that the molecular basis of DM resistance in maize is governed by multi-faceted defense strategies. These include multi-process regulations such as programmed cell death (PCD), regulatory proteins, and transcription factors involved in pathogen defense mechanisms, cell wall organization, homeostasis, and many others. Out of 694 resistant DEGs detected, we narrowed down genes of interest, particularly those highly overexpressed and associated with disease resistance found in other crops. Finally, transcriptome-wide variants and their corresponding impact on gene function were detected for further application in targeted genotyping-by-sequencing, association studies, and marker-assisted DM resistance breeding.
Assessing Risk Factors for Cognitive Decline Using Electronic Health Records: A Scoping Review
Authors: Wang Liqin , Yang Richard , Sha Ziqin , Kuraszkiewicz Anna Maria , Leonik Conrad , Zhou Li , Marshall Gad A.
Published: November 2023

Background

Electronic health records (EHR) provide rich, diverse, longitudinal real-world data, offering valuable opportunities to study antecedent risk factors for cognitive decline. However, the extent to which such records have been utilized to understand the risk factors of cognitive decline remains unclear.

Methods

We conducted a systematic review following PRISMA guidelines. We retrieved relevant articles published between January 1, 2010, and April 30, 2023, from PubMed, Web of Science, and CINAHL. Inclusion criteria were studies utilizing EHR to study risk factors for cognitive decline, including subjective cognitive decline, mild cognitive impairment, and dementia. Each article was screened by at least two reviewers. Data elements were manually extracted based on a predefined schema. The studied risk factors were reported.

Results

Of 1,593 articles identified, 80 research articles were selected. Seventy (87.5%) were retrospective cohort studies, 53 (66.3%) used datasets with greater than 10,000 patients, and 69 (86.3%) used EHR datasets from the United States or United Kingdom. Furthermore, 39 (48.8%) targeted medical conditions, 23 (28.8%) related to medical interventions, and 14 (17.5%) related to lifestyle, socioeconomic status, and environmental factors. The majority of studied medical conditions were associated with an elevated risk of cognitive decline, whereas medical interventions addressing these conditions often reduced the risk.

Conclusion

EHRs have significantly advanced our understanding of medical conditions, interventions, lifestyle, socioeconomic status, and environmental factors related to the risk of cognitive decline.

Highlights

Electronic health records are increasingly analyzed to discern dementia risk factors.

Eighty articles have been published and most of them were retrospective cohort studies.

Most risk factors addressed were related to medical conditions and interventions.

A few articles studied lifestyle, socioeconomic status, and environmental factors.
Compressed sensing expands the multiplexity of imaging mass cytometry
Authors: Hosogane Tsuyoshi , Santana Leonor Schubert , Eling Nils , Moch Holger , Bodenmiller Bernd
Published: November 2023

The multiplexity of current antibody-based imaging is limited by the number of reporters that can be detected simultaneously. Compressed sensing can be used to recover high-dimensional information from low-dimensional measurements when the data has a structure that allows sparse representation. Previously, in composite in situ imaging (CISI) of transcriptomic data, compressed sensing leveraged the gene co-regulation structure that allows sparse representation and recovered spatial expression of 37 RNA species with the measurement of 11 fluorescent channels. Here, we extended the compressed sensing framework to protein expression data measured by imaging mass cytometry (IMC). CISI-IMC accurately recovered spatial expression of 16 proteins from the images of 8 composite channels, which in effect expanded the current multiplexity limit of IMC by 8 channels. With this ratio, up to 80 protein markers could be compressed into currently available 40 isotope channels. Training the CISI-IMC framework using data collected on tissues from various locations in the human body enabled the decompression of composite data from a wide range of tissue types. Our work laid the foundation for much higher plex protein imaging by using CISI.
Novel DNA methylation changes in mouse lungs associated with heavy smoking
Authors: Onuzulu Chinonye Doris , Lee Samantha , Basu Sujata , Comte Jeannette , Hai Yan , Hizon Nikho , Chadha Shivam , Fauni Maria Shenna , Halayko Andrew J. , Pascoe Christopher D. , Jones Meaghan J.
Published: November 2023

Smoking is a potent cause of asthma, chronic obstructive pulmonary disease (COPD) and many other health defects, and changes in DNA methylation (DNAm) have been identified as a potential link between smoking and these health outcomes. However, most links between smoking and DNAm have been made using blood and other easily accessible tissues in humans, while evidence from more directly affected tissues such as the lungs is greatly lacking. Here, we identified DNAm patterns which are altered by smoking directly in the lungs. We used a well-established mouse model to measure the effects of heavy smoking first on lung phenotype immediately after smoking and then after a period of smoking cessation. Next, we determined whether our mouse model could recapitulate previous DNAm patterns observed in smoking humans by measuring DNAm at a candidate gene responsive to cigarette smoke (CS),Cyp1a1.Finally we carried out epigenome-wide DNAm analyses using the newly released Illumina mouse methylation microarrays. Our results recapitulate some of the phenotypes and DNAm patterns observed in human studies but reveal 32 differentially methylated genes specific to the lungs which have not been previously associated with smoking. The affected genes are known to be involved in nicotine dependency, tumorigenesis and metastasis, immune cell dysfunction, lung function decline, and COPD. This research emphasizes the need to study CS-mediated DNAm signatures in directly affected tissues like the lungs, as that may be essential in understanding mechanisms underlying CS-mediated health outcomes.