bluuebunny/crossref_metadata_2025 huggingface dataset:
Occurrence of black queen cell virus in wild bumble bee communities in China
Authors: Xu Jin , Zhang Zhengyi , Guo Yulong , Yang Huipeng , Li Xiaoying , Guo Yueqin , Zeng Huayan , Wu Yueguo , Yao Jun , Li Jilian
Published: April 2024

Wild bumble bees (Hymenoptera: Apidae) play a vital role in agro-ecosystems as important pollinators. However, they are threatened by virus pathogens that are widespread in honey bees. Previous studies have reported that viruses were able to be transmitted across bee genera and caused potential danger to wild bumble bees. China is a global biodiversity hotspot for bumble bees. However, the impact of viruses on the wild bumble bee communities remains elusive. Black queen cell virus (BQCV) is one of the most common honey bee viruses. Here, a total of 72 wild bumble bee samples from 17 geographic regions of China were tested for BQCV. Thirteen positive samples were identified and sequence comparison of partial capsid genes demonstrated a genetic identity of 99.69% to 100%. A phylogenetic tree analysis also showed a close relationship between 13 BQCV isolates and others from a variety of recorded hosts in China. Meanwhile, a distinct evolutionary branch of China isolates was formed when clustering isolates from worldwide bumble bee species. A correlation between BQCV and their geographic locations were observed (P < 0.05). This study not only provides the first evidence of widespread BQCV in wild bumble bee communities in China but also detects a distinct set of genetically identical or closely related BQCV variants that circulate and evolutionarily differ from other countries.
Comparison of Bayesian Coalescent Skyline Plot Models for Inferring Demographic Histories
Authors: Billenstein Ronja J , Höhna Sebastian
Published: April 2024

Bayesian coalescent skyline plot models are widely used to infer demographic histories. The first (non-Bayesian) coalescent skyline plot model assumed a known genealogy as data, while subsequent models and implementations jointly inferred the genealogy and demographic history from sequence data, including heterochronous samples. Overall, there exist multiple different Bayesian coalescent skyline plot models which mainly differ in two key aspects: (i) how changes in population size are modeled through independent or autocorrelated prior distributions, and (ii) how many change-points in the demographic history are used, where they occur and if the number is pre-specified or inferred. The specific impact of each of these choices on the inferred demographic history is not known because of two reasons: first, not all models are implemented in the same software, and second, each model implementation makes specific choices that the biologist cannot influence. To facilitate a detailed evaluation of Bayesian coalescent skyline plot models, we implemented all currently described models in a flexible design into the software RevBayes. Furthermore, we evaluated models and choices on an empirical dataset of horses supplemented by a small simulation study. We find that estimated demographic histories can be grouped broadly into two groups depending on how change-points in the demographic history are specified (either independent of or at coalescent events). Our simulations suggest that models using change-points at coalescent events produce spurious variation near the present, while most models using independent change-points tend to over-smooth the inferred demographic history.
Turf-Type Tall Fescue Brown Patch Resistance as Influenced by Morphological Characteristics
Authors: Powlen Jada S. , Fidanza Michael A. , Kerns James P. , Hoagland Lori A. , Bigelow Cale A.
Published: April 2024

Brown patch (caused by multiple species of Rhizoctonia and Rhizoctonia-like fungi) is one of the major turfgrass diseases impacting turf-type tall fescue [ Schedonorus arundinaceus (Schreb.) Dumort., nom. cons.] lawns during the summer season. Selection of tall fescue cultivars with brown patch resistance is an important cultural management practice to reduce disease severity and limit reliance on fungicides. A greenhouse experiment was conducted to quantify differences in brown patch resistance among 15 tall fescue cultivars and correlate disease resistance with plant morphological characteristics. Prior to R. solani inoculation, leaf blade width, sheath width and length, endophyte stem infection, and relative growth rate were measured. Disease resistance was determined as a percentage of the canopy blighted as measured using digital image techniques. Brown patch severity after 21 days in Experiments 1 and 2 ranged from 36.7 to 72.7% and 20.8 to 41.8%, respectively, among all cultivars. There were significant differences among morphological characteristics for the cultivars. Increased brown patch was associated with cultivars with a faster growth rate, wider sheath width, and decreased sheath length. This study demonstrates the importance of cultivar selection for reducing brown patch severity in tall fescue lawns. Additionally, tall fescue cultivars with higher shoot density and narrow leaves should not be avoided due to concerns of increased brown patch susceptibility.
Facial Skin Rejuvenation Using Poly-dl-Lactic Acid Injected With a Laser-Generated Needle-Free Microjet Injector
Authors: Oh Dong Yeol , Seo Suk Bae , Jang Ye Ji , Park Eun Joo , Kim Kwang Ho
Published: April 2024

BACKGROUND

A laser-induced needle-free microjet injector was developed for rapid, high-speed drug delivery of microliters into the skin.

OBJECTIVE

This study evaluated the clinical rejuvenation effect of repeated dermal injections of the collagen simulator poly-dl-lactic acid (PDLA) using a laser-induced needle-free microjet injector.

METHODS

Five PDLA injection sessions using a laser-induced needle-free microjet injector were conducted in patients concerned about aging skin. Facial uplifting, darkness, redness, roughness, pore size, subjective satisfaction, and side effects were evaluated before each session and 4 weeks after treatment completion. Histological evaluation was also performed with immunohistochemical staining of collagen and elastic fibers.

RESULTS

The clinical results of 27 female patients were evaluated. The treatment resulted in a noticeable skin surface uplifting (0.711 ± 0.42 mm) and significant improvements in darkness (p = .013), redness (p = .009), and roughness (p = .036), with no significant difference in the pore size (p = .770). Patients were reported being satisfied with the overall therapeutic effects, despite mild and tolerable adverse effects. Histological findings revealed growth and thickening of collagen and elastic fibers, with marked increase in collagen I and III levels.

CONCLUSION

Repeated dermal injections of PDLA using a laser-induced microjet injector offer excellent drug delivery, achieving high efficacy in skin rejuvenation, patient satisfaction, and safety.
Prediction Under Interventions: Evaluation of Counterfactual Performance Using Longitudinal Observational Data
Authors: Keogh Ruth H. , Van Geloven Nan
Published: April 2024

Predictions under interventions are estimates of what a person’s risk of an outcome would be if they were to follow a particular treatment strategy, given their individual characteristics. Such predictions can give important input to medical decision-making. However, evaluating the predictive performance of interventional predictions is challenging. Standard ways of evaluating predictive performance do not apply when using observational data, because prediction under interventions involves obtaining predictions of the outcome under conditions that are different from those that are observed for a subset of individuals in the validation dataset. This work describes methods for evaluating counterfactual performance of predictions under interventions for time-to-event outcomes. This means we aim to assess how well predictions would match the validation data if all individuals had followed the treatment strategy under which predictions are made. We focus on counterfactual performance evaluation using longitudinal observational data, and under treatment strategies that involve sustaining a particular treatment regime over time. We introduce an estimation approach using artificial censoring and inverse probability weighting that involves creating a validation dataset mimicking the treatment strategy under which predictions are made. We extend measures of calibration, discrimination (c-index and cumulative/dynamic AUCt) and overall prediction error (Brier score) to allow assessment of counterfactual performance. The methods are evaluated using a simulation study, including scenarios in which the methods should detect poor performance. Applying our methods in the context of liver transplantation shows that our procedure allows quantification of the performance of predictions supporting crucial decisions on organ allocation.
Machine-learning–based plasma metabolomic profiles for predicting long-term complications of cirrhosis
Authors: Guo Chengnan , Liu Zhenqiu , Fan Hong , Wang Haili , Zhang Xin , Zhao Shuzhen , Li Yi , Han Xinyu , Wang Tianye , Chen Xingdong , Zhang Tiejun
Published: April 2024

Background and Aims:

The complications of liver cirrhosis occur after long asymptomatic stages of progressive fibrosis and are generally diagnosed late. We aimed to develop a plasma metabolomic–based score tool to predict these events.

Approach and Results:

We enrolled 64,005 UK biobank participants with metabolomic profiles. Participants were randomly divided into the training (n=43,734) and validation cohorts (n=20,271). Liver cirrhosis complications were defined as hospitalization for liver cirrhosis or presentation with HCC. An interpretable machine-learning framework was applied to learn the metabolomic states extracted from 168 circulating metabolites in the training cohort. An integrated nomogram was developed and compared to conventional and genetic risk scores. We created 3 groups: low-risk, middle-risk, and high-risk through selected cutoffs of the nomogram. The predictive performance was validated through the area under a time-dependent receiver operating characteristic curve (time-dependent AUC), calibration curves, and decision curve analysis. The metabolomic state model could accurately predict the 10-year risk of liver cirrhosis complications in the training cohort (time-dependent AUC: 0.84 [95% CI: 0.82–0.86]), and outperform the fibrosis-4 index (time-dependent AUC difference: 0.06 [0.03–0.10]) and polygenic risk score (0.25 [0.21–0.29]). The nomogram, integrating metabolomic state, aspartate aminotransferase, platelet count, waist/hip ratio, and smoking status showed a time-dependent AUC of 0.930 at 3 years, 0.889 at 5 years, and 0.861 at 10 years in the validation cohort, respectively. The HR in the high-risk group was 43.58 (95% CI: 27.08–70.12) compared with the low-risk group.

Conclusions:

We developed a metabolomic state–integrated nomogram, which enables risk stratification and personalized administration of liver-related events.
SUPERFICIAL AND DEEP VASCULAR COMPLEXES DAMAGED TO DIFFERENT EXTENTS IN ADVANCED STAGES OF DIABETIC RETINOPATHY
Authors: Lee Min-Woo , Jun Ji-Ho , Yu Hwa-Young , Kim Jung-Tae , Song Yong-Yeon
Published: April 2024

Purpose:

To identify the extent of damage to the superficial vascular complex and deep vascular complex as the stage of diabetic retinopathy (DR) increases.

Methods:

Subjects were divided into four groups: patients with type 2 diabetes without DR (Group 1), those with mild-to-moderate nonproliferative DR (Group 2), those with severe-to-very severe nonproliferative DR (Group 3), and those with proliferative DR (Group 4). The vessel densities of the superficial vascular complex (superficial vessel density, SVD) and deep vascular complex (deep vessel density, DVD) and their ratios were compared. Linear regression analyses were used to identify factors associated with the SVD/DVD ratio.

Results:

The SVDs were 25.5% ± 6.1%, 25.1% ± 7.0%, 24.5% ± 9.0%, and 21.6% ± 6.9% (P = 0.048); the DVDs 25.6% ± 5.3%, 23.0% ± 7.0%, 22.3% ± 8.8%, and 17.5% ± 5.0% (P < 0.001); and the SVD/DVD ratios 1.00 ± 0.16, 1.12 ± 0.20, 1.14 ± 0.33, and 1.24 ± 0.27 (P < 0.001) in Groups 1 to 4, respectively. In multivariate analysis, DR severity (B = 7.16, P < 0.001) and the HbA1c level (B = 1.57, P = 0.042) were significantly associated with the SVD/DVD ratio.

Conclusion:

Both the SVD and DVD tended to decrease in the advanced stages of DR, and the SVD/DVD ratio increased, indicating more severe damage to the deep vascular complex than the superficial vascular complex. The ratio was positively associated with the HbA1c level, indicating a significant relationship between that level and DVD rather than SVD damage.
AMALRIC TRIANGULAR SIGN AND CAROTID DOPPLER ULTRASONOGRAPHIC FINDINGS IN CENTRAL RETINAL ARTERY OCCLUSION
Authors: Okubo Maki , Mano Fukutaro , Hashimoto Ryuya , Maeno Takatoshi , Kuniyoshi Kazuki , Kusaka Shunji
Published: April 2024

Purpose:

The aim of this study was to determine the incidence of the Amalric triangular sign (ATS) in patients with central retinal artery occlusion and investigate its association with visual function and carotid Doppler ultrasonography findings.

Methods:

A retrospective chart review was conducted on 21 eyes from 21 patients with complete central retinal artery occlusion. Best-corrected visual acuity and carotid Doppler ultrasonography findings [peak systolic velocity, end-diastolic velocity, and resistance index (RI) = (PSV − EDV)/PSV] were investigated.

Results:

Three patients (14%) exhibited the ATS. Best-corrected visual acuity at first visit was significantly worse in ATS-positive patients than in ATS-negative patients (P = 0.024). Doppler waveform analysis of the common carotid artery showed that ATS-positive patients had a significantly lower end-diastolic velocity [P = 0.009, median 10 (range 9–10) vs. 17 (13–24) m/second] and significantly higher resistance index [P = 0.021, median 0.80 (range 0.79–0.83) vs. 0.72 (0.66–0.82)] than did ATS-negative.

Conclusion:

The Amalric triangular sign was observed in three patients with central retinal artery occlusion, who showed worse best-corrected visual acuity at the first visit than did those without the ATS. Carotid Doppler ultrasonography revealed that ATS-positive patients had a significantly higher resistance index and lower end-diastolic velocity at the common carotid artery than did ATS-negative, indicating steno-occlusive changes in the internal carotid artery.
Hyalinizing clear cell carcinoma of the left main bronchus diagnosed with Ewing sarcoma breakpoint region 1::activating transcription factor 1 fusion: A case report
Authors: Kawachi Riken , Obikane Hiyo , Satoh Daisuke , Shimamura Mie , Nagao Toshitaka , Masuda Shinobu , Sakurai Hiroyuki
Published: April 2024

Rationale:

Hyalinizing clear cell carcinoma (HCCC) of the bronchus is extremely rare. In addition, its rarity makes an accurate histological diagnosis difficult. Herein, we report a case of HCCC in the left main bronchus diagnosed by the detection of Ewing sarcoma breakpoint region 1::activating transcription factor 1 (EWSR1::ATF1) fusion transcript using reverse transcription-polymerase chain reaction (RT-PCR).

Patient concerns:

A 56-year-old woman presented with a tumor obstructing the left main bronchus on physical examination computed tomography. A bronchoscopic biopsy confirmed a malignant tumor but did not provide a definitive diagnosis.

Interventions:

Sleeve resection of the left main bronchus was performed. The intraoperative frozen section was negative for cancer in both the proximal and distal bronchial stumps.

Diagnosis:

General immunohistochemical staining was performed, and mucoepidermoid carcinoma and HCCC were suspected. RT-PCR revealed positive results for EWSR1::ATF1 fusion transcript, and the tumor was finally diagnosed as HCCC.

Outcomes:

The patient was discharged without any postoperative complications. Sixty-five months have passed since surgery, and no cancer recurrence has been observed.

Lessons:

Although hematoxylin and eosin staining and immunostaining alone were not sufficient to distinguish HCCC from mucoepidermoid carcinoma and other malignant tumors, adding genetic testing for EWSR1 rearrangement led to a definitive pathological diagnosis.
Discovering Provider Awareness of Mobility Assistive Technologies and Clinical Guidelines—A Comparative Analysis With Consumer Responses
Authors: Lee Chang Dae , Peterson Sara , Joseph James , McKernan Gina , Cooper Rosemarie , Koontz Alicia M. , Dicianno Brad E. , Cooper Rory A.
Published: April 2024

Objective

This study aims to enhance the accessibility and quality of mobility-assistive technology by investigating and bridging knowledge gaps between mobility-assistive technology providers and consumers with ambulatory limitations.

Design

A survey was conducted among mobility-assistive technology providers in the United States, consisting of sections on awareness, knowledge importance and desire, and knowledge sources. The responses were compared to data collected from consumers in a previous study.

Results

A total of 144 mobility-assistive technology providers participated, with 60% having received academic or professional training in relevant fields. Analysis revealed significant knowledge gaps between providers and consumers, particularly in assistive technology assessment tools and knowledge sources. Moderate gaps were also observed in areas such as clinical practice guidelines, desired mobility-assistive technology information, and knowledge sources. However, the gaps in other areas were relatively small.

Conclusions

This study highlights the knowledge gaps between mobility-assistive technology providers and consumers, hindering the optimal utilization and fulfillment of user needs. Providers possess valuable information that consumers may lack, positioning them as primary knowledge sources. Addressing these gaps through targeted interventions, improved communication channels, and enhanced education can enhance the utilization of mobility-assistive technology and improve outcomes for individuals with ambulatory limitations.
Effect of Extracorporeal Shock Wave on Upper Trapezius Trigger Points in Patients With Cervicogenic Headache
Authors: Hammam Radwa F. , Alshimy Ahmed M. , Elabd Omar M. , Elabd Aliaa M.
Published: April 2024

Objective

A recent study was designed to ascertain the impact of extracorporeal shock wave therapy on upper trapezius trigger points in cervicogenic headaches patients.

Design

A double-blinded randomized controlled trial study, in which 50 participants (11 male and 39 female) aged between 20–40 with cervicogenic headache were subdivided with randomization to group (A), which received traditional physical therapy and sham shock wave therapy, and group (B), which received traditional physical therapy and actual shock wave therapy. All assessments were performed by a therapist before and after the treatment program (4 wks).

Results

There was a significant difference of headache disability index, visual analog scale scores, and upper trapezius electromyographic characteristics with P value <0.05 in both groups, in favor of the shock wave group.

Conclusions

Extracorporeal shock wave therapy could be used for clinical and research concerns because its positive effects on pain suppression, reduction of headache intensity, and restoration of muscle regular activity in cervicogenic headache patients.
Relationship of Body Mass Index on Patient-Reported Outcomes After Platelet-Rich Plasma Versus Microfragmented Adipose Tissue for Knee Osteoarthritis
Authors: Baria Michael , George Reshma , Barker Tyler , Flanigan David , Kaeding Christopher , Magnussen Robert A.
Published: April 2024

Objective

Body mass index is known to contribute to outcomes for patients with knee osteoarthritis. Furthermore, body mass index influences the protein expression of orthobiologic treatments like platelet-rich plasma and microfragmented adipose tissue. We performed a secondary analysis of the association of body mass index with patient-reported outcomes for patients with knee osteoarthritis who received either platelet-rich plasma or microfragmented adipose tissue injections.

Methods

Seventy-one patients with knee osteoarthritis were randomized to receive a single ultrasound-guided injection of platelet-rich plasma or microfragmented adipose tissue. Platelet-rich plasma was created from 180 cc of anticoagulated blood and processed using a double-spin, buffy-coat concentration system. Microfragmented adipose tissue was created using autologous lipoaspirate that was processed according to minimal manipulation guidelines. Patient-reported outcomes and osteoarthritis outcome scores (Knee Osteoarthritis and injury Outcome Score) were tracked for 12 mos.

Results

Forty-nine patients (platelet-rich plasma = 23, microfragmented adipose tissue = 26) completed 12-mo follow-up. Knee Osteoarthritis and injury Outcome Score quality of life and activity of daily living subscores were inversely correlated (both P < 0.05) with body mass index in the microfragmented adipose tissue but not platelet-rich plasmagroup. Knee Osteoarthritis and injury Outcome Score pain and sport subscores showed a trend toward inverse correlation with body mass index in the microfragmented adipose tissue group (P = 0.07 and P = 0.06, respectively), but not platelet-rich plasma.

Conclusions

Body mass index was negatively associated with patient-reported outcomes in patients who received microfragmented adipose tissue injections for knee osteoarthritis, but not for patients receiving platelet-rich plasma.
Missed Opportunities – Characteristics of People who Received a Concurrent HIV/AIDS Diagnosis in New York State from 2016 – 2021
Authors: Rosenthal Mark , Patterson Wendy , Rajulu Deepa T.
Published: April 2024

Background:

Late HIV diagnosis is associated with a wide range of negative outcomes. This study aims to identify characteristics of individuals who received a concurrent diagnosis (CDX) in New York State (NYS) so that more effective interventions can be developed to encourage earlier testing among these populations.

Methods:

The NYS HIV registry was used to identify people who received a CDX from 2016 – 2021. A CDX was a diagnosis that met the criteria for a stage 3 HIV infection within 30 days of the initial HIV diagnosis. Sex at birth, race/ethnicity, transmission risk group, age at diagnosis, region of residence at diagnosis, urbanicity of zip code of diagnosis, and type of diagnosing facility were used as covariates. Bivariate and multivariate risk ratios were calculated to quantify associations between CDX and covariates.

Results:

There were 14,866 people newly diagnosed with HIV in NYS from 2016 – 2021, of which 19.0% had a CDX. Those with female sex at birth, IDU, or MSM/IDU risk were less likely to have a CDX. Increased age, Asian race/ethnicity, residence outside of New York City, and diagnosis at inpatient facilities or emergency rooms were associated with an increased likelihood of a CDX.

Conclusion:

Populations with the highest proportions of CDX were ones that made up a small percentage of all new HIV diagnoses and may not be benefiting as much from current HIV prevention efforts. There are complex interactions between many factors including geographic and social characteristics which may lead to delayed diagnostic testing.
Solitary Pulmonary Perivascular Epithelial Cell Tumor Mimicking Pulmonary Metastasis on 68Ga-DOTATATE PET/CT in a Patient With Pancreatic Neuroendocrine Tumor
Authors: Liang Shuang , Chen Xiaoliang
Published: April 2024

We report the findings of 68Ga-DOTATATE PET/CT in a 56-year-old woman with solitary pulmonary perivascular epithelioid cell tumor. 68Ga-DOTATATE PET/CT showed a lesion with intense uptake in the region of pancreatic head and a solitary nodule with moderate uptake in the left lung. Pancreatic neuroendocrine tumor with pulmonary metastasis was considered. The postoperative pathological results showed a benign perivascular epithelioid cell tumor of the lung. This case emphasizes the need to increase awareness of benign perivascular epithelioid cell tumors in the differential diagnosis of solitary pulmonary nodule with moderate DOTATATE activity.
Mapping combinatorial expression of non-clustered protocadherins in the developing brain identifies novel PCDH19-mediated cell adhesion properties
Authors: Mincheva-Tasheva Stefka , Pfitzner Chandran , Kumar Raman , Kurtsdotter Idha , Scherer Michaela , Ritchie Tarin , Muhr Jonas , Gecz Jozef , Thomas Paul Q.
Published: April 2024

Non-clustered protocadherins (ncPcdhs) are adhesive molecules with spatio-temporally regulated overlapping expression in the developing nervous system. Although their unique role in neurogenesis has been widely studied, their combinatorial role in brain physiology and pathology is poorly understood. Using probabilistic cell typing by
in situ
sequencing, we demonstrate combinatorial inter- and intra-familial expression of ncPcdhs in the developing mouse cortex and hippocampus, at single-cell resolution. We discovered the combinatorial expression of Protocadherin-19 (
Pcdh19
), a protein involved in PCDH19-clustering epilepsy, with
Pcdh1
,
Pcdh9
or Cadherin 13 (
Cdh13
) in excitatory neurons. Using aggregation assays, we demonstrate a code-specific adhesion function of PCDH19; mosaic PCDH19 absence in PCDH19+9 and PCDH19 + CDH13, but not in PCDH19+1 codes, alters cell–cell interaction. Interestingly, we found that PCDH19 as a dominant protein in two heterophilic adhesion codes could promote
trans
-interaction between them. In addition, we discovered increased CDH13-mediated cell adhesion in the presence of PCDH19, suggesting a potential role of PCDH19 as an adhesion mediator of CDH13. Finally, we demonstrated novel
cis
-interactions between PCDH19 and PCDH1, PCDH9 and CDH13. These observations suggest that there is a unique combinatorial code with a cell- and region-specific characteristic where a single molecule defines the heterophilic cell–cell adhesion properties of each code.
Unconventional life history in a migratory shorebird: desegregating reproduction and migration
Authors: Slezak Colby R. , Blomberg Erik J. , Roth Amber M. , Berigan Liam A. , Fish Alexander C. , Darling Rachel , Clements Sarah J. , Balkcom Greg , Carpenter Bobbi , Costanzo Gary , Duguay Jeffrey , Graham Clayton L. , Harvey William , Hook Michael , Howell Douglas L. , Maddox Seth , Meyer Shawn W. , Nichols Theodore C. , Pollard J. Bruce , Roy Christian , Stiller Joshua C. , Straub Jacob N. , Tetreault Mathieu , Tyl Reina , Williams Lisa , Kilburn Jennifer E. , McWilliams Scott R.
Published: April 2024

Conventional life-history theory predicts that energy-demanding events such as reproduction and migration must be temporally segregated to avoid resource limitation. Here, we provide, to our knowledge, the first direct evidence of ‘itinerant breeding’ in a migratory bird, an incredibly rare breeding strategy (less than 0.1% of extant bird species) that involves the temporal overlap of migratory and reproductive periods of the annual cycle. Based on GPS-tracking of over 200 female American woodcock, most female woodcock (greater than 80%) nested more than once (some up to six times) with short re-nest intervals, and females moved northwards on average 800 km between first and second nests, and then smaller distances (
ca
200+ km) between subsequent nesting attempts. Reliance on ephemeral habitat for breeding, ground-nesting and key aspects of life history that reduce both the costs of reproduction and migration probably explain the prevalence of this rare phenotype in woodcock and why itinerant breeding so rarely occurs in other bird species.
Artificial light at night and warming impact grazing rates and gonad index of the sea urchin
Centrostephanus rodgersii
Authors: Caley Amelia , Marzinelli Ezequiel M. , Byrne Maria , Mayer-Pinto Mariana
Published: April 2024

Artificial light at night (ALAN) is a growing threat to coastal habitats, and is likely to exacerbate the impacts of other stressors. Kelp forests are dominant habitats on temperate reefs but are declining due to ocean warming and overgrazing. We tested the independent and interactive effects of ALAN (dark versus ALAN) and warming (ambient versus warm) on grazing rates and gonad index of the sea urchin
Centrostephanus rodgersii.
Within these treatments, urchins were fed either ‘fresh’ kelp or ‘treated’ kelp. Treated kelp (
Ecklonia radiata
) was exposed to the same light and temperature combinations as urchins. We assessed photosynthetic yield, carbon and nitrogen content and C : N ratio of treated kelp to help identify potential drivers behind any effects on urchins. Grazing increased with warming and ALAN for urchins fed fresh kelp, and increased with warming for urchins fed treated kelp. Gonad index was higher in ALAN/ambient and dark/warm treatments compared to dark/ambient treatments for urchins fed fresh kelp. Kelp carbon content was higher in ALAN/ambient treatments than ALAN/warm treatments at one time point. This indicates ocean warming and ALAN may increase urchin grazing pressure on rocky reefs, an important finding for management strategies.
Genome sequence of the plant-growth-promoting bacterium Bacillus velezensis EU07
Authors: Baysal Omur , Studholme David , Jimenez-Quiros Catherine , Tor Mahmut
Published: April 2024

Many Gram-positive spore-forming rhizobacteria of the genus Bacillus show potential as biocontrol biopesticides that promise improved sustainability and ecological safety in agriculture. Here we present a draft-quality genome sequence for Bacillus velezensis EU07, which shows growth-promotion in tomato plants and biocontrol against Fusarium head blight. We found that the genome of EU07 is almost identical to that of the commercially used strain QST713 but identified 46 single-nucleotide differences that distinguish these strains from each other. The availability of this genome sequence will facilitate future efforts to unravel the genetic and molecular basis for its beneficial properties.
Arcicella gelida sp. nov. and Arcicella lustrica sp. nov., isolated from streams in China and re-examining the taxonomic status of all the genera within the families Spirosomataceae and Cytophagaceae
Authors: Lu Huibin , Chen Li , Huang Linpei
Published: April 2024

Three Gram-stain-negative, aerobic, rod-shaped, non-motile strains (DC2WT, DC25WT, and LKC2W) were isolated from streams in China. Comparisons based on the 16S rRNA gene sequences showed that these three strains share 16S rRNA gene sequence similarity values over 97.0 % with the species of genus Arcicella. There was confusion due to the fact that all species of genera Flectobacillus, Aquirufa, and Sandaracinomonas show 16S rRNA gene sequence similarity of over 90.0 % to the above three strains, but the genus Flectobacillus belongs to the family Spirosomataceae and the genera Aquirufa and Sandaracinomonas belong to the family Cytophagaceae. Observing the phylogenetic trees, strains DC2WT, DC25WT, and LKC2W cluster closely with the species of genus Arcicella, but some species within the families Spirosomataceae and Cytophagaceae are not monophyletic. The phylogenomic tree also showed a confused phylogenetic relationships among these non-monophyletic species. Combining the phylogenetic relationships and average nucleotide identity values, the current taxonomic status of all the genera within the families Spirosomataceae and Cytophagaceae were re-examined. The genera ‘Chryseosolibacter’, ‘Dawidia’, and Chryseotalea should belong to the new family Chryseotaleaceae fam. nov., the genera Arcicella, Flectobacillus, Pseudarcicella, Aquirufa, and Sandaracinomonas should belong to the new family Flectobacillaceae fam. nov., the genera Fluviimonas, Taeseokella, Arcticibacterium, Emticicia, Jiulongibacter, Marinilongibacter, Lacihabitans, and Leadbetterella should belong to the new family Leadbetterellaceae fam. nov., the genus Litoribacter should be reassigned to the family Cyclobacteriaceae, and the genera Arundinibacter and Tellurirhabdus should be reassigned to the family Spirosomataceae. Strains DC2WT and DC25WT are reported to represent two novel species of the genus Arcicella, for which the names Arcicella gelida sp. nov. (type strain DC2WT=GDMCC 1.3209T=KCTC 92559T) and Arcicella lustrica sp. nov. (type strain DC25WT=GDMCC 1.3210T=KCTC 92557T) are proposed.
Gut microbiota plays a significant role in gout
Authors: Feng Zhi-Peng , Wang Xiao-Yan , Xin Hong-Yi , Huang Shao-Li , Huang Hong-Yu , Xin Qiang , Zhang Xi-He , Xin Hong-Wu
Published: April 2024

With the development of social economy, the incidence of gout is increasing, which is closely related to people’s increasingly rich diet. Eating a diet high in purine, fat, sugar and low-fibre for a long time further aggravates gout by affecting uric acid metabolism. The renal metabolism mechanism of uric acid has been thoroughly studied. To find a new treatment method for gout, increasing studies have recently been conducted on the mechanism of intestinal excretion, metabolism and absorption of uric acid. The most important research is the relationship between intestinal microbiota and the risk of gout. Gut microbiota represent bacteria that reside in a host’s gastrointestinal tract. The composition of the gut microbiota is associated with protection against pathogen colonization and disease occurrence. This review focuses on how gut microbiota affects gout through uric acid and discusses the types of bacteria that may be involved in the occurrence and progression of gout. We also describe potential therapy for gout by restoring gut microbiota homeostasis and reducing uric acid levels. We hold the perspective that changing intestinal microbiota may become a vital method for effectively preventing or treating gout.
Patterns recovered in phylogenomic analysis of Candida auris and close relatives implicate broad environmental flexibility in Candida/Clavispora clade yeasts
Authors: Schutz Kyle , Melie Tina , Smith Stacey D. , Quandt C. Alisha
Published: April 2024

Fungal pathogens commonly originate from benign or non-pathogenic strains living in the natural environment. The recently emerged human pathogen, Candida auris, is one example of a fungus believed to have originated in the environment and recently transitioned into a clinical setting. To date, however, there is limited evidence about the origins of this species in the natural environment and when it began associating with humans. One approach to overcome this gap is to reconstruct phylogenetic relationships between (1) strains isolated from clinical and non-clinical environments and (2) between species known to cause disease in humans and benign environmental saprobes. C. auris belongs to the Candida/Clavispora clade, a diverse group of 45 yeast species including human pathogens and environmental saprobes. We present a phylogenomic analysis of the Candida/Clavispora clade aimed at understanding the ecological breadth and evolutionary relationships between an expanded sample of environmentally and clinically isolated yeasts. To build a robust framework for investigating these relationships, we developed a whole-genome sequence dataset of 108 isolates representing 18 species, including four newly sequenced species and 18 environmentally isolated strains. Our phylogeny, based on 619 orthologous genes, shows environmentally isolated species and strains interspersed with clinically isolated counterparts, suggesting that there have been many transitions between humans and the natural environment in this clade. Our findings highlight the breadth of environments these yeasts inhabit and imply that many clinically isolated yeasts in this clade could just as easily live outside the human body in diverse natural environments and vice versa.
BRAIN-MAGNET: A novel functional genomics atlas coupled with convolutional neural networks facilitates clinical interpretation of disease relevant variants in non-coding regulatory elements
Authors: Deng Ruizhi , Perenthaler Elena , Nikoncuk Anita , Yousefi Soheil , Lanko Kristina , Schot Rachel , Maresca Michela , Medico-Salsench Eva , Sanderson Leslie E. , Parker Michael J. , van Ijcken Wilfred F.J. , Park Joohyun , Sturm Marc , Haack Tobias B. ,   Genomics England Research Consortium, Roshchupkin Gennady V , Mulugeta Eskeatnaf , Barakat Tahsin Stefan
Published: April 2024

Genome-wide assessment of genetic variation is becoming routine in human genetics, but functional interpretation of non-coding variants both in common and rare diseases remains extremely challenging. Here, we employed the massively parallel reporter assay ChIP- STARR-seq to functionally annotate the activity of >145 thousand non-coding regulatory elements (NCREs) in human neural stem cells, modelling early brain development. Highly active NCREs show increased sequence constraint and harbourde novovariants in individuals affected by neurodevelopmental disorders. They are enriched for transcription factor (TF) motifs including YY1 and p53 family members and for primate-specific transposable elements, providing insights on gene regulatory mechanisms in NSCs. Examining episomal NCRE activity of the same sequences in human embryonic stem cells identified cell type differential activity and primed NCREs, accompanied by a rewiring of the epigenome landscape. Leveraging the experimentally measured NCRE activity and nucleotide composition of the assessed sequences, we built BRAIN-MAGNET, a functionally validated convolutional neural network that predicts NCRE activity based on DNA sequence composition and identifies functionally relevant nucleotides required for NCRE function. The application of BRAIN-MAGNET allows fine-mapping of GWAS loci identified for common neurological traits and prioritizing of possible disease-causing rare non-coding variants in currently genetically unexplained individuals with neurogenetic disorders, including those from the Genomics England 100,000 Genomes project, identifying novel enhanceropathies. We foresee that this NCRE atlas and BRAIN-MAGNET will help reduce missing heritability in human genetics by limiting the search space for functionally relevant non-coding genetic variation.
Insights into Professional Preferences and Rationale for Surgical Sequencing in Managing Hip-Spine Syndrome
Authors: Breuning Carolina , Tian Xinggui , Goronzy Jens , Günther Klaus-Peter , Platz Uwe , Beyer Franziska , Disch Alexander Carl , Lachiewicz Paul F. , Liu Ning , Goodman Stuart B. , Wood Kirkham B. , Zwingenberger Stefan
Published: April 2024

Background

The optimal sequence of hip and spine surgeries for hip-spine syndrome management remains a contentious issue. This study aimed to investigate the preferences and rationale behind the sequence of surgical treatments across various hip-spine syndrome scenarios among potential specialist interviewees.

Methods

A questionnaire survey, featuring five fictional clinical presentations encompassing symptomatic hip osteoarthritis and diverse spinal pathologies, was conducted among German hip and spine surgeons, alongside conducting a cross-national comparison with previous US survey.

Results

German hip and spine surgeons preferred spine-first surgery in hip-spine syndrome scenarios involving neurological deficits, while preferred hip-first in scenarios without such deficits. In contrast, US surgeons demonstrated differing sequencing patterns, highlighting differences between nations. Notably, distinct surgical order preferences were observed among different specialists. Surgeons’ decision-making was primarily influenced by symptom severity and urgency, spine-pelvis-hip biomechanics, and treatment efficacy.

Conclusion

The sequence of hip and spine surgery in various hip-spine syndrome scenarios has different preference patterns, with professional preferences and cross-nation differences, and is guided by the multifaceted considerations involved in surgical decision-making.
Characterising the Modulatory Role of Ikebana in Flower-Dependent Cell Competition
Authors: Marques-Reis Mariana , Gutiérrez-García Andrés , Flores Clara Carlos , Argudo Irene , Stefan Eggel Matthias , Hauert Barbara , Brás-Pereira Catarina , Moreno Eduardo
Published: April 2024

Tissues encompass a quality control mechanism that promotes their optimal state. This mechanism, designated cell competition, is characterised by the elimination of suboptimal yet viable cells when they are near healthier cells within the same tissue compartment.

This study explores Flower-dependent cell competition and introduces Ikebana as a novel player. The differential expression of theflowerisoforms labels cells as winners or losers, influencing their fate in diverse contexts, including eye development, traumatic brain injury, and Alzheimer’s disease. Ikebana, ubiquitously produced in wing imaginal discs and adult brains, modulates loser cell elimination. Reduction ofikebanaexpression correlates with an increased number of loser cells, while its overexpression in the Alzheimer’s disease model reduces the number of Flower LoseB-positive cells.

We suggest that Ikebana protects loser cell elimination, particularly when excessive elimination of loser cells can compromise tissue function. Thus, Ikebana might be a potential therapeutic target for modulating Flower LoseB expression.
A negatively-charged region within carboxy-terminal domain maintains proper CTCF DNA binding
Authors: Liu Lian , Tang Yuanxiao , Zhang Yan , Wu Qiang
Published: April 2024

As an essential regulator of higher-order chromatin structures, CTCF is a highly-conserved DNA binding protein with a central DNA-binding domain of 11 tandem zinc fingers, which are flanked by amino (N-) and carboxy (C-) terminal domains of intrinsically disordered regions. Here we report that CRISPR deletion of the entire C-terminal domain of alternating charge blocks decreases CTCF DNA binding but deletion of the C-terminal fragment of 116 amino acids results in increased CTCF DNA binding and aberrant gene regulation. Through a series of genetic targeting experiments, in conjunction with EMSA, 4C, qPCR, ChIP-seq, and ATAC-seq, we uncovered a negatively-charged region (NCR) responsible for weakening CTCF DNA binding and chromatin accessibility. AlphaFold prediction suggests an autoinhibitory mechanism of CTCF via NCR as a flexible DNA mimic domain, possibly competing with DNA binding for the positively-charged ZF surface area. Thus, the unstructured C-terminal domain plays an intricate role in maintaining proper CTCF-DNA interactions and 3D genome organization.
Aging shapes infection profiles of influenza A virus and SARS-CoV-2 in human lung slices
Authors: Brügger Melanie , Machahua Carlos , Zumkehr Beatrice , Cismaru Christiana , Jandrasits Damian , Dorn Patrick , Marti Thomas M. , Zimmer Gert , Thiel Volker , Funke-Chambour Manuela , Alves Marco P.
Published: April 2024

The recent coronavirus disease 2019 (COVID-19) outbreak revealed the susceptibility of elderly patients to respiratory virus infections, showing cell senescence or subclinical persistent inflammatory profiles and favouring the development of severe pneumonia. In our study, we evaluated the potential influence of lung aging on the efficiency of replication of influenza A virus (IAV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as well as determined the pro-inflammatory and antiviral responses of the distal lung tissue. Using precision-cut lung slices (PCLS) from donors of different ages, we found that pandemic H1N1 and avian H5N1 IAV replicated in the lung parenchyma with high efficacy. In contrast to these IAV strains, SARS-CoV-2 early isolate and Delta variant of concern (VOC) replicated less efficiently in PCLS. Interestingly, both viruses showed reduced replication in PCLS from older compared to younger donors, suggesting that aged lung tissue represents a sub-optimal environment for viral replication. Regardless of the age-dependent viral loads, PCLS responded to infection with both viruses by an induction of IL-6 and IP-10/CXCL10 mRNAs, being highest for H5N1. Finally, while SARS-CoV-2 infection was not causing detectable cell death, IAV infection caused significant cytotoxicity and induced significant early interferon responses. In summary, our findings suggest that aged lung tissue might not favour viral dissemination, pointing to a determinant role of dysregulated immune mechanisms in the development of severe disease.

New & Noteworthy

PCLS from donors of varying ages were exposed to SARS-CoV-2 or IAV. Notably, the latter exhibited the highest replication efficacy, triggering early interferon responses, elevated IL-6 and IP-10/CXCL10 mRNAs expression, and significant cell death compared to SARS-CoV-2. Overall, across all age groups, the pulmonary environment showed sustained immunocompetence. For both viruses, older donor-derived PCLS displayed reduced viral permissiveness, suggesting aged lung tissue might not favour viral dissemination, implying other factors contribute to severe disease development.
Assessment and phenotypic identification of millet germplasm (Setaria italica[L.]) in Liaoning, China
Authors: Xin-tong Li , Wei-Feng He , Hong-hao Wang , Min Xu
Published: April 2024

Aims

This study evaluated millet germplasms in Liaoning Province to support the collection, preservation and innovation of millet germplasm resources.

Methods

The study was conducted from 2018 to 2020, involved the selection of 105 millet germplasm resources from the Germplasm Bank of the Liaoning Academy of Agricultural Sciences (LAAS), the observation and recording of 31 traits, and the application of multivariate analysis methods to assess phenotypic diversity.

Results

From the diversity analysis and correlation analysis, it was found that the tested traits had abundant diversity and complex correlations among them. principal component analysis (PCA) comprehensively analyzed all quantitative traits and extracted 7 principal components. Grey relational analysis (GRA) highlighted the varied contributions of different traits to yield. Through systematic cluster analysis, the resources were categorized into six groups at Euclidean distance of 17.09. K-mean cluster analysis determined the distribution interval and central value of each trait, then identified resources with desirable traits.

Conclusion

The results revealed resources that possess characteristics such as upthrow seedling leaves, more tillers and branches, larger and well-formed ears, and lodging resistance prefer to higher grain yield. It was also discovered that the subear internode length (SIL) could be an indicator for maturity selection. Four specific resources, namely, Dungu No. 1, Xiao-li-xiang, Basen Shengu, and Yuhuanggu No. 1, were identified for further breeding and practical applications.
Behavioral Repertoire of lab-reared early juveniles of the Mexican four-eyed octopus:Octopus maya
Authors: González-Navarrete D.A. , Vergara-Ovalle F. , García-Andaluz P. , Ayala-Guerrero F. , Rosas C. , Vázquez-León P. , Paz-Trejo D.B. , Sánchez-Castillo H.
Published: April 2024

Behavioral studies have predominantly focused on organisms within the phyla Craniata and Arthropoda. Yet, there has been a growing interest in studying the behavior of organisms from alternative phyla, such as mollusks, owing to the research opportunities they offer. Among mollusks, cephalopods have emerged as a prominent subject of inquiry. However, behavioral research on Mexico’s endemic species,Octopus maya (Om), remains conspicuously scarce.Omexhibits favorable attributes for utilization as a standardized animal model in neuroscience research, primarily due to its adaptability to laboratory settings and the successful raising of multiple generations. A comprehensive understanding ofOm’s behavior within laboratory environments is essential to harness its potential as a research model. Thus, the main goal of this study was to establish a comprehensive behavioral catalog forOmunder laboratory conditions. ThirteenOmsubjects (6 to 20 grams) were housed in controlled tank environments. Our findings reveal thatOmexhibits a diverse behavioral repertoire, comprising a minimum of twenty-one distinct behaviors categorized into six behavioral classes. Additionally,Omdisplays discernable diurnal and nocturnal activity patterns, with increased activity levels, altered behavior distributions, and varying activity frequencies predominantly during daylight hours. This expanded knowledge ofOm’s behavior enhances its suitability as a research model organism.