bluuebunny/crossref_metadata_2025_split huggingface dataset:
Syndromes associated with frontotemporal lobar degeneration change response patterns on visual analogue scales
Authors: Williams Rebecca S. , Adams Natalie E. , Hughes Laura E. , Rouse Matthew A. , Murley Alexander G. , Naessens Michelle , Street Duncan , Holland Negin , Rowe James B. 
Published: June 2023

AbstractSelf-report scales are widely used in cognitive neuroscience and psychology. However, they rest on the central assumption that respondents engage meaningfully. We hypothesise that this assumption does not hold for many patients, especially those with syndromes associated with frontotemporal lobar degeneration. In this study we investigated differences in response patterns on a visual analogue scale between people with frontotemporal degeneration and controls. We found that people with syndromes associated with frontotemporal lobar degeneration respond with more invariance and less internal consistency than controls, with Bayes Factors = 15.2 and 14.5 respectively indicating strong evidence for a group difference. There was also evidence that patient responses feature lower entropy. These results have important implications for the interpretation of self-report data in clinical populations. Meta-response markers related to response patterns, rather than the values reported on individual items, may be an informative addition to future research and clinical practise.
A pan-cancer analysis of the role of USP5 in human cancers
Authors: Yan Bokang , Guo Jiaxing , Deng Shuang , Chen Dongliang , Huang Meiyuan 
Published: June 2023

AbstractPosttranslational modifications (PTM) such as acetylation, deubiquitination, and phosphorylation of proteins, play important roles in various kinds of cancer progression. Ubiquitin-specific proteinase 5 (USP5), a unique member of deubiquitinating enzymes (DUBs) which recognizes unanchored polyubiquitin specifically, could regulate the stability of many tumorigenesis-associated proteins to influence cancer initiation and progression. However, the diverse biological significance of USP5 in pan-cancer has not been systematically and comprehensively studied. Here, we explored the role of USP5 in pan-cancer using The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) database, and we also acquired and analyzed data via various software and web platforms such as R, GEPIA2.0, HPA, TISIDB, cBioPortal, UALCAN, TIMER 2.0, CancerSEA and BioGRID. USP5 expression was high in most cancers and differed significantly in different molecular and immune subtypes of cancers. In addition, USP5 had certain diagnostic value in multiple cancers, and high expression of USP5 generally predicted poor prognosis for cancer patients. We also found that the most frequent genetic alterations type of USP5 was mutation, and the DNA methylation level of USP5 decreased in various cancers. Furthermore, USP5 expression correlated with cancer-associated fibroblasts (CAFs), endothelial cells (EC) and genetic markers of immunodulators in cancers. Moreover, the result from single cell sequencing showed that USP5 could regulate several tumor biological behaviors such as apoptosis, DNA damage and metastasis. Gene enrichment analysis indicated “spliceosome” and “RNA splicing” may be the critical mechanism for USP5 to involve in cancer. Taken together, our study elucidates the biological significance of USP5 in the diagnosis, prognosis and immune in human pan-cancer.
A microcomputed tomographic analysis of the morphological variabilities and incidence of extra canals in mandibular first molar teeth in an Egyptian subpopulation
Authors: Saber Shehabeldin Mohamed , Elashiry Mohamed Mohamed , Sadat Shaimaa Mohamed Abu El , Nawar Nawar Naguib 
Published: June 2023

AbstractA well-protected microbial habitat may be present in the root and canal morphology, which is varied and complicated. Before initiating effective root canal treatment, a detailed knowledge of the root and canal anatomical variances in each tooth is a must. This study aimed to investigate the root canal configuration, apical constriction anatomy, location of the apical foramen, dentine thickness, and prevalence of accessory canals in mandibular molar teeth in an Egyptian subpopulation using micro-computed tomography (microCT). A total of 96 mandibular first molars were scanned using microCT, and 3D reconstruction was performed using Mimics software. The root canal configurations of each of the mesial and distal root were classified with two different classification systems. The prevalence and dentin thickness around middle mesial and middle distal canals were investigated. The number, location and anatomy of major apical foramina and the apical constriction anatomy analysed. The number and location of accessory canals were identified. Our findings showed that two separate canals (15%) and one single canal (65%) were the most common configuration in the mesial and distal roots, respectively. More than half of the mesial roots had complex canal configurations and 51% had middle mesial canals. The single apical constriction anatomy was the most common for both canals followed by the parallel anatomy. Disto-lingual and distal locations of the apical foramen are the most common location for both roots. Mandibular molars in Egyptians show a wide range of variations in root canal anatomy with high prevalence of middle mesial canals. Clinicians should be aware of such anatomical variations for successful root canal treatment procedures. A specific access refinement protocol and appropriate shaping parameters should be designated for each case to fulfil the mechanical and biological objectives of root canal treatment without compromising the longevity of treated teeth.
Effects of the depletion of neural progenitors by focal X-ray irradiation on song production and perception in canaries
Authors: Chiver Ioana , dos Santos Ednei B. , Valle Shelley , Lallemand François , Cornil Charlotte A. , Ball Gregory F. , Balthazart Jacques 
Published: June 2023

AbstractThe song control nucleus HVC of songbirds has emerged as a widespread model system to study adult neurogenesis and the factors that modulate the incorporation of new neurons, including seasonal state, sex differences or sex steroid hormone concentrations. However, the specific function of these new neurons born in adulthood remains poorly understood. We implemented a new procedure based on focal X-ray irradiation to deplete neural progenitors in the ventricular zone adjacent to HVC and study the functional consequences. A 23 Gy dose depleted by more than 50 percent the incorporation of BrdU in neural progenitors, a depletion that was confirmed by a significant decrease in doublecortin positive neurons. This depletion of neurogenesis significantly increased the variability of testosterone-induced songs in females and decreased their bandwidth. Expression of the immediate early gene ZENK in secondary auditory areas of the telencephalon that respond to song was also inhibited. These data provide evidence that new neurons in HVC play a role in both song production and perception and that X-ray focal irradiation represents an excellent tool to advance our understanding of adult neurogenesis.
Isolation of saprophytic filamentous fungi from avian fecal samples and assessment of its predatory activity on coccidian oocysts
Authors: Lozano João , Louro Mariana , Almeida Cristina , Victório Ana Cláudia , Melo Pedro , Rodrigues João Paulo , Oliveira Manuela , Paz-Silva Adolfo , Madeira de Carvalho Luís 
Published: June 2023

AbstractFungal strains used in the biocontrol of animal gastrointestinal parasites have been mainly isolated from pasture soil, decaying organic matter, and feces from herbivores and carnivores. However, their isolation from birds and assessment of predatory activity against avian GI parasites has been scarce thus far. This research aimed to isolate filamentous fungi from avian fecal samples and evaluate their predatory activity against coccidia. A pool of 58 fecal samples from chickens, laying hens, and peacocks, previously collected between July 2020-April 2021, were used for isolation of filamentous fungi and assessment of their in vitro predatory activity against coccidian oocysts, using Water-Agar medium and coprocultures. The Willis-flotation technique was also performed to obtain concentrated suspensions of oocysts. A total of seven Mucor isolates was obtained, being the only fungal taxa identified, and all presented lytic activity against coccidia. Isolates FR3, QP2 and SJ1 had significant coccidiostatic efficacies (inhibition of sporulation) higher than 70%, while isolates FR1, QP2 and QP1 had coccidicidal efficacies (destruction of the oocysts) of 22%, 14% and 8%, respectively, after 14 days of incubation, being a gradual and time-dependent process. To our knowledge, this is the first report regarding the isolation of native predatory fungi from avian feces and demonstration of their lytic activity against coccidia.
The causal mutation in ARR3 gene for high myopia and progressive color vision defect
Authors: Gu Lei , Cong Peikuan , Ning Qingyao , Jiang Bo , Wang Jianyong , Cui Hongguang 
Published: June 2023

AbstractThe ARR3 gene, also known as cone arrestin, belongs to the arrestin family and is expressed in cone cells, inactivating phosphorylated-opsins and preventing cone signals. Variants of ARR3 reportedly cause X-linked dominant female-limited early-onset (age < 7 years old) high myopia (< − 6D). Here, we reveal a new mutation (c.228T>A, p.Tyr76*) in ARR3 gene that can cause early-onset high myopia (eoHM) limited to female carriers. Protan/deutan color vision defects were also found in family members, affecting both genders. Using ten years of clinical follow-up data, we identified gradually worsening cone dysfunction/color vision as a key feature among affected individuals. We present a hypothesis that higher visual contrast due to the mosaic of mutated ARR3 expression in cones contributes to the development of myopia in female carriers.
Ultra-high performance liquid chromatography high-resolution mass spectrometry for metabolomic analysis of dental calculus from Duke Alessandro Farnese and Maria D’Aviz
Authors: Riboni Nicolo’ , Bianchi Federica , Mattarozzi Monica , Peracchia Marianna , Meleti Marco , Careri Maria 
Published: June 2023

AbstractDental calculus is a valuable resource for the reconstruction of dietary habits and oral microbiome of past populations. In 2020 the remains of Duke Alessandro Farnese and his wife Maria D’Aviz were exhumed to get novel insights into the causes of death. This study aimed to investigate the dental calculus metabolome of the noble couple by untargeted metabolomics. The pulverized samples were decalcified in a water-formic acid mixture, extracted using methanol/acetonitrile and analyzed by ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS) using a reversed-phase separation followed by electrospray ionization and full scan in positive and negative ion mode. Waters Synapt-G2-Si High-Definition hybrid quadrupole time-of-flight mass spectrometer was used. Significant features were then identified using MSEacquisition mode, recording information on exact mass precursor and fragment ions within the same run. This approach, together with data pre-treatment and multivariate statistical analysis allowed for the identification of compounds able to differentiate between the investigated samples. More than 200 metabolites were identified, being fatty acids, alcohols, aldehydes, phosphatidylcholines, phosphatidylglycerols, ceramides and phosphatidylserines the most abundant classes. Metabolites deriving from food, bacteria and fungi were also determined, providing information on the habits and oral health status of the couple.
Sample size calculation for a NanoString GeoMx spatial transcriptomics experiment to study predictors of fibrosis progression in non-alcoholic fatty liver disease
Authors: Ryaboshapkina Maria , Azzu Vian 
Published: June 2023

AbstractSample size calculation for spatial transcriptomics is a novel and understudied research topic. Prior publications focused on powering spatial transcriptomics studies to detect specific cell populations or spatially variable expression patterns on tissue slides. However, power calculations for translational or clinical studies often relate to the difference between patient groups, and this is poorly described in the literature. Here, we present a stepwise process for sample size calculation to identify predictors of fibrosis progression in non-alcoholic fatty liver disease as a case study. We illustrate how to infer study hypothesis from prior bulk RNA-sequencing data, gather input requirements and perform a simulation study to estimate required sample size to evaluate gene expression differences between patients with stable fibrosis and fibrosis progressors with NanoString GeoMx Whole Transcriptome Atlas assay.
Stripe rust resistance gene(s) postulation in wheat germplasm with the help of differentials and tagged molecular markers
Authors: Haider Mohammad Waris , Kaur Jaspal , Bala Ritu , Singh Sandeep , Srivastava Puja , Sharma Achla , Singh Rohtas , Kumari Jyoti 
Published: June 2023

AbstractThirteen known Yr gene-associated markers pertaining to genes (Yr5,Yr10,Yr15,Yr24/Yr26) were used to identify the genes in selected wheat germplasm which were found resistant under field conditions at two locations in Punjab, India against stripe rust. In field evaluation, 38 genotypes exhibited highly resistant response, with a final rust severity (FRS) ranging from 0 to TR. Seven genotypes expressed a resistant to moderately resistant response with FRS ranging from 5MR–10S. In race-specific phenotying against most prevalent pathotypes of Pucciniastriiformistritici (46S119,110S119 &238S119) by seedling reaction test (SRT) 14 genotypes (29.2%) were found to be immune (IT = 0), 28 genotypes (58.3%) were resistant (IT = 1), and 3 genotypes (6.3%) were moderately resistant (IT = 2). Yr5 was detected in sixteen lines with the help of two markers Xwmc175 and Xgwm120 linked with Yr5. Yr10 was detected in ten lines with the marker Xpsp3000 and Yr15 was detected in fourteen lines with two linked markers; Xgwm413 and Xgwm273. Likewise, Yr24/26 was detected in 15 lines with two linked markers, namely Xbarc181 and Xbarc187. Based on the race specific phenotyping data and marker data, fourteen lines were found to carry a single gene, 16 showed the presence of two gene combinations, and seven genotypes were found to have a combination of three genes. Frequencies of Yr5, Yr15 and Yr26/Yr24 was high among test wheat germplasm in comparison to Yr10.
Effects of a single night of continuous positive airway pressure on spontaneous brain activity in severe obstructive sleep apnea
Authors: Sun Yuanfeng , Lei Fei , Luo Lian , Zou Ke , Tang Xiangdong 
Published: June 2023

AbstractThis study aimed to investigate the effect of a single night of continuous positive airway pressure (CPAP) treatment on spontaneous brain activity and the underlying neuropathological mechanisms in patients with severe obstructive sleep apnea (OSA). The study involved 30 severe OSA patients and 19 healthy controls (HC). Fractional amplitude of low-frequency fluctuation (fALFF) and regional homogeneity (ReHo) methods were employed to evaluate spontaneous brain activity in all participants. Following a single night of CPAP treatment, ReHo values increased in the bilateral caudate and decreased in the right superior frontal gyrus. The fALFF values increased in the left orbital part of the middle frontal gyrus and the right orbital of the inferior frontal gyrus (Frontal_Inf_Orb_R). However, fALFF values decreased in the medial part of the left superior frontal gyrus and the right supramarginal part of the inferior parietal lobe. Pearson correlation analysis revealed a positive relationship between the change in the fALFF in the Frontal_Inf_Orb_R and the change in REM sleep duration (r = 0.437, p = 0.016) following a single night of CPAP treatment. We concluded that observing changes in abnormal fALFF and ReHo in OSA patients before and after a single night of CPAP treatment may enhance our understanding of the neurological mechanisms in patients with severe OSA.
Evidence for a maintenance cost for birds maintaining highly flexible basal, but not summit, metabolic rates
Authors: Swanson David L. , Stager Maria , Vézina François , Liu Jin-Song , McKechnie Andrew E. , Amirkhiz Reza Goljani 
Published: June 2023

AbstractReversible phenotypic flexibility allows organisms to better match phenotypes to prevailing environmental conditions and may produce fitness benefits. Costs and constraints of phenotypic flexibility may limit the capacity for flexible responses but are not well understood nor documented. Costs could include expenses associated with maintaining the flexible system or with generating the flexible response. One potential cost of maintaining a flexible system is an energetic cost reflected in the basal metabolic rate (BMR), with elevated BMR in individuals with more flexible metabolic responses. We accessed data from thermal acclimation studies of birds where BMR and/or Msum(maximum cold-induced metabolic rate) were measured before and after acclimation, as a measure of metabolic flexibility, to test the hypothesis that flexibility in BMR (ΔBMR), Msum(ΔMsum), or metabolic scope (Msum − BMR; ΔScope) is positively correlated with BMR. When temperature treatments lasted at least three weeks, three of six species showed significant positive correlations between ΔBMR and BMR, one species showed a significant negative correlation, and two species showed no significant correlation. ΔMsumand BMR were not significantly correlated for any species and ΔScope and BMR were significantly positively correlated for only one species. These data suggest that support costs exist for maintaining high BMR flexibility for some bird species, but high flexibility in Msumor metabolic scope does not generally incur elevated maintenance costs.
Extended-spectrum beta-lactamases found in Escherichia coli isolates obtained from blood cultures and corresponding stool specimen
Authors: Doerr Nina , Dietze Nadine , Lippmann Norman , Rodloff Arne C. 
Published: June 2023

AbstractWith extended-spectrum β-lactamases (ESBLs) and CTX-M enzymes being on the rise, antimicrobial treatment of enterobacterial infections is becoming more and more challenging. Our study aimed at a molecular characterization of phenotypically ESBL-positiveE. colistrains obtained from blood cultures of patients of the University Hospital of Leipzig (UKL), Germany. The presence of CMY-2, CTX-M-14 and CTX-M-15 was investigated using Streck ARM-D Kit (Streck, USA). Real-time amplifications were performed by QIAGEN Rotor-Gene Q MDx Thermocycler (QIAGEN, Thermo Fisher Scientific, USA). Antibiograms as well as epidemiological data were evaluated. Among 117 cases, 74.4% of the isolates showed a resistance to ciprofloxacin, piperacillin and ceftazidime or cefotaxime while being susceptible to imipenem/meropenem. The proportion of ciprofloxacin resistance was significantly higher than the proportion of ciprofloxacin susceptibility. At least one of the investigated genes was detected in 93.1% of the blood cultureE. coliisolates: CTX-M-15 (66.7%), CTX-M-14 (25.6%) or the plasmid-mediated ampC gene CMY-2 (3.4%). 2.6% were tested positive for two resistance genes. 94 of the corresponding stool specimens tested positive for ESBL producingE. coli(94/112, 83.9%). 79 (79/94, 84%)E. colistrains found in the stool samples matched with the respective patient’s blood culture isolate phenotypically (MALDI-TOF, antibiogram). The distribution of resistance genes was in accordance with recent studies in Germany as well as worldwide. This study provides indications of an endogenous focus of infection and emphasize the importance of screening programs for high-risk patients.
Maternal weight latent trajectories and associations with adverse pregnancy outcomes using a smoothing mixture model
Authors: Faraji Azad Shirin , Biglarian Akbar , Rostami Maryam , Bidhendi-Yarandi Razieh 
Published: June 2023

AbstractClass membership is a critical issue in health data sciences. Different types of statistical models have been widely applied to identify participants within a population with heterogeneous longitudinal trajectories. This study aims to identify latent longitudinal trajectories of maternal weight associated with adverse pregnancy outcomes using smoothing mixture model (SMM). Data were collected from the Khuzestan Vitamin D Deficiency Screening Program in Pregnancy. We applied the data of 877 pregnant women living in Shooshtar city, whose weights during the nine months of pregnancy were available. In the first step, maternal weight was classified and participants were assigned to only one group for which the estimated trajectory is the most similar to the observed one using SMM; then, we examined the associations of identified trajectories with risk of adverse pregnancy endpoints by applying logistic regression. Three latent trajectories for maternal weight during pregnancy were identified and named as low, medium and high weight trajectories. Crude estimated odds ratio (OR) for icterus, preterm delivery, NICU admission and composite neonatal events shows significantly higher risks in trajectory 1 (low weight) compared to trajectory 2 (medium weight) by 69% (OR = 1.69, 95%CI 1.20, 2.39), 82% (OR = 1.82, 95%CI 1.14, 2.87), 77% (OR = 1.77, 95%CI 1.17, 2.43), and 85% (OR = 1.85, 95%CI 1.38, 2.76), respectively. Latent class trajectories of maternal weights can be accurately estimated using SMM. It is a powerful means for researchers to appropriately assign individuals to their class. The U-shaped curve of association between maternal weight gain and risk of maternal complications reveals that the optimum place for pregnant women could be in the middle of the growth curve to minimize the risks. Low maternal weight trajectory compared to high had even a significantly higher hazard for some neonatal adverse events. Therefore, appropriate weight gain is critical for pregnant women.Trial registration International Standard Randomized Controlled Trial Number (ISRCTN): 2014102519660N1; http://www.irct.ir/searchresult.php?keyword=&id=19660&number=1&prt=7805&total=10&m=1 (Archived by WebCite at http://www.webcitation.org/6p3lkqFdV).