bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stochastic gene expression and environmental stressors trigger variable somite segmentation phenotypes
Authors: Keseroglu Kemal , Zinani Oriana Q. H. , Keskin Sevdenur , Seawall Hannah , Alpay Eslim E. , Özbudak Ertuğrul M. 
Published: October 2023

AbstractMutations of several genes cause incomplete penetrance and variable expressivity of phenotypes, which are usually attributed to modifier genes or gene-environment interactions. Here, we show stochastic gene expression underlies the variability of somite segmentation defects in embryos mutant for segmentation clock genes her1 or her7. Phenotypic strength is further augmented by low temperature and hypoxia. By performing live imaging of the segmentation clock reporters, we further show that groups of cells with higher oscillation amplitudes successfully form somites while those with lower amplitudes fail to do so. In unfavorable environments, the number of cycles with high amplitude oscillations and the number of successful segmentations proportionally decrease. These results suggest that individual oscillation cycles stochastically fail to pass a threshold amplitude, resulting in segmentation defects in mutants. Our quantitative methodology is adaptable to investigate variable phenotypes of mutant genes in different tissues.
Androgen receptor is a determinant of melanoma targeted drug resistance
Authors: Samarkina Anastasia , Youssef Markus Kirolos , Ostano Paola , Ghosh Soumitra , Ma Min , Tassone Beatrice , Proust Tatiana , Chiorino Giovanna , Levesque Mitchell P. , Goruppi Sandro , Dotto Gian Paolo 
Published: October 2023

AbstractMelanoma provides a primary benchmark for targeted drug therapy. Most melanomas with BRAFV600 mutations regress in response to BRAF/MEK inhibitors (BRAFi/MEKi). However, nearly all relapse within the first two years, and there is a connection between BRAFi/MEKi-resistance and poor response to immune checkpoint therapy. We reported that androgen receptor (AR) activity is required for melanoma cell proliferation and tumorigenesis. We show here that AR expression is markedly increased in BRAFi-resistant melanoma cells, and in sensitive cells soon after BRAFi exposure. Increased AR expression is sufficient to render melanoma cells BRAFi-resistant, eliciting transcriptional changes of BRAFi-resistant subpopulations, including elevated EGFR and SERPINE1 expression, of likely clinical significance. Inhibition of AR expression or activity blunts changes in gene expression and suppresses proliferation and tumorigenesis of BRAFi-resistant melanoma cells, promoting clusters of CD8+ T cells infiltration and cancer cells killing. Our findings point to targeting AR as possible co-therapeutical approach in melanoma treatment.
FGFR2 is essential for salivary gland duct homeostasis and MAPK-dependent seromucous acinar cell differentiation
Authors: Aure Marit H. , Symonds Jennifer M. , Villapudua Carlos U. , Dodge Joshua T. , Werner Sabine , Knosp Wendy M. , Hoffman Matthew P. 
Published: October 2023

AbstractExocrine acinar cells in salivary glands (SG) are critical for oral health and loss of functional acinar cells is a major clinical challenge. Fibroblast growth factor receptors (FGFR) are essential for early development of multiple organs, including SG. However, the role of FGFR signaling in specific populations later in development and during acinar differentiation are unknown. Here, we use scRNAseq and conditional deletion of murine FGFRs in vivo to identify essential roles for FGFRs in craniofacial, early SG development and progenitor function during duct homeostasis. Importantly, we also discover that FGFR2 via MAPK signaling is critical for seromucous acinar differentiation and secretory gene expression, while FGFR1 is dispensable. We show that FGF7, expressed by myoepithelial cells (MEC), activates the FGFR2-dependent seromucous transcriptional program. Here, we propose a model where MEC-derived FGF7 drives seromucous acinar differentiation, providing a rationale for targeting FGFR2 signaling in regenerative therapies to restore acinar function.
Finite-temperature critical behaviors in 2D long-range quantum Heisenberg model
Authors: Zhao Jiarui , Song Menghan , Qi Yang , Rong Junchen , Meng Zi Yang 
Published: October 2023

AbstractThe Mermin-Wagner theorem states that spontaneous continuous symmetry breaking is prohibited in systems with short-range interactions at spatial dimensionD ≤ 2. For long-range interactions with a power-law form (1/rα), the theorem further forbids ferromagnetic or antiferromagnetic order at finite temperature whenα ≥ 2D. However, the situation forα ∈ (2, 4) atD = 2 is not covered by the theorem. To address this, we conduct large-scale quantum Monte Carlo simulations and field theoretical analysis. Our findings show spontaneous breaking ofSU(2) symmetry in the ferromagnetic Heisenberg model with 1/rα-form long-range interactions atD = 2. We determine critical exponents through finite-size analysis forα < 3 (above the upper critical dimension with Gaussian fixed point) and 3 ≤ α < 4 (below the upper critical dimension with non-Gaussian fixed point). These results reveal new critical behaviors in 2D long-range Heisenberg models, encouraging further experimental studies of quantum materials with long-range interactions beyond the Mermin-Wagner theorem’s scope.
Spatially localised expression of the glutamate decarboxylase gadB in Escherichia coli O157:H7 microcolonies in hydrogel matrices
Authors: Saint Martin Cédric , Caccia Nelly , Darsonval Maud , Gregoire Marina , Combeau Arthur , Jubelin Grégory , Dubois-Brissonnet Florence , Leroy Sabine , Briandet Romain , Desvaux Mickaël 
Published: October 2023

AbstractFunctional diversity within isogenic spatially organised bacterial populations has been shown to trigger emergent community properties such as stress tolerance. Considering gadB gene encoding a key glutamate decarboxylase involved in E. coli tolerance to acidic conditions, we investigated its expression in hydrogels mimicking the texture of some structured food matrices (such as minced meat or soft cheese). Taking advantage of confocal laser scanning microscopy combined with a genetically-engineered dual fluorescent reporter system, it was possible to visualise the spatial patterns of bacterial gene expression from in-gel microcolonies. In E. coli O157:H7 microcolonies, gadB showed radically different expression patterns between neutral (pH 7) or acidic (pH 5) hydrogels. Differential spatial expression was determined in acidic hydrogels with a strong expression of gadB at the microcolony periphery. Strikingly, very similar spatial patterns of gadB expression were further observed for E. coli O157:H7 grown in the presence of L. lactis. Considering the ingestion of contaminated foodstuff, survival of E. coli O157:H7 to acidic stomachal stress (pH 2) was significantly increased for bacterial cells grown in microcolonies in acidic hydrogels compared to planktonic cells. These findings have significant implications for risk assessment and public health as they highlight inherent differences in bacterial physiology and virulence between liquid and structured food products. The contrasting characteristics observed underscore the need to consider the distinct challenges posed by these food types, thereby emphasising the importance of tailored risk mitigation strategies.
Assessment of Surgical Tasks Using Neuroimaging Dataset (ASTaUND)
Authors: Kamat Anil , Eastmond Condell , Gao Yuanyuan , Nemani Arun , Yanik Erim , Cavuoto Lora , Hackett Matthew , Norfleet Jack , Schwaitzberg Steven , De Suvranu , Intes Xavier 
Published: October 2023

AbstractFunctional near-infrared spectroscopy (fNIRS) is a neuroimaging tool for studying brain activity in mobile subjects. Open-access fNIRS datasets are limited to simple and/or motion-restricted tasks. Here, we report a fNIRS dataset acquired on mobile subjects performing Fundamentals of Laparoscopic Surgery (FLS) tasks in a laboratory environment. Demonstrating competency in the FLS tasks is a prerequisite for board certification in general surgery in the United States. The ASTaUND data set was acquired over four different studies. We provide the relevant information about the hardware, FLS task execution protocols, and subject demographics to facilitate the use of this open-access data set. We also provide the concurrent FLS scores, a quantitative metric for surgical skill assessment developed by the FLS committee. This data set is expected to support the growing field of assessing surgical skills via neuroimaging data and provide an example of data processing pipeline for use in realistic, non-restrictive environments.
Dynamic changes in the transcriptome of tRNA-derived small RNAs related with fat metabolism
Authors: Liao Tianci , Gan Mailin , Lei Yuhang , Wang Yan , Chen Lei , Shen Linyuan , Zhu Li 
Published: October 2023

AbstractThe prevalence of obesity and overweight is steadily rising, posing a significant global challenge for humanity. The fundamental cause of obesity and overweight lies in the abnormal accumulation of adipose tissue. While numerous regulatory factors related to fat deposition have been identified in previous studies, a considerable number of regulatory mechanisms remain unknown. tRNA-derived small RNAs (tsRNAs), a novel class of non-coding RNAs, have emerged as significant regulators in various biological processes. In this study, we obtained small RNA sequencing data from subcutaneous white adipose tissue and omental white adipose tissue of lean and obese pigs. In addition, we similarly obtained tsRNAs profiles from scapular brown adipose tissue (BAT), inguinal white adipose tissue (iWAT) and epigonadal white adipose tissue (eWAT) of normal mice. Finally, we successfully identified a large number of expressed tsRNAs in each tissue type and identified tsRNAs conserved in different adipose tissues of pigs and mice. These datasets will be a valuable resource for elucidating the epigenetic mechanisms of fat deposition.
Zaxinone mimics (MiZax) efficiently promote growth and production of potato and strawberry plants under desert climate conditions
Authors: Wang Jian You , Jamil Muhammad , AlOtaibi Turki S. , Abdelaziz Mohamed E. , Ota Tsuyoshi , Ibrahim Omer H. , Berqdar Lamis , Asami Tadao , Ahmed Mousa Magdi Ali , Al-Babili Salim 
Published: October 2023

AbstractClimate changes and the rapid expanding human population have become critical concerns for global food security. One of the promising solutions is the employment of plant growth regulators (PGRs) for increasing crop yield and overcoming adverse growth conditions, such as desert climate. Recently, the apocarotenoid zaxinone and its two mimics (MiZax3 and MiZax5) have shown a promising growth-promoting activity in cereals and vegetable crops under greenhouse and field conditions. Herein, we further investigated the effect of MiZax3 and MiZax5, at different concentrations (5 and 10 µM in 2021; 2.5 and 5 µM in 2022), on the growth and yield of the two valuable vegetable crops, potato and strawberry, in the Kingdom of Saudi of Arabia. Application of both MiZax significantly increased plant agronomic traits, yield components and total yield, in five independent field trials from 2021 to 2022. Remarkably, the amount of applied MiZax was far less than humic acid, a widely applied commercial compound used here for comparison. Hence, our results indicate that MiZax are very promising PGRs that can be applied to promote the growth and yield of vegetable crops even under desert conditions and at relatively low concentrations.
A nomogram for predicting severe myelosuppression in small cell lung cancer patients following the first-line chemotherapy
Authors: Li Yaoyuan , Bao Yanju , Zheng Honggang , Qin Yinggang , Hua Baojin 
Published: October 2023

AbstractThis study aimed at establishing and validating a nomogram to predict the probability of severe myelosuppression in small cell lung cancer (SCLC) patients following the first-line chemotherapy. A total of 179 SCLC cases were screened as the training group and another 124 patients were used for the validation group. Predictors were determined by the smallest Akaike’s information criterion (AIC) in multivariate logistic regression analysis, leading to a new nomogram. The nomogram was validated in both training and validation groups and the predicting value was evaluated by area under the receiver operating characteristics (ROC) curve (AUC), calibration curve, and decision curve analysis (DCA). Age and tumor staging were extracted as predictors to establish a nomogram, which displayed the AUC values as 0.725 and 0.727 in the training and validation groups, respectively. This nomogram exhibited acceptable calibration curves in the two groups and its prediction added more net benefits than the treat-all scheme and treat-none scheme if the range of threshold probability in the DCA was between 15 and 60% in the training and validation groups. Therefore, the nomogram objectively and accurately predict the occurrence of severe myelosuppression in SCLC patients following the first-line chemotherapy.
A multivariate twin study of the genetic association between present moment attention and subjective wellbeing
Authors: Brown Kirk Warren , Aliev Fazil , Eley Thalia C. , Dick Danielle M. , Sawyers Chelsea 
Published: October 2023

AbstractConsiderable evidence supports the role of present-moment attention, a central feature of mindfulness, in subjective wellbeing maintenance and enhancement. Yet it is not clear why such a relation exists. This study examined the genetic and environmental contributions of present-moment attention to subjective wellbeing. Consistent with the “generalist genes hypothesis” and prior evidence, we hypothesized that presence and subjective wellbeing would show a substantial genetic correlation and smaller environmental correlation. Using a large epidemiological sample of healthy 16-year-old twins in the United Kingdom (N = 1136 monozygotic (MZ) and dizygotic (DZ) twin pairs), genetic overlap was found between presence and the cognitive component of subjective wellbeing (life satisfaction), and to a lesser extent, the affective component of subjective wellbeing (operationalized as happiness). The non-shared environmental overlap between these constructs was substantial. This study provides the first evidence known to us showing that present-centered attention, a primary component of mindfulness, has both genetic and environmental overlap with subjective wellbeing. The findings have implications for understanding mechanisms by which presence is associated with positive emotions and life satisfaction, and suggest, pending additional research, that mindfulness-based interventions to enhance wellbeing may be best suited to those with a genetic propensity toward mindful presence.
Electrocardiographic changes during sustained normobaric hypoxia in patients after myocardial infarction
Authors: Kramer Tilmann , Hoenemann Jan-Niklas , Weis Henning , Hoffmann Fabian , Rosenkranz Stephan , Baldus Stephan , Hellmich Martin , Levine Benjamin D. , Jordan Jens , Tank Jens , Limper Ulrich 
Published: October 2023

AbstractThe safety of prolonged high-altitude stays and exercise for physically fit post-myocardial infarction (MI) patients is unclear. Myocardial tissue hypoxia and pulmonary hypertension can affect cardiac function and electrophysiology, possibly contributing to arrhythmias. We included four non-professional male athletes, clinically stable after left ventricular MI (three with ST-segment elevation MI and one with non-ST-segment elevation MI) treated with drug-eluting stents for single-vessel coronary artery disease. Oxygen levels were reduced to a minimum of 11.8%, then restored to 20.9%. We conducted electrocardiography (ECG), ergometry, and echocardiography assessments in normoxic and hypoxic conditions. With an average age of 57.8 ± 3.3 years and MI history 37 to 104 months prior, participants experienced a significant increase in QTc intervals during hypoxia using Bazett’s (from 402 ± 13 to 417 ± 25 ms), Fridericia’s (from 409 ± 12 to 419 ± 19 ms), and Holzmann's formulas (from 103 ± 4 to 107 ± 6%) compared to normoxia. This effect partially reversed during recovery. Echocardiographic signs of pulmonary hypertension during normobaric hypoxia correlated significantly with altered QTc intervals (p < 0.001). Despite good health and complete revascularization following MI, susceptibility to hypoxia-induced QTc prolongation and ventricular ectopic beats persists, especially during physical activity. MI survivors planning high-altitude activities should consult cardiovascular specialists with high-altitude medicine expertise.
Effects of renin–angiotensin inhibitors on renal function and the clinical course in patients with decompensated cirrhosis
Authors: Tergast Tammo L. , Griemsmann Marie , Wedemeyer Heiner , Cornberg Markus , Maasoumy Benjamin 
Published: October 2023

AbstractPatients with decompensated cirrhosis are at risk of developing acute kidney injury (AKI). Studies have suggested that inhibition of the Renin-Angiotensin System (RAS) has certain nephro- and hepatoprotective effects in patients with compensated liver disease. This study aimed to investigate the clinical impact of RAS-Inhibitors in individuals with decompensated liver cirrhosis. Overall, 1181 consecutive hospitalized patients with ascites that underwent paracentesis were considered for this retrospective study. In total, 667 patients with decompensated cirrhosis fulfilled the inclusion criteria and were finally analyzed. RAS-Inhibitor intake was documented in 41 patients (7%). First, 28-day incidences of AKI and grade III AKI of all patients with RAS-Inhibitors were compared to those without intake. Afterwards, propensity score matching was conducted in a 3:1 manner. Here, incidence of further renal endpoints such as need of hemodialysis were analyzed in detail. In the unmatched setting, intake of RAS-Inhibitors was not associated with an increased 28 day-incidence of AKI (P = 0.76) or LTx-free survival (P = 0.60). However, 28 day-incidence of grade III AKI was significantly lower in patients with RAS-Inhibitor intake (P < 0.001). In the matched setting, 28 day-incidence of AKI did not differ (P = 0.81), while grade III AKI was significantly less frequent in the RAS-Inhibitor group (P < 0.001). Need for hemodialysis was also significantly lower in patients with RAS-Inhibitors (P = 0.03) and LTx-free survival was comparable between both groups (P = 0.52). Thus, this study suggests that intake of RAS-Inhibitors is associated with decreased incidences of grade III AKI and need of hemodialysis in patients with decompensated liver disease.
Crustal structure and seismic anisotropy of rift basins in Somaliland
Authors: Ali Mohammed Y. , Ismaiel Mohammad , Yusuf Ibrahim M. , Kaviani Ayoub 
Published: October 2023

AbstractRift margins provide insights into the processes governing the rupture of the continental lithosphere and the subsequence formation of sedimentary basins. The Proterozoic basement underlying Somaliland has been affected by multiple rifting; however, the crustal structure of these rifted basins remains unknown. This study utilized teleseismic receiver function analysis, Bayesian inversion, common conversion point imaging and 2D forward gravity modelling to examine the crust and upper mantle of Somaliland. The results indicate 36.8–38.2 km of crust in southern Somaliland, while the central and northern regions feature thinned crust (~ 21 km) with 5–6 km thick sediments. The joint analysis of radial and transverse components of receiver functions and shear wave splitting revealed fast axis directions trending to 50–56° in the upper mantle, indicating that azimuthal anisotropy is oriented in the regional Africa-Arabia plate motion. Such orientation may have resulted from lattice preferred orientation of olivine from the asthenospheric flow. Additionally, the fast polarization of the crust in central Somaliland is oriented at − 15°, indicating fossil deformation in the thinned crust related to the NW–SE trending Late Jurassic rift event. Further, the fast polarization for stations near the Gulf of Aden is oriented at 75–80°, suggesting crustal deformation associated with the Oligocene rift event. The crustal anisotropy at southern Somaliland revealed fast polarization oriented at − 85°, indicating a preserved far-field response of the WNW-ESE trending Late Cretaceous rift event. Overall, the study provides for the first-time insight into the rift-related extensional strain fabric in the crust and upper mantle anisotropy induced by asthenospheric flow in Somaliland.
Improved prediction of radiation-induced hypothyroidism in nasopharyngeal carcinoma using pre-treatment CT radiomics
Authors: Ritlumlert Napat , Wongwattananard Siriporn , Prayongrat Anussara , Oonsiri Sornjarod , Kitpanit Sarin , Kannarunimit Danita , Chakkabat Chakkapong , Lertbutsayanukul Chawalit , Sriswasdi Sira , Rakvongthai Yothin 
Published: October 2023

AbstractWhen planning radiation therapy, late effects due to the treatment should be considered. One of the most common complications of head and neck radiation therapy is hypothyroidism. Although clinical and dosimetric data are routinely used to assess the risk of hypothyroidism after radiation, the outcome is still unsatisfactory. Medical imaging can provide additional information that improves the prediction of hypothyroidism. In this study, pre-treatment computed tomography (CT) radiomics features of the thyroid gland were combined with clinical and dosimetric data from 220 participants to predict the occurrence of hypothyroidism within 2 years after radiation therapy. The findings demonstrated that the addition of CT radiomics consistently and significantly improves upon conventional model, achieving the highest area under the receiver operating characteristic curve (AUCs) of 0.81 ± 0.06 with a random forest model. Hence, pre-treatment thyroid CT imaging provides useful information that have the potential to improve the ability to predict hypothyroidism after nasopharyngeal radiation therapy.
Association of rs2073618 polymorphism and osteoprotegerin levels with hypertension and cardiovascular risks in patients with type 2 diabetes mellitus
Authors: Sailaja A. Naga , Nanda Nivedita , Suryanarayana B. S. , Pal G. K. 
Published: October 2023

AbstractThere are reports of link of osteoprotegerin (OPG) gene polymorphism to type-2 diabetes (T2D) and hypertension (HTN). The objective of the study was to assess the allele frequency of OPG (rs2073618) gene polymorphism and its association with heart rate variability (HRV) and blood pressure variability profile as CVD risks in diabetes mellitus patients with hypertension undergoing treatment. T2D patients on treatment without hypertension (n = 172), with hypertension (n = 177) and 191 healthy volunteers were recruited for the study. Their blood pressure variability including baroreflex sensitivity (BRS), heart rate variability (HRV), OPG, insulin, lipid profile, receptor-activator for NFkB (RANK), receptor-activator for NFkB-Ligand (RANKL), and tumor necrosis factor-α (TNF-α) were estimated. Allele frequency of OPG (rs2073618) gene polymorphism was assessed from the DNA samples. BRS and HRV indices were decreased, and RANKL/OPG and TNF-α were increased in T2D and T2D + HTN groups, respectively compared to healthy control group. The reduction in BRS was contributed by increased inflammation and reduced SDNN of HRV in GG genotype in T2D + HTN. In GG + GC subgroup, it was additionally contributed by rise in RANKL/OPG level (β − 0.219;p0.008). Presence of mutant GG genotype contributed to the risk of hypertension among T2D patients (OR 3.004) as well as in general population (OR 2.79). It was concluded that CV risks are more in T2D patients with HTN expressing OPG rs2073618 gene polymorphism.