bluuebunny/crossref_metadata_2025 huggingface dataset:
Gray level co-occurrence matrix and wavelet analyses reveal discrete changes in proximal tubule cell nuclei after mild acute kidney injury
Authors: Pantic Igor , Cumic Jelena , Dugalic Stefan , Petroianu Georg A. , Corridon Peter R.
Published: March 2023

Acute kidney injury (AKI) relates to an abrupt reduction in renal function resulting from numerous conditions. Morbidity, mortality, and treatment costs related to AKI are relatively high. This condition is strongly associated with damage to proximal tubule cells (PTCs), generating distinct patterns of transcriptional and epigenetic alterations that result in structural changes in the nuclei of this epithelium. To this date, AKI-related nuclear chromatin redistribution in PTCs is poorly understood, and it is unclear whether changes in PTC chromatin patterns can be detected using conventional microscopy during mild AKI, which can progress to more debilitating forms of injury. In recent years, gray level co-occurrence matrix (GLCM) analysis and discrete wavelet transform (DWT) have emerged as potentially valuable methods for identifying discrete structural changes in nuclear chromatin architecture that are not visible during the conventional histopathological exam. Here we present findings indicating that GLCM and DWT methods can be successfully used in nephrology to detect subtle nuclear morphological alterations associated with mild tissue injury demonstrated in rodents by inducing a mild form of AKI through ischemia–reperfusion injury. Our results show that mild ischemic AKI is associated with the reduction of local textural homogeneity of PTC nuclei quantified by GLCM and the increase of nuclear structural heterogeneity indirectly assessed with DWT energy coefficients. This rodent model allowed us to show that mild ischemic AKI is associated with the significant reduction of textural homogeneity of PTC nuclei, indirectly assessed by GLCM indicators and DWT energy coefficients.
Imaging analysis and predictive nomogram construction for degenerative lumbar spondylolisthesis with severe clinical symptom based on propensity score matching
Authors: He Yi , Wang Wei , Zhou Haiting , Huang Xiaojian , Wang Yinguang , Qu Yunkun , Cheng Hao , You Hongbo
Published: March 2023

Intervertebral disc degeneration, local lumbar segmental morphology changes, and atrophy of multifidus muscle have been considered to be associated with degenerative lumbar spondylolisthesis. However, there remains a great deal of controversy. To further investigate their relationship with degenerative lumbar spondylolisthesis, we conducted a retrospective study that included 67 patients with degenerative spondylolisthesis and 182 control subjects. Propensity score matching was employed to match the case group and the control group. Disc height was evaluated by the anterior disc height index (DHIA) and posterior disc height index (DHIP). Local lumbar segmental morphology was assessed by segmental lordosis (SL). The fatty infiltration and atrophy of multifidus muscle was evaluated by multifidus muscle net content (MFNC). Our results indicate that DHIA, DHIP, SL, and MFNC in the case group were significantly lower than in the control group. Furthermore, the DHIA, DHIP, and MFNC of the slipped segment (L4/5) were lower than those of the non-slipped segment (L3/4). Correlation analysis showed a high relationship between DHIA and MFNC and the degree of degenerative lumbar spondylolisthesis. Logistic regression analysis revealed that DHIA and MFNC might act as protective factors against the development of degenerative lumbar spondylolisthesis. Additionally, a prognostic nomogram was developed and validated to assess the likelihood of patients with severe symptoms requiring surgical intervention.
Novel estimation technique for the carrier-to-noise ratio of wireless medical telemetry using software-defined radio with machine-learning
Authors: Kai Ishida
Published: March 2023

In this study, we developed a novel machine-learning model to estimate the carrier-to-noise ratio (CNR) of wireless medical telemetry (WMT) using time-domain waveform data measured by a low-cost software-defined radio. With automatic estimation of CNR, the management of the electromagnetic environment of WMT can be made easier. Therefore, we proposed a machine-learning method for estimating CNR. According to the performance evaluation results by 5-segment cross-validation on 704 types of measured data, CNR was estimated with 99.5% R-square and 0.844 dB mean absolute error using a gradient boosting regression tree. The gradient boosting decision tree classifiers predicted if the CNR exceeded 30 dB with 99.5% accuracy. The proposed method is effective for investigating electromagnetic environments in clinical settings.
Comprehensive pan-cancer analysis of STAT3 as a prognostic and immunological biomarker
Authors: He Zhibo , Song Biao , Zhu Manling , Liu Jun
Published: March 2023

Numerous studies have indicated that STAT3 plays a key role in promoting oncogenesis and it is considered a potential therapeutic target for cancer treatment; however, there are no reports on STAT3 using pan-cancer analysis. Therefore, it is important to investigate the role of STAT3 in different types of tumors using pan-cancer analysis. In the present study, we used multiple databases to comprehensively analyze the relationship between STAT3 expression and prognosis, different stages of patients with cancer, investigate the clinical value of STAT3 in predicting prognosis, and the relationship between STAT3 genetic alteration and prognosis, drug sensitivity, and STAT3 expression, to determine whether STAT3 participates in tumor immunity, to provide a rationale for STAT3 as a treatment target for a broad-spectrum malignancies. Our results indicate that STAT3 can serve as a prognostic, sensitivity prediction biomarker and a target for immunotherapy, which has been of great value for pan-cancer treatment. Overall, we found that STAT3 significantly predicted cancer prognosis, drug resistance, and immunotherapy, providing a rationale for further experimental studies.
Associations of cognitive impairment with self-isolation and access to health and care during the COVID-19 pandemic in England
Authors: Beach Brian , Steel Nicholas , Steptoe Andrew , Zaninotto Paola
Published: March 2023

This research explored experiences across three cognitive function groups (no impairment, mild impairment, and dementia) with respect to shielding (either self-isolating or staying at home), COVID-19 infection, and access to health/care services during the COVID-19 pandemic. Analyses were conducted using data from the English Longitudinal Study of Ageing (ELSA) COVID-19 sub-study collected in 2020. We report bivariate estimates across our outcomes of interest by cognitive function group along with multivariate regression results adjusting for demographic, socioeconomic, geographic, and health characteristics. Rates of shielding were high across all cognitive function groups and three measured time points (April, June/July, and Nov/Dec 2020), ranging from 74.6% (95% confidence interval 72.9–76.2) for no impairment in Nov/Dec to 96.7% (92.0–98.7) for dementia in April (bivariate analysis). 44.1% (33.5–55.3) of those with dementia experienced disruption in access to community health services by June/July compared to 34.9% (33.2–36.7) for no impairment. A higher proportion of those with mild impairment reported hospital-based cancellations in June/July (23.1% (20.1–26.4)) and Nov/Dec (16.3% (13.4–19.7)) than those with no impairment (18.0% (16.6–19.4) and 11.7% (10.6–12.9)). Multivariate adjusted models found that those with dementia were 2.4 (1.1–5.0) times more likely than those with no impairment to be shielding in June/July. All other multivariate analyses found no statistically significant differences between cognitive function groups. People with dementia were more likely than people with no impairment to be shielding early in the pandemic, but importantly they were no more likely to experience disruption to services or hospital treatment.
Mitochondrion-targeted antioxidant SkQ1 prevents rapid animal death caused by highly diverse shocks
Authors: Skulachev V. P. , Vyssokikh M. Yu. , Chernyak B. V. , Averina O. A. , Andreev-Andrievskiy A. A. , Zinovkin R. A. , Lyamzaev K. G. , Marey M. V. , Egorov M. V. , Frolova O. J. , Zorov D. B. , Skulachev M. V. , Sadovnichii V. A.
Published: March 2023

The response to stress involves the activation of pathways leading either to protection from the stress origin, eventually resulting in development of stress resistance, or activation of the rapid death of the organism. Here we hypothesize that mitochondrial reactive oxygen species (mtROS) play a key role in stress-induced programmed death of the organism, which we called “phenoptosis” in 1997. We demonstrate that the synthetic mitochondria-targeted antioxidant SkQ1 (which specifically abolishes mtROS) prevents rapid death of mice caused by four mechanistically very different shocks: (a) bacterial lipopolysaccharide (LPS) shock, (b) shock in response to intravenous mitochondrial injection, (c) cold shock, and (d) toxic shock caused by the penetrating cation C12TPP. Importantly, under all these stresses mortality was associated with a strong elevation of the levels of pro-inflammatory cytokines and administration of SkQ1 was able to switch off the cytokine storms. Since the main effect of SkQ1 is the neutralization of mtROS, this study provides evidence for the role of mtROS in the activation of innate immune responses mediating stress-induced death of the organism. We propose that SkQ1 may be used clinically to support patients in critical conditions, such as septic shock, extensive trauma, cooling, and severe infection by bacteria or viruses.
IntelliSleepScorer, a software package with a graphic user interface for automated sleep stage scoring in mice based on a light gradient boosting machine algorithm
Authors: Wang Lei A. , Kern Ryan , Yu Eunah , Choi Soonwook , Pan Jen Q.
Published: March 2023

Machine learning has been applied in recent years to categorize sleep stages (NREM, REM, and wake) using electroencephalogram (EEG) recordings; however, a well-validated sleep scoring automatic pipeline in rodent research is still not publicly available. Here, we present IntelliSleepScorer, a software package with a graphic user interface to score sleep stages automatically in mice. IntelliSleepScorer uses the light gradient boosting machine (LightGBM) to score sleep stages for each epoch of recordings. We developed LightGBM models using a large cohort of data, which consisted of 5776 h of sleep EEG and electromyogram (EMG) signals across 519 unique recordings from 124 mice. The LightGBM model achieved an overall accuracy of 95.2% and a Cohen’s kappa of 0.91, which outperforms the baseline models such as the logistic regression model (accuracy = 93.3%, kappa = 0.88) and the random forest model (accuracy = 94.3%, kappa = 0.89). The overall performance of the LightGBM model as well as the performance across different sleep stages are on par with that of the human experts. Most importantly, we validated the generalizability of the LightGBM models: (1) The LightGBM model performed well on two publicly available, independent datasets (kappa >  = 0.80), which have different sampling frequency and epoch lengths; (2) The LightGBM model performed well on data recorded at a lower sampling frequency (kappa = 0.90); (3) The performance of the LightGBM model is not affected by the light/dark cycle; and (4) A modified LightGBM model performed well on data containing only one EEG and one EMG electrode (kappa >  = 0.89). Taken together, the LightGBM models offer state-of-the-art performance for automatic sleep stage scoring in mice. Last, we implemented the IntelliSleepScorer software package based on the validated model to provide an out-of-box solution to sleep researchers (available for download at https://sites.broadinstitute.org/pan-lab/resources).
Modeling of land subsidence using GIS-based artificial neural network in Yunlin County, Taiwan
Authors: Ku Cheng-Yu , Liu Chih-Yu
Published: March 2023

In this study, the land subsidence in Yunlin County, Taiwan, was modeled using an artificial neural network (ANN). Maps of the fine-grained soil percentage, average maximum drainage path length, agricultural land use percentage, electricity consumption of wells, and accumulated land subsidence depth were produced through geographic information system spatial analysis for 5607 cells in the study area. An ANN model based on a backpropagation neural network was developed to predict the accumulated land subsidence depth. A comparison of the model predictions with ground-truth leveling survey data indicated that the developed model had high accuracy. Moreover, the developed model was used to investigate the relationship of electricity consumption reduction with reductions in the total area of land with severe subsidence (> 4 cm per year); the relationship was approximately linear. In particular, the optimal results were obtained when decreasing the electricity consumption from 80 to 70% of the current value, with the area of severe land subsidence decreasing by 13.66%.
Effectiveness of high-flow nasal cannulae compared with noninvasive positive-pressure ventilation in preventing reintubation in patients receiving prolonged mechanical ventilation
Authors: Tseng Chi-Wei , Chao Ke-Yun , Wu Hsiu-Li , Lin Chen-Chun , Hsu Han-Shui
Published: March 2023

Many intensive care unit patients who undergo endotracheal extubation experience extubation failure and require reintubation. Because of the high mortality rate associated with reintubation, postextubation respiratory management is crucial, especially for high-risk populations. We conducted the present study to compare the effectiveness of oxygen therapy administered using high-flow nasal cannulae (HFNC) and noninvasive positive pressure ventilation (NIPPV) in preventing reintubation among patients receiving prolonged mechanical ventilation (PMV). This single-center, prospective, unblinded randomized controlled trial was at the respiratory care center (RCC). Participants were randomized to an HFNC group or an NIPPV group (20 patients in each) and received noninvasive respiratory support (NRS) administered using their assigned method. The primary outcome was reintubation within7 days after extubation. None of the patients in the NIPPV group required reintubation, whereas 5 (25%) of the patients in the HFNC group required reintubation (P = 0.047). The 90-day mortality rates of the NIPPV and HFNC groups (four patients [20%] vs. two patients [10%], respectively) did not differ significantly. No significant differences in length of RCC stay, length of hospital stay, time to liberation from NRS, and ventilator-free days at 28-day were identified. The time to event outcome analysis also revealed that the risk of reintubation in the HFNC group was higher than that in the NIPPV group (P = 0.018). Although HFNC is becoming increasingly common as a form of postextubation NRS, HFNC may not be as effective as NIPPV in preventing reintubation among patients who have been receiving PMV for at least 2 weeks. Additional studies evaluating HFNC as an alternative to NIPPV for patients receiving PMV are warranted.

ClinicalTrial.gov ID: NCT04564859; IRB number: 20160901R.

Trial registration: ClinicalTrial.gov (https://clinicaltrials.gov/ct2/show/NCT04564859).
A retrospective study on comparison of clinical characteristics and outcomes of diabetic ketoacidosis patients with and without acute pancreatitis
Authors: Khan Adeel Ahmad , Ata Fateen , Yousaf Zohaib , Aljafar Mohamad Safwan , Seijari Mohammed Najdat , Matarneh Ahmad , Dakkak Bassel , Halabiya Malik , Muthanna Bassam , Maliyakkal Abdul Majeed , Kartha Anand
Published: March 2023

The co-existence of diabetic ketoacidosis (DKA) with acute pancreatitis (AP) is associated with unfavorable clinical outcomes. However, diagnosing AP in DKA patients is challenging and often missed due to overlapping symptoms. The aim of this retrospective observational study was to compare the clinical characteristics and outcomes of patients with concomitant DKA and AP or DKA alone. Data of patients with DKA admitted between January 2015 to August 2021 to four hospitals in Qatar was extracted from the electronic health record (Cerner). American Diabetes Association criteria and Atlanta criteria were used for DKA and AP diagnosis, respectively. Independent T-test or Mann–Whitney U test was used to analyze continuous variables, whereas categorical variables were analyzed via Chi-square or Fischer exact tests as appropriate. Univariate and multivariate logistic regression models were generated to assess the correlations. A p-value of < 0.05 was considered statistically significant. Of 936 patients with DKA, 84 (9.0%) had coexisting AP. AP was most common in the Asian race (66%, p < 0.001). Patients with DKA and AP were older, had higher admission anion-gap, white cell count, hemoglobin (hb), neutrophil/lymphocyte ratio, urea, creatinine, maximum blood glucose during the episode, total cholesterol and triglyceride level (TGL) (p < 0.05). They had a lower admission venous pH and bicarbonate at 6 h. Patients in the DKA with AP group also had a longer length of stay (LOS), DKA duration and a higher rate of ICU admission (p-values ≤ 0.001). In-hospital mortality, 3-month all-cause readmission, 6-month and 12-month DKA recurrence did not differ between the two groups. Univariate logistic regression analysis showed age, Asian ethnicity, male gender, T2D, admission WBC count, hb, urea, creatinine, potassium, venous pH, bicarbonate, anion gap, total cholesterol, TGL and LDL level were significantly associated with the development of DKA with AP (p < 0.05). In multivariate logistic regression analysis, age and total cholesterol level were associated with concomitant DKA and AP (p < 0.05). Patients with concomitant DKA and AP have more severe derangement in markers of DKA severity, inflammation, kidney injury and metabolic profile, along with a longer DKA duration, LOS and requirement for ICU support compared to DKA patients without AP. This highlights the clinical significance of diagnosing the co-existence of DKA with AP, as the combination results in significantly worse clinical outcomes and greater healthcare utilization than in patients with only DKA.
Effect of redroot pigweed interference on antioxidant enzyme and light response of common bean (Phaseolus vulgaris L.) depends on cultivars and growth stages
Authors: Tabatabaiepour Seyede Zahra , Tahmasebi Zahra , Taab Alireza , Rashidi-Monfared Sajad
Published: March 2023

Redroot Pigweed (Amaranthus retroflexus L.) is an important weed that is highly competitive with common bean. Photosynthetic pigments, the activity of antioxidant enzymes, the relative expression of a number of antioxidant enzyme and light response genes, were studied in three of common bean cultivars and in V4 and R7 stages under Redroot Pigweed free and infested. The presence of weeds reduced the content of chlorophyll, relative chlorophyll and anthocyanin of common bean leaves. With the increase of weed competition, the expression of antioxidant genes and enzymes increased, which indicates the increase of their activity in order to reduce the amount of reactive oxygen species. Among the studied antioxidant enzymes, the activity of catalase and ascorbate peroxidase produced in the leaves was higher than that of superoxide dismutase. With the increase of weed interference, the expression of phytochrome interacting factor 3 (PIF3) gene as a positive regulator of light signals is increased and the expression of phytochrome rapidly regulated1 (PAR1) gene as a negative regulator is decreased. Chlorophyll a/b-binding protein (CAB1) and auxin-responsive protein IAA8 (IAA8) genes also down-regulated with increasing competition. Along with the decrease of CAB expression in the conditions of competition with weeds, the chlorophyll a, b content also decreased. Correlation between gene expression and physiological traits related to them highlights the prominent role of CWCP in maintaining yield potential.
New evidence for regional pastoral practice and social complexity in the Eastern Tianshan Mountains in the first millennium BCE
Authors: Wang Yuxuan , Monteith Francesca , Xi Tongyuan , Ren Meng , Li Daren , Hu Songmei , Wang Jianxin , Festa Marcella , Ma Jian
Published: March 2023

Mobile pastoralism was a key lifeway in the Late Bronze and Iron Age of Northwest China and played a crucial role in the regional socio-cultural development, as well as the formation of transregional networks. In this paper we analyse the complete faunal assemblage from House F2 in Shirenzigou, on the Eastern Tianshan Mountains, in combination with radiocarbon dating and spatial analysis, to explore local animal resources exploitation strategies and related socio-economic implications. Our results show an intensive multipurpose caprine management, while the exploitation of other domestic taxa, cattle, horses and dogs, was limited. This pastoral economy was supplemented with some hunting. The differentiated use of space in F2 indicates that basic domestic tasks were carried out in the structure, however its position within the landscape and the predominance of bone tools related to warfare and socialization activities, suggests that it was not an ordinary dwelling, it may also have served as a watch post for the summer encampment within the gully. Our findings constitute an important contribution on the discussion on animal resources exploitation strategies and their relationship with evolving socio-economic complexity in the Eastern Tianshan region in the late first millennium BCE.
Spectrochemical approach combined with symptoms data to diagnose fibromyalgia through paper spray ionization mass spectrometry (PSI-MS) and multivariate classification
Authors: Alves Marcelo V. S. , Maciel Lanaia I. L. , Passos João O. S. , Morais Camilo L. M. , dos Santos Marfran C. D. , Lima Leomir A. S. , Vaz Boniek G. , Pegado Rodrigo , Lima Kássio M. G.
Published: March 2023

This study performs a chemical investigation of blood plasma samples from patients with and without fibromyalgia, combined with some of the symptoms and their levels of intensity used in the diagnosis of this disease. The symptoms evaluated were: visual analogue pain scale (VAS); fibromyalgia impact questionnaire (FIQ); Hamilton anxiety rating scale (HAM); Tampa Scale for Kinesiophobia (TAMPA); quality of life Questionnaire—physical and mental health (QL); and Pain Catastrophizing Scale (CAT). Plasma samples were analyzed by paper spray ionization mass spectrometry (PSI-MS). Spectral data were organized into datasets and related to each of the symptoms measured. The datasets were submitted to multivariate classification using supervised models such as principal component analysis with linear discriminant analysis (PCA-LDA), successive projections algorithm with linear discriminant analysis (SPA-LDA), genetic algorithm with linear discriminant analysis (GA-LDA) and their versions with quadratic discriminant analysis (PCA/SPA/GA-QDA) and support vector machines (PCA/SPA/GA-SVM). These algorithm combinations were performed aiming the best class separation. Good discrimination between the controls and fibromyalgia samples were observed using PCA-LDA, where the spectral data associated with the CAT symptom achieved 100% classification sensitivity, and associated with the VAS symptom achieved 100% classification specificity, with both symptoms at the moderate level of intensity. The spectral variable at 579 m/z was found to be substantially significant for classification according to the PCA loadings. According to the human metabolites database, this variable can be associated with a LysoPC compound, which comprises a class of metabolites already evidenced in other studies for fibromyalgia diagnosis. This study proposed an investigation of spectral data combined with clinical data to compare the classification ability of different datasets. The good classification results obtained confirm this technique is as a good analytical tool for the detection of fibromyalgia, and provides theoretical support for other studies about fibromyalgia diagnosis.
Physiological responses of three field-grown species (Ceratonia siliqua, Eucalyptus camaldulensis, and Moringa oleifera) to water deficits in a Mediterranean semi-arid climate
Authors: Ezzine Hasna , Metougui Mohamed Louay , Boukcim Hassan , Abbas Younes
Published: March 2023

Reforestation of degraded drylands calls for the selection of species with the capacity to withstand water scarcity. In this current study we have assessed, the physiological responses of three field-grown species (Ceratonia siliqua, Eucalyptus camaldulensis and Moringa oleifera) to water deficits in semi-arid regions in order to suggest a potential species for rehabilitation programs. The physiological behavior of the given species was studied in three irrigation schemes: subsurface drip irrigation (applied weekly), tank irrigation (applied monthly), and unirrigated plants. In a stressed state, an assessment of relative water content (RWC), water potential (pre-dawn water potential PWP and midday water potential MWP) and stomatal conductance revealed three contrasting physiological responses. First, C. siliqua stomata remained open with a high RWC at low water potentials. Consequently, this species tolerated water deficits by decreasing its leaf water potential, primarily associated with osmotic adjustment. On the other hand, E. camaldulensis was found to be a drought-avoider species, mutated to a water-saving strategy by complete stomatal closure. Finally, for the extreme case, M. oleifera showed leaf shedding under water deficit conditions. These different physiological responses allowed these species to survive water deficits, and consequently, could be considered suitable candidates for rehabilitating degraded semi-arid areas.
Characteristics and varieties of gases enclathrated in natural gas hydrates retrieved at Lake Baikal
Authors: Hachikubo Akihiro , Minami Hirotsugu , Sakagami Hirotoshi , Yamashita Satoshi , Krylov Alexey , Kalmychkov Gennadiy , Poort Jeffrey , De Batist Marc , Manakov Andrey , Khlystov Oleg
Published: March 2023

Molecular and stable isotope compositions of hydrate-bound gases collected from 59 hydrate-bearing sites between 2005 to 2019 in the southern and central sub-basins of Lake Baikal are reported. The δ2H of the hydrate-bound methane is distributed between − 310‰ and − 270‰, approximately 120‰ lower than its value in the marine environment, due to the difference in δ2H between the lake water and seawater. Hydrate-bound gases originate from microbial (primary and secondary), thermogenic, and mixed gas sources. Gas hydrates with microbial ethane (δ13C: − 60‰, δ2H: between − 310‰ and − 250‰) were retrieved at approximately one-third of the total sites, and their stable isotope compositions were lower than those of thermogenic ethane (δ13C: − 25‰, δ2H: − 210‰). The low δ2H of ethane, which has rarely been reported, suggests for the first time that lake water with low hydrogen isotope ratios affects the formation process of microbial ethane as well as methane. Structure II hydrates containing enclathrated methane and ethane were collected from eight sites. In thermogenic gas, hydrocarbons heavier than ethane are biodegraded, resulting in a unique system of mixed methane-ethane gases. The decomposition and recrystallization of the hydrates that enclathrate methane and ethane resulted in the formation of structure II hydrates due to the enrichment of ethane.
Estimating aspect ratio of the distal femur and proximal tibia in the Emirati population from MRI scans of the knee: a preliminary experience
Authors: Prithishkumar Ivan James , Abdulwahab Taiceer , Mohammad Alshafi , Albelooshi Ali
Published: March 2023

Size and shape of knee implants play an important role in the success of total knee arthroplasty. Several studies have identified anthropometric differences of the distal femur and proximal tibia between the genders and ethnicities. Ill-fitting prosthesis can cause overhang or under-fit resulting in persistence of pain, periprosthetic fracture and decreased range of motion. The purpose of this study was to estimate the aspect ratio of distal femur and proximal tibia in the Emirati population and determine whether gender differences exist within this group. Magnetic resonance imaging datasets of unilateral knees scans performed on adult Emirati patients at a tertiary care hospital were retrospectively examined. Knee parameters were obtained from 65 males and 46 females (n = 111). Females showed significantly smaller AP and ML dimensions of distal femur and lower aspect ratios compared to males (p < 0.001). Proximal tibial dimensions (AP and ML) of Emirati women are also significantly smaller compared to men. However, aspect ratio of proximal tibia did not show gender variation (p = 0.956) within the Emirati population. Emirati knees showed significant gender differences in bony dimensions and aspect ratio of the knee, and also have smaller aspect ratios when compared with most other population groups.
Pan-cancer genomic analysis shows hemizygous PTEN loss tumors are associated with immune evasion and poor outcome
Authors: Vidotto T. , Melo C. M. , Lautert-Dutra W. , Chaves L. P. , Reis R. B. , Squire J. A.
Published: March 2023

In tumors, somatic mutations of the PTEN suppressor gene are associated with advanced disease, chemotherapy resistance, and poor survival. PTEN loss of function may occur by inactivating mutation, by deletion, either affecting one copy (hemizygous loss) leading to reduced gene expression or loss of both copies (homozygous) with expression absent. Various murine models have shown that minor reductions in PTEN protein levels strongly influence tumorigenesis. Most PTEN biomarker assays dichotomize PTEN (i.e. presence vs. absence) ignoring the role of one copy loss. We performed a PTEN copy number analysis of 9793 TCGA cases from 30 different tumor types. There were 419 (4.28%) homozygous and 2484 (25.37%) hemizygous PTEN losses. Hemizygous deletions led to reduced PTEN gene expression, accompanied by increased levels of instability and aneuploidy across tumor genomes. Outcome analysis of the pan-cancer cohort showed that losing one copy of PTEN reduced survival to comparable levels as complete loss, and was associated with transcriptomic changes controlling immune response and the tumor microenvironment. Immune cell abundances were significantly altered for PTEN loss, with changes in head and neck, cervix, stomach, prostate, brain, and colon more evident in hemizygous loss tumors. These data suggest that reduced expression of PTEN in tumors with hemizygous loss leads to tumor progression and influences anticancer immune response pathways.
Epigenetic modification of gene expression in cancer cells by terahertz demethylation
Authors: Cheon Hwayeong , Hur Junho K. , Hwang Woochang , Yang Hee-Jin , Son Joo-Hiuk
Published: March 2023

Terahertz (THz) radiation can affect the degree of DNA methylation, the spectral characteristics of which exist in the terahertz region. DNA methylation is an epigenetic modification in which a methyl (CH3) group is attached to cytosine, a nucleobase in human DNA. Appropriately controlled DNA methylation leads to proper regulation of gene expression. However, abnormal gene expression that departs from controlled genetic transcription through aberrant DNA methylation may occur in cancer or other diseases. In this study, we demonstrate the modification of gene expression in cells by THz demethylation using resonant THz radiation. Using an enzyme-linked immunosorbent assay, we observed changes in the degree of global DNA methylation in the SK-MEL-3 melanoma cell line under irradiation with 1.6-THz radiation with limited spectral bandwidth. Resonant THz radiation demethylated living melanoma cells by 19%, with no significant occurrence of apurinic/apyrimidinic sites, and the demethylation ratio was linearly proportional to the power of THz radiation. THz demethylation downregulates FOS, JUN, and CXCL8 genes, which are involved in cancer and apoptosis pathways. Our results show that THz demethylation has the potential to be a gene expression modifier with promising applications in cancer treatment.
Microwave demonstration of Purcell effect enhanced radiation efficiency
Authors: Stanfield L. D. , Powell A. W. , Horsley S. A. R. , Sambles J. R. , Hibbins A. P.
Published: March 2023

We experimentally demonstrate a Purcell effect-based design technique for improved impedance matching, and thus enhanced the reflection coefficient from a small microwave emitter. Using an iterative process centred on comparing the phase of the radiated field of the emitter in air with that of the emitter in a dielectric environment, we optimise the structure of a dielectric hemisphere above a ground plane surrounding a small monopolar microwave emitter in order to maximise its radiation efficiency. The optimised system shows very strong coupling between the emitter and two omnidirectional radiation modes at 1.99 GHz and 2.84 GHz, yielding Purcell enhancement factors of 1762 and 411 times increase respectively, and near perfect radiation efficiency.
Evaluation of local oxygen flux produced by photoelectrochemical hydroxide oxidation by scanning electrochemical microscopy
Authors: Gupta Bhavana , Aziz Ariba , Sundriyal Shashank , Shrivastav Vishal , Melvin Ambrose A. , Holdynski Marcin , Nogala Wojciech
Published: March 2023

Several in-situ electrochemical approaches have been developed for performing a localized photoelectrochemical investigation of the photoanode. One of the techniques is scanning electrochemical microscopy (SECM), which probes local heterogeneous reaction kinetics and fluxes of generated species. In traditional SECM analysis of photocatalysts, evaluation of the influence of radiation on the rate of studied reaction requires an additional dark background experiment. Here, using SECM and an inverted optical microscope, we demonstrate the determination of O2 flux caused by light-driven photoelectrocatalytic water splitting. Photocatalytic signal and dark background are recorded in a single SECM image. We used an indium tin oxide electrode modified with hematite (α-Fe2O3) by electrodeposition as a model sample. The light-driven flux of oxygen is calculated by analysis of SECM image recorded in substrate generation/tip collection mode. In photoelectrochemistry, the qualitative and quantitative knowledge of oxygen evolution will open new doors for understanding the local effects of dopants and hole scavengers in a straightforward and conventional manner.
Effectiveness of a transactional model-based education programme for enhancing stress-coping skills in industrial workers: a randomized controlled trial
Authors: Kaveh Mohammad Hossein , Mehrazin Farnaz , Cousins Rosanna , Mokarami Hamidreza
Published: March 2023

The aim of this study was to examine the effectiveness of a stress management educational intervention programme based on the Transactional Model of Stress and Coping (TMSC) among industrial workers. Participants were 106 employees of a power plant in Iran, randomly assigned into an intervention group and a control group. The intervention comprised active and participatory methods to enhance employees coping skills and it was delivered in six face-to-face sessions. Data was collected using the Ways of Coping Questionnaire, the Multidimensional Scale of Perceived Social Support, the Perceived Stress Scale, and the Spiritual Well-Being Scale at baseline and three months after the intervention. We found mean scores of distancing, self-controlling, seeking social support, escape-avoidance, planned problem-solving, positive reappraisal, total coping skills, perceived social support, and spiritual well-being significantly differed at follow-up compared to baseline in the intervention group, but not in the control group. There was also a significant difference in the mean score of perceived stress between the two groups. We conclude that the educational intervention based on the TMSC was effective in improving coping skills and reducing perceived stress. We suggest that interventions based on the TMSC model can be supportive in workplaces where job stress is common.
Long-term intensive management reduced the soil quality of a Carya dabieshanensis forest
Authors: Huang Cheng , Fu Songling , Ma Xiaomin , Ma Xiaoxiang , Ren Xiaoliang , Tian Xinxin , Tong Yinhao , Yuan Feiyang , Liu Hua
Published: March 2023

The evaluation of soil quality can provide new insights into the sustainable management of forests. This study investigated the effects of three types of forest management intensities (non-management (CK), extensive management (EM), and intensive management (IM)), and five management durations (0, 3, 8, 15, and 20 years) on the soil quality of a Carya dabieshanensis forest. Further, minimum data sets (MDS) and optimized minimum data sets (OMDS) were established to evaluate the soil quality index (SQI). A total of 20 soil indicators representing its physical, chemical, and biological properties were measured for the 0–30 cm layer. Using one-way ANOVA and principal component analysis (PCA), the total data set (TDS), the minimum data set (MDS), and optimized minimum data set (OMDS) were established. The MDS and OMDS contained three (alkali hydrolyzed nitrogen (AN), soil microbial biomass nitrogen (SMBN), and pH) and four (total phosphorus (TP), soil organic carbon (SOC), AN, and bulk density (BD)) soil indicators, respectively. The SQI derived from the OMDS and TDS exhibited a stronger correlation (r = 0.94, p < 0.01), which was suitable for evaluating the soil quality of the C. dabieshanensis forest. The evaluation results revealed that the soil quality was highest during the early stage of intensive management (IM-3), and the SQI of each soil layer was 0.81 ± 0.13, 0.47 ± 0.11, and 0.38 ± 0.07, respectively. With extended management times, the degree of soil acidification increased, and the nutrient content decreased. Compared with the untreated forest land the soil pH, SOC, and TP decreased by 2.64–6.24%, 29.43–33.04%, and 43.63–47.27%, respectively, following 20 years of management, while the SQI of each soil layer decreased to 0.35 ± 0.09, 0.16 ± 0.02 and 0.12 ± 0.06, respectively. In contrast to extensive management, the soil quality deteriorated more rapidly under longer management and intensive supervision. The OMDS established in this study provides a reference for the assessment of soil quality in C. dabieshanensis forests. In addition, it is suggested that the managers of C. dabieshanensis forests should implement measures such as increasing the amount of P-rich organic fertilizer and restoring vegetation to increase soil nutrient resources for the gradual restoration of soil quality.
Early cellular events and potential regulators of cellulase induction in Penicillium janthinellum NCIM 1366
Authors: Christopher Meera , Sreeja-Raju AthiraRaj , Abraham Amith , Gokhale Digambar Vitthal , Pandey Ashok , Sukumaran Rajeev K.
Published: March 2023

Cellulase production by fungi is tightly regulated in response to environmental cues, and understanding this mechanism is a key pre-requisite in the efforts to improve cellulase secretion. Based on UniProt descriptions of secreted Carbohydrate Active enZymes (CAZymes), 13 proteins of the cellulase hyper-producer Penicillium janthinellum NCIM 1366 (PJ-1366) were annotated as cellulases- 4 cellobiohydrolases (CBH), 7 endoglucanases (EG) and 2 beta glucosidases (BGL). Cellulase, xylanase, BGL and peroxidase activities were higher for cultures grown on a combination of cellulose and wheat bran, while EG was stimulated by disaccharides. Docking studies indicated that the most abundant BGL- Bgl2- has different binding sites for the substrate cellobiose and the product glucose, which helps to alleviate feedback inhibition, probably accounting for the low level of glucose tolerance exhibited. Out of the 758 transcription factors (TFs) differentially expressed on cellulose induction, 13 TFs were identified whose binding site frequencies on the promoter regions of the cellulases positively correlated with their abundance in the secretome. Further, correlation analysis of the transcriptional response of these regulators and TF-binding sites on their promoters indicated that cellulase expression is possibly preceded by up-regulation of 12 TFs and down-regulation of 16 TFs, which cumulatively regulate transcription, translation, nutrient metabolism and stress response.
A finite element analysis of different postures and intra-abdominal pressures for the uterine ligaments in maintaining the normal position of uterus
Authors: Chen Jialan , Zhang Junfeng , Wang Fan
Published: March 2023

Uterine prolapse is a common gynecological disease, which seriously affects the quality of life and physical and mental health of elderly women. The aim of this study was to analyze the influence of different conditions (intra-abdominal pressure (IAP) and posture) on stress and displacement of uterine ligaments using the finite element method, and evaluate the contribution of uterine ligaments on uterus. The three-dimensional (3D) models of retroverted uterus and its accessory ligaments were established, loads and constraints were set in ABAQUS software, and the stress and displacement of uterine ligaments were calculated. The uterine displacement increased with the increase of IAP, and then the stress and displacement of each uterine ligament also increased. The uterine displacement was in the order of forward < upright < backward with different postures, and USL, CL and RL got larger values when the body was backward, while BL got a larger value when the body was forward. With the same condition, the stress of the uterine ligaments was in the order of USL > BL > CL > RL, and the displacement of the ligaments was in the order of BL > RL > USL > CL. The contribution of each uterine ligament changing with different IAP and postures was studied through finite element analysis, and the research results were consistent with the clinical data, which can provide a basis for exploring the mechanism of uterine prolapse.
Collateral activity of the CRISPR/RfxCas13d system in human cells
Authors: Shi Peiguo , Murphy Michael R. , Aparicio Alexis O. , Kesner Jordan S. , Fang Zhou , Chen Ziheng , Trehan Aditi , Guo Yang , Wu Xuebing
Published: March 2023

CRISPR/Cas13 systems are increasingly used for programmable targeting of RNAs. While Cas13 nucleases are capable of degrading both target RNAs and bystander RNAs in vitro and in bacteria, initial studies fail to detect collateral degradation of non-target RNAs in eukaryotic cells. Here we show that RfxCas13d, also known as CasRx, a widely used Cas13 system, can cause collateral transcriptome destruction when targeting abundant reporter RNA and endogenous RNAs, resulting in proliferation defect in target cells. While these results call for caution of using RfxCas13d for targeted RNA knockdown, we demonstrated that the collateral activity can be harnessed for selective depletion of a specific cell population defined by a marker RNA in an in vitro setting.
A custom-made AAV1 variant (AAV1-T593K) enables efficient transduction of Japanese quail neurons in vitro and in vivo
Authors: Zoabi Shaden , Andreyanov Michael , Heinrich Ronit , Ron Shaked , Carmi Ido , Gutfreund Yoram , Berlin Shai
Published: March 2023

The widespread use of rodents in neuroscience has prompted the development of optimized viral variants for transduction of brain cells, in vivo. However, many of the viruses developed are less efficient in other model organisms, with birds being among the most resistant to transduction by current viral tools. Resultantly, the use of genetically-encoded tools and methods in avian species is markedly lower than in rodents; likely holding the field back. We sought to bridge this gap by developing custom viruses towards the transduction of brain cells of the Japanese quail. We first develop a protocol for culturing primary neurons and glia from quail embryos, followed by characterization of cultures via immunostaining, single cell mRNA sequencing, patch clamp electrophysiology and calcium imaging. We then leveraged the cultures for the rapid screening of various viruses, only to find that all yielded poor to no infection of cells in vitro. However, few infected neurons were obtained by AAV1 and AAV2. Scrutiny of the sequence of the AAV receptor found in quails led us to rationally design a custom-made AAV variant (AAV1-T593K; AAV1*) that exhibits improved transduction efficiencies in vitro and in vivo (14- and five-fold, respectively). Together, we present unique culturing method, transcriptomic profiles of quail’s brain cells and a custom-tailored AAV1 for transduction of quail neurons in vitro and in vivo.
Machine-learning-powered extraction of molecular diffusivity from single-molecule images for super-resolution mapping
Authors: Park Ha H. , Wang Bowen , Moon Suhong , Jepson Tyler , Xu Ke
Published: March 2023

While critical to biological processes, molecular diffusion is difficult to quantify, and spatial mapping of local diffusivity is even more challenging. Here we report a machine-learning-enabled approach, pixels-to-diffusivity (Pix2D), to directly extract the diffusion coefficient D from single-molecule images, and consequently enable super-resolved D spatial mapping. Working with single-molecule images recorded at a fixed framerate under typical single-molecule localization microscopy (SMLM) conditions, Pix2D exploits the often undesired yet evident motion blur, i.e., the convolution of single-molecule motion trajectory during the frame recording time with the diffraction-limited point spread function (PSF) of the microscope. Whereas the stochastic nature of diffusion imprints diverse diffusion trajectories to different molecules diffusing at the same given D, we construct a convolutional neural network (CNN) model that takes a stack of single-molecule images as the input and evaluates a D-value as the output. We thus validate robust D evaluation and spatial mapping with simulated data, and with experimental data successfully characterize D differences for supported lipid bilayers of different compositions and resolve gel and fluidic phases at the nanoscale.
Rapid and sensitive detection of Staphylococcus aureus via an all-in-one staggered strand exchange amplification platform
Authors: Zhang Jian , Han Xiangning , Wang Ye , Mu Xiaofeng , Shi Chao , Li Yong , Ma Cuiping
Published: March 2023

A staggered strand exchange amplification (SSEA) method was developed by employing a DNA polymerase and two sets of forward and reverse primers arranged in tandem that invade the denaturation bubbles of double-stranded DNA.
Modulated oxygen vacancies in europia clusters/black phosphorus induced signal amplification for efficient chemiluminescence sensing
Authors: Gong Hui , Zhao Dayang , Zhou Yu , Zhou Yuxian , Gou Jing , Liu Houjing
Published: March 2023

In this work, we proposed an oxygen vacancy engineering strategy to boost the chemiluminescence (CL) efficiency in europia clusters/black phosphorus quantum dots (Eu2O3/BPQDs), which could dramatically amplify the NaClO CL emission through electron transfer.
A new computational tool for interpreting the infrared spectra of molecular complexes
Authors: Iglesias-Reguant Alex , Reis Heribert , Medveď Miroslav , Luis Josep M. , Zaleśny Robert
Published: March 2023

A new computational tool enables associating the changes in IR spectra occurring upon complex formation with individual types of intermolecular interactions (electrostatic, exchange, induction, and dispersion).
Infrared action spectroscopy of the deprotonated formic acid trimer, trapped in helium nanodroplets
Authors: Taccone Martín I. , Thomas Daniel A. , Ober Katja , Gewinner Sandy , Schöllkopf Wieland , Meijer Gerard , von Helden Gert
Published: March 2023

Hydrogen bonding interactions are essential in the structural stabilization and physicochemical properties of complex molecular systems, and carboxylic acid functional groups are common participants in these motifs.