bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glycome profiling and immunohistochemistry uncover spaceflight-induced changes in non-cellulosic cell wall components in Arabidopsis thaliana seedling roots
Authors: Blancaflor Elison , Nakashima Jin , Pattathil Sivakumar , Avci Utku , Chin Sabrina , Sparks J. Alan , Hahn Michael , Gilroy Simon 
Published: March 2023

Abstract
A large and diverse library of glycan-directed monoclonal antibodies (mAbs) was used to determine if plant cell walls are modified by low-gravity conditions encountered during spaceflight. This method called glycome profiling (glycomics) revealed global differences in non-cellulosic cell wall epitopes in Arabidopsis thaliana root extracts recovered from RNA purification columns between seedlings grown on the International Space Station-based Vegetable Production System and paired ground (1-g) controls. Immunohistochemistry on 11-day-old seedling primary root sections showed that ten of twenty-two mAbs that exhibited spaceflight-induced increases in binding through glycomics, labeled space-grown roots more intensely than those from the ground. The ten mAbs recognized xyloglucan, xylan, and arabinogalactan epitopes. Notably, three xylem-enriched unsubstituted xylan backbone epitopes were more intensely labeled in space-grown roots than in ground-grown roots, suggesting that the spaceflight environment accelerated root secondary cell wall formation. This study highlights the feasibility of glycomics for high-throughput evaluation of cell wall glycans using only root high alkaline extracts from RNA purification columns, and subsequent validation of these results by immunohistochemistry. This approach will benefit plant space biological studies because it extends the analyses possible from the limited amounts of samples returned from spaceflight and help uncover microgravity-induced tissue-specific changes in plant cell walls.
Investigation of air pollution during COVID-19 pandemic using satellite and on-site measurment data in six provinces in Iran
Authors: Shahne Maryam Zare , Noori Amirhossein , Attar Mehdi Alizadeh 
Published: March 2023

Abstract
Introduction: Iran has been one of the countries with the highest rates of COVID-19 cases, such that over 7 million cases have been recorded for this illness, and more than 140000 people died because of the COVID-19 pandemic up to May 2022 in Iran. Studies have been conducted to investigate the association between exposure to poor air quality and the increasing rate of morbidity and mortality due to COVID-19.
Materials and methods:
In the present study, the temporal variation of Sentinel-5P TROPOMI-derived air pollutants (NO2 and SO2,) and MODIS-derived AOD were examined by using satellite missions in six major air pollution’ hotspots provinces, including Isfahan, Tabriz, Mashhad, Tehran, Ahvaz, and Gilan in Iran for contemporaneous time periods before (as a baseline period and pre-lockdown year), and during the epidemic, including the first wave lockdown period of the COVID-19 outbreak, from the 22nd of February, 2019, to the 22nd of February, 2021. Moreover, the satellite data were compared with field measurements in these periods.
Results: The results revealed that the mean ratio of NO2 and SO2 has not varied drastically in the considered provinces. These column concentration ratios for all months were within the range of +2%(Tehran) to -6% (Tabriz). In comparison, the ratio of variance is more considerable, especially for Gilan province, a tourist attraction province, even in travel restrictions and lockdowns in Iran. The AOD distribution map and its trend illustrated that Gilan, Khorasan-Razavi, and Tabriz had become more pollutants after the outbreak due to changes in tourist patterns and emission inventories. The results have provided a monthly RMSE of 2.5*10-5, 1.4*10-4, and 1.8*10-4, for NOx, SOx, and AOD, respectively.
Base on wavelet transform, implemented on ground-measurment of PM2.5, the PM2.5 concentration increased in early 2021 (especially Februray) from the value in baseline period, due to eased restriction and expansion of public COVID-19 vaccine in all considered provinces.
Conclusions: The results of this study provide helpful insight to air pollution conditions during the COVID-19 pandemic in Iran. It is also could assist air pollution policymakers to plan effective control strategies in a similar situation.
Predicting IDH mutation status as well as Ki-67 and p53 expression in high-grade gliomas using amide proton transfer-weighted and arterial spin labeling MRI
Authors: Chen Ling , Li Yao , Zhang Jinhuan , Li Shuanghong , Huang Lizhao , Tang Lifang , Wu Min , Zhu Li , Zeng Zisan , Li Tao 
Published: March 2023

Abstract
This study aimed to explore the efficiency of APT imaging and ASL perfusion for evaluating IDH mutation status as well as Ki-67 and p53 expression in patients with high-grade gliomas. Sixty patients with newly diagnosed HGGs were retrospectively analyzed. All subjects were divided into IDH mutation subgroups, Ki-67 index subgroups, and p53 expression subgroups based on the pathological results. rAPTw and rCBF values were compared among different molecular types. ROC curve analysis was used to assess the predictive ability of imaging parameters. Our results showed that significant differences in rAPTw and rCBF values were observed between IDH mutation subgroups and Ki-67 expression subgroups. rAPTw and rCBF values showed no significant association with p53 expression. The AUC of rAPTw and rCBF for predicting IDH mutation status were 0.854 and 0.87, respectively; for Ki-67 index, the AUC values were 0.75 and 0.727, respectively. Combined use of rAPTw and rCBF values showed better predictive ability for IDH mutation and Ki-67 expression status compared to their individual predictive ability. In conclusion, APTw and ASL could be valuable MRI biomarkers for identifying IDH mutation status and Ki-67 index in HGGs, but they may not be useful for assessing p53 expression.
Comprehensive analysis of a prognostic immune-related gene signature in esophageal carcinoma predicts disease prognosis and treatment response
Authors: Jiang Chenhao , Ren Yilin , Xue Lele , Li Fanping , Wang Zhe , Zhang Anzhi , Li Ya , Xie Yufang , Li Jiangfen , Yang Kaige , Liang Weihua , Zhang Haijun , Li Man , Yang Lan , Li Feng , Hu Jian Ming 
Published: March 2023

Abstract
Background: Esophageal cancer (EC) is a lethal disease with dismal survival rates. The tumor immune microenvironment plays a key contributor to the poor prognosis of EC. Here, we aimed to identify an immune-associated gene biomarker signature in EC and explore potential therapeutic strategies.
Methods: We combined the publicly available TCGA dataset with qRT-PCR results and constructed an immune-related 3-genemodel related to the survival of patients with EC. Kaplan-Meier survival analysis and time-dependent receiver operating curve (ROC) were then conducted to determine the predictive performance of the model, followed by clinical validation and nomogram establishment using Cox regression analysis. The underlying molecular mechanisms were explored with gene set enrichment analysis and tumor mutational burden (TMB). Finally, the immune microenvironment landscape was described with ESTIMATE and CIBERSORT, and the TIDE algorithm and the pRRophetic package were used to evaluated the model’s ability to predict immunotherapeutic and chemotherapeutic efficacy for different EC patient sub-groups.
Results: We identified a 3-gene signature that significantly associated with poor overall survival in the TCGA and clinical data sets. And the EC samples were divided into the high- and low-risk groups depending on their risk scores. Then, a nomogram was established which included the gene model, clinical stage and positive lymph node metastasis for potential clinical translation. There were significant differences in the tumor immune microenvironment, TMB and metabolic pathways between the two groups. Cell type composition analysis found that M0 Macrophages, CD8 T cell and other immune cells not only have increased abundance in the tumor, but also can be reflected by the model. Additionally, while low-risk patients were found to benefit more from immunotherapy, high-risk patients with a worse prognosis could benefit more from the application of agents such as Bryostatin.1and FH535.
Conclusion: We report a novel gene model which reveals the driving immune-related factors in EC. These factors may act as immunotherapeutic biomarkers and potential therapeutic targets for novel EC treatments.
Projected Climate Extremes over Agro-climatic Zones of Ganga River Basin under 1.5, 2 and 3-degree Global Warming Levels
Authors: Singh Harsh Vardhan , Joshi Nitin , Suryavanshi Shakti 
Published: March 2023

Abstract
In the present study, we have evaluated the extreme precipitation and temperature indices over the 10 agro-climatic zones falling under Ganga River basin (GRB)utilizing a high resolution daily gridded temperature and precipitation multi-model ensembled CMIP6 dataset (0.25°x0.25°) under global warming levels of 1.5°C, 2°C, and 3°C.We found that annual daily minimum temperature(TNN) showing higher rise of about 67% than maximum temperature (TXX)of 48%in GRB. The basin also experiences a greater increase in the frequency of warm nights (TN90P) of about 67.71% compared to warm days (TX90P) of 29.1% for 3°C global warming level.Along with extreme indices, population exposed due to the impact of the extreme maximum temperature has also been analysed for progressive warming levels. Population exposure to extreme temperature event (TXX) has been analysed with 20-year return period using GEV distribution method. The study concludes that exposed population to extreme temperature event experienced an increase from 46.99–52.16% for whole Ganga Basin. Consecutive Dry Days (CDD) and Consecutive Wet Days (CWD) both show a significant increasing trend, but CWD has significant increase in majority of the zones, while CDD show significant decreasing trend for some of the zones for three warming levels periods.Extreme climate indices help to understand the frequency and intensity of the extreme weather events such as heavy rainfall, droughts, heatwaves etc. to develop early warning systems and adaptation strategies to mitigate such events.
PIK3CA Mutational Profiling in a Patient Cohort with HR+/HER2- Advanced Metastatic Breast Cancer at a Tertiary Cancer Center
Authors: ALSMADI OSAMA , Abdel-Razeq Hikmat , Talab Yazan , Abdulelah Hazem , Shaheen Zeena , Tbakhi Abdelghani 
Published: March 2023

Abstract
Common PIK3CA gene activating mutations can be found in 20–30% of all breast cancer cases, and regarded as predictive markers for therapeutic response to PI3K inhibitors. The therascreen PIK3CA mutation companion assay and the alpha-specific PI3K inhibitor, Alpelisib, are FDA-approved for selecting and treating patients with advanced PIK3CA-mutated metastatic breast cancer. The main objective behind this report was to investigate the composition and proportion of PIK3CA mutations using a PIK3CA mutation Therascreen RT-PCR assay, in a patient cohort with receptor-positive/HER2-negative (HR+/HER2) metastatic breast cancer, who were diagnosed and treated at King Hussein Cancer Center (KHCC). Patients with PIK3CA-mutated tumors represented 39.4% (91/231) of all patients. Four PIK3CA mutations comprised 86.8% of all PIK3CA mutations; mainly H1047R (33.3%), E545K (20.9%), E542K (24.2%), and H1047L (8.8%). The four main mutations map to the helical and kinase domains of the PIK3CA encoded protein. C420R was found in only one patient, and E545A was found in two patients. Nine of the 91 mutated patients had shown double PIK3CA mutations (9.9%). In conclusion, PIK3CA is frequently mutated in multiple types of cancers at known ‘Hot-spots’, mainly in the kinase and helical modular domains, which was found consistent with our findings. PIK3CA mutational signature in our metastatic breast cancer cohort varied with a 39.4% (91/231) positivity rate. The PIK3CA mutational screening panel did not capture mutations in the remaining 140 (60.6%) cases; these patients may be mutated in other genes related to breast cancer, or in PIK3CA loci not covered by the Therascreen assay. Survival and clinical outcomes in association with PIK3CA mutational profiles shall be addressed in a follow-up investigation for this patients’ cohort.
Predictive value of renal resistance index on the timing of CRRT weaning in patients with acute kidney injury in ICU
Authors: Zhang Zhuo , Xu Yan , Ma Yibo , Pu Hao , Zhou Shujun , Li Wen 
Published: March 2023

Abstract
Background: Few studies have been undertaken to establish the optimal time for discontinuing continuous renal replacement therapy (CRRT) in individuals with acute kidney injury (AKI). This study aimed to find prospective renal biomarkers or clinical signs that could indicate successful CRRT deconditioning.
Methods： A prospective observational study was carried out on 45 patients wt CRRT who discontinued following renal recovery. When patients did not require CRRT for at least 7 days, they were regarded as successfully discharged. Patients who resumed dialysis within seven days were deemed unsuccessful.
Results: 24 (53.3%) of the 45 patients examined were successfully released from CRRT. The 24-h urine volume after weaning cessation, the renal resistance index (RRI) after cessation, and the creatinine ratio on the day of weaning and the day following weaning were determined to be variables impacting the effectiveness of CRRT cessation in a multivariate model. The RRI AUC-ROC after CRRT discontinuation was 0.872 (0.76 -0.99), and the 24-h urine volume AUC-ROC was 0.929. (0.84-1.00). The AUC-ROC for the 24-h urine volume after CRRT discontinuation was 0.929 (0.84-1.00), and the creatinine ratio on the first day following CRRT cessation vs the day of weaning was 0.643 (0.476-0.810).
Conclusions: RRI was the main risk factor of successful CRRT weaning.
Single-step discovery of high-affinity RNA ligands by UltraSelex
Authors: Zhang Yaqing , Jiang Yuan , Kuster David , Ye Qiwei , Huang Wenhao , Fürbacher Simon , Zhang Jingye , Tang Zhipeng , Ibberson David , Wild Klemens , Sinning Irmgard , Hyman Anthony , Jäschke Andres 
Published: March 2023

Abstract

Aptamers, nucleic acid ligands against specific targets, have emerged as drug candidates, sensors, imaging tools, and nanotechnology building blocks. The most successful method for their development has been SELEX (Systematic Evolution of Ligands by EXponential Enrichment), an iterative procedure that is labor- and time-intensive and often enriches candidates for criteria other than those desired. Here we present UltraSelex, a non-iterative method that combines biochemical partitioning, high-throughput sequencing, and computational background minimization through statistical rank modeling. This approach avoids the common bias for abundant sequences and selects high-affinity ligands, even if they are extremely scarce. In six independent UltraSelex experiments (three towards each target), we discovered high-affinity aptamers for a fluorogenic silicon rhodamine dye, and a protein target, the SARS-CoV-2 RNA-dependent RNA polymerase. These aptamers enabled live-cell RNA imaging and efficient enzyme inhibition, respectively. The wet-lab partitioning part of UltraSelex can be completed in a few hours, and including sequencing and rank modeling via a public web server, the identification of lead candidates can be accomplished in about one day. UltraSelex provides a rapid route to novel drug candidates and diagnostic tools with greatly improved performance.
Tob negatively regulates NF-κB activation in breast cancer through its association with the TNF receptor complex.
Authors: Yamamoto Tadashi , Tokumasu Miho , Sato Atsuko , Ito-Kureha Taku , Yamamoto Mizuki , Ohmine Nao , Semba Kentaro , Inoue Jun-ichiro 
Published: March 2023

Abstract
NF-κB mediates transcriptional regulation crucial to many biological functions, and elevated NF-κB activity leads to autoimmune and inflammatory diseases, as well as cancer. Since highly aggressive breast cancers have few therapeutic molecular targets, clarification of key molecular mechanisms of NF-κB signaling would facilitate development of more effective therapy. In this report, we show that Tob, a member of the Tob/BTG family of antiproliferative proteins, acts as a negative regulator of the NF-κB signal in breast cancer. Studies with 35 human breast cancer cell lines reveal that Tob expression is negatively correlated with NF-κB activity. Analysis of The Cancer Genome Atlas (TCGA) database of clinical samples reveals an inverse correlation between Tob expression and NF-κB activity. Tob2, another member of the Tob/BTG family, shows no such negative correlations. Furthermore, in TNF-α treated cells, Tob associates with TNF receptor complex I to suppress polyubiquitylation of RIPK1, which results in repression of NF-kB activity. Therefore, Tob functions as a negative regulator of the NF-κB pathway and may serve as a therapeutic target for aggressive breast cancer.
Statistical Comparison among Brain Networks with Popular Network Measurement Algorithms
Authors: Pran Rakib Hassan 
Published: March 2023

Abstract
In this research, a number of popular network
measurement algorithms have been applied to several brain
networks (based on applicability of algorithms) for finding out
statistical correlation among these popular network
measurements which will help scientists to understand these
popular network measurement algorithms and their
applicability to brain networks. By analyzing the results of
correlations among these network measurement algorithms,
statistical comparison among selected brain networks has also
been summarized. Besides that, to understand each brain
network, the visualization of each brain network and each
brain network’s degree distribution histogram have been
extrapolated. Six network measurement algorithms have been
chosen to apply time to time on sixteen brain networks based
on applicability of these network measurement algorithms and
the results of these network measurements are put into a
correlation method to show the relationship among these six
network measurement algorithms for each brain network. At
the end, the results of the correlations have been summarized
to show the statistical comparison among these sixteen brain
networks.
Optic nerve sheath diameter as a new noninvasive marker for predicting the prognosis of patients with acute ischemic stroke in the intensive care unit
Authors: Wang Cuicui , Xing Yingqi , Li Cong , Chen Hongxiu , Meng Yan , Liu Ying , Zhang Jie , Wang Lijuan 
Published: March 2023

Abstract
Objective: Intracranial hypertension is linked to poor prognosis after acute ischemic stroke (AIS). Intracranial pressure can be evaluated by using the ultrasonographic optic nerve sheath diameter (ONSD) and transcranial Doppler (TCD). This study aims to determine whether ONSD and TCD parameters could noninvasively predict the prognosis of AIS patients.
Design: Prospective observational blinded study.
Setting: Neurology intensive care unit (ICU).
Patients: Consecutive patients with AIS.
Interventions: ONSD and TCD parameters of 81 AIS patients were obtained upon admission. The Glasgow Outcome Scale scores were evaluated at the 6-month follow-up. The clinical differences between the poor and good prognosis groups were compared. The association between variables and prognosis was assessed, and the cutoff values for the Glasgow Coma Scale (GCS) score and ONSD for predicting poor prognoses were analyzed.
Measurements and main results: At the 6-month follow-up, 54 patients had poor prognosis; the ONSDs of the poor and good prognosis groups were 5.45±0.38 and 4.96±0.32, respectively (P<0.001). There were no significant differences in TCD parameters between the two groups. ONSD (odds ratio [OR] 1.4; 95% confidence interval [CI], 1.2–1.7; P<0.001) and GCS score (OR, 0.7; 95% CI, 0.5–0.9; P=0.003) were independent factors influencing poor prognosis. The best ONSD cutoff value for poor prognosis was 5.21 mm; the sensitivity, specificity, and area under the curve were 87.0%, 82.1%, and 0.862, respectively.
Conclusions: Ultrasonographic measurement of ONSD may be a new prognostic indicator of functional outcomes in ICU AIS patients. However, TCD parameters have no significant prognostic value for AIS patients.
A fractional-order Wilson-Cowan formulation of cortical disinhibition
Authors: González-Ramírez Laura Rocío 
Published: March 2023

Abstract
This work presents a fractional-order Wilson-Cowan model derivation under Caputo’s formalism, considering an order of 0 < α ≤ 1. To that end, we propose memory-dependent response functions and average neuronal excitation functions that permit us to naturally arrive to a fractional-order model that incorporates past dynamics into the description of synaptically coupled neuronal populations' activity. We then focus on a particular example to analyze the fractional-order dynamics of the disinhibited cortex. This system mimics cortical activity during neurological disorders such as epileptic seizures, which allows brain dynamics to transition to a hyperexcited activity state. In the first-order mathematical model, we recover traditional results showing a transition from a low-level activity state to a plausibly pathological high-level activity state as an external factor modifies cortical inhibition. On the other hand, under the fractional-order formulation, we establish novel results showing that the system resists such transition as the order is decreased, permitting the possibility of staying in the low-activity state even with increased disinhibition. Furthermore, considering the memory index interpretation of the fractional-order model motivation here developed, our results establish that by increasing the memory index, the system becomes more resistant to transitioning towards the high-level activity state. That is, a possible effect of the memory index is to stabilize neuronal activity. To summarize our results, we present a two-parameter structural portrait describing the system’s dynamics dependent on a proposed disinhibition parameter and the order. We also explore numerical model simulations to validate our results.