bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tracing TET1 expression in prostate cancer: discovery of malignant cells with a distinct oncogenic signature
Authors: Schagdarsurengin U. , Luo C. , Slanina H. , Sheridan D. , Füssel S. , Böğürcü-Seidel N. , Gattenloehner S. , Baretton G. B. , Hofbauer L. C. , Wagenlehner F. , Dansranjav T. 
Published: November 2021

Abstract
Background
Ten–eleven translocation methylcytosine dioxygenase 1 (TET1) is involved in DNA demethylation and transcriptional regulation, plays a key role in the maintenance of stem cell pluripotency, and is dysregulated in malignant cells. The identification of cancer stem cells (CSCs) driving tumor growth and metastasis is the primary objective of biomarker discovery in aggressive prostate cancer (PCa). In this context, we analyzed TET1 expression in PCa.

Methods
A large-scale immunohistochemical analysis of TET1 was performed in normal prostate (NOR) and PCa using conventional slides (50 PCa specimens) and tissue microarrays (669 NOR and 1371 PCa tissue cores from 371 PCa specimens). Western blotting, RT-qPCR, and 450 K methylation array analyses were performed on PCa cell lines. Genome-wide correlation, gene regulatory network, and functional genomics studies were performed using publicly available data sources and bioinformatics tools.

Results
In NOR, TET1 was exclusively expressed in normal cytokeratin 903 (CK903)–positive basal cells. In PCa, TET1 was frequently detected in alpha-methylacyl-CoA racemase (AMACR)–positive tumor cell clusters and was detectable at all tumor stages and Gleason scores. Pearson’s correlation analyses of PCa revealed 626 TET1-coactivated genes (r > 0.5) primarily encoding chromatin remodeling and mitotic factors. Moreover, signaling pathways regulating antiviral processes (62 zinc finger, ZNF, antiviral proteins) and the pluripotency of stem cells were activated. A significant proportion of detected genes exhibited TET1-correlated promoter hypomethylation. There were 161 genes encoding transcription factors (TFs), of which 133 were ZNF-TFs with promoter binding sites in TET1 and in the vast majority of TET1-coactivated genes.

Conclusions
TET1-expressing cells are an integral part of PCa and may represent CSCs with oncogenic potential.
Intermittent hypoxia treatment alleviates memory impairment in the 6-month-old APPswe/PS1dE9 mice and reduces amyloid beta accumulation and inflammation in the brain
Authors: Yue Xiangpei , Zhou Yanzhao , Qiao Meng , Zhao Xingnan , Huang Xin , Zhao Tong , Cheng Xiang , Fan Ming , Zhao Yongqi , Chen Ruoli , Zhu Lingling 
Published: November 2021

Abstract
Background
Alzheimer’s disease (AD) is a progressive, degenerative, and terminal disease without cure. There is an urgent need for a new strategy to treat AD. The aim of this study was to investigate the effects of intermittent hypoxic treatment (IHT) on cognitive functions in a mouse model of AD and unravel the mechanism of action of IHT.

Methods
Six-month-old APPswe/PS1dE9 (APP/PS1) male mice were exposed to hypoxic environment (14.3% O2) 4 h/day for 14 days or 28 days. Cognitive functions were measured by Morris water maze test after either 14 days or 42 days of interval. Thereafter the distribution of amyloid plaque and microglial activation were determined by mouse brain immunohistochemistry, while the amyloid beta (Aβ) and inflammatory cytokines were measured by ELISA and Western Blot. Microarray was used for studying gene expressions in the hippocampus.

Results
IHT for 14 days or 28 days significantly improved the spatial memory ability of the 6-month-old APP/PS1 mice. The memory improvement by 14 days IHT lasted to 14 days, but not to 42 days. The level of Aβ plaques and neurofilament accumulations was reduced markedly after the IHT exposure. IHT reduced the pro-inflammatory cytokines IL-1β, IL-6 levels, and β-secretase cleavage of APP processing which implies reduced Aβ production. Microarray analysis revealed a large number of genes in the hippocampus were significantly altered which are known to be metabolism-regulated genes.

Conclusions
This study provides evidence of the beneficial effect of IHT on the progression of AD by alleviating memory impairment, reducing Aβ accumulation and inflammation in the brain. IHT can be developed as a novel measure to relieve the progression of AD by targeting multiple pathways in the AD pathogenesis.
Prevalence of anemia and its associated factors among married women in 19 sub-Saharan African countries
Authors: Zegeye Betregiorgis , Anyiam Felix Emeka , Ahinkorah Bright Opoku , Ameyaw Edward Kwabena , Budu Eugene , Seidu Abdul-Aziz , Yaya Sanni 
Published: November 2021

Abstract
Background
Sub-Saharan Africa (SSA) remains the region with the highest burden of anemia globally. Since anemia has both health and non-health-related consequences, its reduction is one of the Sustainable Development Goals. Therefore, this study aimed to examine the prevalence of anemia and its associated factors among married women in SSA.

Methods
Using Stata version-14 software, the analysis was done on 89,029 married women from the Demographic and Health Surveys of 19 countries in SSA. Pearson Chi-Square test and Binary logistic regression analyses were used to examine the factors associated with anemia. The results were presented using adjusted Odds Ratio (aOR) at a 95% Confidence Interval (CI). A p-value less than or equal to 0.05 (p ≤ 0.05) was considered statistically significant.

Results
The pooled analysis showed that 49.7% of married women were anemic. Of these, 1.04% and 15.05% were severely and moderately anemic respectively, and the rest 33.61% were mildly anemic. Husband education (primary school-aOR = 0.84, 95% CI; 0.71–0.99), wealth index (middle-aOR = 0.81, 95% CI; 0.68–0.96, richer-aOR = 0.69, 95% CI; 0.57–0.84, richest-aOR = 0.68, 95% CI; 0.51–0.91), modern contraceptive use (yes-aOR = 0.68, 95% CI; 0.56–0.81) and religion (Muslim-aOR = 1.27, 95% CI; 1.11–1.46, others-aOR = 0.73, 95% CI; 0.59–0.90) were factors associated with anemia among married women.

Conclusion
The findings show that nearly half of the married women are affected by anemia. Enhancing partners’ educational levels, and economic empowerment of women, strengthening family planning services, and working with religious leaders to reduce the perception and religious beliefs related to food restrictions can be the main focus to reduce the burden of anemia among married women in SSA.
Quality of life among Syrian refugees in Germany: a cross-sectional pilot study
Authors: Al Masri Feras , Müller Mattea , Nebl Josefine , Greupner Theresa , Hahn Andreas , Straka Dorothee 
Published: November 2021

Abstract
Background
More than 10 million Syrians have left their homes and sought refuge in neighboring countries, including Europe, since the beginning of the Syrian conflict in March 2011, and immigration continues to this day. This cross-sectional study included Syrian refugees residing in and around Hannover, Germany. We investigated whether general socioeconomic factors (e.g. age, sex, housing, asylum duration) were predictive factors for the quality of life (QOL) of Syrian refugees in Germany.

Methods
The QOL of Syrian refugees was assessed using the WHOQOL-BREF tool, a questionnaire assessing the QOL in four domains: Physical health, psychological, social relationships and environment. A total of 114 Syrian refugees, aged between 18 and 45 years, who obtained one of the following statuses, asylum, refugee protection or subsidiary protection, were included. The QOL domain and total scores of Syrian refugees in Germany were compared with a Western norm and Sub-Saharan population. Data were analyzed with the Spearman Rho correlation coefficient, Kruskal–Wallis and Mann–Whitney U test and multivariate linear regression.

Results
More than 65% of the participants (62.3% male, 37.7% female) were between 18 and 29 years old, and 45% had lived in Germany for less than four years. The lowest QOL score was reported in the social relationship’s domain (60.5%), while the psychological score was lowest in participants aged 40–45 years (P = 0.011). The age was significantly negatively associated with physical health (P = 0.010), psychological (P <  0.001) and the total QOL (P = 0.005). Asylum duration was associated with the environment domain (P = 0.040), the short-time refugees were less satisfied than the longtime refugees, and with aspects of the psychological domain in Enjoying life and Concentration ability (P <  0.001 and P = 0.033, respectively), yet was not associated with total QOL or total domain scores. There were significant associations between housing and the psychological domain (P = 0.032) and housing and the social relationship domain (P <  0.001). The refugees who living in camps registered a lower score in psychological than residents of apartments and houses, and the single refugees had a higher score than those married and divorced (P = 0.032 and P = 0.035, respectively).

Conclusions
The Syrian refugees participating in this study showed a low QOL score in the assessment of all domains compared to the normal population, especially regarding social relations and psychological; it was associated with socioeconomic factors, such as housing, asylum duration and marital status. This calls for urgent societal and political efforts to strengthen the social living conditions of Syrian refugees in Germany.
A hospital-wide outbreak of IMI-17-producing Enterobacter ludwigii in an Israeli hospital
Authors: Schechner Vered , Levytskyi Katya , Shalom Ohad , Yalek Alexander , Adler Amos 
Published: November 2021

Absract
Background
To describe the course and intervention of an hospital-wide IMI-Producing Enterobacter ludwigii outbreak.

Methods
This was an outbreak interventional study, done at a tertiary care center in Tel-Aviv, Israel. Data was collected on the course of the outbreak and the demographic and clinical characteristics of all patients involved in the outbreak. The intervention measures included patients’ cohorting, contact isolation precautions, environmental cleaning and screening of contacts. The molecular features and phylogeny of outbreak-related isolates were studied by whole-genome based analysis.

Results
The outbreak included 34 patients that were colonized by IMI-Producing E. ludwigii and were identified in 24 wards throughout the hospital. Colonization was identified in the first 72 h of admission in 13/34 patients (38.2%). Most patients (91.2%) were admitted from home and had relatively low level of comorbidities. The majority of them (88%) had no recent use of invasive catheters and none had previous carriage of other multi-drug resistant bacteria. All available isolates harbored the blaIMI-17 allele and belonged to Sequence-Type 385. With the exception of two isolates, all isolates were closely related with less than a 20-SNP difference between them.

Conclusions
This outbreak had most likely originated in the community and subsequently disseminated inside our institution. More studies are required in order to elucidate the epidemiology of IMI-Producing E. ludwigii and the possible role of environmental sources in its dissemination.
The cytotoxicity and apoptotic effects of verbascoside on breast cancer 4T1 cell line
Authors: Daneshforouz Atena , Nazemi Samad , Gholami Omid , Kafami Marzieh , Amin Bahareh 
Published: November 2021

Abstract
Background
Despite significant advancements in breast cancer therapy, novel drugs with lower side effects are still being demanded. In this regard, we investigated the anti-cancer features of verbascoside in 4 T1 mouse mammary tumor cell.

Methods
First, MTT assay was performed with various concentrations (ranging between 5 to 200 μM) of verbascoside and IC50 was calculated. Then the expression of Bax, Bcl-2, and caspase-3 was evaluated in treated 4 T1 cells. In addition, we investigated the expression of TLR4, MyD88, and NF-κB to ascertain the underlying mechanism of the anti-proliferative feature of verbascoside. Also, flow cytometry followed by double PI and Annexin V was conducted to confirm the apoptosis-inducing effect of verbascoside.

Results
Our results from MTT assay showed verbascoside inhibits proliferation of 4 T1 cancer cells (IC50 117 μM) while is safe for normal HEK293T cells. By qRT-PCR, we observed that verbascoside treatment (100, 117 and, 130 μM) increases the expression of caspase-3 and Bax while reduces the expression of Bcl-2. Also, verbascoside (100, 117 and, 130 μM) increased the expression of TLR4 only at 130 μM dose and the expression of MyD88 whereas reduced the expression of NF-κB at mRNA level. Flow cytometry analysis also confirmed verbascoside induces apoptosis in 4 T1 cells at 117 μM.

Conclusion
Taken together, our data showed verbascoside is a safe natural compound for normal cells while has apoptosis-inducing feature through TLR4 axis on 4 T1 cells.
Latitudinal- and height-dependent long-term climatology of propagating quasi-16-day waves in the troposphere and stratosphere
Authors: Tang Wentao , Zhang Shaodong , Huang Chunming , Huang Kaiming , Gong Yun , Gan Quan 
Published: November 2021

AbstractThe global amplitude of the westward propagating quasi-16-day waves (16DW) with wavenumber 1 (Q16W1), the strongest component of 16DW, are derived from the European Centre for Medium-Range Weather Forecasts ERA-Interim reanalysis temperature and zonal wind data sets from February 1979 to January 2018. In terms of temperature and zonal wind, strong climatologically average amplitudes of Q16W1 appear in the upper stratosphere at mid–high latitudes in both hemispheres, and the wave amplitude is stronger in the Northern Hemisphere (NH) than in the Southern Hemisphere (SH). Multivariate linear regression is separately applied to calculate the responses of the Q16W1 temperature and zonal wind amplitudes to the QBO (quasi-biennial oscillation), ENSO (El Niño-Southern Oscillation), solar activity and linear trends of the Q16W1 amplitude. The QBO signatures of the Q16W1 temperature and zonal wind amplitudes are mainly located in the stratosphere. The Q16W1 has significant QBO responses at low latitudes. In addition, only the temperature amplitude presents a larger QBO signature in its strongest climatological amplitude region. No significant responses to ENSO and solar activity are observed in temperature and zonal wind amplitudes. The linear trends of the monthly mean Q16W1 temperature and zonal wind amplitude are generally positive, especially in the mid-upper stratosphere. The trend is asymmetric about the equator and significantly stronger in the NH than in the SH. The seasonal variation in the trend of the temperature amplitude is studied and illustrated to be stronger in winter and weaker in spring and autumn. Further investigation suggests that the background and local instability trends contribute most of the increasing trend of the Q16W1 amplitude. In winter in both hemispheres, a weakening trend of eastward zonal wind provides more favourable background wind for Q16W1 upward propagation, in autumn and winter in the NH and in spring, autumn and winter in the SH, and the increasing trend of local instability may enhance wave excitation.

Graphical Abstract
Creating a training set for artificial intelligence from initial segmentations of airways
Authors: Dudurych Ivan , Garcia-Uceda Antonio , Saghir Zaigham , Tiddens Harm A. W. M. , Vliegenthart Rozemarijn , de Bruijne Marleen 
Published: November 2021

AbstractAirways segmentation is important for research about pulmonary disease but require a large amount of time by trained specialists. We used an openly available software to improve airways segmentations obtained from an artificial intelligence (AI) tool and retrained the tool to get a better performance. Fifteen initial airway segmentations from low-dose chest computed tomography scans were obtained with a 3D-Unet AI tool previously trained on Danish Lung Cancer Screening Trial and Erasmus-MC Sophia datasets. Segmentations were manually corrected in 3D Slicer. The corrected airway segmentations were used to retrain the 3D-Unet. Airway measurements were automatically obtained and included count, airway length and luminal diameter per generation from the segmentations. Correcting segmentations required 2–4 h per scan. Manually corrected segmentations had more branches (p < 0.001), longer airways (p < 0.001) and smaller luminal diameters (p = 0.004) than initial segmentations. Segmentations from retrained 3D-Unets trended towards more branches and longer airways compared to the initial segmentations. The largest changes were seen in airways from 6th generation onwards. Manual correction results in significantly improved segmentations and is potentially a useful and time-efficient method to improve the AI tool performance on a specific hospital or research dataset.
An insight into Alzheimer’s disease and its on-setting novel genes
Authors: Vigneswaran Jaanaky , Muthukumar Sivaloganathan Anogh , Shafras Mohamed , Pant Geetika 
Published: November 2021

AbstractAccording to the World Health Organisation, as of 2019, globally around 50 million people suffer from dementia, with approximately another 10 million getting added to the list every year, wherein Alzheimer’s disease (AD) stands responsible for almost a whopping 60–70% for the existing number of cases. Alzheimer’s disease is one of the progressive, cognitive-declining, age-dependent, neurodegenerative diseases which is distinguished by histopathological symptoms, such as formation of amyloid plaque, senile plaque, neurofibrillary tangles, etc. Majorly four vital transcripts are identified in the AD complications which include Amyloid precursor protein (APP), Apolipoprotein E (ApoE), and two multi-pass transmembrane domain proteins—Presenilin 1 and 2. In addition, the formation of the abnormal filaments such as amyloid beta (Aβ) and tau and their tangling with some necessary factors contributing to the formation of plaques, neuroinflammation, and apoptosis which in turn leads to the emergence of AD. Although multiple molecular mechanisms have been elucidated so far, they are still counted as hypotheses ending with neuronal death on the basal forebrain and hippocampal area which results in AD. This review article is aimed at addressing the overview of the molecular mechanisms surrounding AD and the functional forms of the genes associated with it.
Berries instead of bears: new insight into gastronomic attractiveness of Russian Siberia
Authors: Ermolaev Vladimir A. , Ruban Dmitry A. , Yashalova Natalia N. 
Published: November 2021

AbstractActive use of berries in regional cuisines underlines gastronomic specifics of Russia. The present study focuses on three regions of Russian Siberia and establishes that edible berries are numerous there and determine specifics of the regional cuisine rooted into the cultural traditions. These cultural and gastronomic traditions developed during four centuries by Russian settlers in Siberia who adapted to severe natural conditions, explored new food resources, and interacted with the local peoples. If so, berries and berry products can be regarded as a kind of ethnic food. Modern berries-based tourism (bacatourism) initiatives and, particularly, berry picking and tasting at you-pick farms and raspberry festival are registered on the study territory. Sellers tend to position berry products as typically Siberian, which permits their use as regional, quasi-ethnic souvenirs. Berries determine significant gastronomic attractiveness of Southern Siberia, and further exploitation of this potential can contribute to sustainable development of this vast territory and maintaining its cultural identity within the broad and diverse Russian space.
Changes in the level of oxidative stress markers in Indian catfish (Wallago attu) infected with Isoparorchis hypselobagri
Authors: Sahreen Anam , Fatima Kaneez , Zainab Tahmina , Saifullah Mohammad Khalid 
Published: November 2021

Abstract
Background
Helminth infection and infestation in fishes are detrimental and have a major effect on fish health and fish production. Among various factors, parasitic infections are known to modulate antioxidant defences in fish. Similar to other aerobic animals,
fish are also susceptible to the effect of reactive oxygen species and thus have well established intrinsic and efficient antioxidant defences. ‘Oxidative stress markers are an important indicator of the physiological state of the parasite and its host’. Indian catfish,
Wallago attu is a freshwater fish that serves as the definitive host of the adult piscine trematode Isoparorchis hypselobagri. Our two years prevalence data signifies the intensity of the problem revealing a minimum of 5.5% and a maximum of 54% I. hypselobagri infection in Indian catfish W. attu (unpublished data). The present study aimed to achieve baseline data attributed to changes in some oxidative markers due to parasitic infection.

Results
During the present study, the level of enzyme activities of Catalase (CAT), Glutathione reductase (GR), Glutathione-S-transferase (GST), Glutathione peroxidase (GPx), Superoxide dismutase (SOD) and lipid peroxidation was investigated to explore the pathogenic impact on the fish host. The level of these oxidative stress markers was monitored in the swim bladder, liver, intestine and muscle of the host. We also recorded the enzyme activities in the parasite I. hypselobagri. Analysis of data revealed an elevation in GST, SOD, GR, GPx and CAT activity in the infected host tissue as compared to the non-infected fish. Further, we observed presence of GST, SOD, GR and GPx enzymes in the parasite I. hypselobagri while CAT did not show any enzyme activity.

Conclusions
Increased level of enzyme activity in liver, muscle and intestine of infected host has been recorded which indicates increased oxidative stress in the host due to parasitic invasion. The presence of antioxidant enzymes in the parasites suggests an active antioxidant defence system to avoid immune responses to long term survival and establishment in their host.
A dictionary learning method for seismic data compression
Authors: Faouzi Zizi Mohammed Outhmane , Turquais Pierre 
Published: November 2021

For a marine seismic survey, the recorded and processed data size can reach several terabytes. Storing seismic data sets is costly, and transferring them between storage devices can be challenging. Dictionary learning (DL) has been shown to provide representations with a high level of sparsity. This method stores the shape of the redundant events once and represents each occurrence of these events with a single sparse coefficient. Therefore, an efficient DL-based compression workflow, which is specifically designed for seismic data, is developed here. This compression method differs from conventional compression methods in three respects: (1) The transform domain is not predefined but data-driven, (2) the redundancy in seismic data is fully exploited by learning small-sized dictionaries from local windows of the seismic shot gathers, and (3) two modes (i.e., two different parameterizations) are proposed depending on the geophysical application. Based on a test seismic data set, we have determined superior performance of our workflow in terms of compression ratio (CR) for a wide range of signal-to-residual ratios, such as the zfp software or algorithms from the Seismic Unix package. Using a more realistic data set of marine seismic acquisition, we evaluate the capability of our workflow to preserve the seismic signal for different applications. For applications such as near-real-time transmission and long-term data storage, we observe insignificant signal leakage on a 2D line stack when the DL method reaches a CR higher than 20. For other applications, such as visual quality control of shot gathers, our method preserves the visual aspect of the data even when a CR of 95 is reached.