bluuebunny/crossref_metadata_2025_split huggingface dataset:
TIMP2 is associated with prognosis and immune infiltrates of gastric and colon cancer
Authors: Jian Fang , Yanhong Jiao , Limeng Wei , Guoping Niu , Yiqin Tian , Hao Lin , Zhaoji Pan 
Published: April 2022

Abstract
Tissue inhibitor of metalloproteinase-2 (TIMP2) is an inhibitor among the tissue inhibitors of metalloproteinase (TIMP) family members, is associated with the progression of a variety of tumors. However, the association of TIMP2 with cancer prognosis and tumor-infiltrating lymphocytes remains unclear. TIMP2 expression was analyzed by Tumor Immune Estimation Resource (TIMER), TNMplot, Gene Expression Profiling Interactive Analysis (GEPIA) database and 50 paired gastric cancer tissues. We evaluated the influence of TIMP2 on clinical prognosis using Kaplan-Meier plotter, the PrognoScan database, GEPIA and TCGA data. The correlation of TIMP2 with tumor immune infiltrates and with the set of gene markers of immune infiltrates was investigated by TIMER and GEPIA. TIMP2 is highly expressed in gastric cancer and low expressed in colon cancer. High TIMP2 expression was significantly correlated with poor overall survival (OS, hazard ratio [HR] = 1.38, 95% confidence interval [CI]: [1.16–1.63]; P = 0.0002) and progression-free survival (PFS, HR = 1.39, 95% CI: [1.14–1.7]; P = 0.0012) in gastric cancers. Specifically, high TIMP2 expression was associated with poorer OS and PFS, but not with OS and PFS in stage 1 (OS HR = 1.96, P = 0.29; PFS HR = 0.43, P = 0.19) and stage 2 (OS HR = 1.59, P = 0.12; PFS HR = 1.47, P = 0.2) and stage N0 patients (OS HR = 1.6, P = 0.35; PFS HR = 1.56, P = 0.38) of gastric cancer patients. There was a significant positive correlation between TIMP2 expression and different type of immune cells, including CD4 + T cells, CD8 + T cells, macrophages, Neutrophils, and dendritic cells in stomach adenocarcinoma (STAD) and colon adenocarcinoma (COAD). Moreover, TIMP2 expression was strongly correlated with different sets of immune markers. These results suggest that TIMP2 is associated with prognosis and level of immune infiltrating in a variety of cancers, especially colon and gastric cancer patients. Moreover, expression of TIMP2 potentially contributes to regulation of tumor-associated macrophages (TAMs), dendritic cells, T cell exhaustion and Tregs in colon and gastric cancer. These findings suggest that TIMP2 may serve as a prognostic biomarker for predicting prognosis and immune infiltration in gastric and colon cancer.
Privacy Risks of Whole-Slide Image Sharing in Digital Pathology
Authors: Holub Petr , Müller Heimo , Bíl Tomáš , Pireddu Luca , Plass Markus , Praßer Fabian , Schlünder Irene , Zatloukal Kurt , Nenutil Rudolf , Brázdil Tomáš 
Published: April 2022

Abstract
Access to large volumes of so called whole-slide images, high-resolution scans of complete pathological slides, has become a cornerstone of development of novel artificial intelligence methods in digital pathology, but has broader impact for medical research and education/training. However, a methodology based on risk analysis for sharing such imaging data and applying the principle "as open as possible and as closed as necessary" is still lacking. In this article we develop a model for privacy risk analysis for whole-slide images, which focuses primarily on identity disclosure attacks, as these are the most important from a regulatory perspective. We develop a mathematical model for risk assessment and design a taxonomy of whole-slide images with respect to privacy risks. Based on these risk assessment model and the taxonomy, we design a series of experiments to demonstrate the risks on real-world imaging data. Finally, we develop guidelines for risk assessment and recommendations for low-risk sharing of whole-slide image data.
Heterogeneity in prevalence of subclinical Plasmodium falciparum and Plasmodium vivax infections but no parasite genomic clustering in the Chittagong Hill Tracts, Bangladesh
Authors: Huwe Tiffany , Kibria Mohammad Golam , Johora Fatema Tuj , Phru Ching Swe , Jahan Nusrat , Hossain Mohammad Sharif , Khan Wasif Ali , Price Ric N , Ley Benedikt , Alam Mohammad Shafiul , Koepfli Cristian 
Published: April 2022

Abstract
BackgroundMalaria remains endemic in Bangladesh, with the majority of cases occurring in forested, mountainous region in the Chittagong Hill Tracts (CHT). This area is home to Bengali and diverse groups of indigenous people (Pahari) residing largely in mono-ethnic villages.Methods1002 individuals of the 9 most prominent Pahari and the Bengali population were randomly selected and screened by RDT and qPCR. Parasites were genotyped by msp2 and deep sequencing of 5 amplicons (ama1-D3, cpmp, cpp, csp, and msp7) for P. falciparum (n=20), and by microsatellite (MS) typing of ten loci and amplicon sequencing of msp1 for P. vivax (n=21). Population structure was analyzed using STRUCTURE software. Identity-by-state (IBS) was calculated as a measure of parasite relatedness and used to generate relatedness networks. ResultsThe prevalence of Plasmodium falciparum and Plasmodium vivax infection was 0.7% by RDT (Pf: 6/1002; Pv: 0/1002, mixed: 1/1002) and 4% by qPCR (Pf: 21/1002; Pv: 16/1002, mixed: 5/1002). Infections were highly clustered, with 64% (27/42) of infections occurring in only two Pahari groups, the Khumi and Mro. Diversity was high; expected heterozygosity was 0.93 for P. falciparum and 0.81 for P. vivax. 85.7% (18/21) of P. vivax and 25% (5/20) of P. falciparum infections were polyclonal. No population structure was evident for either species, suggesting high transmission and gene flow among Pahari groups. ConclusionsHigh subclinical infection prevalence and genetic diversity mirror ongoing transmission. Control activities should be specifically directed to Pahari groups at greatest risk.
A multipole-based effect catalog system for the systematic identification of potential measurands
Authors: Welzbacher Peter , Kirchner Eckhard , Vorwerk-Handing Gunnar 
Published: April 2022

Abstract
Caused by the constantly progressing digitalization in engineering, a significant demand for information about characteristic process and state variables of technical systems arises, e.g. as basis for digital twins or predictive maintenance. However, since it is oftentimes neither obvious what nor how to measure, the integration of measuring functions, in particular in terms of a retrofit, represents a current major challenge in mechanical engineering. In order to overcome this challenge, an approach for the systematic identification of potential measurands is provided in this contribution. For this purpose, the approach of physical effect catalogs is taken up and used for the systematic identification of potential measurands, starting from a physical variable to be determined. Existing catalog systems have two major limitations with respect to the intended identification of cause-effect relationships: on the one hand, existing effect catalogs assume an effect to be realized and not a cause and, on the other hand, a consideration of design parameters of a technical system is not intended. These limitations are overcome by linking the basic ideas of existing catalog systems with the fundamentals of multipole-based modeling. In this way, a multipole-based effect catalog system is developed. The developed catalog system creates the basis to systematically include the changes and transformations of a process or state variable to be determined in a technical system into the identification of potential measurands.
Dynamical geography and transition paths of Sargassum in the tropical Atlanti
Authors: Beron-Vera Francisco J. , Olascoaga Maria J. , Putman Nathan F. , Triñanes Joaquin , Lumpkin Rick , Goni Gustavo 
Published: April 2022

Abstract
By analyzing a time-homogeneous Markov chain constructed using trajectories of undrogued drifting buoys from the NOAA's Global Drifter Program, we find that probability density can distribute in a manner that resembles very closely the recently observed recurrent belt of high Sargassum density in the tropical Atlantic between 5-10oN coined the Great Atlantic Sargassum Belt (GASB). A spectral analysis of the associated transition matrix further unveils a forward attracting almost-invariant set in the northwestern Gulf of Mexico with a corresponding basin of attraction disconnected from the Sargasso Sea, but including the nutrient-rich regions around the Amazon and Orinoco rivers mouths and also the upwelling system off the northern coast of west Africa. This represents a data-based inference of potential remote sources of Sargassum recurrently invading the Intra-Americas Seas (IAS). By further applying Transition Path Theory (TPT) on the data-derived Markov chain model, two potential pathways for Sargassum into the IAS from the upwelling system off the coast of Africa are revealed. One TPT-inferred pathway takes place along the GASB. The second pathway is more southern and slower, first going through the Gulf of Guinea, then across the tropical Atlantic toward the mouth of the Amazon River, and finally along the northeastern South American margin. The existence of such a southern TPT-inferred pathway may have consequences for bloom stimulation by nutrients from river runoff.
A comparison of serum copper levels in patients with papillary thyroid carcinoma, nodular goiter, and healthy volunteers
Authors: Maneeprasopchoke Prachya , Phousamran Phoupong , Pongsapich Warut , Pithuksurachai Paveena , Worrakulpanit Jakrit , Keawvijit Tippanate , Poungvarin Naravat , Amornpichetkul Kanchana , Chongkolwatana Cheerasook 
Published: April 2022

Abstract
Serum copper (Cu) is an essential trace element that plays a key role in thyroid hormone production. An inappropriate level of serum Cu might be related to development of both benign and malignant thyroid neoplasm. Nodular goiter and papillary thyroid carcinoma (PTC) are common benign and malignant tumors of the thyroid, respectively. This study aims to compare the serum Cu levels of healthy women with women with PTC or nodular goiter. A total of 205 Thai women were recruited for this cross-sectional study. The reference group was comprised of 100 healthy volunteers. There were 61 nodular goiter and 41 PTC patients that had been treated with surgery. Serum Cu was measured using an atomic absorption spectrophotometer and the three groups were compared. The serum Cu levels of the PTC, nodular goiter and the reference group were 0.99 ± 0.27 µg/ml, 1.07 ± 0.26 µg/ml and 1.00 ± 0.30 µg/ml, respectively. The results were not statistically different (P = 0.26). A post hoc subgroup analysis in the PTC group showed serum Cu levels were significantly higher in the blood vessel invasion group (P = 0.01) and the BRAFV600E mutation group (P = 0.04), but no relationships between serum Cu and other aggressive histopathology were observed. The serum Cu levels of patients with PTC and nodular goiter were not different and did not differ significantly from the reference group. Thus, serum Cu cannot be applied to stratify risk in indeterminate thyroid nodules. Nevertheless, higher serum Cu levels were associated with blood vessel invasion and BRAFV600E mutation in PTC. Therefore, this trace element might have a potential role in prognostication of PTC.
Primary Clear Cell Carcinoma of the Pancreas
Authors: Kang Yoo Na 
Published: April 2022

Abstract
The most common malignant tumor of the pancreas is ductal adenocarcinoma. Focal clear cell changes in the ductal component of pancreatic ductal adenocarcinoma are rarely observed. Clear cell carcinomas composed almost entirely of clear tumor cells are very rare. We present a case of a 72-year-old man with a pancreatic mass, which was detected on abdominal computed tomography (CT), and a history of hepatitis B, hepatitis C, and hepatocellular carcinoma. He had received treatment with Zeffix, peginterferon, ribavirin, and radiofrequency ablation twice until 2 years prior. One year prior, follow-up contrast-enhanced abdominal CT revealed a newly developed pancreatic mass. Laparoscopic radical antegrade modular pancreato-splenectomy was performed under the clinical diagnosis of pancreatic ductal adenocarcinoma. An ill-defined white-to-tan firm solid mass was observed in the pancreas, approximately 2.0 cm in diameter. The tumor cells showed > 90 % clear cell features, with large round to oval nuclei and abundant clear cytoplasms, and well-defined cell membranes. Immunohistochemical staining revealed that the tumor cells were positive for pan-cytokeratin, cytokeratin 7, cytokeratin 19, HNF-1β, MUC-1, and p53. We excluded the possibility of metastatic clear renal cell carcinoma, neuroendocrine carcinoma, perivascular epithelioid cell tumor, malignant melanoma, and sarcoma because immunohistochemical staining of the tumor cells did not reveal the presence of vimentin, chromogranin, synaptophysin, and HMB45. Consequently, his condition was diagnosed as primary clear cell carcinoma of the pancreas, and he received postoperative radiotherapy and folfirinox chemotherapy after surgery. However, 11 months after surgery, a newly developed hepatic metastatic lesion was detected.
Extra-osseous Primary Ewing’s Sarcoma of the Lungs Mistakenly Diagnosed and Managed as Hemothorax: An Extremely Aggressive and Fatal Rare Tumor with an Unusual Site
Authors: Osman Ahmed Adam , Bashir Ahmed Muhammad , Mutlu Eren , Ibrahim Ismail Gedi 
Published: April 2022

Abstract
Extraosseous Ewing's sarcoma of the lungs is a rare soft tissue tumor of pediatric and adolescent usually found in the extremities. In this case report, we describe such a case in a four year-old-male child presented with shortness of breath, cough, left side chest pain, and hemoptysis for two months. We reviewed clinical, radiological and pathological findings for this rare malignancy. This rare and fatal malignancy has been misdiagnosed and managed inappropriately because of low suspicion of index of taking this into the differential diagnosis.
Acoustic observations of lava fountain activity during the 2021 Fagradalsfjall eruption, Iceland
Authors: Lamb Oliver , Gestrich Julia , Barnie Talfan , Jónsdóttir Kristín , Ducrocq Cécile , Shore Michael , Lees Jonathan , Lee Stephen 
Published: April 2022

Abstract
The 2021 eruption within the Fagradalsfjall volcanic system in Iceland provided a rare opportunity to record acoustic data generated by a basaltic fissure. Eruptive activity in May 2021 was defined by a sequence of repetitive lava fountaining activity. Here we describe key observations and analysis conducted on acoustic data recorded by a four-element infrasound microphone array near the eruption site. Detailed inspection of acoustic waveforms and comparisons with seismic data and lava fountain height measurements revealed a complex eruptive sequence during each lava fountain event: acoustic tremor during peak lava fountaining was followed by a transition to Strombolian-style activity with distinct high-amplitude impulsive waveforms. Quantitative comparisons to jet noise spectra finds complex turbulence acoustics during each event, with evidence of variations in the wavefield centred on peak lava fountain heights. Strombolian explosions could mostly be modelled by oscillations of bursting gas slugs at the top the magma column, with a minor number of events exhibiting Helmholtz resonance behaviour instead. We find an increase in bubble radii between early and late May, suggesting a widening of the upper conduit during the lava fountain sequence. Finally, we propose that higher acoustic amplitudes, in addition to a wider conduit in late May, indicates higher gas flux through the conduit culminating in shorter lava fountain events. This study highlights the value of deploying acoustic sensors for providing additional constraints on eruption dynamics and source parameters during effusive fissure eruptions in Iceland and elsewhere.
Identification of key molecules and significant signaling pathways in HNRNPK regulated lung cancer cells
Authors: Guo Hongmei , Wang Mengshan 
Published: April 2022

Abstract
Lung cancer is the primary cause of cancer deaths in the United States. Many potential therapeutic targets for which drugs are constantly under development. Heterogeneous nuclear ribonucleoprotein K (HNRNPK) is a regulatory protein that is related to various cancer development. However, the mechanism is still not clear. Here, our objective is to identify the key molecules and signaling pathways by analyzing the RNA-seq data. The GSE197946 was created by the Illumina HiSeq 2000 (Homo sapiens). The KEGG and GO analyses revealed Apelin signaling pathway and Oxytocin signaling pathway were the main changed biological processes. Moreover, we further identified several interactive genes including EGFR, FOS, NOTCH1, EGR1, MMP2, ITGAM, PRKACB, ICAM1, H6PD, and SPP1. Our study may provide novel insights into the treatment of lung cancer.
The interplay of hormonal and infectious factors in the pathogenesis of complicated pregnancy
Authors: Amiraslanova M. M. , Zemlina N. S. , Kuznetsova I. V. 
Published: April 2022

Introduction. The causes for adverse pregnancy outcomes are usually complex and, in some cases, can worsen each other.Aim. To assess the role and establish the interplay of hormonal and infectious factors in the pathological course of pregnancy in women with threatened spontaneous miscarriage.Materials and methods. A total 120 pregnant women were enrolled for the observational prospective study, in which they were divided into 4 groups. Group 1 included 32 patients with threatened spontaneous miscarriage and hyperandrogenism (HA), who received glucocorticosteroids (GCS); group 2 included 28 patients with threatened spontaneous miscarriage and HA, who did not receive GCS; group 3 included 30 patients with threatened spontaneous miscarriage without HA; group 4 (control) included 30 women with a physiological course of pregnancy. The following examination methods were used: clinical assessment of the course of pregnancy; measurement of the serum levels of dehydroepiandrosterone sulfate (DHEA-S), 17-hydroxyprogesterone (17-OHP) and total testosterone at weeks 5 to 8, 9 to 12, 13 to 18, 19 to 24 and 25 to 32 of gestation; microbiological tests of vaginal discharge.Results. The evaluation of androgenic status showed that the levels of the tested hormonal parameters in women with HA significantly exceeded those of the control group, while the changes in 17-OHP and testosterone secretion was comparable to that in women without HA, and DHEA-S level decreased to control values by the third trimester. The use of corticosteroids was associated with significant changes in the values and secretion levels of 17-OHP and DHEA-S, but not testosterone; DHEA-S levels decreased to the values that were significantly lower as compared to all groups in the third trimester of pregnancy.Conclusions. Vaginal infections play an important role in the genesis of gestational failures. Hyperandrogenism exacerbates the problem of miscarriage, however, the use of corticosteroids does not result in improved hormonal characteristics and clinical pregnancy outcomes, deteriorating the vaginal biocenosis.
Pregnancy outcomes and thyroid dysfunction: preterm birth risk assessment
Authors: Mateykovich E. A. , Chernova A. L. , Shevlyukova T. P. , Sukhanov A. A. 
Published: April 2022

Introduction. Subclinical hypothyroidism occurs in 2–3% of pregnant women and is often associated with pregnancy complications, including preterm birth.Aim – to study correlations between thyroid dysfunction and pregnancy outcomes.Materials and methods. 64 clinical cases of managing pregnant women in the Perinatal Center (Tyumen) were analyzed for 2017– 2021: 28 women with thyroid-stimulating hormone (TSH) > 2.5 mU/l, 36 women with TSH ≤ 2.5 mU/l) during the entire period of pregnancy. Quantitative features are described by absolute and relative (percentage) indicators. The probability of outcome depending on the presence of a clinical-amnestic factor was assessed by determining the relative risk (RR) and 95% confidence interval (CI). The level of statistical significance in testing the null hypothesis is p < 0.05.Results. There were no differences in pregnant women with and without subclinical hypothyroidism when considering such medical and social factors as age, marital status, work, education, nicotine addiction, obesity, kidney disease. An increased risk of preterm delivery was found in patients with a TSH level > 2.5 mU/l: RR 1.41 (0.59–3.37), especially against the background of a positive test for antibodies to thyroperoxidase: RR 1.63 (0.62–4.28). In the absence of treatment, the risk of early delivery, preterm birth, preeclampsia was revealed.Conclusions. A universal approach to determining the threshold values of TSH for the diagnosis of subclinical hypothyroidism in pregnant women, to the need and tactics of its treatment has not been developed. Diseases of the thyroid gland are endemic for Western Siberia, often associated with iron deficiency anemia, their high frequency in the anamnesis of pregnant women is noted. Establishing a correlation between subclinical hypothyroidism, hormonal correction and pregnancy complications requires further research. An obstacle is the lack of proper diagnosis of the TSH level in women who give birth on an emergency basis in early gestational periods.
An innovative approach to the prevention and treatment of acute respiratory tract infections in children
Authors: Larkova I. A. , Revyakina V. A. 
Published: April 2022

The problem of prevention and treatment of acute respiratory infections of the upper respiratory tract remains extremely at the top. Although viruses are the etiological factor in more than 90% of acute respiratory infections, the fact of the active use of antibiotics in the treatment of patients with this patology, along with the lack of effective antiviral agents can cause increasing concern, since this is assocatied with an increase in bacterial resistance, sensitization and inflammatory diseases and therefore requires the development of completely different alternative methods of treatment. Since the discovery of the human microbiome over the past two decades, not only the microbiota as a participant in the infectious process, but also probiotics as a factor in managing the immune responses of the macroorganism in viral infections have been actively studied. In addition, the antiviral activity of different probiotic strains has been demonstrated in the scientific literature, which explains the interest of the scientific community in the use of probiotics in acute respiratory infections, especially since probiotics have shown not only efficacy, but aalso high safety in patients of different age groups, including infants. Thus, the literature review showed that the currently available data both from clinical studies and experimental work on the use of probiotics in acute respiratory infections indicate the potential of such an innovative strategy not only for the prevention but also for the treatment of the acute period of the disease, which should be the basis for its wider use in real practice.