bluuebunny/crossref_metadata_2025_split huggingface dataset:
STEEL enables high-resolution delineation of spatiotemporal transcriptomic data
Authors: Chen Yamao , Zhou Shengyu , Li Ming , Zhao Fangqing , Qi Ji 
Published: January 2022

Abstract
Advances in spatial transcriptomics enlarge the use of single cell technologies to unveil the expression landscape of the tissues with valuable spatial context. However, computational tools developed for single-cell transcriptomics have great limits in dealing with spatial transcriptomic data with high noise on detected transcript signals. Here we propose an unsupervised and manifold learning-based algorithm, STEEL, which identifies different cell types from spatial transcriptome by clustering cells/beads exhibiting both highly similar gene expression profiles and close spatial distance in the manner of graphs. Comprehensive evaluation of STEEL on various spatial transcriptomic datasets from 10X Visium platform demonstrates that it not only achieves a high resolution to characterize fine structures of mouse brain, but also enables the integration of multiple tissue slides individually analyzed into a larger one. STEEL outperforms previous methods to effectively distinguish different cell types of various tissues on Slide-seq datasets, featuring in higher bead density but lower transcript detection efficiency. Application of STEEL on spatial transcriptomes of early-stage mouse embryos (E9.5 to E12.5) successfully delineates a progressive development landscape of tissues from ectoderm, mesoderm and endoderm layers, and futher profiles dynamic changes on cell differentiation in heart and other organs. With the advancement of spatial transcriptome technologies, our method will have great applicability in high-resolution cell type identification and unbiased spatiotemporal data integration.
Triple negative apocrine breast carcinoma has better prognosis despite poor response to neoadjuvant chemotherapy
Authors: Hu Taobo , Liu Yiqiang , Hu Xuejiao Lina , Zhao Guiyang , Wang Shu , Long Mengping 
Published: January 2022

Abstract
Background: Apocrine carcinoma is a rare subtype of invasive ductal breast cancer that shows apocrine differentiation and largely with triple negative immunohistology. Triple negative breast cancers are known to have a more aggressive clinical course. However, unlike the most other types, it is reported that triple negative apocrine carcinoma has a better prognosis. Due to scarcity of reported studies, our knowledges for its clinical behavior, prognosis and response to therapy are very limited. Methods: In this study, we retrospectively retrieved 41 triple negative apocrine carcinoma cases from our breast cancer database with an average follow up 32.8 months.Results: It was found that triple negative apocrine carcinoma had poorer response to neoadjuvant therapy, but better prognosis compared with other non-apocrine types of triple negative breast cancer. Meanwhile, triple negative apocrine carcinoma has a low proliferative nature as indicated by its low Ki67 index. Analysis of SEER database showed that chemotherapy did not improve breast cancer specific survival in TNAC patients. Conclusions: Our results suggest that triple negative apocrine carcinoma is a special subtype of triple negative breast cancer for which de-escalation of chemotherapy should be considered.
A multi-part strategy for introgression of exotic germplasm into elite plant breeding programs using genomic selection
Authors: Breider Irene S. , Gaynor R. Chris , Gorjanc Gregor , Thorn Steve , Pandey Manish K. , Varshney Rajeev K. , Hickey John M. 
Published: January 2022

Abstract
Some of the most economically important traits in plant breeding show highly polygenic inheritance. Genetic variation is a key determinant of the rates of genetic improvement in selective breeding programs. Rapid progress in genetic improvement comes at the cost of a rapid loss of genetic variation. Germplasm available through expired Plant Variety Protection (exPVP) lines is a potential resource of variation previously lost in elite breeding programs. Introgression for polygenic traits is challenging, as many genes have a small effect on the trait of interest. Here we propose a way to overcome these challenges with a multi-part pre-breeding program that has feedback pathways to optimise recurrent genomic selection. The multi-part breeding program consists of three components, namely a bridging component, population improvement, and product development. Parameters influencing the multi-part program were optimised with the use of a grid search. Haploblock effect and origin were investigated. Results showed that the introgression of exPVP germplasm using an optimised multi-part breeding strategy resulted in 1.53 times higher genetic gain compared to a two-part breeding program. Higher gain was achieved through reducing the performance gap between exPVP and elite germplasm and breaking down linkage drag. Both first and subsequent introgression events showed to be successful. In conclusion, the multi-part breeding strategy has a potential to improve long-term genetic gain for polygenic traits and therefore, potential to contribute to global food security.
Determinants of Rural Women’s Nutrition Security Status in Northwest Ethiopia
Authors: Teshome Fentaw , Andaregie Adino , Astatkie Tessema 
Published: January 2022

Abstract

Background: Nutrition security of women is one of the most vital foundations for overall development and wellbeing of society. Since understanding the factors that influence the nutrition security of women is very important for implementing appropriate interventions, this study was conducted to determine the determinants of the nutrition security status of rural women in Northwest Ethiopia. Methods: Survey data were collected from 197 rural women randomly selected using a two-stage sampling method (Cluster sampling in the first stage and Stratified random sampling in the second stage). Data in the two outcomes (nutritionally secured whose BMI ≥ 18.5, and nutritionally insecure whose BMI < 18.5 kg/m2) were analyzed using Binary Logit regression model to determine the significance of the determinants on women’s nutrition security status. Results: The study showed that 72.6% of the women in the study area were nutritionally insecure. Results of the statistical analysis revealed that family size (negative effect), and women’s daily feed frequency, the consumption of milk, fruits and vegetables, and animal products, and women empowerment (all positive effect) were the significant determinants of the nutrition security status of rural women. The weight, the height, and the BMI of nutritionally insecure women (44 kg, 1.45 m, and 15.8 kg/m2, respectively) were significantly lower than those of nutritionally secured women (50.8 kg, 1.55 m, and 21.1 kg/m2, respectively). Conclusions: This is the first study on the determinants of rural women’s nutrition security status using social and demographic data collected at the grass root level and analyzed using an advanced econometric model. The findings of the study show the need for government and other stakeholders’ interventions to increase access to nutritious food products and to provide trainings on feeding culture and dietary diversity to women. The findings of this study can help the Government of Ethiopia to achieve its National Development Priorities in line with the Sustainable Development Goals (SDGs) of UN, particularly Goals 2, 3 and 5.
Global distribution of mcr gene variants in 214,095 metagenomic samples
Authors: Martiny Hannah-Marie , Munk Patrick , Brinch Christian , Szarvas Judit , Aarestrup Frank , Petersen Thomas 
Published: January 2022

Abstract
Since the initial discovery of a mobilized colistin resistance gene (mcr-1), several other variants have been reported, some of which might have circulated a while before being discovered. Metagenomic data provides an opportunity to re-analyze available older data to understand the evolutionary history of recently discovered antimicrobial resistance genes (ARGs). Here, we present a large-scale metagenomic study of 442 Tbp of sequencing reads from 214,095 samples to identify the host and geographical distribution and genomic context of nine mcr gene variants (mcr-1 to mcr-9). Our results show that the dissemination of each variant is not uniform. Instead, the source and location play a role in the spread. Despite the very diverse distribution, the genomic background of the mcr genes remains unchanged as the same mobile genetic elements and plasmid replicons occur. This work emphasizes the importance of sharing genomic data for surveillance of ARGs in our fight against antimicrobial resistance.
Ma's Bamboo-Based Medicinal Moxibustion Therapy of Low Back Pain in Lumbar Disc Herniation: Study Protocol for a Randomized Controlled Trial
Authors: Wang Xian-Zhu , Cui Jin , FU Jing , Xue Kai-Yang , Chen Ping-Nan , Xiao Cai-Hong 
Published: January 2022

Abstract
Background

Lumbar disc herniation (LDH) is a common and frequently-occurring disease in clinic. Low back pain and sciatica are the presenting symptoms of LDH. To some extent, it can be considered that measures with the capability to improve low back pain or sciatica have the potential to treat LDH. Ma's bamboo-based medicinal moxibustion therapy can effectively reduce the degree of low back pain and has been widely used. Studies of small sample size have seen significant improvement on pain relief.
Methods/design:

The trial is a multicenter, randomized, parallel-group, non-inferiority study. Three hundred and twelve patients will be randomly assigned to a Ma's bamboo-based medicinal moxibustion group (n=156) and an acupuncture group (n=156).Patients in each group will receive treatment every day,6 times a week, 12 times in total. Follow-up will be conducted 14 days after treatment. The primary outcome will be the visual analogue scale(VAS)at baseline, after 6 times of treatment,the end of treatment, and follow-up. the secondary outcomes will include Oswestry disability indexes (ODI) ,modified Japanese Orthopaedic Association low back pain (M-JOA) score,serum β-endorphin (β-EP) and serum substance P (SP). β-EP and SP as well as safety evaluation indexes (routine blood test, liver and kidney function, and ECG) will be measure at baseline and after the end of treatment.
Discussion

The results of the trial will compare the efficacy on low back pain in LDH between Ma's bamboo-based medicinal moxibustion group and acupuncture group and will be expected to make a systematic and objective evaluation on the clinical efficacy and safety of Ma's bamboo-based medicinal moxibustion therapy.
Trial registration:

ChiCTR, ChiCTR2000038725. Registered on 29 September 2020.
KOLEKSI MANUSKRIP INDONESIA DALAM KATALOG ONLINE EROPA DAN URGENSI DIGITALISASI
Authors: Aimah Rhomayda Alfa 
Published: January 2022

Outside Indonesia, Indonesian manuscripts are preserved in universities, libraries and museums in various parts of the globe. And the exact number of collections is not known as various projects of manuscript digitization and cataloging continue to emerge. This paper discusses two things. First, remarkable European institutions preserving Indonesian manuscripts will be reviewed. We will look at their manuscript collections and to what extent they deal with the digitized collections. Secondly, as a great number of Indonesian digitized manuscripts in Europe is accessible online and free of charge, this paper will study how digitizing Indonesian manuscript becomes crucial. It argues that comprehensive manuscript digitization is – for now – the main goal of preservation.

Manuskrip Indonesia tidak hanya tersimpan di Indonesia, jumlah pastinya tidak diketahui dan terus berubah karena katalogisasi naskah-naskah tersebut masih terus dilakukan di lembaga-lembaga yang menyimpannya – universitas, museum maupun perpustakaan – di berbagai belahan dunia. Artikel ini membahas dua hal: Yang pertama, akan dijabarkan lembaga-lembaga penting yang menyimpan naskah-naskah kuno Indonesia dan memiliki sistem preservasi dan katalogisasi yang unggul; Yang kedua, mengingat sebagian dari koleksi digital di Eropa tersebut bahkan dapat diakses secara online dan tidak berbayar, artikel ini juga mengkaji pentingnya digitalisasi naskah. Argumen yang dimunculkan adalah digitalisasi naskah yang komprehensif merupakan tujuan utama preservasi untuk saat ini.
Sovereign Futures in Neshnabé Speculative Fiction
Authors: TOPASH-CALDWELL BLAIRE 
Published: January 2022

Abstract
Film has been the primary way dominant society has consumed inaccurate and problematic symbols, images, and stereotypes of Native peoples for over one hundred years. Indigenous-made films, on the other hand, reclaim Indigenous representational space or ‘visual sovereignty’ through narratives of Indigenous experience that highlight culturally relevant stories and contemporary issues they face. In particular, Indigenous-made speculative fiction inspires contemplations of Indigenous agency in alternative realities. Indigenous futurisms expressed in works of speculative fiction is a rejection of theoretical, institutional, and political projects that imagined Indigenous peoples in the past and excluded them from the future. Through a survey of Neshnabé speculative fiction and other art, this article argues that Indigenous futurisms constitute creative approaches to sovereignty in a multiplicity of potential futures and is an analytical framework that illuminates the ever-expanding contours of Indigenous sovereignty in order to imagine an otherwise to present and past circumstances of Indigenous existence.
Wpływ Higieny Rąk Personelu Medycznego na Transmisję Czynników Etiologicznych Zakażeń Związanych z Opieką Zdrowotną
Authors: Szarek Klaudia , Kabała Monika , Martirosian Gajane 
Published: January 2022

Streszczenie
Prawidłowo przeprowadzona procedura mycia i dezynfekcji rąk, wśród pracowników jednostek medycznych jest jedną z podstawowych zasad zapobiegania zakażeniom związanym z opieka zdrowotną, które znacznie wydłużają hospitalizację, generując większe koszty. Celem pracy było dokonanie przeglądu dostępnej literatury na temat źródeł szerzenia się zakażeń szpitalnych w kontekście higieny rąk personelu. Ocena, czy procedury te są wykonywane prawidłowo oraz czy ręce i paznokcie mają wpływ na rozprzestrzenianie się drobnoustrojów w środowisku szpitalnym. Literatury szukano w bazach danych PubMed oraz Google Schoolar, wpisując odpowiednie słowa kluczowe. Zebrane dane literaturowe jednoznacznie wskazują jak istotną rolę w przerwaniu łańcucha epidemiologicznego zakażeń szpitalnych ma prawidłowa procedura mycia rąk; krótkie oraz niepomalowane paznokcie a także brak biżuterii na rękach personelu szpitalnego.
Spicy Plant Raw Materials in Choux Dough
Authors: Kopylova Anastasiia , Davydenko Nataliia , Sapozhnikov Aleksandr , Loseva Anna 
Published: January 2022

Introduction. Semi-finished choux dough has neither vitamins nor minerals. However, its nutritional value can be increased by adding vegetable raw materials. The research objective was to evaluate the possibilities of using spicy vegetable raw materials in the formulation of semi-finished choux dough.
Study objects and methods. The study featured fresh parsley (Petroselinum crispum), basil (Ocimum), celery (Apium) leaves and stems, and IR-dried powder of celery stalks. Standard research methods were used to determine the sensory, physico-chemical, and nutritional properties of the resulting choux samples.
Results and discussion. Classical semi-finished choux dough with craquelin served as control sample. Fresh spicy vegetable raw materials degraded the sensory characteristics of the product. However, powdered celery stalks did not interfere with the taste of the choux dough. They were added in the amount of 2.5, 5.0, and 7.5% by weight of wheat flour. The celery powder gave the dough a sour-spicy flavor, as well as increased the content of vitamins B (up to 10%) and beta-carotene (up to 70%) in the finished product.
Conclusion. The sample with 5% of IR-dried celery powder proved optimal for choux dough. It increased the content of vitamin B2 and beta-carotene, thus improving the nutritional value of the semi-finished product. In future, the powder can be tested as part of bakery filling in combination with ingredients that mask the typical celery taste.
Quality and Optimal Shelf Life of Late Season Green Cabbage
Authors: Ivanova Maria , Yanchenko Elena , Yanchenko Aleksey , Virchenko Ivan 
Published: January 2022

Introduction. Green cabbage has a short shelf life. As a result, it becomes scarce by March and April, often due to miscalculated sell-by-date. The research objective was to establish qualitative indicators and optimal shelf life of late season green cabbage. Study objects and methods. The study featured eleven late season varieties of green cabbage grown in alluvial meadow soil using N150P150K180 as fertilizer. The samples (25 cabbage heads) were put in layers into wooden containers with a capacity of 200–250 kg each and stored at 0...+1°C and a relative humidity of 90–95% for 7 months. By the end of storage, the samples were tested for the yield of marketable products, weight loss, diseases, etc.
Results and discussion. The highest yield belonged to Gertsoginya F1 (80.4%), Kilaton F1 (78.6%), and Beaumont Agro F1 (77.7%). The optimal shelf life did not exceed 5–6 months. The yield of commercial products depended on the solid matter content (r = 0.81) and, to a lesser degree, on the average content of ascorbic acid (r = 0.52), monosaccharides (r = 0.55), and nitrates (r = 0.55). The weight loss had a negative mean relationship with the content of solids (r = –0.55), ascorbic acid (r = –0.49), and nitrates (r = –0.59).
Conclusion. The optimal shelf life for most varieties and hybrids of green cabbage proved to be 4–5 months, whereas for Beau Monde Agro F1, Gertsoginya F1, Idilliya F1, and Kilaton F1, it was 5–6 months. Further research might reveal hybrids with longer shelf life.
Technological Potential of Saratov Spring Durum Wheat Grain
Authors: Sadygova Madina , Gaponov Sergei , Shutareva Galina , Tsetva Natalya , Kirillova Tatyana , Filina Darya 
Published: January 2022

Introduction. Durum wheat is vital for high-quality pasta production. The present research tested the high technological potential of durum wheat varieties developed in the Saratov region. The research objective was to study the effect of the quality of durum wheat on the quality of pasta.
Study objects and methods. The study featured durum wheat of the following varieties: Saratovskaya Zolotistaya, Valentina, Nik, Krasnokutka 13, Luch 25, Pamyati Vasilchuka, Bezenchukskaya 182 and Annushka. The experiment involved an original PSL-13 press for standard spaghetti with a diameter of 1.8 mm. The content of protein, raw gluten, and their quality were determined by standard methods. The cooking properties of the pasta were evaluated according to the method developed in the South-Eastern Federal Agricultural Research Center.
Results and discussion. The indicators of raw gluten and protein are known to correlate. The samples of Saratovskaya Zolotistaya and Luch 25 had a high protein content of 15.3 and 15.6%, respectively, as well as a high content of raw gluten (33.2 and 35.1%, respectively). The raw gluten of Saratov varieties proved to be much better than in the control samples. The indicator of microSDs sedimentation was 30–36 mm. The strength of spaghetti followed the increase in crude gluten (33–35%) and protein (15.3–15.6%), which is typical of this type of pasta. The strength, coefficient of determination (R2 = 0.98), and sharing force (R2 = 0.92) depended on the protein content.
Conclusion. The study established the following optimal selection criteria for durum wheat varieties to be used in strong spaghetti production: virtuosity – 80%, raw gluten – 33–35%, protein content – 5–7% higher than normal, raw gluten – 72–80 units.
Reclamation of Post-Technological Landscapes: International Experience
Authors: Asyakina Lyudmila , Dyshlyuk Lyubov , Prosekov Alexander 
Published: January 2022

Introduction. Anthropogenic activities cause large-scale environmental problems. The growing volumes of toxic emissions contribute to soil, water, and air pollution, thus posing a serious threat to all living systems and the global ecosystem. New reclamation methods are a relevant research topic as they help to restore and preserve ecosystems.
Study objects and methods. The research covered sixteen years of scientific publications from PubMed of the National Center for Biotechnology Information (USA), Elsevier (Scopus, ScienceDirect), Web of Science, and the national electronic library service eLibrary.ru.
Results and discussion. The authors reviewed various scientific publications to define the main technogenic objects that have a toxic effect on biota. Soil is more vulnerable to destructive effects, and mining wastes are responsible for the largest share of technogenically disturbed objects. Pollutants include many compounds, such as heavy metals, hydrocarbons, sulfur compounds, acids, etc. Reclamation technologies reduce the man-induced impact on the environment, e.g. pollutants can be completely or partially destroyed, processed into non-toxic products, completely removed, stabilized into less toxic forms, etc. This review provides information on the main methods of reclamation of disturbed soils and substantiates the prospect of developing integrated reclamation technologies.
Conclusion. The present review featured the main pollutants of anthropogenic origin and the traditional soil reclamation methods. The most prospective new technologies of soil reclamation appeared to be a combination of such biological methods as phytoremediation, bioaugmentation, and biostimulation.