bluuebunny/crossref_metadata_2025 huggingface dataset:
High-dose radiation associated with improved survival in IDH-wildtype low-grade glioma
Authors: Liu Shuai , Liu Yanwei , Li Guanzhang , Feng Jin , Chen Li , Qiu Xiaoguang
Published: April 2021

Background

As molecular advances have deepened the knowledge on low-grade glioma (LGG), we investigated the effect of higher radiation dose on the survival of IDH-wildtype (IDHwt) LGG.

Methods

In the current study, 52 IDHwt LGG patients who received radiotherapy were enrolled from the Chinese Glioma Genome Atlas dataset. Radiation doses > 54 Gy were defined as high-dose, whereas doses ≤ 54 Gy were defined as low-dose. We performed univariate and multivariate survival analyses to examine the prognostic role of high-dose radiotherapy.

Results

In total, the radiation dose ranged from 48.6 Gy to 61.2 Gy, with a median of 55.8 Gy, and 31 patients were grouped into high-dose radiation. Univariate survival analysis indicated that high-dose radiotherapy (p = 0.015), tumors located in the frontal lobe (p = 0.009), and pathology of astrocytoma (p = 0.037) were significantly prognostic factors for overall survival. In multivariate survival analysis, high-dose radiotherapy (p = 0.028) and tumors located in the frontal lobe (p = 0.016) were independently associated with better overall survival.

Conclusions

In conclusion, high-dose radiotherapy independently improved the survival of IDHwt LGG. This can guide treatments for glioma with known molecular characteristics.
The effects of gender, educational level, and personality on online learning outcomes during the COVID-19 pandemic
Authors: Yu Zhonggen
Published: April 2021

With the rampant pandemic of COVID-19, an increasing number of people are acquiring knowledge through online learning approaches. This study aims to investigate how to improve online learning effectiveness during this special time. Through a mixed design, this study revealed the effect of educational levels, gender, and personality traits on online learning outcomes. It was concluded that postgraduates (N = 599) outperformed undergraduates (N = 553) in online learning, learners (N = 1152) with strong personality traits such as agreeableness, conscientiousness, and openness to a new experience outperformed those with strong extraversion and neuroticism. Future research could improve interpersonal interactions and encourage learners to post words in the online discussion forum, focus on how to design scaffolding online learning and how to improve the quality and dynamic of the online contents, and highlight blended learning rather than either merely online or traditional face-to-face learning.
Temporal morphometric analyses of Pila globosa in India for its use in aquaculture and food industry
Authors: Panda Falguni , Pati Samar Gourav , Bal Abhipsa , Mathur Shivangi , Nirmaladevi Ramalingam , Paital Biswaranjan
Published: April 2021

Background

Although the apple snail Pila globosa is used as indicator species for human consumption locally and as fish feed, research on it in general is very scanty. It is used in food industry, in aquaculture as fish bait and used as food in many regions of India and many other countries, but research on it has been started in the 1970s. Only 40 articles are available on this organism in PubMed indicating an urgent need of basic research on it especially work on its spatiotemporal morphometry Therefore, sampling of P. globosa was done from different parts of India in different seasons (summer, winter and rainy), and different morphometric studies were performed on this organism to draw baseline information. Analysis was conducted to study morphometry, the relationship between shell length and the weight and relative condition factor of Indian apple snail Pila globosa collected from five zones (east, west, north, south and centre) of India during 2018–2019 year.

Results

The shell length (SL) (46.5 ± 13.33), shell width (SW) (40.22±11.5 mm), spire length (SPL) (2.99±0.15 mm), base length (BL) (12.53±2.94 mm), aperture length (AL) (21.95±4.36 mm), aperture width (AW) (2.74±0.47 mm) and shell weight (WT) (31.08±13.76 g) were observed to be varied among the individual sampled across India. Different relationships for SL/SW (Log SW=0.9889 Log SL + 0.9444), SL/SPL (Log SPL = 0.1452 Log SL+0.3815), SL/BL (Log BL=0.7789 Log SL+0.5814), SL/AL (Log AL= 0.6518 Log SL+0.9111) and SL/AW (Log AW=0.4475 Log SL+0.1422) were observed by considering shell length as basic index. The relationship between shell length and shell weight was found to be Log WT=2.0263 Log SL+0.1098. The relative condition factor revealed uninterrupted and good environmental condition observed for apple snails. A negative allometric growth pattern was observed from the length–weight relationship.

Conclusion

The environments of apple snail in India are not contaminated, and the results can be used as baseline data in aquaculture for model analysis and can be used as a reference for drawing relationship among different morphometric indices of P. globosa in India, as there is no such information available on it. The data can also be used for mass scale production of P. globosa for consumption by human and use in aquatic industries as fish feed.
The melittology research in Northern Africa and the Middle East: past and present situations
Authors: Shebl Mohamed A. , Ben Abdelkader Faten , Bendifallah Leila , Benachour Karima , Bataw Ali A. , Bufliga Emsaed M. , Osman Mohamed A. , Kamel Soliman M.
Published: April 2021

Background

More than 20,000 species in the superfamily Apoidea have been identified worldwide. This superfamily includes the most important group of insect pollinators that contribute to the integrity of ecosystems.

Main body

We have gathered in this paper data from many previous works in Northern Africa and Middle East regions. Some of these data are date from many years ago and others are recent. We present here a non-exhaustive list of some common Apoid species. In addition, certain previous studies that were published and other current research opportunities were suggested.

Conclusion

Although there are many bee experts in the Arab world, i.e., in apiculture, however, a few researchers are interested in melittology even though it seems that this region represents a large bee diversity.
Embolization for massive bleeding due to spontaneous left external iliac vein rupture: report of a successful case
Authors: Sueyoshi Eijun , Sakamoto Ichiro , Uetani Masataka
Published: April 2021

Background

Spontaneous rupture of the iliac vein has rarely been reported. Its associated hypovolemic shock-related symptoms and signs, including syncope and hypotension, have been observed in most of these cases. Successful transcatheter venous embolization for massive bleeding due to spontaneous rupture of the external iliac vein was herein reported.

Case presentation

An 82-year-old female patient developed sudden left lower abdominal and back pain. Immediately, she lost consciousness and went into shock. CT images of her abdomen revealed a huge retroperitoneal hematoma, with leakage of contrast medium in the hematoma in the left flank. These findings suggested left external iliac vein rupture.

Open surgery was considered; however, since the patient’s condition may have deteriorated further due to the time needed to prepare for surgery, including general anesthesia, transcatheter venous embolization of the left iliac vein was selected. A 5.2-Fr compliant balloon catheter (nominal diameter of 10 mm) was inflated at the distal site of the external iliac vein to reduce extravasation. N-butyl-2-cyanoacrylate (NBCA) was mixed with Lipiodol at a ratio of 1:2. The left Iliac vein was filled and completely embolized with the NBCA/Lipiodol mixture (total injected volume, 5 mL) using a 1.8-Fr microcatheter. After embolization, the patient quickly. An inferior vena cava filter was placed 1 day after embolization.

Conclusion

Spontaneous rupture of the iliac vein is a very rare and lethal condition. Transcatheter venous embolization may control potentially life-threatening bleeding. Rapid bleeding control in a critical condition is facilitated by this minimally invasive approach.
Fortification performance of polyurethane coating in outdoor historical ironworks
Authors: Reda Y. , Abdelbar M. , El-Shamy A. M.
Published: April 2021

Background

Ironworks in the tomb of Suleiman Pasha Al-Faransawi (located in the old Cairo, Egypt) were exposed in the open-air are susceptible to various corrosion factors, which be contingent on the environmental conditions wherein the artifacts are displayed and the existence of a protective layer or not. Examinations and analysis were conducted to identify the structure and type of the alloys used in making the decorative ironworks, to identify the manufacturing technique and decoration, and to study the nature of rust compounds. This has been achieved by using metallographic microscopy, X-ray diffraction, and a carbon–sulfur analyzer. Many protection approaches have been worked such as varnishes, waxes, and oils, but they have had many disadvantages. The aim of this paper is to assess the competence of polyurethane coating by using electrochemical measurements (electrochemical impedance spectroscopy (EIS) and potentiodynamic polarization) in the fortification of ironworks exposed in the outdoor environment.

Results

The results confirmed that the decorative ironworks were manufactured from wrought and gray cast iron. The main corrosion products identified by XRD are goethite, akageneite, and maghemite. Lead oxide hydrate refers to old lead paints (red primer) which have been applied to protect the ironworks. Quartz and calcite are the products of heavy dust particles that covered the surface.

Conclusion

The data proved that the polyurethane is acting as a good protective coating for the decorative ironworks exposed in an uncontrolled environment. The 2% is considered as the recommended dose for this polymer for the minimum corrosion rate of the ironworks.
Effect of milk replacer allowance on calf faecal bacterial community profiles and fermentation
Authors: Kumar Sandeep , Khan M. Ajmal , Beijer Emma , Liu Jinxin , Lowe Katherine K. , Young Wayne , Mills David A. , Moon Christina D.
Published: April 2021

Background

The nutrition of calves from birth until weaning is predominantly from liquid (milk or milk-based) feeds. Liquid feed allowances are often restricted during artificial rearing to accelerate the development of the rumen by promoting solid feed intake. Liquid feeds bypass the rumen and are digested in the lower digestive tract, however, the influence of different types of milk feeds, and their allowances, on the calf hindgut microbiota is not well understood. In this study, faecal samples from 199 calves raised on three different allowances of milk replacer: 10% of initial bodyweight (LA), 20% of initial bodyweight (HA), and ad libitum (ADLIB), were collected just prior to weaning. Bacterial community structures and fermentation products were analysed, and their relationships with calf growth and health parameters were examined to identify potential interactions between diet, gut microbiota and calf performance.

Results

Differences in the total concentrations of short-chain fatty acids were not observed, but higher milk replacer allowances increased the concentrations of branched short-chain fatty acids and decreased acetate to propionate ratios. The bacterial communities were dominated by Ruminococcaceae, Lachnospiraceae and Bacteroides, and the bacterial diversity of the ADLIB diet group was greater than that of the other diet groups. Faecalibacterium was over three times more abundant in the ADLIB compared to the LA group, and its abundance correlated strongly with girth and body weight gains. Milk replacer intake correlated strongly with Peptococcus and Blautia, which also correlated with body weight gain. Bifidobacterium averaged less than 1% abundance, however its levels, and those of Clostridium sensu stricto 1, correlated strongly with initial serum protein levels, which are an indicator of colostrum intake and passive transfer of immunoglobulins in early life.

Conclusions

Higher milk replacer intakes in calves increased hindgut bacterial diversity and resulted in bacterial communities and short chain fatty acid profiles associated with greater protein fermentation. Increased abundances of beneficial bacteria such as Faecalibacterium, were also observed, which may contribute to development and growth. Moreover, correlations between microbial taxa and initial serum protein levels suggest that colostrum intake in the first days of life may influence microbiota composition at pre-weaning.
Awareness and use of family planning methods among women in Northern Saudi Arabia
Authors: Alenezi Ghzl Ghazi , Haridi Hassan Kasim
Published: April 2021

Background

Evaluation of awareness and use of family planning methods is important to improve services and policies. This study aimed to assess awareness and use of family planning methods among women in an urban community in the north of Saudi Arabia.

A cross-sectional study was carried out in a maternity hospital and 12 primary health care (PHC) centers in Hail City between December 1st, 2019, and May 30, 2020.

Results

Four hundred married sexually active women aged 18–49 years were interviewed using a pretested structured questionnaire. The mean age of the participant was 32.0±7.5 years, 73.5% were university educated, and 58% were housewives. More than two-thirds of them (67.6%) had ≥3 living children. Most women (85%) ever used, and 66.5% were currently using any method of contraception; however, only one in five who get counseling for the contraceptive method used, and 40% of the last births were unplanned for. Almost all women reported unavailable family planning clinics in their primary healthcare centers. Most participants (83.0%) desired to have >3 children, which indicates that the main purpose of family planning was child spacing rather than limitation. Relying on natural methods as being safer (36.3%), desire to have more children (19%), being afraid from side effects (15.3%), and possibility of difficulty getting pregnant or might cause infertility (13.0%) were reasons the participants viewed for unsung modern contraceptives.

Conclusion

This study revealed that most women in urban Hail community, northern Saudi Arabia, were aware about and have a positive attitude towards family planning. The majority of the participants ever used, and two-thirds were currently using any contraceptive method/s, which is higher than the national estimate for Saudi Arabia. However, only one in five counseled by healthcare providers for the type of contraceptive method used. Unavailability of family planning services in primary health care centers impedes getting professional counseling. It is imperious to consider family planning clinics to provide quality family planning services.
Screening for dysphagia in dysphonic patients with non-neoplastic vocal fold lesions by Arabic EAT-10: cross-sectional study
Authors: Ghandour Hassan Hosny , Hadhoud Yara Hany , ElFiky Yomna Hassan
Published: April 2021

Background

Dysphagia is described as any disruption in the normal swallowing starting from the preparatory transport of a bolus from the oral cavity through both pharynx and esophagus down to the stomach. The purpose of this study is to detect the different symptoms of Dysphagia in dysphonic patients with non-neoplastic vocal fold lesions to consider the potential benefit of swallowing therapy hand in hand with the voice intervention strategies.

Methods

The Arabic Eating Assessment Tool-10 (A-EAT-10) was applied on 50 patients with age ranging from 15 to 50 years diagnosed as being dysphonic secondary to non-neoplastic vocal fold lesions on objective and clinical measures. Patients with a score above three will be considered to have dysphagia.

Results

Application of Arabic EAT-10 on dysphonic patients with minimal associated pathological lesions revealed swallowing difficulties that are not due to their vocal pathological condition. In the current study, 12 patients from the studied sample (24% of the patients) complained of phonasthenic symptoms and these symptoms may be misinterpreted by the patients as dysphagia. Symptoms of comorbid phonasthenia may be misinterpreted by the patients as dysphagia.

Conclusions

Although non-neoplastic vocal fold lesions are not the etiological factor for dysphagia, these group of patients still complains on subjective screening tools like A-EAT-10. The dysphagic symptoms in this group of patients may be related to the comorbid phonasthenia, and treatment of phonasthenia by voice therapy could alleviate these symptoms.
Introduction to this special section: The role of geophysics in a net-zero-carbon world
Authors: Falcon-Suarez Ismael Himar , Bathija Arpita Pal
Published: April 2021

Human activities are changing the earth's climate, causing increasingly disruptive social and ecological impacts. These impacts can be reduced if global carbon dioxide (CO2) emissions reach net zero in the near future. A net-zero-carbon world can be achieved by using energy more efficiently and responsibly; transitioning toward energy sources, products, and services that minimize greenhouse gas release; and implementing existing and novel technologies to remove and store CO2 from the atmosphere.
Seismic-derived geomechanical properties of potential CO2 storage reservoir and cap rock in Smeaheia area, northern North Sea
Authors: Fawad Manzar , Rahman Md Jamilur , Mondol Nazmul Haque
Published: April 2021

Geologic CO2 storage site selection requires reservoir, seal, and overburden investigation to prevent injection- and storage-related risks. Three-dimensional geomechanical modeling and flow simulation are crucial to evaluate these mechanical-failure-related consequences; however, the model input parameters are limited and challenging to estimate. This study focuses on geomechanical properties extracted from seismic-derived elastic property cubes. The studied reservoirs (Middle Jurassic Sognefjord, Fensfjord, and Krossfjord formation sandstones) and cap rocks (Heather and Draupne formation shales) are located in the Smeaheia area, northern North Sea, and are evaluated for a potential CO2 storage site. From the elastic property cubes, i.e., acoustic impedance, P- to S-wave velocity ratio, and bulk density, we obtained geomechanical property cubes of Young's modulus, Poisson's ratio, shear modulus, lambda-rho, and mu-rho. Petrophysical property cubes such as porosity and shale volume were also available and were extracted from the elastic property cubes using deterministic methods. We evaluated the geomechanical properties to observe their relationship with depth, compaction/cementation, and petrophysical properties to characterize the cap and reservoir rocks. We found good coherence between the geomechanical and petrophysical properties and their relationship with compaction as a function of depth. The brittleness analyses using elastic property crossplots reveal that both the cap and reservoir rocks are mainly ductile to less ductile, posing lower fracturing risk during CO2 injection. This also indicates lower risks of associated microseismic and possible CO2 leakage.
A direct noise attenuation approach in processing of land continuous records
Authors: Li Chengbo , Mosher Charles C. , Zhang Yu
Published: April 2021

Blended source acquisition has drawn great attention in industry due to its increased efficiency and reduced overall cost for acquiring seismic data. It eliminates the requirement of a minimum time (usually determined by record length) between adjacent shots and allows multiple sources to be activated simultaneously and independently. Conventional processing simply converts continuous records into fixed-length records using the source excitation time and then applies traditional denoising techniques to the fixed-length records. Source excitation time is used to extract fixed-length records that are the equivalent of traditional synchronous recording. Here, we elaborate on the usage of continuous records for land noise attenuation. Compared to conventional common shot/receiver/midpoint/offset domains, continuous records represent the data in the naturally recorded domain. This domain offers flexible and much longer record lengths to work with and, moreover, enables exploiting the characteristics of noise prior to correlation, shot slicing, or other preprocessing. We limit our discussions to the techniques and methods for attenuating coherent environmental and source-generated noise on vibroseis data. We have found that incoherent noise can be handled effectively by traditional noise suppression methods after deblending. We illustrate the effectiveness of noise attenuation in the continuously recorded domain for three different types of noise using field examples from the North Slope of Alaska and the Permian Basin.
Reviews
Authors: Krebes Edward S.
Published: April 2021

Classical Mechanics in Geophysical Fluid Dynamics, by Osamu Morita, ISBN 978-0-367-26649-3, 2019, CRC Press, 320 p.
Next Steps: Sequencing Therapies in Metastatic Kidney Cancer in the Contemporary Era
Authors: Schmidt Andrew L. , Tabakin Alexandra L. , Singer Eric A. , Choueiri Toni K. , McKay Rana R.
Published: April 2021

Systemic therapy for first-line metastatic renal cell carcinoma has evolved toward immune checkpoint blockade combinations incorporating a PD-1/L1 inhibitor along with CTLA-4 inhibition or VEGF-targeted therapy. The new treatment paradigm that integrates immunotherapy for treatment-naïve advanced metastatic renal cell carcinoma creates a new therapeutic challenge for clinicians including the optimal way to integrate multidisciplinary care involving surgery, radiotherapy, and application of contemporaneous systemic treatment in subsequent lines of therapy following discontinuation of combination therapy. We outline the available data for the multidisciplinary management of metastatic renal cell carcinoma, systemic therapy options in the post–immune checkpoint blockade setting, and novel therapies in development for advanced renal cell carcinoma. We provide practical considerations to assist clinicians in treatment choice and map future directions for progress.
Implementation of a Quality Improvement Project to Increase Access to Dietitian Services for Patients With Gastrointestinal Cancer in a Safety-Net Hospital System
Authors: Levonyak Nicholas S. , Hodges Mary P. , Haaf Nicole , Mhoon Verca , Lopez Ricardo , Little Jones Amy , Sanjeevaiah Aravind , Kainthla Radhika , Beg Muhammad Shaalan , Kazmi Syed M.
Published: April 2021

PURPOSE:

Rates of malnutrition are high in patients with GI cancer, leading to poor outcomes. The aim of our project was to increase the rate of documented dietitian assessment in patients with GI cancer at Parkland Health and Hospital System from 5% to 25%.

METHODS:

Three PDSA cycles were conducted after identifying barriers to dietitian services. A registered dietitian was assigned to the GI oncology clinic during the first cycle, an adapted Malnutrition Screening Tool was implemented through the electronic medical record during the second cycle, and clinical staff training was performed during the third cycle. New patients with GI cancer seen by the registered dietitian had weight, Eastern Cooperative Oncology Group performance status, and serum albumin recorded at initial visit and 3-month follow-up. Paired t tests were performed. Emergency department visits and hospital admissions were also recorded during this time.

RESULTS:

Through these interventions, the percentage of patients with GI cancer with documented assessment by the registered dietitian increased from 5.1% in October 2018 prior to our interventions to 21.8% in July 2019 and has sustained in the 15%-20% range thereafter. From May to July 2019, there were 63 new patients with GI cancer seen by a registered dietitian. No significant difference was observed in average difference in weight and serum albumin level at initial visit and 3-month follow-up.

CONCLUSION:

A nutrition-focused quality improvement project led to a more than three-fold increase in the rate of documented dietitian assessment in patients with GI cancer.
Quantum tunneling from a Bardeen black hole
Authors: Xiang Li , Xie Yi
Published: April 2021

The tunneling probability of a Schwarzschild black hole is ill-defined, if the second-order WKB approximation is considered. In this letter, the second-order tunneling probability of a Bardeen black hole is carefully investigated, and it is found to be regularized by the magnetic charge q. When the black hole entropy is maintained to be non-negative and monotonic increasing, the magnetic charge is restricted by

. The minimal probability refers to such a transition that the final state is a black hole remnant of Planck length.
Optimal vaccination program for two infectious diseases with cross-immunity spreading on a network
Authors: Ye Yang , Zhang Qingpeng , Cao Zhidong , Dajun Zeng Daniel
Published: April 2021

There are often multiple diseases with cross-immunity competing for vaccination resources. Here we investigate the optimal vaccination program in a two-layer Susceptible-Infected-Removed (SIR) model, where two diseases with cross-immunity spread in the same population, and vaccines for both diseases are available. We identify three scenarios of the optimal vaccination program, which prevents the outbreaks of both diseases at the minimum cost. We analytically derive a criterion to specify the optimal program based on the costs for different vaccines.
Non-parametric sign prediction of high-dimensional correlation matrix coefficients
Authors: Bongiorno Christian , Challet Damien
Published: April 2021

We introduce a method to predict which correlation matrix coefficients are likely to change their signs in the future in the high-dimensional regime, i.e., when the number of features is larger than the number of samples per feature. The stability of correlation signs, two-by-two relationships, is found to depend on three-by-three relationships inspired by Heider social cohesion theory in this regime. We apply our method to US and Hong Kong equities historical data to illustrate how the structure of correlation matrices influences the stability of the sign of its coefficients.
Perioperative Management of Flecainide: A Problem-Based Learning Discussion
Authors: Acker Leah , Bova Campbell Kristen , Naglee Colleen , Taicher Brad , Bronshteyn Yuriy S.
Published: April 2021

Flecainide is a first-line antiarrhythmic drug used to treat atrial arrhythmias and/or supraventricular tachycardia in those without coronary artery disease or structural heart disease. Even though it is an older antiarrhythmic, flecainide accounted for 1.6 million prescriptions in the United States in 2016, and its utilization is generally increasing. Despite its popularity, flecainide may predispose patients to rapid atrial flutter with resultant hemodynamic compromise, particularly in the physiologically stressful perioperative period. This article reviews the pharmacology of flecainide, describes problematic arrhythmias that may arise specifically during flecainide use, and offers recommendations for perioperative flecainide management.
Teaching Medical Students to Create Anesthetic Plans Using a Branched-Chain Learning Module
Authors: Buhl Lauren K. , Wong Vanessa , Jones Stephanie B.
Published: April 2021

It is challenging to include medical students in the anesthetic decision-making process during their introductory clinical rotation in anesthesiology. Furthermore, the rotation is often too brief to even expose students to the variety inherent in anesthesia practice. We created a web-based, branched-chain learning module (BCLM) for medical students with alternate narratives and patient outcomes based on their anesthetic choices. In semistructured group interviews, students described how the BCLM met its educational objectives and gave constructive feedback on several ways to improve their experience with it, guiding the future use of BCLMs in medical education.
Diversity and robustness of bone morphogenetic protein pattern formation
Authors: Madamanchi Aasakiran , Mullins Mary C. , Umulis David M.
Published: April 2021

Pattern formation by bone morphogenetic proteins (BMPs) demonstrates remarkable plasticity and utility in several contexts, such as early embryonic development, tissue patterning and the maintenance of stem cell niches. BMPs pattern tissues over many temporal and spatial scales: BMP gradients as short as 1-2 cell diameters maintain the stem cell niche of the Drosophila germarium over a 24-h cycle, and BMP gradients of several hundred microns establish dorsal-ventral tissue specification in Drosophila, zebrafish and Xenopus embryos in timescales between 30 min and several hours. The mechanisms that shape BMP signaling gradients are also incredibly diverse. Although ligand diffusion plays a dominant role in forming the gradient, a cast of diffusible and non-diffusible regulators modulate gradient formation and confer robustness, including scale invariance and adaptability to perturbations in gene expression and growth. In this Review, we document the diverse ways that BMP gradients are formed and refined, and we identify the core principles that they share to achieve reliable performance.
Data science in cell imaging
Authors: Driscoll Meghan K. , Zaritsky Assaf
Published: April 2021

Cell imaging has entered the ‘Big Data’ era. New technologies in light microscopy and molecular biology have led to an explosion in high-content, dynamic and multidimensional imaging data. Similar to the ‘omics’ fields two decades ago, our current ability to process, visualize, integrate and mine this new generation of cell imaging data is becoming a critical bottleneck in advancing cell biology. Computation, traditionally used to quantitatively test specific hypotheses, must now also enable iterative hypothesis generation and testing by deciphering hidden biologically meaningful patterns in complex, dynamic or high-dimensional cell image data. Data science is uniquely positioned to aid in this process. In this Perspective, we survey the rapidly expanding new field of data science in cell imaging. Specifically, we highlight how data science tools are used within current image analysis pipelines, propose a computation-first approach to derive new hypotheses from cell image data, identify challenges and describe the next frontiers where we believe data science will make an impact. We also outline steps to ensure broad access to these powerful tools – democratizing infrastructure availability, developing sensitive, robust and usable tools, and promoting interdisciplinary training to both familiarize biologists with data science and expose data scientists to cell imaging.
Contextual behavioural plasticity in Italian agile frog (Rana latastei) tadpoles exposed to native and alien predator cues
Authors: Gazzola Andrea , Balestrieri Alessandro , Scribano Giovanni , Fontana Andrea , Pellitteri-Rosa Daniele
Published: April 2021

Predation is a strong driver for the evolution of prey behaviour. To properly assess the actual risk of predation, anuran tadpoles mostly rely on water-borne chemical cues, and their ability to evaluate environmental information is even more crucial when potential predators consist of unknown alien species. Behavioural plasticity – that is, the capacity to express changes in behaviour in response to different environmental stimuli – is crucial to cope with predation risk. We explored the defensive behaviour of Italian agile frog (Rana latastei) tadpoles when exposed to the chemical cues of two predator species, one native (dragonfly larvae) and one alien (red swamp crayfish). Firstly, we observed whether a plastic life history trait (i.e. hatching time) might be affected by native predatory cues. Secondly, we recorded a suite of behavioural responses (activity level, lateralization and sinuosity) to each cue. For assessing lateralization and sinuosity, we developed a C++ code for the automatic analysis of digitally recorded tadpole tracks. Hatching time seemed not to be affected by the potential risk of predation, while both predator species and diet affected tadpoles’ defensive behaviour. Tadpoles responded to a predator threat by two main defensive strategies: freezing and ‘zig-zagging’. While the first behaviour had previously been reported, the analysis of individual trajectories indicated that tadpoles can also increase path complexity, probably to prevent predators from anticipating their location. We also recorded a decrease in lateralization intensity, which suggests that under predation risk, tadpoles tend to scrutinize the surrounding environment equally on both sides.
Distance estimation by Asian honey bees in two visually different landscapes
Authors: George Ebi Antony , Thulasi Neethu , Kohl Patrick L. , Suresh Sachin , Rutschmann Benjamin , Brockmann Axel
Published: April 2021

Honey bees estimate distances to food sources using image motion experienced on the flight path and they use this measure to tune the waggle phase duration in their dance communication. Most studies on the dance-related odometer are based on experiments with Apis mellifera foragers trained in small tunnels with black and white patterns, which allows the creation of quantifiable changes in optic flow. In this study, we determined the waggle phase duration-distance curves of two Asian honey bee species, Apisflorea and Apiscerana, in two different natural environments with clear differences in the vegetation conditions and hence visual contrast. We found that the dense vegetation condition (with higher contrast) elicited a more rapid increase in the waggle phase duration with distance than the sparse vegetation condition in A. florea but not in A. cerana. Our findings suggest that contrast sensitivity of the waggle dance odometer might vary among honey bee species.
The Impact of Preoperative Breast MRI on Surgical Margin Status in Breast Cancer Patients Recalled at Biennial Screening Mammography: An Observational Cohort Study
Authors: Gommers Jessie J. J. , Duijm Lucien E. M. , Bult Peter , Strobbe Luc J. A. , Kuipers Toon P. , Hooijen Marianne J. H. , Mann Ritse M. , Voogd Adri C.
Published: April 2021

Background

This study aimed to examine the association between preoperative magnetic resonance imaging (MRI) and surgical margin involvement, as well as to determine the factors associated with positive resection margins in screen-detected breast cancer patients undergoing breast-conserving surgery (BCS).

Methods

Breast cancer patients eligible for BCS and diagnosed after biennial screening mammography in the south of The Netherlands (2008–2017) were retrospectively included. Missing values were imputed and multivariable regression analyses were performed to analyze whether preoperative MRI was related to margin involvement after BCS, as well as to examine what factors were associated with positive resection margins, defined as more than focally (>4 mm) involved.

Results

Overall, 2483 patients with invasive breast cancer were enrolled, of whom 123 (5.0%) had more than focally involved resection margins. In multivariable regression analyses, preoperative MRI was associated with a reduced risk of positive resection margins after BCS (adjusted odds ratio [OR] 0.56, 95% confidence interval [CI] 0.33–0.96). Lobular histology (adjusted OR 2.86, 95% CI 1.68–4.87), large tumor size (per millimeter increase, adjusted OR 1.05, 95% CI 1.03–1.07), high (>75%) mammographic density (adjusted OR 3.61, 95% CI 1.07–12.12), and the presence of microcalcifications (adjusted OR 4.45, 95% CI 2.69–7.37) and architectural distortions (adjusted OR 1.85, 95% CI 1.01–3.40) were independently associated with positive resection margins after BCS.

Conclusions

Preoperative MRI was associated with lower risk of positive resection margins in patients with invasive breast cancer eligible for BCS using multivariable analysis. Furthermore, specific mammographic characteristics and tumor characteristics were independently associated with positive resection margins after BCS.
Nitrogenization of Biomass-Derived Porous Carbon Microtubes Promotes Capacitive Deionization Performance
Authors: Sheng Xinran , Xu Xingtao , Wu Yue , Zhang Xiaojie , Lin Peng , Eid Kamel , Abdullah Aboubakr M , Li Zhengtong , Yang Tao , Nanjundan Ashok Kumar , Yamauchi Yusuke
Published: April 2021

Nitrogenization of porous carbon provides an effective methodology to promote capacitive deionization (CDI) performance. Exploring a new class of nitrogen-doped porous carbons from waste biomass over commercially available activated carbons is of significant interest in CDI. In this contribution, we present the preparation of nitrogen-doped porous carbon microtubes (N-CMTs) by pyrolyzing willow catkins, a naturally abundant biomass with urea as the nitrogen source. Due to the naturally occurring hollow microtube structure and the high nitrogen content, the as-prepared N-CMTs show an enhanced desalination performance compared to undoped samples. A high deionization capacity of 16.78 mg g−1 predicted by Langmuir isotherm and a stable cycling performance over ten cycles are observed. The result advocates the importance and significance of naturally developed architectures and chemistry for practical CDI application.
A noncanonical microRNA derived from the snaR-A noncoding RNA targets a metastasis inhibitor
Authors: Stribling Daniel , Lei Yi , Guardia Casey M. , Li Lu , Fields Christopher J. , Nowialis Pawel , Opavsky Rene , Renne Rolf , Xie Mingyi
Published: April 2021

MicroRNAs (miRNAs) are small noncoding RNAs that function as critical posttranscriptional regulators in various biological processes. While most miRNAs are generated from processing of long primary transcripts via sequential Drosha and Dicer cleavage, some miRNAs that bypass Drosha cleavage can be transcribed as part of another small noncoding RNA. Here, we develop the target-oriented miRNA discovery (TOMiD) bioinformatic analysis method to identify Drosha-independent miRNAs from Argonaute crosslinking and sequencing of hybrids (Ago-CLASH) data sets. Using this technique, we discovered a novel miRNA derived from a primate specific noncoding RNA, the small NF90 associated RNA A (snaR-A). The miRNA derived from snaR-A (miR-snaR) arises independently of Drosha processing but requires Exportin-5 and Dicer for biogenesis. We identify that miR-snaR is concurrently up-regulated with the full snaR-A transcript in cancer cells. Functionally, miR-snaR associates with Ago proteins and targets NME1, a key metastasis inhibitor, contributing to snaR-A's role in promoting cancer cell migration. Our findings suggest a functional link between a novel miRNA and its precursor noncoding RNA.
Ο ρόλος της μοριακής κυτταρολογίας στη διαχείριση γυναικών με παθολογία ενδομητρίου
Authors: Κουρέας Νικόλαος
Published: April 2021

Σκοπός: Σκοπός της παρούσης μελέτης είναι να διερευνηθεί η αξία της κυτταρολογίας υγρής φάσης στη διαγνωστική προσπέλαση αλλοιώσεων ενδομητρίου, η αξιοπιστία της τεχνικής αυτής στην εφαρμογή τεχνικών μοριακής βιολογίας και η διερεύνηση του ρόλου της μοριακής κυτταρολογίας υγρής φάσης ως πρωτογενούς δοκιμασίας ταξινόμησης γυναικών με παθολογία ενδομητρίου. Υλικό – Μέθοδοι: Μελετήθηκαν 866 ιστολογικά επιβεβαιωμένα ενδομητρικά δείγματα από γυναίκες ηλικίας 19 έως 89 ετών. Σε 61 από αυτά προσδιορίστηκε το επίπεδο μεθυλίωσης του γονιδίου GALR1 και υπολογίστηκε η μέση μεθυλίωση.Το σύνολο των δειγμάτων ταξινομήθηκε κυτταρολογικά σε 6 κατηγορίες βάσει συγκεκριμένων κριτηρίων και η κυτταρολογική ταξινόμηση συγκρίθηκε με την ιστολογική διάγνωση των δειγμάτων. Από 109 ιστολογικά επιβεβαιωμένα δείγματα, επιλέχθηκαν 49 κυτταρολογικά δείγματα υγρής φάσης στα οποία μελετήθηκε η έκφραση 8 miRNA. Τα υπόλοιπα εξήντα δείγματα αφορούσαν σε κύβους παραφίνης (FFPE, Formaldehyde Fixed-Paraffin Embedded) και χρησιμοποιήθηκαν για να προσδιοριστούν τα επίπεδα έκφρασης των ίδιων miRNA. Αποτελέσματα: Με τη μεθυλίωση του γονιδίου GALR1 ήταν δυνατόν να ταξινομηθούν σωστά 8 από τις 9 καλοήθεις περιπτώσεις και 20 από τις 21 κακοήθεις περιπτώσεις. Συνολική ακρίβεια 93,33%, ευαισθησία 95,24%, και εξειδίκευση 88,89%.Σύμφωνα με τα αποτελέσματα της κυτταρολογικής ταξινόμησης, ο κίνδυνος κακοήθειας με σχετικό εύρος αξιοπιστίας 95% είναι για τις κυτταρολογικά καλοήθεις περιπτώσεις 1,42% ± 0,98%, για τις περιπτώσεις ACE-L 4,30% ± 4,12%, για τις περιπτώσεις ACE-H 89,80% ± 8,47% και για τις κυτταρολογικά κακοήθεις περιπτώσεις 97,81% ± 2,45%. Ειδικότερα, ο κίνδυνος κακοήθειας για την κατηγορία ACE-U είναι 44,44% ± 32,46%, ενώ το υψηλό εύρος αξιοπιστίας αποδίδεται στο γεγονότος ότι αυτή η κατηγορία περιελάμβανε μόνο εννέα περιπτώσεις (1,04% όλων των διαγνώσεων). Η έκφραση 7 miRNAs ήταν σημαντικά υψηλότερη σε κακοήθη δείγματα, ενώ η συνδυαστική χρήση τριών miRNAs επέτρεψε την αξιολόγηση 4 ιστολογικά επαληθευμένων καρκινωμάτων ως κακοήθη ενώ η κυτταρολογική αξιολόγηση τα είχε κατατάξει ως ανεπαρκή (n=3) ή καλοήθη (n=1). Συμπέρασμα: Η παρούσα εργασία αποδεικνύει ότι η κυτταρολογία υγρής φάσης είναι μια αξιόπιστη μέθοδος δειγματοληψίας που είναι καλά ανεκτή, εύκολη στη χρήση, λιγότερο επώδυνη από τη βιοψία, η οποία επιτρέπει την εφαρμογή τεχνικών μοριακής βιολογίας όπως η μεθυλίωση του GALR1 γονιδίου και η έκφραση των miRNAs και την πρωτογενή ταξινόμηση γυναικών με ενδομητρική παθολογία, γεγονός που την καθιστά πολύτιμο εργαλείο στη διαχείριση γυναικών με παθολογία ενδομητρίου.
Using historical and citizen science data to improve knowledge about the occurrence of the elusive sandbar shark Carcharhinus plumbeus (Chondrichthyes – Carcharhinidae) in the Adriatic Sea
Authors: JAMBURA PATRICK L. , ĆETKOVIĆ ILIJA , KRIWET JÜRGEN , TÜRTSCHER JULIA
Published: April 2021

The Mediterranean Sea is an extinction hotspot for sharks, skates, and rays, with at least half of all species being threatened. The sandbar shark Carcharhinus plumbeus is among the most threatened species and is declared endangered (EN) in the Mediterranean according to the IUCN Red List of Threatened Species. The Adriatic Sea was previously proposed to be an important nursery area for this species based on sporadic sightings of neonates and juveniles. However, this species is generally considered to be rare in this region, and reports of its presence are scarce. Here, we present new records for the sandbar shark in the Adriatic Sea and review spatial and temporal data accumulated from literature, museum specimens, and citizen science initiatives in an attempt to assess the distribution and seasonality of this species. The majority of the records were from neonate and juvenile sandbar sharks, and three hotspots for their occurrence could be identified: (1) the Emilia-Romagna region, (2) the Veneto region, and (3) the Gulf of Trieste. Our data indicate a high concentration of sandbar sharks around the delta of the Po river, emphasising the need for scientific surveys in this confined area in order to confirm a possible nursery ground. Data collected by citizen science initiatives reveal that this species is still present in the Adriatic Sea and might be more abundant than previously thought, underlining the potential of citizen science as a valuable tool to monitor the distribution of rare and endangered species.
Toward the widespread application of low-cost technologies in coastal ocean observing (Internet of Things for the Ocean)
Authors: MARCELLI MARCO , PIERMATTEI VIVIANA , GERIN RICCARDO , BRUNETTI FABIO , PIETROSEMOLI ERMANNO , ADDO SAM , BOUDAYA LOBDA , COLEMAN RICHARD , NUBI OLULUNMI AYOOLA , JOJANNES RICK , SARKER SUBRATA , SOHOU ZACHARIE , ZENNARO MARCO , WHILTSHIRE KAREN , CRISE ALESSANDRO
Published: April 2021

The ability to access user-friendly, low-cost instrumentation remains a limiting factor in coastal ocean observing. The majority of currently available marine observation equipment is difficult to deploy, costly to operate, and requires specific technical skills. Moreover, a harmonized observation program for the world’s coastal waters has not yet been established despite the efforts of the global ocean organizations. Global observational systems are mainly focused on open ocean waters and do not include coastal and shelf areas, where models and satellites require large data sets for their calibration and validation. Fortunately, recent technological advances have created opportunities to improve sensors, platforms, and communications that will enable a step-change in coastal ocean observing, which will be driven by a decreasing cost of the components, the availability of cheap housing, low-cost controller/data loggers based on embedded systems, and low/no subscription costs for LPWAN communication systems. Considering the above necessities and opportunities, POGO’s OpenMODs project identified a series of general needs/requirements to be met in an Open science development framework. In order to satisfy monitoring and research necessities, the sensors to be implemented must be easily interfaced with the data acquisition and transmission system, as well as compliant with accuracy and stability requirements. Here we propose an approach to co-design a cost-effective observing modular instrument architecture based on available low-cost measurement and data transmission technologies, able to be mounted/operated on various platforms. This instrument can fit the needs of a large community that includes scientific research (including those in developing countries), non-scientific stakeholders, and educators.
Species and habitats of conservation interest in the Ecologically and Biologically Significant Area of the Strait of Sicily: a contribution towards the creation of a Specially Protected Areas of Mediterranean Importance
Authors: CONSOLI PIERPAOLO , ALTOBELLI CHIARA , PERZIA PATRIZIA , BO MARZIA , ROSSO ANTONIETTA , ALONGI GIUSEPPINA , SERIO DONATELLA , CANESE SIMONEPIETRO , ROMEO TERESA , ANDALORO FRANCO
Published: April 2021

In 2015, the Strait of Sicily, which includes several banks, was candidate as a future Specially Protected Area of Mediterranean Importance (SPAMI) by the Contracting Parties of the Barcelona Convention. In this context, the present study aims to provide the first biological and ecological characterisation of this poorly known area, focusing on habitats and species of conservation concern. Surveys were carried through a remotely operated vehicle (ROV) and allowed the identification of 19 habitat types, mostly considered of priority interest by the SPA/BD Protocol of the Barcelona Convention. A total of 269 taxa were also identified, mostly Porifera, Cnidaria and Pisces, among which 115 species are of conservation concern according to the International Union for Conservation of Nature (IUCN) Red Lists, the Habitats Directive, the Bern Convention, the SPA/BD Protocol and CITES. ROV surveys allowed some interesting observations on poorly known species and habitats. Results underlined that remarkable discrepancies in species conservation status assessment that exist between the several lists of protected species considered. The IUCN Red Lists, although not legally binding for European States, are the most complete, but, in spite of this, the conservation policies in the EU are largely focused on the Habitats Directive, which is really not exhaustive. An exhaustive and legally binding instrument to protect species of conservation concern at European scale is highly recommended. Acquired results could be useful for the delimitation of a future SPAMI or a network of Marine Protected Areas (including the investigated banks) and the identification of zones within them suitable for different area-based management measures.