bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient reaction deletion algorithms for redesign of constraint-based metabolic networks for metabolite production with weak coupling
Authors: Tamura Takeyuki 
Published: February 2020

Abstract
Background: Metabolic network analysis through flux balance is an established method for the computational redesign of production strains in metabolic engineering. The computational redesign is often based on reaction deletions from the original wild type networks. A key principle often used in this method is the production of target metabolites as by-products of cell growth. From a viewpoint of bioinformatics, it is very important to prepare a set of algorithms that can determine reaction deletions that achieve growth coupling whatever network topologies, target metabolites and parameter values will be considered in the future. Recently, the strong coupling-based method was used to demonstrate that the coupling of growth and production is possible for nearly all metabolites through reaction deletions in genome-scale metabolic models of Escherichia coli and Saccharomyces cerevisiae under aerobic conditions. However, when growing S. cerevisiae under anaerobic conditions, deletion strategies using the strong coupling-based method were possible for only 3.9% of all metabolites. Therefore, it is necessary to develop algorithms that can achieve growth coupling by reaction deletions for the conditions that the strong coupling-based method was not efficient.
Results: We developed an algorithm that could calculate the reaction deletions that achieve the coupling of growth and production for 91.3% metabolites in genome-scale models of S. cerevisiae under anaerobic conditions. This analysis was conducted for the worst-case scenario using flux variability analysis. To demonstrate the feasibility of the coupling, we derived appropriate reaction deletions using the new algorithm for target production in which the search space was divided into small cubes (CubeProd).
Conclusions: We developed a novel algorithm, CubeProd, to demonstrate that growth coupling is possible for most metabolites in S.cerevisiae under anaerobic conditions. This may imply that growth coupling is possible by reaction deletions for most target metabolites in any genome-scale constraint-based metabolic networks. The developed software, CubeProd, implemented in MATLAB, and the obtained reaction deletion strategies are freely available.
The association of water supply, sanitation and hygiene interventions and childhood malnutrition in Kersa and Omo Nada districts of Jimma Zone, Ethiopia: A case-control study
Authors: Soboksa Negasa Eshete , Gari Sirak Robele , Hailu Abebe Beyene , Alemu Bezatu Mengistie 
Published: February 2020

Abstract
Background: Malnutrition is the widely known nutritional disorder and one of the leading causes of morbidity and mortality among children in developing countries like Ethiopia. About 50% of under-nutrition around the world is associated with infections caused by unsafe water, inadequate sanitation or insufficient hygiene. However, there are limited available data which associate water supply, sanitation and hygiene practices and childhood malnutrition in Ethiopia particularly in the study area. Therefore, the objective of this study was designed to examine the association of water supply, sanitation and hygiene interventions and childhood malnutrition.Methods: Case-control study design was conducted from December 2018 to January 2019 Kersa and Omo Nada districts of Jimma Zone, Southwest Ethiopia. Randomly 126 cases and 252 controls were selected from the malnourished children and normal children, respectively. A pretested, structured, interviewer-administered questionnaire was used. Bivariate and multivariable logistic regression analyses were used to identify the study variables associated with childhood malnutrition and to adjust for confounders. The crude and adjusted odds ratios with 95% confidence interval was calculated to assess the level of significance and reported for each confounding variable.Results: The results of this study showed that children living with mothers/caregivers lack of formal education were found to have 57% times less likely developed malnourished, compared to those living with mother/caregiver who attended secondary and above (AOR = 0.57; 95% CI: 0.26-1.24). The odds of having malnutrition were increased among children who were breastfed after one hour of birth (AOR=2.60; 95% CI: 1.02-6.65) and children who had diarrhea (AOR=9.50; 95% CI: 5.19-17.36).Collecting water from a distance of less than/equal to one kilometer (AOR=2.52; 95% CI: 0.56-11.39), defecating in open pit(AOR=1.33; 95% CI: 0.62-2.83),under-five children open field defecation practices (AOR=1.17; 95% CI: 0.42-3.23) and lack of hand washing at critical times (AOR=2.38; 95% CI: 1.07-5.29) were positively associated with childhood malnutrition. Conclusion: We conclude that improvement in the initiation of breastfeeding within one hour, diarrhea prevention, use of improved latrine and hand washing at critical times is needed to improve the nutritional status of children.
The Impact of Summer Vacation on Children’s Obesogenic Behaviors and Body Mass Index: A natural experiment.
Authors: Weaver R Glenn , Armstrong Bridget , Hunt Ethan , Beets Michael , Brazendale Keith , Dugger Roddrick , Turner-McGrievy Gabrielle , Pate Russell , Maydeu-Olivares Alberto , Saelens Brian , Youngstedt Shawn 
Published: February 2020

Abstract
Background: Children’s BMI gain accelerates during summer. The Structured Days Hypothesis posits that the lack of the school day during summer vacation negatively impacts children’s obesogenic behaviors (i.e., physical activity, screen time, diet, sleep). This natural experiment examined the impact of summer vacation on children’s obesogenic behaviors and body mass index (BMI). Methods: Elementary-aged children (n=285, grade=1-5, 48.7% male, 57.4% African American) attending a year-round (n=97) and two match-paired traditional schools (n=188) participated in this study. Obesogenic behaviors were collected during three conditions: Condition 1) all children attend school, Condition 2) year-round children attend school while traditional children were on summer vacation, and Condition 3) summer vacation for all children. Changes in BMI z-score were collected for the corresponding school years and summers. Multi-level mixed effects regressions estimated obesogenic behaviors and monthly zBMI changes. It was hypothesized that children would experience unhealthy changes in obesogenic behaviors when entering summer vacation because the absence of the school day (i.e., Condition 1 vs. 2 for traditional school children and 2 vs. 3 for year-round school children). Results: From Condition 1 to 2 traditional school children experienced statistically significantly greater unhealthy changes in daily minutes sedentary (∆=24.2, 95CI=10.2, 38.2), screen time minutes (∆=33.7, 95CI=17.2, 50.3), sleep midpoint time (∆=73:43, 95CI=65:33, 81:53), and sleep efficiency percentage (-∆=0.7, 95CI=-1.1, -0.3) when compared to year-round school children. Alternatively, from Condition 2 to 3 traditional school children experienced statistically significantly smaller unhealthy changes in daily minutes sedentary (∆=-54.5, 95CI=-70.9, -38.0), MVPA minutes (∆=11.4, 95CI=3.7, 19.1), screen time minutes (∆=-46.5, 95CI=-63.0, -30.0), sleep midpoint time (∆=-95:54, 95CI=-106:22, -85:26), and sleep efficiency percentage (-∆=0.7, 95CI=-1.1, -0.3) when compared to year-round school children. Monthly zBMI gain accelerated during summer for traditional (∆=0.033 95CI=0.019, 0.047) but not year-round school children (∆=0.004, 95CI=-0.014, 0.023).Conclusions: This study suggests that the lack of the school day during summer vacation negatively impacts sedentary behaviors, sleep timing, and screen time. Changes in sedentary behaviors, screen time, and sleep midpoint may contribute to accelerated summer BMI gain. Providing structured programming during summer vacation may positively impact these behaviors, and in turn, mitigate accelerated summer BMI gain.
Recurrence of ovarian squamous cell carcinoma with MET gene copy number variation: a case report and review of literature
Authors: Dong Xuhui , Yuan Lei , Yao Liangqing 
Published: February 2020

Abstract
Background: Malignant transformation such as ovarian squamous cell carcinoma (SCC) in ovarian mature cystic teratoma (OMCT) is a rare tumor. The gene mutation of ovarian SCC remains unclear. We herein report a recurrent case of ovarian squamous cell carcinoma with MET gene copy number variation. Case presentation: A 60-year-old woman presented with recurrence of ovarian SCC 8 months after primary surgery. Adhesiolysis, right abdominal wall mass excision, prosthetics, enterectomy, enterostomy and partial cystectomy were performed by laparoscope. Pathologic examination demonstrated metastatic squamous cell carcinoma in ileocecus, rectum and abdominal wall muscle. MET gene copy number was elevated with copy number of six in this case. Postoperatively, the patient was treated with four cycles of combination chemotherapy with docetaxel and carboplatin. The patient was free of disease at 20 months’ follow-up. Conclusions: Optimal cytoreductive surgery combined with platinum-based chemotherapy is recommended currently for not only primary tumor but also recurrence. For patients with malignant transformation in OMCT, prompt diagnosis and individualized treatment are crucial for better prognosis. Increased copy number of MET may be correlated with her poor PFS and can be a potential therapeutic target for this case.
Papillary thyroid cancer with para-aortic lymph node metastasis discovered incidentally during work-up of metastatic colon cancer: a case report
Authors: Wang Yi , Zhou Rongjing , Xie Shangnao 
Published: February 2020

Abstract
Background: Papillary thyroid cancer usually manifests an indolent behavior and infrequently causes rare distant metastases, with the exclusion of lung and bone metastases. Metastasis to the para-aortic lymph node from papillary thyroid cancer is extremely rare. Case presentation: The present study reports a case of a 71-year-old Chinese female with para-aortic lymph node metastasis from papillary thyroid cancer 12 months following total thyroidectomy, and synchronous intra-abdominal metastasis from colon cancer 18 months following right hemicolectomy. The patient was administered chemotherapy combined with targeted therapy post-operation. She developed lung metastasis and intra-abdominal relapse 6 months after the operation, and died of progressive disease 12 months after presentation. Conclusion: This study is the first to report a case of para-aortic lymph node metastasis from papillary thyroid cancer. Keywords: Papillary thyroid cancer, Lymph node, Metastasis
A rare primary leiomyosarcoma of the thyroid gland: a case report and literature review
Authors: Hao Shuai , Huang Miao , Tian Wuguo , Zhao Jianjie , Gao Bo , Luo Donglin 
Published: February 2020

Abstract
Background Primary thyroid leiomyosarcoma(LMS) is very rare, with only 30 cases reported worldwide. Thyroid LMS should be diagnosed with caution and comprehensively evaluated considering clinical, imaging, and pathological data. It is a kind of fatal tumor with an extremely poor prognosis and lacks effective treatment regimens, and most patients die within 1 year of diagnosis. Here, we present a case report on a patient with Primary thyroid LMS. Case presentation A 76-year-old woman presented with hoarseness, dysphagia, and dyspnea when lying down for the past 1 month visited our hospital. She had a history of right neck masses in the past 2 years. A hard, irregular tumor of approximately 8 cm × 5 cm × 5 cm was observed on the right lobe of the thyroid, the boundary between which and the surrounding tissues was unclear. The tumor anteriorly invaded the cervical muscles and interiorly invaded the right walls of the trachea and esophagus. Most tumor tissues were excised, a curative operation seemed impossible. Immunohistochemically, the tumor cells were positive for Calponin, vimentin and SMA, but negative for EMA, CK, P53, Desmin and S-100. Tumor recurrence and progression were considered two months after surgery, the patient refused follow-up treatment for personal reasons and died 4 months after surgery. Conclusion Thyroid LMS accounting for merely 0.014% of primary thyroid tumors of unknown etiology. The diagnosis can only be confirmed upon a lack of evidence regarding epithelial differentiation or other types of sarcoma differentiation and when immunohistochemistry yields positive smooth muscle markers. Primary thyroid LMS is primarily surgically resected and no other effective treatment currently available. Disease progression is rapid, the prognosis is poor, and the 1-year survival rate is <10%. In the present study, a rare case of a 76-year-old female patient diagnosed with thyroid LMS was reported and a review of the literature is presented.
Development of Pathological Super-resolution Images using Artificial Intelligence based on Whole Slide Image
Authors: Deng Yang , Feng Min , Jiang Yong , Zhou Yanyan , Qing Hangyu , Xiang Fei , Wang Yizhe , Bao Ji , Bu Hong 
Published: February 2020

Abstract
Background: Pathology plays a very important role in the cancer diagnosis, as the gold standard for the identification of tumors. The rapid development of digital pathology (DP) which based on Whole Slide Image (WSI) has led to many improvements in telepathological consultation, digital management, and computer-assisted diagnosis by artificial intelligence (AI). In DP, the common digitization strategy is to scan the pathology slice with X20 or X40 objective. Usually, the X40's WSI is 4 times bigger than the X20's, and obviously, the storage space and transmission time of the data should be 4 times. These increased costs will be great negative factor in the popularization of DP. But at the same time, some cases have to use the high magnification WSI for reliable diagnosis. Methods: In this article, we present a novel super-resolution process which could be used for WSI through Deep Learning. This process powered by AI, have the ability to switch X20 WSI to X40 without loss of whole and locally features. Furthermore, we collect the examples of WSI data of patients with 100 uterine leiomyosarcoma and adult granulosa cell tumor (AGCT) of ovary respectively, which are used to test our super-resolution process. Results: We used the peak signal-to-noise ratio (PSNR), the structural similarity (SSIM), and the Blind/Referenceless Image Spatial QUality Evaluator (BRISQUE) to test the resulting X40 WSI synthesized by the super-resolution (SR), which were 42.03, 0.99 and 49.22 . Then, we tested our SR images from subjective evaluation of the pathologist's perspective, and tested that if the pathologists could objectively distinguish the images between SR and high-resolution (HR), to further confirm the consistency between our SR images and the real HR images. Conclusions: The testing results indicate that the X40 WSI synthesized by the super-resolution matches the performance of the one generated from the X40 objective in diagnosis of both tumors. We believe that this is a reliable method can be used in a variety of tumors' digital slides, and will be available for a large scale in clinical pathology as an innovative technique.
Detecting abnormal fundus images by employing deep transfer learning
Authors: Yu Yan , Chen Xiao , Zhu Xiang-Bing , Zhang Peng-Fei , Hou Yin-Fen , Zhang Rong-Rong , Wu Chang-Fan 
Published: February 2020

Abstract
Background: To develop and validate a deep transfer learning (DTL) algorithm for detecting abnormalities in fundus images from nonmydriatic fundus photography examinations.
Methods : A total of 1,295 fundus images from January 2017 to December 2018 at Yijishan Hospital of Wannan Medical College were collected for developing and validating the deep transfer learning algorithm in detecting abnormal fundus images. The DTL model was developed by using 929 (normal 254, abnormal 402) fundus images, including normal fundus images and abnormal fundus images, the latter including maculopathy, optic neuropathy, vascular lesion, choroidal lesions, vitreous disease, and cataracts. We tested our model using a subset of the publicly available Messidor dataset (using 366 images) and evaluated the testing performance of the DTL model for detecting abnormal fundus images.
Results : In the internal validation dataset (n=273 images), the AUC, sensitivity, accuracy, and specificity of the DTL for correctly classified fundus images were 0.997, 97.41%, 97.07%, and 96.82%, respectively. For the test dataset (n=273 images), the AUC, sensitivity, accuracy, and specificity of the DTL for correctly classifying fundus images were 0.926, 88.17%, 87.18%, and 86.67%, respectively.
Conclusion : In the evaluation, the DTL presented high sensitivity and specificity for detecting abnormal fundus-related diseases. Further research is necessary to improve this method and evaluate the applicability of the DTL in the community health care center.
Key words : Fundus images; Deep transfer learning; Developing and validation; Artificial intelligence.
Metamorphic amphiboles in the Ironwood Iron-Formation, Gogebic Iron Range, Wisconsin: Implications for potential resource development
Authors: Green Carlin J. , Seal Robert R. , Piatak Nadine M. , Cannon William F. , McAleer Ryan J. , Nord Julia A. 
Published: February 2020

Abstract
The Paleoproterozoic Ironwood Iron-Formation, a Superior-type banded iron formation located in the western Gogebic Iron Range in Wisconsin, is one of the largest undeveloped iron ore resources in the United States. Interest in the development of this resource is complicated by potential environmental and health effects related to the presence of amphibole minerals in the Ironwood, a consequence of Mesoproterozoic contact metamorphism. The presence of these amphiboles and their contact metamorphic origin have long been recognized; however, recent interest in this resource has highlighted the lack of detailed knowledge on their distribution, mineral chemistry, and morphology. Optical microscopy, X-ray diffraction, scanning electron microscopy, and electron microprobe analysis were utilized to investigate the origin, distribution, morphology, and chemistry of amphiboles in the Ironwood.
Amphibole is present in the western portion of the study area due to regional-scale contact meta-morphism associated with the intrusion of the 1.1 Ga Mellen Intrusive Complex. Locally amphibole is also present, adjacent to diabase and/or gabbro dikes and sills in the lower-grade Ironwood in the eastern portion of the study area. In both localities, amphiboles in the Ironwood most commonly developed in massive and prismatic habits, and locally assumed a fibrous habit. Fibrous amphiboles were recognized locally in the two potential ore zones of the Ironwood but were not observed in the portion likely to be waste rock. Massive and prismatic amphiboles show a wide range of Mg# [molar Mg/(Mg+Fe2+)] values (0.06 to 0.87), whereas Mg# values of fibrous amphiboles are restricted from 0.14 to 0.35. Factors that influenced the compositional variability of amphiboles in the Ironwood may have included temperature of formation, morphology, bulk chemistry of the iron formation, and variations in prograde and retrograde metamorphism. The presence of amphiboles in the Ironwood is a known issue that will need to be factored into any future mine plans. This study provides an objective assessment of the distribution and character of amphiboles in the Ironwood to aid all decision-makers in any future resource development scenarios.
Gender Differences in Fear of Missing out Experiences among Undergraduate Students in Oman
Authors: Qutishat Mohammed Ghalib 
Published: February 2020

BACKGROUND:
Students with fear of missing out (FOMO) are profoundly connected and updated with others via constant social media connections to satisfy their needs and self-recognition. They use social media platforms to build new relationships, belong to some social group, remain fully informed, and fulfill their affiliation needs, which can increase their urge to spend more time visiting other people’s profiles and comparing their life achievements with others. Thus, this study has been conceptualized to investigate gender differences of FOMO experiences among undergraduate students in Oman.

METHODS:
A descriptive correlational and cross-sectional study design was chosen to achieve the research purpose among Sultan Qaboos University (SQU) undergraduate students. The total sample was 339. The experiences of fear of missing out was measured by using the Fear of Missing Out scale. The items were measured on a 5-point Likert-scale ranging from (“not at all true of me”) (“extremely true of me”).

RESULTS:
The mean age was approximately 21.56 years. Our study shows a homogeneous gender variation (female 50.15% (n=170), and male 49.85% (n=169)). However, the majority of the participants were single (93.5%), lived out-campus (56%), and in their 5th academic year (33.92%).

:
Males scored higher fear of missing out than females 24.8693 and 22.829, respectively, the results of this study possess a significant gender differences in the experiences of fear of missing out (p = 0.009).

CONCLUSION:
The university students surveyed experienced a moderate level of FOMO. However. Males scored a higher level of fear of missing out than females. They focus more on expanding social connections compared to females. Factors such as culture, norms, and self-image may play a role in experiencing FOMO, more studies are required in that claim.
An In vivo Immunohistochemical Study on MacroH2A.1 in Lung and Lymph-Node Tissues Exposed to an Asbestiform Fiber
Authors: Loreto Carla , Lombardo Claudia , Caltabiano Rosario , Ledda Caterina , Hagnas Maria , Filetti Vera , Rapisarda Venerando 
Published: February 2020

Aims:
The aim of this study was to investigate MacroH2A.1 immunoexpression
in tissues of sheep exposed to FE.

Background:
The correlation between asbestiform fibers, lung cancer, pleural
mesothelioma, and other lung diseases is already well established as the
pathophisiological pathophysiological respiratory mechanisms involved by inhalation of
Fluoro-edenite (FE). The latter is represented by cell proliferation and inducing the
release of growth factors, cytokines, and reactive oxygen and nitrite species, with DNA
damage that causes chronic inflammation and carcinogenesis. MacroH2A.1, and histone
variant, seems to play a role in sensing the metabolic state of the cell and linking it with
chromatin. Physiologically, MacroH2A.1 is expressed at low levels in stem cells and it
became upregulated during differentiation, preventing reprogramming of induced
pluripotent stem cells and after nuclear transfer. In particular, MacroH2A.1 has been
shown to explicate a potent antitumor mechanism in vivo as it results upregulated in
senescent cells determining a permanent growth-arrest.

Objective:
Evaluate the possible role of the histone variant in the organism in response
to deep insight understanding the mechanisms of toxicity and the cellular response to
FE.

Methods:
Lung and lymph nodes of exposed sheep were selected. Samples were
processed for histological and immunihistochemical immunohistochemical evaluations.
Densitometric, morphometric, and statistical analysis analyses were conducted.

Results:
Tissue sections of FE exposed sheep demonstrated overexpression of
MacroH2A.1 vs unexposed samples. The data suggest an involvement of these this
molecule in the cellular response triggered by FE directed exposure.

Conclusion:
In this contest, MacroH2A.1 overexpression supports its function as an
epigenetic stabilizer that helps to establish and maintain differentiated states.