bluuebunny/crossref_metadata_2025_split huggingface dataset:
South-Seeking Magnetic Bacteria
Authors: Kirschvink J. L. 
Published: April 2021

ABSTRACT
During the past few years, a wide variety of living organisms have been found which biologically synthesize the ferrimagnetic mineral, magnetite (Fe3O4) First discovered as a biogenic material in the teeth of a primitive mollusc, the chiton (Polyplacophora, Lowenstam 1962), it has since been found as an organic precipitate in magnetically sensitive honey bees (Gould, Kirschvink & Deffeyes, 1978), homing pigeons (Walcott, Gould & Kirschvink, 1979) and bacteria (Frankel, Blakemore & Wolfe, 1979). In all of these organisms (except the chiton), the magnetite is apparently used to orient with or detect the direction and intensity of the earth’s magnetic field (Kirschvink, 1979; Kirschvink & Gould, in review).
Status of Surgical Management of Borderline Ovarian Tumors in France: are Recommendations Being Followed? Multicentric French Study by the FRANCOGYN Group
Authors: Lecointre Lise , Bund Virginie , Sangnier Eva , Ouldamer Lobna , Bendifallah Sofiane , Koskas Martin , Bolze Pierre-Adrien , Collinet Pierre , Canlorbe Geoffroy , Touboul Cyril , Huchon Cyrille , Coutant Charles , Faller Emilie , Boisramé Thomas , Gantzer Justine , Demarchi Martin , Lavoué Vincent , Akladios Chérif 
Published: April 2021

Abstract
Background
Borderline ovarian tumors (BOTs) are tumors with a favorable prognosis but whose management by consensus is essential to limit the risk of invasive recurrence. This study aimed to conduct an inventory of surgical practices for BOT in France and to evaluate the conformity of the treatment according to the current French guidelines.

Methods
This retrospective, multicenter cohort study included nine referral centers of France between January 2001 and December 2018. It analyzed all patients with serous and mucinous BOT who had undergone surgery. A peritoneal staging in accordance with the recommendations was defined by performance of a peritoneal cytology, an omentectomy, and at least one peritoneal biopsy.

Results
The study included 332 patients. A laparoscopy was performed in 79.5% of the cases. Treatment was conservative in 31.9% of the cases. The recurrence rate was significantly increased after conservative treatment (17.3% vs 3.1%; p < 0.001). Peritoneal cytology was performed for 95.5%, omentectomy for 83.1%, and at least one biopsy for 82.2% of the patients. The overall recurrence rate was 7.8%, and the recurrence was invasive in 1.2% of the cases. No link was found between the recurrence rate and the conformity of peritoneal staging. The overall rate of staging noncompliance was 22.9%.

Conclusion
The current standards for BOT management seem to be well applied.
Development of Off-On Switching 19F MRI Probes for Cathepsin K Activity Detection
Authors: Konishi Yuki , Okunishi Atsuya , Sugihara Fuminori , Nakamura Tatsuya , Akazawa Kazuki , Minoshima Masafumi , Kikuchi Kazuya 
Published: April 2021

Abstract
Cathepsin K is a protease expressed in osteoclasts that degrades bone tissue, such as type I collagen fibers. Overexpression of cathepsin K is involved in osteoporosis, rheumatoid arthritis, and bone metastasis. Therefore, detecting cathepsin K activity is important for understanding the mechanism of these diseases and developing new drugs. However, current chemical probes cannot be employed for the detection of cathepsin K activity in animal deep-tissue. In this study, we developed novel 19F magnetic resonance imaging (MRI) probes (FLAME-(Gd-X), X = Acp, Deg, Deg2) to detect cathepsin K. In FLAME-(Gd-X), the Gd3+ complex was modified on the surface of perfluorocarbon-encapsulated silica nanoparticles through cathepsin K substrate and three different hydrophobic/hydrophilic linkers. The 19F NMR signal intensities of these probes were suppressed by the paramagnetic relaxation enhancement (PRE) effect of the Gd3+ complexes. The 19F MRI signal intensities of FLAME-Gd-Acp and FLAME-Gd-Deg specifically increased with the substrate cleavage by cathepsin K. The 19F MRI probes based on the PRE effect can be applied to the in vivo detection of cathepsin K activity.
Dates fruits effects on blood glucose among patients with diabetes mellitus: A review and meta-analysis
Authors: Mirghani Hyder Osman 
Published: April 2021

Background & Objective: Dates fruit is known for its great nutritional value and two to three servings of dates fruit/day are beneficial for patients with diabetes. However, some may advice against this cheap and widely available fruit consumption. Besides, 12% of the population Worldwide are either suffering or are at risk of developing diabetes, but no previous meta-analysis has assessed this important issue. Thus, the study aimed to investigate the effects of date’s fruit on glycemia among patients with diabetes.
Methods: A systematic literature search was conducted in PubMed, Medline, EBSCO, Cochrane, and Google Scholar databases for trials published in English from the first published article up to December 2020. The following keywords were used: “dates fruit and glycemic control”, “dates fruit and blood glucose”, “dates fruit and HbA1c” without limitations regarding the date of publication.
Results: Out of the 942 references identified, only 10 cohorts from five full texts were included, a reduction of Fasting plasma glucose (FPG), odd ratio, -24.79, 95% CI=-34.75, -14.83 P =0.002. I2 for heterogeneity=79%, P <0.00001 and postprandial plasma glucose (PPPG), odd ratio -28.19, 95% CI=-60.66-4.29, P =<0.0001. I2 for heterogeneity=92%, P=0.09) was observed. While the effect on HbA1c was neutral, odd ratio, -.20, 95% CI=-.46 -.06, P=0.13. I2 for heterogeneity=0. %, P=0.55.
Conclusion: Dates fruit was beneficial regarding glycemic control among patients with diabetes, physician may not need to restrict its use among patients with diabetes. The small number of the included studies and the heterogeneity observed in PPPG and FPG sub-analysis limited the current results. Further trials assessing the glycemic indices of various types of dates fruit are needed.
doi: https://doi.org/10.12669/pjms.37.4.4112
How to cite this:Mirghani HO. Dates fruits effects on blood glucose among patients with diabetes mellitus: A review and meta-analysis. Pak J Med Sci. 2021;37(4):1230-1236. doi: https://doi.org/10.12669/pjms.37.4.4112
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Incidence of acute pulmonary embolism among patients hospitalized with COVID-19: a systematic review and meta-analysis
Authors: Munner Mohamed S. , Ritchie Charles A. , Elkhidir Ibrahim H. , Mohammadat Doaa T. , Ahmed Hussein J. , Altayeb Khalid A. , Yassin Rawan Z. , Hassan Riyan M. , Hamad Saada A. , Nimir Mohammed , Hamid Osman S. , Johnson Margaret M. , Narula Tathagat , Erben Young , Tawk Rabih G. , Miller David A. , Gupta Vivek , Devcic Zlatko , Freeman William D. , Toskich Beau B. 
Published: April 2021

Background: Coronavirus disease 2019 (COVID-19) is a global pandemic, which is associated with venous thromboembolism and pulmonary embolism (PE). This study aimed to estimate the pooled incidence of PE among patients hospitalized with COVID-19 within the published literature. Methods: This systematic review and meta-analysis was performed according to PRISMA guidelines. An electronic search using MEDLINE /PubMed, ScienceDirect, Cochrane, and OpenGray databases was conducted May 19th, 2020. Eligible studies included sufficient data to calculate the incidence of PE diagnosed during hospitalization in patients with COVID-19. Case reports were excluded. Quality was assessed using the Newcastle-Ottawa scale (observational cohort and case-control), AXIS tool (cross-sectional), and quality assessment tool (case series). Demographics and PE incidence data were extracted from the included studies and analyzed with R language. The pooled incidence of PE in patients hospitalized with COVID-19 was calculated. Results: The database search identified 128 records. Ten observational studies were eligible and were included in the meta-analysis with a total of 1722 patients (mean age= 63.36). .The incidence of PE was noted to be higher in males. The D-dimer levels were specified between PE group and non-PE group in only three studies, while the remaining either reported it improperly or had missing data.The pooled PE incidence in patients hospitalized with COVID-19 was 17% (95% CI: 0.1-0.26). There was a high degree of study heterogeneity (I2 = 94%, p<0.01). Conclusion: The pooled PE incidence in patients hospitalized with COVID-19 is 17%. This increased incidence is greater than that previously reported in the general population of non-COVID-19. Attention and further investigation of this risk is warranted.
Bioimage analysis workflows: community resources to navigate through a complex ecosystem
Authors: Paul-Gilloteaux Perrine , Tosi Sébastien , Hériché Jean-Karim , Gaignard Alban , Ménager Hervé , Marée Raphaël , Baecker Volker , Klemm Anna , Kalaš Matúš , Zhang Chong , Miura Kota , Colombelli Julien 
Published: April 2021

Workflows are the keystone of bioimage analysis, and the NEUBIAS (Network of European BioImage AnalystS) community is trying to gather the actors of this field and organize the information around them. One of its most recent outputs is the opening of the F1000Research NEUBIAS gateway, whose main objective is to offer a channel of publication for bioimage analysis workflows and associated resources. In this paper we want to express some personal opinions and recommendations related to finding, handling and developing bioimage analysis workflows. The emergence of "big data” in bioimaging and resource-intensive analysis algorithms make local data storage and computing solutions a limiting factor. At the same time, the need for data sharing with collaborators and a general shift towards remote work, have created new challenges and avenues for the execution and sharing of bioimage analysis workflows. These challenges are to reproducibly run workflows in remote environments, in particular when their components come from different software packages, but also to document them and link their parameters and results by following the FAIR principles (Findable, Accessible, Interoperable, Reusable) to foster open and reproducible science. In this opinion paper, we focus on giving some directions to the reader to tackle these challenges and navigate through this complex ecosystem, in order to find and use workflows, and to compare workflows addressing the same problem. We also discuss tools to run workflows in the cloud and on High Performance Computing resources, and suggest ways to make these workflows FAIR.
Demonstration of various optical directed logic operations by using an integrated photonic circuit
Authors: Xiao Huifu , Han Xu , Jiang Yongheng , Ren Guanghui , Mitchell Arnan , Gao Daqiang , Yang Jianhong , Tian Yonghui 
Published: April 2021

Optical directed logic is a novel logic operation scheme that employs electrical signals as operands to control the working states of optical switches to perform the logic operations. In this Letter, we propose and demonstrate an integrated photonic circuit which can implement five different optical logic operations by utilizing two optical modes. The proposed device is fabricated on a silicon-on-insulator substrate by using electron beam lithography and inductively coupled plasma etching processes. The static experimental results show that the fabricated device can implement five different operations correctly—XOR, XNOR, NOR, NOT, and AND—from which we can see that the signal-to-noise ratios are larger than 17.6 dB over the entire C band for all five logic functions. At last, all five logic operations with the speed of 10 Kbps are demonstrated. The proposed device with simple structure, large bandwidth, and versatility would be a promising candidate for information processing in optical mode division multiplexing networks.
How geographic access to care shapes disease burden: The current impact of post-exposure prophylaxis and potential for expanded access to prevent human rabies deaths in Madagascar
Authors: Rajeev Malavika , Guis Hélène , Edosoa Glenn Torrencelli , Hanitriniaina Chantal , Randrianarijaona Anjasoa , Mangahasimbola Reziky Tiandraza , Hierink Fleur , Ramiandrasoa Ravo , Nely José , Heraud Jean-Michel , Andriamandimby Soa Fy , Baril Laurence , Metcalf C. Jessica E. , Hampson Katie 
Published: April 2021

Background
Post-exposure prophylaxis (PEP) is highly effective at preventing human rabies deaths, however access to PEP is limited in many rabies endemic countries. The 2018 decision by Gavi to add human rabies vaccine to its investment portfolio should expand PEP availability and reduce rabies deaths. We explore how geographic access to PEP impacts the rabies burden in Madagascar and the potential benefits of improved provisioning.

Methodology & principal findings
We use spatially resolved data on numbers of bite patients seeking PEP across Madagascar and estimates of travel times to the closest clinic providing PEP (N = 31) in a Bayesian regression framework to estimate how geographic access predicts reported bite incidence. We find that travel times strongly predict reported bite incidence across the country. Using resulting estimates in an adapted decision tree, we extrapolate rabies deaths and reporting and find that geographic access to PEP shapes burden sub-nationally. We estimate 960 human rabies deaths annually (95% Prediction Intervals (PI): 790–1120), with PEP averting an additional 800 deaths (95% PI: 640–970) each year. Under these assumptions, we find that expanding PEP to one clinic per district (83 additional clinics) could reduce deaths by 19%, but even with all major primary clinics provisioning PEP (1733 additional clinics), we still expect substantial rabies mortality. Our quantitative estimates are most sensitive to assumptions of underlying rabies exposure incidence, but qualitative patterns of the impacts of travel times and expanded PEP access are robust.

Conclusions & significance
PEP is effective at preventing rabies deaths, and in the absence of strong surveillance, targeting underserved populations may be the most equitable way to provision PEP. Given the potential for countries to use Gavi funding to expand access to PEP in the coming years, this framework could be used as a first step to guide expansion and improve targeting of interventions in similar endemic settings where PEP access is geographically restricted and baseline data on rabies risk is lacking. While better PEP access should save many lives, improved outreach, surveillance, and dog vaccination will be necessary, and if rolled out with Gavi investment, could catalyze progress towards achieving zero rabies deaths.
Diagnostic accuracy of the WHO clinical definitions for dengue and implications for surveillance: A systematic review and meta-analysis
Authors: Raafat Nader , Loganathan Shanghavie , Mukaka Mavuto , Blacksell Stuart D. , Maude Richard James 
Published: April 2021

Background
Dengue is the world’s most common mosquito-borne virus but remains diagnostically challenging due to its nonspecific presentation. Access to laboratory confirmation is limited and thus most reported figures are based on clinical diagnosis alone, the accuracy of which is uncertain. This systematic review assesses the diagnostic accuracy of the traditional (1997) and revised (2009) WHO clinical case definitions for dengue fever, the basis for most national guidelines.

Methodology/Principal findings
PubMed, EMBASE, Scopus, OpenGrey, and the annual Dengue Bulletin were searched for studies assessing the diagnostic accuracy of the unmodified clinical criteria. Two reviewers (NR/SL) independently assessed eligibility, extracted data, and evaluated risk of bias using a modified QUADAS-2. Additional records were found by citation network analysis. A meta-analysis was done using a bivariate mixed-effects regression model. Studies that modified criteria were analysed separately. This systematic review protocol was registered on PROSPERO (CRD42020165998). We identified 11 and 12 datasets assessing the 1997 and 2009 definition, respectively, and 6 using modified criteria. Sensitivity was 93% (95% CI: 77–98) and 93% (95% CI: 86–96) for the 1997 and 2009 definitions, respectively. Specificity was 29% (95% CI: 8–65) and 31% (95% CI: 18–48) for the 1997 and 2009 definitions, respectively. Diagnostic performance suffered at the extremes of age. No modification significantly improved accuracy.

Conclusions/Significance
Diagnostic accuracy of clinical criteria is poor, with significant implications for surveillance and public health responses for dengue control. As the basis for most reported figures, this has relevance to policymakers planning resource allocation and researchers modelling transmission, particularly during COVID-19.
Prognostic and clinicopathological significance of C-reactive protein/albumin ratio (CAR) in patients with gastric cancer: A meta-analysis
Authors: Yu Junhua , Liu Huiling , Zeng Xueyun , Zhao Yujun , Jiang Dejun , Lu Hang , Qian Jun 
Published: April 2021

Background
In recent years, many studies have explored the potential prognostic utility of C-reactive protein/albumin ratio (CAR) in patients with gastric cancer (GC), however, the results remain conflicting. We thus performed a meta-analysis to determine the association of CAR and prognosis of GC.

Methods
This meta-analysis was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Statement. PubMed, Web of science, Embase, and Cochrane Library were searched. Hazard ratios (HRs) and 95% confidence intervals (CIs) for overall survival (OS) and cancer-specific survival (CSS) of included studies were pooled to estimate the prognostic value of CAR.

Results
Eight studies with a total of 3,216 patients were included in this meta-analysis. High CAR was significantly associated with poor OS (HR = 1.59, 95%CI = 1.36–1.85, p<0.001) and worse CSS (HR = 1.65, 95%CI = 1.21–2.25, p = 0.002). In addition, high CAR was significantly associated with male sex (OR = 1.80, 95%CI = 1.31–2.47, p<0.001), advanced tumor stage (OR = 2.14, 95%CI = 1.48–3.09, p<0.001), and tumor size ≥3cm (OR = 2.69, 95%CI = 1.84–3.93, p<0.001).

Conclusion
Elevated pretreatment CAR is a prognostic marker of poor OS and CSS in patients with GC. Furthermore, high CAR levels are associated with clinicopathological features reflecting tumor progression.
Disease-dependent variations in the timing and causes of readmissions in Germany: A claims data analysis for six different conditions
Authors: Ruff Carmen , Gerharz Alexander , Groll Andreas , Stoll Felicitas , Wirbka Lucas , Haefeli Walter E. , Meid Andreas D. 
Published: April 2021

Background
Hospital readmissions place a major burden on patients and health care systems worldwide, but little is known about patterns and timing of readmissions in Germany.

Methods
We used German health insurance claims (AOK, 2011–2016) of patients ≥ 65 years hospitalized for acute myocardial infarction (AMI), heart failure (HF), a composite of stroke, transient ischemic attack, or atrial fibrillation (S/AF), chronic obstructive pulmonary disease (COPD), type 2 diabetes mellitus, or osteoporosis to identify hospital readmissions within 30 or 90 days. Readmissions were classified into all-cause, specific, and non-specific and their characteristics were analyzed.

Results
Within 30 and 90 days, about 14–22% and 27–41% index admissions were readmitted for any reason, respectively. HF and S/AF contributed most index cases, and HF and COPD accounted for most all-cause readmissions. Distributions and ratios of specific to non-specific readmissions were disease-specific with highest specific readmissions rates among COPD and AMI.

Conclusion
German claims are well-suited to investigate readmission causes if longer periods than 30 days are evaluated. Conditions closely related with the primary disease are the most frequent readmission causes, but multiple comorbidities among readmitted cases suggest that a multidisciplinary care approach should be implemented vigorously addressing comorbidities already during the index hospitalization.
A scoping review of internal hospital crises and disasters in the Netherlands, 2000–2020
Authors: Klokman Vincent W. , Barten Dennis G. , Peters Nathalie A. L. R. , Versteegen Marieke G. J. , Wijnands Jaap J. J. , van Osch Frits H. M. , Gaakeer Menno I. , Tan Edward C. T. H. , Boin Arjen 
Published: April 2021

BackgroundInternal hospital crises and disasters (IHCDs) are events that disrupt the routine functioning of a hospital while threatening the well-being of patients and staff. IHCDs may cause hospital closure, evacuations of patients and loss of healthcare capacity. The consequences may be ruinous for local communities. Although IHCDs occur with regularity, information on the frequency and types of these events is scarcely published in the medical literature. However, gray literature and popular media reports are widely available. We therefore conducted a scoping review of these literature sources to identify and characterize the IHCDs that occurred in Dutch hospitals from 2000 to 2020. The aim is to develop a systematic understanding of the frequency of the various types of IHCDs occurring in a prosperous nation such as the Netherlands.MethodsA systematic scoping review of news articles retrieved from the LexisNexis database, Google, Google News, PubMed and EMBASE between 2000 and 2020. All articles mentioning the closure of a hospital department in the Netherlands were analyzed.ResultsA total of 134 IHCDs were identified in a 20-year time period. Of these IHCDs, there were 96 (71.6%) emergency department closures, 76 (56.7%) operation room closures, 56 (41.8%) evacuations, 26 (17.9%) reports of injured persons, and 2 (1.5%) reported casualties. Cascading events of multiple failures transpired in 39 (29.1%) IHCDs. The primary causes of IHCDs (as reported) were information and communication technology (ICT) failures, technical failures, fires, power failures, and hazardous material warnings. An average of 6.7 IHCDs occurred per year. From 2000–2009 there were 32 IHCDs, of which one concerned a primary ICT failure. Of the 102 IHCDs between 2010–2019, 32 were primary ICT failures.ConclusionsIHCDs occur with some regularity in the Netherlands and have marked effects on hospital critical care departments, particularly emergency departments. Cascading events of multiple failures transpire nearly a third of the time, limiting the ability of a hospital to stave off closure due to failure. Emergency managers should therefore prioritize the risk of ICT failures and cascading events and train hospital staff accordingly.