bluuebunny/crossref_metadata_2025_split huggingface dataset:
Middle Miocene Temperature and Productivity Evolution at a Northeast Atlantic Shelf Site (IODP U1318, Porcupine Basin): Global and Regional Changes
Authors: Sangiorgi Francesca , Quaijtaal Willemijn , Donders Timme H. , Schouten Stefan , Louwye Stephen 
Published: June 2021

AbstractWe present a high‐resolution multiproxy middle Miocene sea surface temperature (SST) and productivity (SSP) reconstruction of Integrated Ocean Drilling Program Site U1318, from the upper slope edge (∼400 m water depth) of the Porcupine Basin continental margin, eastern North Atlantic Ocean. Biomarker and dinoflagellate cyst proxies reveal warm and mostly stratified waters during the Miocene Climatic Optimum (MCO) that cooled ∼3°C across the Miocene Climate Transition (MCT). The organic biomarker (TEX86 and ) paleothermometers document a series of 11 transient cooling events (CEs), superimposed on the long‐term climate evolution. These CEs are associated with increases in cold‐water dinocysts and correlate to global benthic δ18O shifts, including the Mi‐2, Mi‐3, and Mi‐4 events. Most CEs are also associated with increases in primary productivity. A prolonged interval of high SSP between ∼13.8 and 13.6 Ma supports the idea that carbon production (and burial) in shallow areas represents a feedback mechanism contributing to long‐term atmospheric CO2 decline and cooling during the MCT. SST comparison in three North Atlantic sites (Azores Site 608, Porcupine Basin Site U1318, and Rockall Plateau Site 982) reveals that MCO SSTs are much warmer at Site 608 than at the other two sites. The low‐resolution SST record of Site 982 shows no decrease in temperature around the MCT. This may be linked to contemporaneous tectonic changes in the Tethys, Central American, and Arctic Seaways impacting local ocean circulation, superimposed on global drivers of climate change.
Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome sequences
Authors: Mizuno Fuzuki , Gojobori Jun , Kumagai Masahiko , Baba Hisao , Taniguchi Yasuhiro , Kondo Osamu , Matsushita Masami , Matsushita Takayuki , Matsuda Fumihiko , Higasa Koichiro , Hayashi Michiko , Wang Li , Kurosaki Kunihiko , Ueda Shintaroh 
Published: June 2021

AbstractThe Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome (mitochondrial genome) sequence from Palaeolithic human remains. We also obtained those of Neolithic (the hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome sequence was not found to be a direct ancestor of any of Jomon, Yayoi, and present-day Japanese people. However, it was an ancestral type of haplogroup M, a basal group of the haplogroup M. Therefore, our results indicate continuity in the maternal gene pool from the Palaeolithic to present-day Japanese. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.
Leveraging attention‐based visual clue extraction for image classification
Authors: Cui Yunbo , Du Youtian , Wang Xue , Wang Hang , Su Chang 
Published: June 2021

AbstractDeep learning‐based approaches have made considerable progress in image classification tasks, but most of the approaches lack interpretability, especially in revealing the decisive information causing the categorization of images. This paper seeks to answer the question of what clues encode the discriminative visual information between image categories and can help improve the classification performance. To this end, an attention‐based clue extraction network (ACENet) is introduced to mine the decisive local visual information for image classification. ACENet constructs a clue‐attention mechanism, that is global‐local attention, between the image and visual clue proposals extracted from it and then introduces a contrastive loss defined over the achieved discrete attention distribution to increase the discriminability of clue proposals. The loss encourages considerable attention to be devoted to discriminative clue proposals, that is those similar within the same category and dissimilar across categories. The experimental results for the Negative Web Image (NWI) dataset and the public ImageNet2012 dataset demonstrate that ACENet can extract true clues to improve the image classification performance and outperforms the baselines and the state‐of‐the‐art methods.
Scalable Synthesis of l-allo-Enduracididine: The Unusual Amino Acid Present in Teixobactin
Authors: Chandrasekhar Srivari , Gangathade Namdeo , Nayani Kiranmai , Bukya Hemalatha , Mainkar Prathama S. 
Published: June 2021

AbstractA scalable synthesis of l-allo-enduracididine is achieved from commercially available (S)-glycidol in ten linear steps involving well-established synthetic transformations. The synthetic route is flexible and can be used to synthesize all four diastereomers by changing the stereochemistry of glycidol and Sharpless asymmetric dihydroxylation reagent.
Suitability of Hybrid and Landrace Maize Plants Within Conventional and Organic-Polyculture Maize Agroecosystems for Hosting Parasitic Wasps
Authors: Moya-Raygoza Gustavo , Figueroa-Bautista Pedro 
Published: June 2021

Abstract
Polycultures and conventional monoculture have different effects on insect pests and natural enemies. Little is known about the parasitoid response to landrace and hybrid plants damaged by insect pests within organic-polyculture agroecosystems vs. monoculture ones. The aim of the present study was to compare the suitability of these agroecosystems for hosting parasitic wasps by evaluating the parasitism rate, parasitoid abundance, and species composition on landrace and hybrid maize races within organic-polyculture and conventional maize agroecosystems. This study was performed within the Mesoamerican region where maize was originally domesticated and where the maize insect pest Dalbulus maidis (DeLong) (Hemiptera: Cicadellidae) originated. Maize plants of landrace and hybrid varieties were used to attract egg parasitoids of D. maidis within each of the two agroecosystems; conventional maize monoculture and an organic-polyculture of landrace maize, beans, and squash, which also included weed plants. Four treatments were conducted in this field experiment: 1) landrace-within organic agroecosystem, 2) hybrid-within organic agroecosystem, 3) landrace-within conventional agroecosystem, and 4) hybrid-within conventional agroecosystem. A community of parasitic wasps, of which the micro-wasp Paracentrobia sp. (Hymenoptera: Trichogrammatidae) was the most abundant member, was found attacking the D. maidis eggs in both agroecosystems. The parasitism rate and parasitoid abundance were similar among the four treatments. However, the abundance of parasitoids was greater in the conventional maize monoculture. Bait plants (landrace and hybrid maize) within each agroecosystem did not show differences in either parasitoid abundance or parasitism rate.
peakPantheR, an R package for large-scale targeted extraction and integration of annotated metabolic features in LC–MS profiling datasets
Authors: Wolfer Arnaud M , D S Correia Gonçalo , Sands Caroline J , Camuzeaux Stephane , Yuen Ada H Y , Chekmeneva Elena , Takáts Zoltán , Pearce Jake T M , Lewis Matthew R 
Published: June 2021

Abstract

Summary
Untargeted liquid chromatography–mass spectrometry (LC–MS) profiling assays are capable of measuring thousands of chemical compounds in a single sample, but unreliable feature extraction and metabolite identification remain considerable barriers to their interpretation and usefulness. peakPantheR (Peak Picking and ANnoTation of High-resolution Experiments in R) is an R package for the targeted extraction and integration of annotated features from LC–MS profiling experiments. It takes advantage of chromatographic and spectral databases and prior information of sample matrix composition to generate annotated and interpretable metabolic phenotypic datasets and power workflows for real-time data quality assessment.

Availability and implementation
peakPantheR is available via Bioconductor (https://bioconductor.org/packages/peakPantheR/). Documentation and worked examples are available at https://phenomecentre.github.io/peakPantheR.github.io/ and https://github.com/phenomecentre/metabotyping-dementia-urine.

Supplementary information
Supplementary data are available at Bioinformatics online.
Major hepatectomy with combined vascular resection for perihilar cholangiocarcinoma
Authors: Sugiura T , Uesaka K , Okamura Y , Ito T , Yamamoto Y , Ashida R , Ohgi K , Otsuka S , Nakagawa M , Aramaki T , Asakura K 
Published: June 2021

Abstract

Background
Hepatectomy with vascular resection (VR) for perihilar cholangiocarcinoma (PHCC) is a challenging procedure. However, only a few reports on this procedure have been published and its clinical significance has not been fully evaluated.

Methods
Patients undergoing surgical resection for PHCC from 2002–2017 were studied. The surgical outcomes of VR and non-VR groups were compared.

Results
Some 238 patients were included. VR was performed in 85 patients. The resected vessels were hepatic artery alone (31 patients), portal vein alone (37 patients) or both (17 patients). The morbidity rates were almost the same in the VR (49.4 per cent) and non-VR (43.8 per cent) groups (P = 0.404). The mortality rates of VR (3.5 per cent) and non-VR (3.3 per cent) were also comparable (P &gt; 0.999). The median survival time (MST) was 45 months in the non-VR group and 36 months in VR group (P = 0.124). Among patients in whom tumour involvement was suspected on preoperative imaging and whose carbohydrate antigen 19-9 (CA19-9) value was 37 U/ml or less, MST in the VR group was significantly longer than that in the non-VR group (50 versus 34 months, P = 0.017). In contrast, when the CA19-9 value was greater than 37 U/ml, MST of the VR and non-VR groups was comparable (28 versus 29 months, P = 0.520).

Conclusion
Hepatectomy with VR for PHCC can be performed in a highly specialized hepatobiliary centre with equivalent short- and long-term outcomes to hepatectomy without VR.
Loss of Yap/Taz in cardiac fibroblasts attenuates adverse remodelling and improves cardiac function
Authors: Mia Masum M , Cibi Dasan Mary , Ghani Siti Aishah Binte Abdul , Singh Anamika , Tee Nicole , Sivakumar Viswanathan , Bogireddi Hanumakumar , Cook Stuart A , Mao Junhao , Singh Manvendra K 
Published: June 2021

Abstract

Aims
Fibrosis is associated with all forms of adult cardiac diseases including myocardial infarction (MI). In response to MI, the heart undergoes ventricular remodelling that leads to fibrotic scar due to excessive deposition of extracellular matrix mostly produced by myofibroblasts. The structural and mechanical properties of the fibrotic scar are critical determinants of heart function. Yes-associated protein (Yap) and transcriptional coactivator with PDZ-binding motif (Taz) are the key effectors of the Hippo signalling pathway and are crucial for cardiomyocyte proliferation during cardiac development and regeneration. However, their role in cardiac fibroblasts, regulating post-MI fibrotic and fibroinflammatory response, is not well established.

Methods and results
Using mouse model, we demonstrate that Yap/Taz are activated in cardiac fibroblasts after MI and fibroblasts-specific deletion of Yap/Taz using Col1a2Cre(ER)T mice reduces post-MI fibrotic and fibroinflammatory response and improves cardiac function. Consistently, Yap overexpression elevated post-MI fibrotic response. Gene expression profiling shows significant downregulation of several cytokines involved in post-MI cardiac remodelling. Furthermore, Yap/Taz directly regulate the promoter activity of pro-fibrotic cytokine interleukin-33 (IL33) in cardiac fibroblasts. Blocking of IL33 receptor ST2 using the neutralizing antibody abrogates the Yap-induced pro-fibrotic response in cardiac fibroblasts. We demonstrate that the altered fibroinflammatory programme not only affects the nature of cardiac fibroblasts but also the polarization as well as infiltration of macrophages in the infarcted hearts. Furthermore, we demonstrate that Yap/Taz act downstream of both Wnt and TGFβ signalling pathways in regulating cardiac fibroblasts activation and fibroinflammatory response.

Conclusion
We demonstrate that Yap/Taz play an important role in controlling MI-induced cardiac fibrosis by modulating fibroblasts proliferation, transdifferentiation into myofibroblasts, and fibroinflammatory programme.
Persisting burden and challenges of rheumatic heart disease
Authors: Marijon Eloi , Mocumbi Ana , Narayanan Kumar , Jouven Xavier , Celermajer David S 
Published: June 2021

Abstract
Rheumatic heart disease (RHD) is the result of episodes of acute rheumatic fever with valvular (and other cardiac) damage caused by an abnormal immune response to group A streptococcal infections, usually during childhood and adolescence. As a result of improved living conditions and the introduction of penicillin, RHD was almost eradicated in the developed world by the 1980s. However, being a disease of poverty, its burden remains disproportionately high in the developing world, despite being a fundamentally preventable disease. Rheumatic heart disease generates relatively little attention from the medical and science communities, in contrast to other common infectious problems (such as malaria, HIV, tuberculosis), despite the major cardiovascular morbidity/mortality burden imposed by RHD. This relative neglect and paucity of funding have probably contributed to limited fundamental medical advances in this field for over 50 years. Given the importance of prevention before the onset of major valvular damage, the main challenges for RHD prevention are improving social circumstances, early diagnosis, and effective delivery of antibiotic prophylaxis. Early identification through ultrasound of silent, subclinical rheumatic valve lesions could provide an opportunity for early intervention. Simple echocardiographic diagnostic criteria and appropriately trained personnel can be valuable aids in large-scale public health efforts. In addition, a better understanding of the immunogenic determinants of the disease may provide potential routes to vaccine development and other novel therapies.
Accuracy of a Self-Administered Online Cognitive Assessment in Detecting Amnestic Mild Cognitive Impairment
Authors: Paterson Theone S E , Sivajohan Brintha , Gardner Sandra , Binns Malcolm A , Stokes Kathryn A , Freedman Morris , Levine Brian , Troyer Angela K 
Published: June 2021

Abstract

Objectives
Our aim was to validate the online Brain Health Assessment (BHA) for detection of amnestic mild cognitive impairment (aMCI) compared to gold-standard neuropsychological assessment. We compared the diagnostic accuracy of the BHA to the Montreal Cognitive Assessment (MoCA).

Methods
Using a cross-sectional design, community-dwelling older adults completed a neuropsychological assessment, were diagnosed as normal cognition (NC) or aMCI, and completed the BHA and MoCA. Both logistic regression (LR) and penalized logistic regression (PLR) analyses determined BHA and demographic variables predicting aMCI; MoCA variables were similarly modeled. Diagnostic accuracy was compared using area under the receiver operating characteristic curve (ROC AUC) analyses.

Results
Ninety-one participants met inclusion criteria (51 aMCI, 40 NC). PLR modeling for the BHA indicated Face–Name Association, Spatial Working Memory, and age-predicted aMCI (ROC AUC = 0.76; 95% confidence interval [CI]: 0.66–0.86). Optimal cut-points resulted in 21% classified as aMCI (positive), 23% negative, and 56% inconclusive. For the MoCA, digits, abstraction, delayed recall, orientation, and age predicted aMCI (ROC AUC = 0.71; 95% CI: 0.61–0.82). Optimal cut-points resulted in 22% classified positive, 8% negative, and 70% inconclusive (LR results presented within). The BHA model classified fewer participants into the inconclusive category and more as negative for aMCI, compared to the MoCA model (Stuart–Maxwell p = .004).

Discussion
The self-administered BHA provides similar detection of aMCI as a clinician-administered screener (MoCA), with fewer participants classified inconclusively. The BHA has the potential to save practitioners time and decrease unnecessary referrals for a comprehensive assessment to determine the presence of aMCI.
Role of data from cost and other economic analyses in healthcare decision-making for HIV, TB and sexual/reproductive health programmes in South Africa
Authors: Murphy Joshua P , Kgowedi Sharon , Naidoo Nalini , Girdwood Sarah , Jamieson Lise , Soeteman Djøra , Resch Stephen , Meyer-Rath Gesine 
Published: June 2021

Abstract
An increasing focus on the use of the results of cost analyses and other economic evaluations in health programme decision-making by governments, donors and technical support partners working in low- and middle-income countries is accompanied by recognition that this use is impeded by several factors, including the lack of skills, data and coordination between spheres of the government. We describe our experience generating economic evaluation data for human immunodeficiency virus, tuberculosis and sexual/reproductive health programmes in South Africa alongside the results of a series of in-depth interviews (IDIs) among decision-makers within the South African government and implementing organizations (data users) and producers of economic evaluations (data producers). We summarize results across (1) the process of implementing a new intervention; (2) barriers to the use of cost data and suggested solutions and (3) the transferability of experiences to the planned South African implementation of universal health coverage (UHC). Based on our experience and the IDIs, we suggest concrete steps towards the improvement of economic data use in the planning and the establishment of structures mandated under the transition to UHC. Our key recommendations include the following: (1) compile a publicly available and regularly updated in-country cost repository; (2) increase the availability of programmatic outcomes data at the aggregate level; (3) agree upon and implement a set of primary decision criteria for the adoption and funding of interventions; (4) combine the efforts of health economics institutions into a stringent system for health technology assessments and (5) improve the link between national and provincial planning and budgeting.
Aligning an interface terminology to the Logical Observation Identifiers Names and Codes (LOINC®)
Authors: Nikiema Jean Noël , Griffier Romain , Jouhet Vianney , Mougin Fleur 
Published: June 2021

Abstract

Objective
Our study consists in aligning the interface terminology of the Bordeaux university hospital (TLAB) to the Logical Observation Identifiers Names and Codes (LOINC). The objective was to facilitate the shared and integrated use of biological results with other health information systems.

Materials and Methods
We used an innovative approach based on a decomposition and re-composition of LOINC concepts according to the transversal relations that may be described between LOINC concepts and their definitional attributes. TLAB entities were first anchored to LOINC attributes and then aligned to LOINC concepts through the appropriate combination of definitional attributes. Finally, using laboratory results of the Bordeaux data-warehouse, an instance-based filtering process has been applied.

Results
We found a small overlap between the tokens constituting the labels of TLAB and LOINC. However, the TLAB entities have been easily aligned to LOINC attributes. Thus, 99.8% of TLAB entities have been related to a LOINC analyte and 61.0% to a LOINC system. A total of 55.4% of used TLAB entities in the hospital data-warehouse have been mapped to LOINC concepts. We performed a manual evaluation of all 1-1 mappings between TLAB entities and LOINC concepts and obtained a precision of 0.59.

Conclusion
We aligned TLAB and LOINC with reasonable performances, given the poor quality of TLAB labels. In terms of interoperability, the alignment of interface terminologies with LOINC could be improved through a more formal LOINC structure. This would allow queries on LOINC attributes rather than on LOINC concepts only.
Use of Infrared Thermography for Assessment of Burn Depth and Healing Potential: A Systematic Review
Authors: Dang Justin , Lin Matthew , Tan Calvin , Pham Christopher H , Huang Samantha , Hulsebos Ian F , Yenikomshian Haig , Gillenwater Justin 
Published: June 2021

Abstract
Burn wound depth assessments are an important component of determining patient prognosis and making appropriate management decisions. Clinical appraisal of the burn wound by an experienced burn surgeon is standard of care but has limitations. Infrared (IR) thermography is a technology in burn care that can provide a noninvasive, quantitative method of evaluating burn wound depth. IR thermography utilizes a specialized camera that can capture the IR emissivity of the skin, and the resulting images can be analyzed to determine burn depth and healing potential of a burn wound. Though IR thermography has great potential for burn wound assessment, its use for this has not been well documented. Thus, we have conducted a systematic review of the current use of IR thermography to assess burn depth and healing potential. A systematic review and meta-analysis of the literature was performed on PubMed and Google Scholar between June 2020 and December 2020 using the following keywords: FLIR, FLIR ONE, thermography, forward looking infrared, thermal imaging + burn*, burn wound assessment, burn depth, burn wound depth, burn depth assessment, healing potential, burn healing potential. A meta-analysis was performed on the mean sensitivity and specificity of the ability of IR thermography for predicting healing potential. Inclusion criteria were articles investigating the use of IR thermography for burn wound assessments in adults and pediatric patients. Reviews and non-English articles were excluded. A total of 19 articles were included in the final review. Statistically significant correlations were found between IR thermography and laser Doppler imaging (LDI) in 4/4 clinical studies. A case report of a single patient found that IR thermography was more accurate than LDI for assessing burn depth. Five articles investigated the ability of IR thermography to predict healing time, with four reporting statistically significant results. Temperature differences between burnt and unburnt skin were found in 2/2 articles. IR thermography was compared to clinical assessment in five articles, with varying results regarding accuracy of clinical assessment compared to thermography. Mean sensitivity and specificity of the ability of IR thermography to determine healing potential &lt;15 days was 44.5 and 98.8, respectively. Mean sensitivity and specificity of the ability of FLIR to determine healing potential &lt;21 days was 51.2 and 77.9, respectively. IR thermography is an accurate, simple, and cost-effective method of burn wound assessment. FLIR has been demonstrated to have significant correlations with other methods of assessing burns such as LDI and can be utilized to accurately assess burn depth and healing potential. However, the technology needs more standardization and validation before it can achieve widespread adoption in clinical practice.