bluuebunny/crossref_metadata_2025_split huggingface dataset:
A review of access and benefit‐sharing measures and literature in key aquaculture‐producing countries
Authors: Humphries Fran , Benzie John A.H. , Lawson Charles , Morrison Clare 
Published: January 2021

AbstractCountries increasingly use access and benefit‐sharing laws as a tool for the conservation and sustainable use of biological resources and associated traditional knowledge. These laws generally require the recipient of resources/knowledge to obtain the provider country’s prior informed consent before collection, use or transfer and to share the benefits from their use with the provider. The aim of this literature review is to comprehensively analyse access and benefit‐sharing laws and literature about the top five aquaculture‐producing countries – China, India, Indonesia, Viet Nam and Bangladesh – to identify research trends and gaps in relation to accessing and sharing the benefits of aquaculture genetic resources and associated traditional knowledge. Using a systematic quantitative literature review methodology, we found only 5% of the literature examined the implications of access and benefit‐sharing for aquaculture and these only related to publications about India’s arrangements. While the other countries had literature about their legal measures and literature about informal genetic resource sharing practices in aquaculture, none of them connected the two research topics. None of the countries had literature analysing the implications of access and benefit‐sharing in relation to traditional knowledge associated with aquaculture. We conclude that given these are the top global producers accounting for up to 80% of all aquaculture products, urgent research is needed to fill the literature gaps to assess whether access and benefit‐sharing as a legal/policy tool is achieving conservation and sustainable use goals for aquaculture genetic resources.
A Probabilistic Fatigue Damage Model for Aluminum 6061-T6 10-Gauge Sheet-Type Material
Authors: Le Xiaobin 
Published: January 2021

Abstract
The 6061-T6 10-gauge sheet-type flat fatigue specimen was designed, manufactured, and tested on an Instron 8081 fatigue test machine. The fatigue tests were performed under five different cyclic axial loads with 195 tests. This paper will display how to use these 195 test data under different cyclic axial loads to build a probabilistic fatigue damage model. The model is validated by the results obtained from the traditional P-S-N curve approach. One advantage of this probabilistic fatigue damage model is that it can calculate the reliability of a component under any type of cyclic loads at any cyclic load level.
Propagation of Shock Wave at the Cavitation Bubble Expansion Stage Induced by a Nanosecond Laser Pulse
Authors: Geng Siyuan , Yao Zhifeng , Zhong Qiang , Du Yuxin , Xiao Ruofu , Wang Fujun 
Published: January 2021

Abstract
The objective of this paper is to reveal the attenuation characteristics of a shock wave after optical breakdown in water, with laser pulses of 12-ns duration. A high time-resolved shadowgraph method is applied to capture the temporal evolutions of the cavitation bubble wall and shock wave. The experiments are carried out on a single bubble generated far away from the free surface and the rigid walls with laser pulse energies of 22 mJ, 45 mJ, and 60 mJ. The results show that a high, time-resolved, wave front velocity of the shock wave is identified, and the maximum velocity can reach up to around 4000 m/s. An asymmetric shock wave is observed at the very start of the bubble expansion stage, and the process of the sharp attenuation of wave front velocity down to sound velocity is accomplished within 310 ns. The possible relationship of the cavitation bubble and the shock wave is discussed and a prediction model, using the maximum bubble radius and the corresponding time calculated by the Gilmore model, is proposed to calculate the location of the wave front.
On the Pressure Losses Through Multistage Perforated Plates
Authors: La Rosa Davide Maria , Rossi Marco Maria Agostino , Ferrarese Giacomo , Malavasi Stefano 
Published: January 2021

Abstract
Perforated plates are commonly used for flow control in pressurized systems. In different industrial applications, these devices are also used in series (multistage perforated plates) to manage high pressure drop or reduce cavitation occurrence in industrial pipes and enhance efficiency of gas turbines in power plants. Based on analysis of literature and modeling considerations, a functional relationship that describes the dimensionless pressure loss for multistage perforated plates is proposed in this paper. Moreover, numerical investigation of the influence of the spacing between perforated plates for two identical-stage plates with aligned and misaligned holes is carried out by simulating a wide range of Reynolds number in turbulent flow regime. The obtained results include the trend of the pressure loss coefficient as the spacing between the two perforated plates varies for both cases of aligned and misaligned holes. The numerical achievements also show that for small spacing, the pressure loss coefficient is very different from that caused by two independent plates and is strongly influenced by the alignment between the holes of the two plates. By increasing the spacing, the behavior of the losses caused by the two-stage plates tends to that of two independent plates. A critical spacing between the plates has also been defined, beyond which the pressure losses are independent from the alignment of the holes.
Pilus Production in Acinetobacter baumannii Is Growth Phase Dependent and Essential for Natural Transformation
Authors: Vesel Nina , Blokesch Melanie 
Published: January 2021

ABSTRACT
Acinetobacter baumannii is a severe threat to human health as a frequently multidrug-resistant hospital-acquired pathogen. Part of the danger from this bacterium comes from its genome plasticity and ability to evolve quickly by taking up and recombining external DNA into its own genome in a process called natural competence for transformation. This mode of horizontal gene transfer is one of the major ways that bacteria can acquire new antimicrobial resistances and toxic traits. Because these processes in A. baumannii are not well studied, we herein characterized new aspects of natural transformability in this species that include the species’ competence window. We uncovered a strong correlation with a growth phase-dependent synthesis of a type IV pilus (TFP), which constitutes the central part of competence-induced DNA uptake machinery. We used bacterial genetics and microscopy to demonstrate that the TFP is essential for the natural transformability and surface motility of A. baumannii, whereas pilus-unrelated proteins of the DNA uptake complex do not affect the motility phenotype. Furthermore, TFP biogenesis and assembly is subject to input from two regulatory systems that are homologous to Pseudomonas aeruginosa, namely, the PilSR two-component system and the Pil-Chp chemosensory system. We demonstrated that these systems affect not only the piliation status of cells but also their ability to take up DNA for transformation. Importantly, we report on discrepancies between TFP biogenesis and natural transformability within the same genus by comparing data for our work on A. baumannii to data reported for Acinetobacter baylyi, the latter of which served for decades as a model for natural competence.
IMPORTANCE Rapid bacterial evolution has alarming negative impacts on animal and human health which can occur when pathogens acquire antimicrobial resistance traits. As a major cause of antibiotic-resistant opportunistic infections, A. baumannii is a high-priority health threat which has motivated renewed interest in studying how this pathogen acquires new, dangerous traits. In this study, we deciphered a specific time window in which these bacteria can acquire new DNA and correlated that with its ability to produce the external appendages that contribute to the DNA acquisition process. These cell appendages function doubly for motility on surfaces and for DNA uptake. Collectively, we showed that A. baumannii is similar in its TFP production to Pseudomonas aeruginosa, though it differs from the well-studied species A. baylyi.
Age and deposition of the Fort Crittenden Formation: A window into Late Cretaceous Laramide and Cenozoic tectonics in southeastern Arizona
Authors: Caylor Emilia A. , Carrapa Barbara , Sundell Kurt , DeCelles Peter G. , Smith Joshua M. 
Published: January 2021

AbstractThe Upper Cretaceous Fort Crittenden Formation exposed in the Santa Rita and Huachuca Mountains of southeastern Arizona is a syntectonic deposit that has been associated with Laramide tectonic activity. However, the spatio-temporal relationships among Cretaceous sedimentation, magmatism, basement exhumation, and possible flat slab-related processes in the southern Laramide region remain poorly understood. Age controls for uplift and erosion of local topography and syntectonic deposition in response to deformation remain particularly poor. The Fort Crittenden Formation comprises 800–2500 m of locally derived fluvial to alluvial fan sedimentary rocks and records paleodrainage reorganization in response to active tectonics. Changes in sedimentary facies, provenance, and paleoflow suggest deposition in a tectonically partitioned intraforeland basin. New detrital zircon data constrain the timing of deposition of the Fort Crittenden Formation between ca. 86 Ma and ca. 76 Ma. The lack of depositional age zircons throughout the majority of the Fort Crittenden Formation is consistent with a magmatic lull in the Cordilleran arc between ca. 90 Ma and ca. 76 Ma. The overlying Salero Formation and Late Cretaceous intrusions are expressions of renewed magmatism in southeastern Arizona at ca. 75 Ma. New Lu-Hf data indicate that magmas evolved from contamination of old juvenile crust. When interpreted in conjunction with other regional data sets, our study indicates that the Laramide deformation front migrated eastward into southwestern New Mexico by 75 Ma. Thermal modeling of apatite fission track and (U-Th)/He data from granitic clasts are consistent with Late Cretaceous–Paleocene (ca. 76–55 Ma) heating related to magmatism and cooling and exhumation during the Eocene and Oligocene.
Penetrating abdominal injury: UK military experience from the Afghanistan conflict
Authors: Leong MJ , Edgar I , Terry M 
Published: January 2021

AbstractAimsTo identify the prevalence, injury patterns and mortality of penetrating abdominal injury in patients treated at the UK Role 3 Medical Treatment Facility (MTF) in Camp Bastion, Afghanistan.MethodsAll patients with a penetrating abdominal injury were identified from the UK Joint Theatre Trauma Registry (JTTR). Demographics, predicted survival and observed mortality were compared. Sub-group analyses of UK military patients were conducted, comparing changes in survival as the campaign progressed and identifying the anatomical distribution of abdominal injuries.ResultsBetween June 2006 and June 2013, 1331 of the 8558 (16%) patients recorded on the JTTR had a penetrating abdominal injury; 393 were UK military, of whom 175 (45%) survived. 71% of UK military fatalities had the maximum New Injury Severity Score (NISS) of 75 compared to 4.6% of UK military survivors. The survival rate of UK military patients increased in the later stages of the campaign. Fatal injury in UK military patients was associated with significant vascular or hepatic injuries.ConclusionsThis study has defined the epidemiology of penetrating abdominal injury in a modern conflict. Continued training and further research into injury prevention and management will help to ensure that the improved outcomes observed in Afghanistan continue on future operations.
BET proteins are associated with the induction of small airway fibrosis in COPD
Authors: Zakarya Razia , Chan Yik L , Rutting Sandra , Reddy Karosham , Bozier Jack , Woldhuis Roy R , Xenaki Dikaia , Van Ly David , Chen Hui , Brandsma Corry-Anke , Adcock Ian M , Oliver Brian G 
Published: January 2021

Rationale
In COPD, small airway fibrosis occurs due to increased extracellular matrix (ECM) deposition in and around the airway smooth muscle (ASM) layer. Studies of immune cells and peripheral lung tissue have shown that epigenetic changes occur in COPD but it is unknown whether airway mesenchymal cells are reprogrammed.

Objectives
Determine if COPD ASM cells have a unique epigenetic response to profibrotic cytokine transforming growth factor β1 (TGF-β1).

Methods

Primary human ASM cells from COPD and non-COPD smoking patients were stimulated with TGF-β1. Gene array analysis performed to identify differences in ECM expression. Airway accumulation of collagen 15α1 and tenascin-C proteins was assessed. Aforementioned ASM cells were stimulated with TGF-β1 ± epigenetic inhibitors with qPCR quantification of
COL15A1
and
TNC
. Global histone acetyltransferase (HAT) and histone deacetylase (HDAC) activity were assessed. chromatin immunoprecipitation (ChIP)-qPCR for histone H3 and H4 acetylation at
COL15A1
and
TNC
promoters was carried out. Effects of bromoterminal and extraterminal domain (BET) inhibitor JQ1(+) on expression and acetylation of ECM target genes were assessed.

Measurements and main results

COPD ASM show significantly higher
COL15A1
and
TNC
expression in vitro and the same trend for higher levels of collagen 15α1 and tenascin-c deposited in COPD airways in vivo. Epigenetic screening indicated differential response to HDAC inhibition. ChIP-qPCR revealed histone H4 acetylation at
COL15A1
and
TNC
promoters in COPD ASM only. ChIP-qPCR found JQ1(+) pretreatment significantly abrogated TGF-β1 induced histone H4 acetylation at
COL15A1
and
TNC
.

Conclusions

BET protein binding to acetylated histones is important in TGF-β1 induced expression of
COL15A1
and
TNC
and maintenance of TGF-β1 induced histone H4 acetylation in cell progeny.
Effects of nonstandard interaction on temporal and spatial correlations in neutrino oscillations
Authors: Sarkar Trisha , Dixit Khushboo 
Published: January 2021

AbstractEffects of physics beyond the standard model in the neutrino sector are conveniently incorporated through non-standard interaction parameters. Assuming new physics in the form of dimension-6 vector operators, a recent global analysis of neutrino oscillation data including results from COHERENT experiment suggests two favourable new physics scenarios. These are LMA-Light (with normal mass ordering) and LMA-Dark (with inverted mass ordering) sectors of parameters. In this work, we study the effects of new physics solutions on Leggett–Garg-type (LGtI) inequality which quantifies temporal correlations in the system along with flavour entropy and genuine tripartite entanglement which can be considered as measures of spatial correlations. We show that the violation of LGtI for $$\nu _{\mu }$$

ν
μ

energy around 3 GeV in the DUNE experimental set-up can not only be an indication of presence of new physics but such a new physics is expected to be in the form of LMA-Dark sector with inverted ordering. Further, we show that the LMA-Light solution, in general, decreases the values of all measures of quantum correlations in comparison to their SM predictions. On the other hand, the Dark solution can significantly enhance the values of these measures.
Meshless Numerical Analysis of Phase Change Problems in Artificial Freezing Technology Applied in Geo-Media
Authors: Chen Peipei , Yang Guangchang , Wu Nan 
Published: January 2021

Numerical solutions to heat conduction problems involving phase change have traditionally been obtained using the grid-based finite difference or finite element methods. However, due to the unique mathematical form of the equations and the limitations of the grid algorithm, difficulties may arise in solutions. In this study, smooth particle hydrodynamics (SPH) method is used to calculate heat conduction with phase change so as to obtain reasonable numerical solutions. An SPH-based program is presented, and its practicality and reliability are verified through a benchmark problem. Based on the unidirectional freezing test, the validity and accuracy of the soil freezing model considering the phase change effect is verified compared with the finite element results. Then, artificial freezing technology is applied in geo-media, where the heat conduction with phase change during soil freezing is simulated. The temperature distribution characteristics around freezing pipes and the development of thermal regime of characteristic points with time are obtained. The frozen front development is analyzed, considering different freezing-pipe temperatures and different thermal parameters for the media. The findings of this study may provide a reference for the design of future engineering applications using artificial freezing technology.
Biomarker Discovery in Patients with Immunotherapy-Treated Melanoma with Imaging Mass Cytometry
Authors: Martinez-Morilla Sandra , Villarroel-Espindola Franz , Wong Pok Fai , Toki Maria I. , Aung Thazin Nwe , Pelekanou Vasiliki , Bourke-Martin Brian , Schalper Kurt A. , Kluger Harriet M. , Rimm David L. 
Published: January 2021

Abstract

Purpose:
Imaging mass cytometry (IMC) is among the first tools with the capacity for multiplex analysis of more than 40 targets, which provides a novel approach to biomarker discovery. Here, we used IMC to characterize the tumor microenvironment of patients with metastatic melanoma who received immunotherapy in efforts to find indicative factors of treatment response. In spite of the new power of IMC, the image analysis aspects are still limited by the challenges of cell segmentation.

Experimental Design:
Here, rather than segment, we performed image analysis using a newly designed version of the AQUA software to measure marker intensity in molecularly defined compartments: tumor cells, stroma, T cells, B cells, and macrophages. IMC data were compared with quantitative immunofluorescence (QIF) and digital spatial profiling.

Results:
Validation of IMC results for immune markers was confirmed by regression with additional multiplexing methods and outcome assessment. Multivariable analyses by each compartment revealed significant associations of 12 markers for progression-free survival and seven markers for overall survival (OS). The most compelling indicative biomarker, beta2-microglobulin (B2M), was confirmed by correlation with OS by QIF in the discovery cohort and validated in an independent published cohort profiled by mRNA expression.

Conclusions:
Using digital image analysis based on pixel colocalization to assess IMC data allowed us to quantitively measure 25 markers simultaneously on formalin-fixed, paraffin-embedded tissue microarray samples. In addition to showing high concordance with other multiplexing technologies, we identified a series of potentially indicative biomarkers for immunotherapy in metastatic melanoma, including B2M.
Development and Multiple Validation of the Protein Multi-marker Panel for Diagnosis of Pancreatic Cancer
Authors: Kim Yoseop , Yeo Injoon , Huh Iksoo , Kim Jaenyeon , Han Dohyun , Jang Jin-Young , Kim Youngsoo 
Published: January 2021

Abstract

Purpose:
To develop and validate a protein-based, multi-marker panel that provides superior pancreatic ductal adenocarcinoma (PDAC) detection abilities with sufficient diagnostic performance.

Experimental Design:
A total of 959 plasma samples from patients at multiple medical centers were used. To construct an optimal, diagnostic, multi-marker panel, we applied data preprocessing procedure to biomarker candidates. The multi-marker panel was developed using a training set comprised of 261 PDAC cases and 290 controls. Subsequent evaluations were performed in a validation set comprised of 65 PDAC cases and 72 controls. Further validation was performed in an independent set comprised of 75 PDAC cases and 47 controls.

Results:
A multi-marker panel containing 14 proteins was developed. The multi-marker panel achieved AUCs of 0.977 and 0.953 for the training set and validation set, respectively. In an independent validation set, the multi-marker panel yielded an AUC of 0.928. The diagnostic performance of the multi-marker panel showed significant improvements compared with carbohydrate antigen (CA) 19-9 alone (training set AUC = 0.977 vs. 0.872, P &lt; 0.001; validation set AUC = 0.953 vs. 0.832, P &lt; 0.01; independent validation set AUC = 0.928 vs. 0.771, P &lt; 0.001). When the multi-marker panel and CA 19-9 were combined, the diagnostic performance of the combined panel was improved for all sets.

Conclusions:
This multi-marker panel and the combined panel showed statistically significant improvements in diagnostic performance compared with CA 19-9 alone and has the potential to complement CA 19-9 as a diagnostic marker in clinical practice.
Neoadjuvant Chemoradiotherapy Combined with Atezolizumab for Resectable Esophageal Adenocarcinoma: A Single-arm Phase II Feasibility Trial (PERFECT)
Authors: van den Ende Tom , de Clercq Nicolien C. , van Berge Henegouwen Mark I. , Gisbertz Suzanne S. , Geijsen E.D. , Verhoeven R.H.A. , Meijer Sybren L. , Schokker Sandor , Dings M.P.G. , Bergman Jacques J.G.H.M. , Haj Mohammad Nadia , Ruurda Jelle P. , van Hillegersberg Richard , Mook Stella , Nieuwdorp Max , de Gruijl Tanja D. , Soeratram Tanya T.D. , Ylstra Bauke , van Grieken Nicole C.T. , Bijlsma Maarten F. , Hulshof Maarten C.C.M. , van Laarhoven H.W.M. 
Published: January 2021

Abstract

Purpose:
The CROSS trial established neoadjuvant chemoradiotherapy (nCRT) for patients with resectable esophageal adenocarcinoma (rEAC). In the PERFECT trial, we investigated the feasibility and efficacy of nCRT combined with programmed-death ligand-1 (PD-L1) inhibition for rEAC.

Patients and Methods:
Patients with rEAC received nCRT according to the CROSS regimen combined with five cycles of atezolizumab (1,200 mg). The primary endpoint was the feasibility of administering five cycles of atezolizumab in ≥75% patients. A propensity score–matched nCRT cohort was used to compare pathologic response, overall survival, and progression-free survival. Exploratory biomarker analysis was performed on repeated tumor biopsies.

Results:
We enrolled 40 patients of whom 85% received all cycles of atezolizumab. Immune-related adverse events of any grade were observed in 6 patients. In total, 83% proceeded to surgery. Reasons for not undergoing surgery were progression (n = 4), patient choice (n = 2), and death (n = 1). The pathologic complete response rate was 25% (10/40). No statistically significant difference in response or survival was found between the PERFECT and the nCRT cohort. Baseline expression of an established IFNγ signature was higher in responders compared with nonresponders (P = 0.043). On-treatment nonresponders showed either a high number of cytotoxic lymphocytes (CTL) with a transcriptional signature consistent with expression of immune checkpoints, or a low number of CTLs.

Conclusions:
Combining nCRT with atezolizumab is feasible in patients with rEAC. On the basis of our exploratory biomarker study, future studies are necessary to elucidate the potential of neoadjuvant immunotherapy in patient subgroups.
See related commentary by Catenacci, p. 3269
First record of Touit melanonotus (Wied, 1820) (Aves: Psittaciformes: Psittacidae) in Cantareira State Park, Brazil: new colonization or simply unnoticed?
Authors: Melo Marcos Antônio , De Almeida Braga David 
Published: January 2021

Although the avifauna of Cantareira State Park (CSP), Brazil has been studied for 120 years, the Brown-backed Parrotlet Touit melanonotus had not been recorded. Here, we present the first record and diet items (fruits of Ocotea sp.) in CSP, discussing the potential for this psittacid going unnoticed in this area for a long period.